BIO 240 FINAL

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what is evolution

"Evolution is change in heritable traits of biological populations over successive generations"

Incomplete lineage sorting in the western lowland gorilla

'Kamilah' genome sequences 170Gbp sequence has evidence of ILS and suggests gorillas are more closely related to chimps than humans for the alleles sampled Potentially because of ancestral hybridisation events This contradicts the known species tree

What is nucleotide diversity and use

(Pi) frequency at which randomly chosen allele pairs will differ at a given site Calculated at putatively neutral sites of the genome Measure of polymorphism Can be used to compare levels of diversity between populations and species Higher nucleotide diversity = more polymorphic

drift reduces genetic variation in a population

- Alleles are lost at a faster rate in small populations - Alternative allele is fixed

what is a phylogenetic tree

- a diagrammatic depiction of biological entities that are connected through common descent; - constructed using characters that result from common ancestry these reflect evolutionary history.

Mutation generates variation

-Mutation rates for any gene are low -with genome size and population size many new mutations arise each generation (humans: ca. 9.8 billion new mutations) -Source of variation for selection and drift to act

Mutation-selection balane

-equilibrium frequency reached through tug-of-war between negative selection and new mutation -explains persistence of rare deleterious mutations in populations

Fixation Index

-genetic structure that indicates population differentiation -based on genetic polymorphisms -high Fst: high degree of differentiation between populations =(variation in a sub pop)/(variation in all populations)

isolating barriers

-geographic: extrinsic properties of landscape that prevent gene glow (allopatry) -reproductive: features of organisms that prevent interbreeding (even in sympatry)

Hardy Weinberg Equilibrium Assumptions

-no new mutations -no migration -large pop. -random mating bt genotypes -all genotypes have same fitness = no natural selection

push and pull of drift and migration

-population subdivision enhances the effects of genetic drift (divergence in allele frequencies) -gene flow (migration) counteracts subdivision by homogenizing allele frequencies

A given autosomal locus has three possible alleles (A1, A2, and A3). Assuming that the numbers of individuals with the six possible genotypes are as follows, what would be the frequency of the A1 allele in the population? A1A1 = 30 A1A2 = 27 A2A2 = 12 A1A3 = 17 A2A3 = 10 A3A3 = 4 What would be the frequency of the A2A2 genotype? Assume the population is under Hardy-Weinberg equilibrium.

.09

Consider gene A in a population in which the frequency of the a allele is 0.3 and the inbreeding coefficient is 0.25. What is the frequency of aa individuals in this population?

.1425

A given autosomal locus has three possible alleles (A1, A2, and A3). Assuming that the numbers of individuals with the six possible genotypes are as follows A1A1 = 30 A1A2 = 27 A2A2 = 12 A1A3 = 17 A2A3 = 10 A3A3 = 4 What is the frequency of A3 allele in the population?

.175

A given autosomal locus has three possible alleles (A1, A2, and A3). Assuming that the numbers of individuals with the six possible genotypes are as follows, what would be the frequency of the A1 allele in the population? A1A1 = 30 A1A2 = 27 A2A2 = 12 A1A3 = 17 A2A3 = 10 A3A3 = 4 What would be the frequency of the A1A3 genotype? Assume the population is under Hardy-Weinberg equilibrium.

.182

.305

Consider gene A in a population in which the frequency of the a allele is 0.3 and the inbreeding coefficient is 0.25. What is the frequency of Aa individuals in this population?

.315

A recessive disease afflicts 1 in 12 individuals in a population. If the population is in Hardy-Weinberg equilibrium, what is the frequency of carriers in this population?

.42

In a large, randomly mating population, the following genotypes were found to produce the mean numbers of offspring shown. Genotype # offspring FF 50 Ff 28 ff 22 What is the selection coefficient (s) for the Ff genotype?

.44

.52

Consider gene A in a population in which the frequency of the a allele is 0.3 and the inbreeding coefficient is 0.25. What is the frequency of AA individuals in this population?

.5425

A population in HW equillibrium is taken into the lab for an experiment in which inbreeding occurs. The inbreeding coefficient is 0.6. The original population is genotyped to determine the alleles present at the A locus, and the following frequencies of the three genotypes is observed: AA 0.49 Aa 0.42 aa 0.09 What is the expected frequency of the AA genotype in the next generation?

.616

The MN blood group is examined in a population, and the following numbers of genotypes are observed: 5 MM 25 MN 20 NN What is the frequency of the N allele in the population?

.65

A recessive disease afflicts 1 in 12 individuals in a population. If the population is in Hardy-Weinberg equilibrium, what is the frequency of the dominant allele (p)?

The mean number of offspring produced by each of three genotypes is shown below. 10 MM 30 MN 50 NN What is the selection coefficient for the genotype NN?

Scale for Fst values

0 = no divergence and 1 = fixed difference 0-0.1 = weak differentiation 0.1-0.25. = moderate differentiation >0.25 = strong differentiation Strong differentiation level depends on how closely related two populations are More closely related = fewer differences and lower significance level

The mean number of offspring produced by each of three genotypes is shown below. What is the fitness (W) for the genotype MM? 10 MM 30 MN 50 NN

0.20

A given autosomal locus has three possible alleles (A1, A2, and A3). Assuming that the numbers of individuals with the six possible genotypes are as follows, what would be the frequency of the A1 allele in the population? A1A1 = 30 A1A2 = 27 A2A2 = 12 A1A3 = 17 A2A3 = 10 A3A3 = 4 What would be the frequency of the A1A1 genotype? Assume the population is under Hardy-Weinberg equilibrium.

0.27

What is the predicted response to selection (R) if the narrow-sense heritability is 0.2 and the selection difference is 2.9?

0.6

0.7

In a large, randomly mating population, the following genotypes were found to produce the mean numbers of offspring shown. Genotype # offspring FF 50 Ff 28 ff 22 What is the fitness of the FF genotype?

How do we calculate expected heterozygosity

1 - sum of allele frequency for each allele in a population

Overall strategy for testing the prediction that genes behind adaptive phenotypic differences are more divergent than neutral genes

1) genotype individuals from divergent populations at many loci 2) estimate neutral distribution for Fst 3) compare observed and expected distributions 4) outlier loci with Fst values outside of expected distribution are potentially influenced by selection

How do we test if genes for adaptive phenotypic differences are more differentiated than most

1) need a measure for differentiation 2) an expectation for neutral genes 3) an expectation for genes under divergent selection 4) ways to sample differentiation of many different genes

5 big questions in molecular genetics..

1. What is the cauee of variability 2. What genes are involved 3. Is variability adaptive or evolved by chance 4. Does it affect fitness and evolution 5. Can we make use of it eg conservation/medicine/crop improvement

pop response to selection may level off after many gen.s, why?

1. genetic variation runs out: homozygous Va = 0, h^2 = 0 2. natural selection opposes further change

Kurzweil's Six Epochs of Evolution

1. physics and chemistry 2. biology 3. brains 4. technology 5. merger of technology and human intelligence 6. the universe wakes up

The response to selection of flower size in a plant species is studied. Flower size is measured in the population and an average of 30.4 mm is obtained. A set of plants with average flower size of 34.13 mm are allowed to interbreed and a their offspring have a mean flower size of 32.21 mm. What is the response to selection?

1.81 mm

Allele q of Spinal Muscular Atrophy occurs

1/100 in human population

Sequencing exons and the cause of dm in Belgian blue

11bp frame shifting deletion results in a truncated protein with 102 fewer amino acids expected to be non functional 14 full blood Belgian blues are homozygous for this mutations and out of 120 non dm muscle cattle only one had this allele likely to be a change mutation (homoplasy)

In an analysis of 120 SNPs, 80 are monomorphic. What is the percentage of polymorphic loci?

120 - 80 = 40 polymorphic 40/120 x100 = 33.33%

Kumar and Subramanian, 2002 study into K and T

17,208 protein coding DNA sequences in 5,669 nuclear genes from 326 placental mammals Divergence time (T) and evolutionary distance (K) show a linear relationship consistent with predictions of neutral model Evolutionary distance = sequence divergence at synonymous sites likely to b neutrally evolving (K)

On average, each chicken in a population produces 4 eggs a week. A farmer selects for increased egg production, whereby only chickens producing more than 8 eggs per week are allowed to reproduce (average egg production per chicken in the reproducing chickens is 9). The next generation of chickens produces an average of 7 eggs per week per chicken. What is the response to selection?

FY blood group locus polymorphism and H value

3 major blood groups FYo FYa and FYb FYb is ancestral and differs from FYo by a single non coding base change FYo = confers malaria resistance = fixed in sub Saharan Africa Prediction it is driven to fixation by strong positive selection Deficiency of variation at FY locus in sub Saharan African groups H is negative and p <0.05 = suggesting selection is acting

Does the Oldfield mouse p gene explain all variation in escape tunnel?

30% increase in escape tunnel building in P gene As behaviour is exhibited 100% of the time there may be other influences in the genome Complex behaviours can evolve from distinct genetic behaviour

On average, each chicken in a population produces 5 eggs a week. A farmer selects for increased egg production, whereby only chickens producing more than 8 eggs per week are allowed to reproduce (average egg production per chicken in the reproducing chickens is 9). The next generation of chickens produces an average of 7 eggs per week per chicken. What is the selection differential?

Calculating divergence time of the G6PD gene

5022bp segment w 59 diffs, U is known 59/5022 = K =0.0117 T = 0.0117 /2U T / average generation time in years gives the year since divergence

Results of finch GWAS

6/15 most differentiated region are in loci known to affect beak/craniofacial development Major locus for beak shape identified ALX1 ALX1 had largest Fst and is associated with craniofacial development in humans Groups separated into blunt and pointy beaks Flat region of nucleotide diversity in region with ALX1 in broad beak birds and low diversity in haplotypes = evidence for selective sweep and positive selection of ALX1

Findings on study of geospiza fortis genotyping

62 individuals genotypes Highly significant association between genotype and degree of beak pointedness (p < 0.0001) Balancing selection may maintain variation to allow birds to cope with changing environments

Fate of most mutations in bacteria

655 mutations identified as different from ancestral type Only 28 had a positive effect Majority of mutations are deleterious so selection is constantly working against negative mutations to maintain fitness

How do we interpret C value? Eg C = 1 - 0.33 = 0.77

77% of non synonymous diversity is removed by purifying selection

What has been found by studies into height heritability and QTLs

80% of human height is heritable but most studies only find loci to explain 2-4% of variation with allelic substitutions only altering height by 2-5mm A meta analysis found 697 loci that explain 16% of variation More loci with association to trait on larger chromosome suggesting genes affecting height are evenly distributed across the genome

Did innocenti and morrow identify SBGE in drosophila

91% (17,350) genes showed sex biased gene expression ~7,500 showed > 2 fold differences in expression between males and females

Method of genotyping polygyne fire ants

92 million Illumina RAD sequence reads from 92 haploid sons of Bb queens 2796 markers across 16 chromosomes Non combining region encompassing 285 markers Same region found in 3 other families

What is Jukes Cantor?

A correction for multiple hits Assuming mutations all have equal probability K is smaller than Kjc As K increases, the distance between K and Kjc increases because as more time passes more multiple hits will occur, it is more likely that mutations will occur at the same site

What is incomplete lineage sorting

A limitation to phylogenetic analysis Gene trees using K are based on certain sequences Potential inconsistencies arise as different genes may produce different trees Causing the gene tree to differ from the known species tree

High values for heterozygosity (or expected heterozygosity) at a genetic locus in a population indicates that there is:

A lot of genetic variation

What is Fst

A measure of differentiation and distinctness of populations Compared inbreeding (expected heterozygosity) in sub population (Hs) to total population (Ht)

What is a transition

A mutation from a purine to another purine or pyramidine to another pyramidine More common than transversion so U is higher

Founder effect

A new population is started by a small number of individuals that by chance do not represent the gene pool of the larger source population

What is a supergene

A number of tightly linked genes that are not affected by recombination

Horn size in soay sheep

A quantitative trait with heritability of 0.35 Genotype has additive effect in horn length and circumference Substituting H0 for H+ makes horns 40mm longer

What is genetic drift

A random process that occurs in all populations but is more important in small populations Chance events that affect survival and reproductive success of individuals irrespective of how well adapted they are. Genetic drift does not produce adaptations!

What is a phenogram

A tree representing similarity or distance but may not represent historical relationships eg convergence

Why is the neutral theory useful

Acts as a null hypothesis against which data in molecular variation and evolution can be tested We can reject the neutral theory to argue selection is acting

What is calibration and some methods of doing it

Adding a timescale to a phylogenetic tree Fossils, biogeographic events and molecular clock H

what are the four bases

Adenine - Thymine Guanine - Cytosine

How do lohmueller's results support theoretical predictions

All 3 types of non synonymous mutations segregate at higher frequencies in the European sample than African Bottlenecks and reduction of Ne in European sample has lead to increased burden of deleterious alleles due to reduced efficacy of selection Supports prediction that selection is less effective in populations with smaller Ne and deleterious alleles segregate at higher frequencies in populations with lower Ne

Lohmueller results

All non synonymous mutations including benign segregate at significantly lower frequencies than neutral On average non synonymous mutations have a damaging effect on fitness Those predicted to have a more damaging effect in the protein are on average more deleterious

Darwin's logic for natural selection fact 1

All species have great potential fertility that their population size would increase exponentially if all individuals that were born reproduced successfully

Why might alleles have very high Fst values

Allele May be under strong positive selection or linked to an allele under strong positive selection

Why is populations genetics theoretical?

Allele frequency changes have long time scales and are not directly observable Fitness differences between genotypes May be too small to measure in a lab but are visible to evolutionary forces

What is Lewontins paradox?

Although actual population size can vary over many orders of magnitude Level of variability in neutral genetic diversity is much more restricted

Mutation-Selection balance

An equilibrium in allele frequency occurs when new copies of the allele arises by mutation at exactly the same rate they are eliminated by natural selection

How might the Out of Africa hypothesis explain low Ne in humans

Ancestral human population with low Ne lived in restricted areas of Africa Repeated bottlenecks in human history as small groups colonised new areas Recent rapid population expansion in <1000 generations, which is not long enough for effects of rapid growth to be reflected in nucleotide diversity

Features of human height

Archetypal polygenic (QTL) trait Normally distributed and highly heritable Francis Galton first studied human height and heritability in the mid 1800s

Advantageous alleles

Are swept to fixation by natural selection

Effect of purifying selection on allele frequency

As selection against an allele increases (it's negative fitness effects becomes larger) its frequency decreases Purifying selection is very effective, as it become stronger there is a very steep drop off in allele frequency

How do we calculate synonymous diversity

Assuming synonymous mutations are neutral synonymous diversity = SD = 4NeU

What is linkage mapping

Basic way of finding the genes underlying traits using closely related parents species or inbred lines of the same species Developed in the late 1920s

Neutral Mutations

Become fixed or lost by chance

What tends to happen to beneficial mutations

Beneficial mutations tend to increase in frequency over time They segregate at higher frequencies than neutral variants as are more likely to become fixed

What happens to KA when non synonymous changes are strongly beneficial

Beneficial non synonymous changes have higher fixation probabilities as they segregate at higher frequencies KA is elevated as more substitutions will occur

Bifurcation vs multifurcation

Bi = each node has 2 descendent lineages Multi = each node has 2 or more descendent lineages

what is bootstrapping?

Bootstrapping, resampling alignment with replacement, Can summarise trees for node support Slow

What is an ultra metric tree

Branch length represents time

What is an additive tree?

Branches represent evolutionary distance/change (K) These tree would have longer branches for rodents than primates

Chippendale experiment into genetic correlation in drosophila

Bred hemiclonal lines and measured the relative fitness of males and females Juveniles showed positive correlation, fitness increases in both sexes Adults show negative correlation when increased fitness in one sex reduced fitness in the other = sexually antagonistic

What is C

C = selective constraint, proportion of non synonymous mutations expected to be so strongly deleterious that fixation probability is 0 Amount of non synonymous variation removed by purifying selection

Estimated selective constraints (C) are different in different parts of the genome Where is C highest and lowest and what does this mean

C is highest for non synonymous subs in exons (~0.7) Non synonymous in exons > synonymous in exons (0.23) > 3' UTR (0.15) > 5' UTR (0.14) > introns (<0.1) As distance from transcribed region increases selective constraints decrease Exons are more conserved than introns and flanking coding regions

what is midpoint rooting

Calculate all of the tip-to-tip distances, select the longest then place the root half-way between these two tips

How do we calculate observed and expected heterozygosity values for total population

Calculate genotype frequencies in sub populations and add together to find total population Use allele frequency in total population to calculate expected genotype frequency Compare where significantly different to each other using chi squared test

Prugnolle et al, 2005 and the serial dilution model

Calculated mean genetic diversity of 51 human populations using 377 microsatellite markers and plotted against distance from east Africa in km Negative correlation between distance and mean genetic diversity

Consequences of adaptive phenotypic differentiation

Can lead to formation of different ecomorphs and sub populations Eg cichlids colours and water depths Aphids adapted to different host plants Monkey flowers and different pollinators

What is evolution

Changes in allele frequency over time Allele frequencies can inc or dec from gen to gen caused by genetic drift or selection

Why might there be high Fst peaks in non coding regions

Changes to non coding region may not be as damaging as coding regions so selection is less strong here Weaker selection = increases Fst (as shown by strength of purifying selection in different genomic regions) High Fst in non coding regions is common for diverging sub-species

Example of Population Bottleneck

Cheetah Population

How can we estimate K from sequence data?

Compare 2 homologous sequences and calculate proportion of nucleotide sites that differ D = differences L = length of sequence K = D/L

Yang et al 2006 evidence for wed biased gene expression

Compared gene expression in liver cells for male and female mice Red = over expressed & green = under-expressed Clear evidence of males and females differentials expressing genes

What does Tajimas D show us?

Compares relative frequency of low and intermediate frequency variants Excess of low frequency variants relative to neutral model and D<0 Excess of intermediate frequency variants and D>0

Eory et al, 2010 comparison of human and chimp genomes method

Comparison used ancestral repeats in intervening regions in place of Ks as a neutral reference to calculate divergence ARs are transposable elements inserted into genome of common ancestor (45% mammalian genome = ARs) ARs appear to be neutrally evolving

How is linkage mapping carried out?

Construct a linkage map by crossing 2 parental types Cross heterozygous F1 generation to create a F2 generation all genetically different to each other due to recombination between parental genomes Requires 100s of F2 individuals

what can analogy be due to

Convergence (e.g. wings in birds and bats; DNA sequence in echolocation genes in bats and dolphins) Reversal/secondary loss (e.g. snakes resemble fish in lacking legs; loss of pigmentation and eye gene function in cave animals)

What is the molecular clock and cytochrome b example

DNA and protein sequences evolve at a rate that is relatively constant across time and among different organisms Shorter generation times = faster rates of evolution Cytochrome b has 2% rule with 2% divergence occurring for every million years of separation

sequencing data-> variation in base pair sequence of DNA using microsatellites: short repetitive DNA sequences, highly variable, # of repeats varies bt indivs, show more recent evolution DNA sequences: (SNPs) are described whole genome, chose markers/sequences, deeper evolutionary relationships

DNA molecular variation

what are extinct organisms

DNA not usually available, oldest ancient DNA: Orlando et al. 2013, horse ancient DNA, ~700,000 ya Morphology available for the 99% of life that is no longer with us.

what is multiple sequence alignment

DNA sequences from more closely related populations will be more similar to each other than they are to more distantly related populations

How to we collect data for site frequency spectra

DNA sequences from n individuals containing a certain number of polymorphic sites Calculate how many times a derived allele at each polymorphic site is present in a population Eg singletons are present only once in a population at a given site Same process for doubles/triples

What was found in the phylogenetic tree of finches

Deep divergence between broad and point beaked birds Phylogenies show near allele fixation in groups with different phenotype All blunt except 1 homozygous for B All rest except 3 homozygous for b Short branch lengths for broad beak (B) are consistent with selective sweep

What tends to happen to deleterious mutations

Deleterious mutations tend to decrease in frequency over time They segregate at lower frequencies than neutral variants and are less likely to become fixed

Why might the incidence of human diseases vary in different populations

Deleterious variants segregating at higher frequencies in populations with smaller Ne eg cystic fibrosis is more common in Europe than Africa and Asia (40 per 100,000 Europeans and 1/100,000 Asians) Sickle cell anaemia is maintained by balancing selection in Africa (270/100,000 African Americans and 2/100,000 European Americans) Differences in disease incidence is a combination of selection and drift

What happens when mutation, selection and genetic drift interact?

Deleterious, netural or advantageous alleles can appear

What can confound interpretations of significant D and H values

Demographic changes can cause false positives

What factors play a key role in determining level of nucleotide diversity

Demography and Ne, smaller Ne = reduced nucleotide diversity as variability lost due to drift is greater, bottlenecks U, lower U = lower diversity Selection = positive/purifying act to reduce diversity while balancing maintains it

How can the molecular clock allow us insight into molecular evolution

Departures from the constant substitution rate give us insight into mechanisms that may be impacting molecular evolution

What is evolutionary biology?

Descent with Modification Species change overtime Lineages split and diverge new life forms derive from older forms life forms are related

Why are differences in allele frequency not a useful measure of differentiation?

Difference of 0.5 could be 0.8&0.3 or 0.5&0 which is compete differentiation by allele fixation

What is polymorphism and what is the cause

Differences between members of the same species AKA diversity Before alleles become fixed a population is polymorphic Polymorphism is due to segregating variants and can tell us about more recent evolutionary past

What is divergence

Differences between organisms of different species Divergence is due to substitutions and can tell us about more distant evolutionary past (species lineages splitting)

Results from mice linkage mapping

Different chromosomes cause genetic variation for different tunnel types Oldfield P gene causes longer entrance tunnel and higher probability of escape tunnel Swapping deer mice allele for this = 30% increase of escape tunnel building At least 3 regions explain variation in entrance tunnel length 1 region explains most of the variation in presence/absence of escape tunnel

Selection coefficient (s) values for different types of mutations

Different mutations will have different effects in fitness S = 0 mutation is neutral and subject to drift S > 0 mutation is beneficial S < 0 mutations is deleterious

what is meant by mitochondrial DNA

Different regions provide resolution at different evolutionary depths; DNA sequence based (via PCR/Sanger or NGS);

Effect of no recombination on b chromosome in polygyne fire ants

Differential gene expression common in this region Mutations beneficial to b form can remain associated with it Deleterious mutations can also accumulate = lethal in homozygous form

Genetic Drift

Differential reproductive success that happens by chance, not related to phenotype/genotype

What factors affect levels of polymorphism

Diversity = 4NeU so higher mutation rate = higher diversity and higher population size = higher diversity As species differ in Ne and U, polymorphism is different for different species and populations

WF equation for nucleotide diversity

E(pi) = 4Ne U

Example of Ne vs nucleotide diversity vs census size in ecoli vs humans

Ecoli have a much larger population size than humans Ecoli have a nucleotide diversity only 20x larger than humans and an Ne 2000x larger Difference in nucleotide diversity is much less than difference in effective population size This difference can't be explain by differences in U alone

How can we identify when confounding factors are affecting D and H values

Effects of positive selection will be localised with nucleotide diversity depressed close to selected regions whereas effects of demography are genome wide We can look for outlier genes with reduced diversity or use models less sensitive to demography such as composite DH models

How can we figure out K for different kinds of substitutions

Eg K A -> G is number of A->G mutations / total number of A sites Same procedure for other kinds of mutations

Deleterious alleles

Eliminated by natural selection

What is the generation time effect hypothesis

Errors in DNA replication in the germ line is a major source of mutations and therefore variation Species with shorter generation times have more germ like replications per year and more replication errors per unit time This causes a higher mutation rate per unit time Since K = 2TU, K is greater in species with shorter generation times

How do you date trees using molecular clocks?

Estimate DNA substitutions between sequences calibrate rate the substitutions have occurred using time points use rate of substitution to estimate divergence times

Example used for SNPs

Estimating ethnic origin Predicting physical traits Degraded DNA samples More common than microsatellites

What would happen if genetic drift is the only evolutionary process in a finite population?

Eventually one allele will drift to fixation (p=1) and all other alleles will be lost

Blue skies point of view as to why polymorphism is interesting

Evolution requires heritable genetic variation How is this variation created and maintained and what is the genetic basis of adaptation We can infer evolutionary history

Darwin's logic for natural selection fact 2

Except for minor annual fluctuations and occasional major fluctuations, populations normally display stability

How do we identify areas where evolutionary forces may be acting on the genome using Fst

Exceptions from normal distribution Eg very low Fst or very high Fst

What happened to D upon fixation of beneficial alleles

Excess of low frequency variants and defect of intermediate frequency variants in regions nearby to selected gene D should be negative which indicated that allele may be under positive selection

What happens to Fay and Wu's H when beneficial alleles become fixed

Excess of neutral high frequency variants relative to neutral model in regions near to selected allele H becomes negative

What is double muscle in Belgians blues and the cause?

Exhibits double muscle phenotype = 20-25% higher muscle mass and inc feed efficiency Segregated as single autosomal locus called muscular hyper trophy Mh = region of bovine chromosome 2 = homologous to human But unknown which gene in this genomic region and which mutation is responsible for dm

RXFP2 gene

Explains variability in a discreet and quantitative trait in soay sheep Unlike human height, a single gene explains most of the variation in a quantitative trait

How can we study the effect of selection on the fate of non neutral genetic variants

Extend the WF model to include selection

Cheetah population

Extremely low genetic diversity, and its the lowest polymorphism of cats. Only explanation is the cheetahs has same/very similar genotypes caused by bottleneck

Non-random mating, mutation, migration, genetic drift, and natural selection all change allele frequencies in a population and thus play a role in evolution.

The intercross QTL mapping method is the method most frequently used for genetic studies of human disease.

True or False, theres low genetic variation between populations

False

True or False: An E. coli strain referred to as lac- cannot produce its own lactose.

False

True or False: Chromosomes are replicated during the G1 phase of the cell cycle.

False

True or False: Cysteine and guanine are two of the bases in DNA.

False

True or False: Genes on the X and Y chromosomes are inherited in an autosomal fashion.

False

True or False: In meiosis, the equational division comes before the reductional division.

False

True or False: One of the phases of meiosis resembles a mitosis and this phase is meiosis I.

False

True or False: Sex chromosomes are prone to non-disjunction because they do not pair with each other in meiosis.

False

True or False: Transformation requires that bacteria make contact via a pilus structure.

False

True or false, genetic drift does lead to adaptation

False

What are hemiclonal lines

Family lines that have been extensively inbred to individuals are essentially clones

How do we carry out UPGMA

Firstly calculate K for all species comparisons Those with smallest K (most closely related) are joined Branch length is mean K/2 Next work out mean K from the species in the group for all the remaining species, next closely related is added as next branch (length = mean K/2) Repeat for remaining species

How likely are different kinds of mutations to become fixed?

Fixation probability for a neutral mutation is = to its initial frequency = 1/2n Beneficial mutation FP = > 1/2n Deleterious mutation FP = < 1/2n Fixation probability is a function of the fitness effect of the new mutation

Missouri Ozarks - Collard Lizards

Fragmentation of formerly widespread habitat caused lizard population isolation in small populations that diverge by genetic drift

How can we calculate Fst

Fst = (Ht - Hs)/Ht

How do we calculate expected Fst from n and m at equilibrium

Fst = 1/(1+4Nm) One migrant per generation gives an Fst of 0.2 This is an expectation, when we sample many neutral loci, they will vary around this value and produce a normal distribution

How does Fst change with migration as selection

Fst decreases as migration increases (more gene flow slows divergence) Fst increases as selection increases

Expectations for Fst for alleles under selection

Fst will be higher than neutral alleles It can be hard to distinguish between selected allele and alleles linked to selected alleles High Fst is an indication of something acting in the genome

GDF8 myostatin gene in mice and relevance to double muscle in Belgian blues

GDF8 = negative regulator of skeletal muscle in mice, knock out = similar phenotype to dm with 2-3 fold higher muscle mass Generally very conserved between species esp C terminal residues = implies functional conservation Null myostatin mice and dm Belgian blues = similar phenotype Myostatin and mh have similar map positions on bovine genome

Method for study on beak divergence for Darwin's finches

GWAS on sequences genome of 120 birds from 15 species Fst estimated at 15kb intervals

What is the SLC24A5 gene in humans and form in European and African populations

Gene influences skin pigmentation levels Non synonymous mutation changes ancestral Ala111 to Thr111 Thr111 is skin lightening and has 98.7-100% prevalence in Europeans Ala111 ranges from 93-100% in Africans Lighter skin aids vitamin D synthesis and is adaptive in areas with less sunlight Prediction that the derived alleles should be under strong positive selection in Europe

What if the GTR method

General time reversal model that allows each possible base change to have its own mutation rate and each base to have different frequencies in DNA sequence when estimating K and correcting for multiple hits

Sexual conflict hypothesis in soay sheep

Genes associated with small horns have a fitness advantage in females No evidence of fitness differences between 3 female genotypes

Trade off hypothesis for soay sheep

Genes associated with small horns have other benefits in males Scurs = reduces reproductive success due to lack of sexually selected trait Normal horns have good reproductive success but lower survival Heterozygous have high reproductive success and longer survival Heterozygous advantage in males as overall lifetime fitness is greater Form of balancing selection maintains scur allele in population

Genetics behind adaptive phenotypic differences

Genes behind adaptive phenotypic differences are likely to be more differentiated than most (neutral genes)

Change in frequency of alleles in a finite population due to chance alone

Genetic Drift

Heterozygosisty is a measure of what?

Genetic Variation

Which of the following statements is not true of genetic drift?

Genetic drift is minimal when p and q are equal.

Utilitarian point of view as to why polymorphism is interesting

Genetic variation underlies phenotypic differences Eg disease predisposition, economically important traits, improvement of domesticated crops and conservation Locating genes and regions of interest for further research

What is an extended phenotype

Genetically controlled innate trait that shapes the environment and is heritable eg burrowing/nesting/web spinning behaviours

3 hypotheses as to how scurs are maintained in soay sheep populations

Genic capture Sexual conflicts Trade off

Universal hierarchy, genes -> environment -> selection

Genome = heritable genetic elements that contain functional genetic elements eg genes/regulatory elements that perform biological functions by producing molecules and pathways that lead to phenotype Phenotype interacts with environment and interactions affect fitness Different genome = different fitness Natural selection and other forces acts on differences and shape evolution

Method of genome sequencing

Genome is fragmented and forms a library Sequencers generate short reads, the length depends on the sequencer used Reads are aligned to a reference genome and SNP calling occurs

What is GWAS

Genome wide association studies Tests for association of markers across the genome with the trait Can explain the genetic basis of quantitative traits

What is a selective sweep

Genomic regions close to a positively selected loci will be caught up due to linkage and inherited along with the selected gene

Method of genotyping monogyne fire ants

Genotype-by-sequencing 121 Illumina RAD sequence reads for 87 haploid sons of BB queens 4983 markers across all 16 chromosomes Nothing of note found

parapatric speciation

Geographic barrier only partially separates populations Some gene flow possible

what is some evidence for evolution

Geographic distribution of organisms Palaeontology - transitional animals Comparative anatomy - homology

What is a Manhattan plot

Graph of chromosome position against -log(P) value = statistical association between SNP and trait Each dot is a SNP marker Skyscrapers are regions with strong association that explain variation Has a horizontal genome wide significance level, SNPs above this are likely to be associated with the trait

Cooper et al, 1995 and grasshopper populations

Grasshopper population genetic distance estimated using nuclear non coding sequence markers Western and northern populations show great eats similarity to Turkish and Balkan populations suggesting these populations founded these populations Geographical barriers eg the alps can prevent migration and coalescence

What causes the differences between polygyne and monogyne fire ants

Heterotrophic chromosomes B and b caused by a large non combining region due to a inversion Create a supergene including GP-9 and other genes causing differences in many traits

Why does GWAS require a higher marker density than linkage mapping?

Higher amount of recombination has occurs, more markers ensures better coverage around the trait in question This means GWAS is finer resolution that linkage mapping

What is a site frequency spectrum

Histogram showing the frequency (proportion) of polymorphic sites when a SNP is present i times in a population

What does genetic similarity depend on

History of separation and gene flow

what is the key to building a reliable phylogenetic tree

Homologous characters

Genic capture hypothesis in soay sheep

Horns are determined by many genes of small effect and horns are an indicator of quality Linkage mapping shows that 75% trait variation in horns can be explained by the RXFP2 gene Horns are not a QTL

how are DNA sequences used to track evolutionary histories

How changes attract and how they change overtime

What is the rate of substitution

How many of the newly arising mutations per generation will become fixed in a population The rate of accumulation is dependent on the neutral mutation rate

2 questions polymorphism studies help us answer

How much variation is there at an average locus in a natural population To what extent does natural selection as opposed to mutation/drift determine the frequency of allelic variants in a population

What questions do we aim to answer by studying sequence evolution

How to measure variability, how much variation is there and what determines the level How can variability tell us about how genome evolution occurs and what determines he process of genome evolution

What are Hs and Ht

Hs = sub population inbreeding (variation within populations) Ht = total population inbreeding (variation between populations

GWAS of horn types in soay sheep

Hugely significant peak on chromosome 10 RXFP2 gene shows significant association with horn types via a nearby SNP marker Very strong evidence RXFP2 is horn locus This SNP explains the presence/scurs/absence of a horn trait

What questions can mapping help us to address

Human medicine Animal and crop breeding Behavioural ecology Speciation and evolution Fundamental quantitative genetics and testing assumptions

Purifying selection in humans and drosophila

Humans 0.041/0.086 = 0.4767 1-0.4767 = 52% Drosophila = 0.12/1.54 = 0.0779 1-0.0779 = 92% Selection is stronger in drosophila and this is consistent with differences in Ne that we see

Human and drosophila SD vs NSD

Humans: SD = 0.086%, NSD = 0.041% Drosophila: SD = 0.12%, NSD = 1.54% Clear evidence of selection against non synonymous diversity

Kiernan et al 2007 study into repeated bottleneck in human history

Hypothesis: non African populations should have experienced more frequent and deeper bottlenecks and therefore have lower Ne and nucleotide diversity Estimated nucleotide diversity using SNPs from hapmap project Africans = 0.084%, Europeans = 0.06%, Asians = 0.057% Humans colonised the world in steps and each new habitat was founded by a small founding population = bottleneck

How much sex biased gene expression is due to sexual antagonism

I&M found that only 8.5% of sex biased transcripts were from sexually antagonistic loci Much of SBGE is a footprint of resolved conflict and not ongoing antagonism

How can we use DNA sequence data to construct phylogenetic trees

Identify SNPs and other sequence changes and use the maximum parsimony principle to test which genetic tree is likely to be correct Trees with the fewest evolutionary steps are favoured

Can we infer patterns of point mutations from K data

If evolution is neutral we can detect patterns of point mutations from nucleotide substitutions as K = 2TU U = K/2T

Problems with sequencer error

Illumina sequencers have high error rate of 0.1-0.01 per base, this can be higher than the level of variability in genomes eg humans = 0.001 Therefore it can be difficult to tell if SNP is genuine difference or an artefact of sequencing

Feature of molecular evolution of important regions and result

Important regions evolve slower as more non synonymous variation is removed by purifying selection (C) These areas are more conserved between species

What is the expected number of new mutations per generation

In a population of n diploid individuals, if neutral mutation rate is U per site per generation then per generation number of new mutations = 2nu

Starting frequency and likely fixation probability of new mutations

In a population with n diploid individuals the starting frequency for a new mutations is 1/2n as mutations begin as a single haplotype Fixation probability is low and mutations are more likely to become lost than fixed

What is slippage mutation

In microsatellites where alleles are defined by the number of repeats it contains slippage mutation is the loss/gain of a repeat between generations This causes microsatellites to have a much higher mutation rate than SNPs

what is natural selection

Individuals whose inherited traits give them a greater chance of surviving and reproducing tend to leave more offspring;

Example of pyrimethamine antimalarial drug and positive selection, causal mutation and study

Introduced in South Asia in 1970s and resistance spread to fixation in 6 years Induced by point mutation in active site of parasite's dihydrofolate reductase on chromosome 4 Strong positive selection for resistance genes as they have large fitness effect Expected heterozygosity estimated at 33 microsatellite loci for 61 parasites Nucleotide diversity is greatly reduced closer to dhfr locus Deviation from neutral diversity = evidence of selection acting

What is the long term effect of gene flow if migrants leave no offspring?

Introduces new combinations of genes by "shuffling" genetic variation every generation. Can be beneficial, neutral or harmful

How is sexual antagonism (conflict) exhibited in red deer

Island species w no migration make them a good model species, males hold territories and female harems Expectation that fittest male has fittest offspring, true for same sex offspring Negative correlation for female offspring = sexual conflict in gene expression

Why study soay sheep

Island species with >8000 individuals studied with many having genomes sequenced Life history, genetics, morphology, parasites etc known Interesting as it is unusual to have polymorphic variation in horns (usually present or absent)

Genetic drift at small population sizes occurs in what 3 situations?

Isolated Small Populations Bottleneck Effect Founder Effect

What do we require for a relative rate test and result of primate/rodent compared to marsupials tree

It can be difficult to find data about the ancestor of the 2 lineages so we use an out group Rate of evolution in the primate lineage is about 9% slower than rodent lineage

Usefulness of Fst

It is an indication and not a fact and is relative to the populations studied May be beneficial to combine with an objective measure of diversity such as nucleotide diversity This would make it more reliable when making assumptions about evolution

Limitations of non population genetics models

It is not always clear which trait should be measured (physiological or adaptive) We need to rule our chance mutations We need to find out which genes are involved and whether gene function is knocked out or just changed

How do we calculate K

K = 2T (rate of substitution) SO K = 2TU

Problems with using K to construct phylogenetic trees

K may underestimate genetic distance due to multiple hits

What is KA and how is it calculated

KA = non synonymous substitutions per non synonymous site Proportion C don't get fixed so KA = 2TU(1-C)

How can we determine when positive selection is likely to have driven an allele to fixation

KA will be significantly greater than KS

How do we calculate C

KA/Ks = 2TU(1-C)/2TU = 1-C C = 1-(KA/KS)

How do we calculate Kjc

Kjc = (3/4) ln [1- (4/3)K]

How can biogeographic events be used for calibration

Known geographical times of events such as island separation can help us date divergence as adaptive radiations often occur after geographic separation

Genetic basis of discrete horn trait in soay sheep

Known to be caused by a single gene on chromosome 2 Comparing genotype and phenotype, genotype predicts phenotype accurately but not perfectly so a large part but not complete control of the trait is genetic

Marker types for linkage mapping and GWAS and number required

LM = microsatellites and AFLPs (amplified fragment length polymorphisms), 100- a few thousand required GWAS = SNPs, many more required 5000-1.5 mil or more

Genomic study of SLC24A5 gene in humans

Largest contiguous region of low diversity in European genome corresponds to this gene Very low mean diversity around the SLC24A5 locus D = -2.9759 in Europeans (p<0.001) = strong evidence of positive selection D in Africans is not significantly different to 0

What is a Densitree

Less transparent tree tips Root = more transparency, less certainty

Effect of synonymous mutations

Likely to be negative as they don't impact the amino acid sequence

How does positive selection affect genomic diversity and effect of recombination

Linkage causes positive selection to reduce nucleotide diversity in areas close to a selected gene due to selective sweep Upon fixation of a beneficial allele, diversity in nearby regions is severely reduced Recombination can introduce new diversity into the area linked with beneficial allele and increase nucleotide diversity at these sites

Two methods for gene mapping

Linkage mapping and GWAS

What is the serial dilution model?

Liu et al 2006, populations residing further from the birthplace of humans in Africa should have lower diversity

Resolution of lm and gwas

Lm = rough, can map QTLs to approximate parts of chromosomes GWAS = finer, QTLs can be mapped to within individual genes

Role of recombination in lm and gwas

Lm = test relies on recombination between markers and QTL within generations in the study GWAS = relies on ancestral recombination events between markers and QTL

Mutations

Long term effects are the raw material of evolution

Buri 1956 and genetic drift

Looked at frequency of brown eye bw75 allele in 109 drosophila populations with 16 starting individuals Initial frequency of 0.5 Populations spread apart and many lost variation

Why does large population size cause incomplete lineage sorting

Loss of genetic variation due to drift is slower in large populations this maintains polymorphisms longer and reduces chances of complete coalescence in internal branches Lineage origin can be unclear with no distinct nodes from ancestral population

3 things genetic drift leads to in a finite population

Loss of variability Fluctuation of allele frequency over time Isolated populations diverge even in the absence of selection

If inbreeding in sub populations is high, how does this affect Fst?

Low level of expected heterozygosity due to increased homozygosity so Hs is smaller Therefore Fst is larger and populations are more divergent

Problem with scurs in soay sheep population

Males with normal horns have higher reproductive success and therefore higher fitness so how are scurs maintained?

Horn phenotypes in soay sheep

Males: normal = 87%, scurs (preformed/asymmetric) = 13% Females: normal = 32%, scurs = 29%, polled = 39%

what are the various methods of sequence alignment

Manual - by eye Automatic - computer local alignment - Smith and Waterman algorithm and more

Fst findings in heliconius

Many significant Fst peaks outside of coding areas Fst corresponding to colour gene = 0.8 Very high indicating strong differentiation between populations Likely to be under selection

Why might alleles have very low Fst values

May be locked in inversions and unable to recombine and segregate = persistence in populations May be subject to very strong purifying selection if they perform an essential biological function

What would we expect Ne to be in populations with fluctuating population size?

Me would be closer to the minimum population size and low as diversity will be reduced when population has small size

Aims of innocenti and morrow 2010

Measure whether sex biased gene expression occurs and if sex biased genes are associated with fitness and cause conflict

PAML and TRIM5a

Method used to identify important region Significant patches compared between species Measured infection rates between different cell lines Rhesus TRIM showed lowest infection rates, replacing with human 13aa sequence increased infection rates and deletion of whole 13aa sequence vastly increased infection rates Therefore the 13aa sequence must be necessary for restriction or HIV

What does allele frequency in sub populations depend on

Migration and strength of selection

Example of Habitat Fragmentation

Missouri Ozarks - Collard Lizards

How do we genotype a mapping cross

Molecular markers throughout the genome distinguish between parents Statistical tests along chromosome to test markers association with trait F2 have 3 genotype possibilities = homo parent 1, hereto or homo parent 2 If trait mean is the same for each genotype it indicates there is no QTL Genotypes with significantly diff trait means = marker is close to gene that influences trait

Social forms of fire ants

Monogyne =BB, one queen that is large and fecund Polygyne = Bb, multiple smaller and less fecund queens, recognise and kill BB queen GP-9 gene controls social form and affects many traits including behaviour, size, fecundity and social form

Benefits and drawbacks of using while DNA sequences to identify gene differentiation

More costly More detail and able to detect larger mutations

Why might counting substitutions underestimate K?

More distantly related species have more substitutions as T is higher Multiple hits: subs occurring at the same site are more likely in distantly related species Multiple hits will lead to K being underestimated

what are shared derived characters?

More intuitive than morphologicala data Shared derived character = bony Amniotes from amphibians = egg

what are some examples of traits that can't be inherited

Morphological traits might not be heritable (phenotypic plasticity). e.g. human height DNA sequences always heritable.

how do you reduce/avoid homoplasy

Morphology subdivide into multiple characters; choose characters not associated with adaptation to a particular niche (e.g. body shape in aquatic animals, limb size/shape (locomotory mode), Molecular choose "housekeeping" genes - genes related to cellular function, not genes associated with adaptation to a particular niche; score lots of characters (sequence more!);

What is the cost and ease of data

Morphology used to be much cheaper than DNA sequencing - not any more! Morphology requires specialised anatomical knowledge but the number of specialists are few

How are sexually dimorphism traits genetically correlated?

Most correlations are >1 so as the trait increases in males it also increases in females Negative correlation over all, so the more dimorphism a species is, the weaker the genetic correlation

what is meant by DNA sequence alignment

Most fundamental step of molecular analysis, yet often least critically analysed. Need to make sure all "bits" of DNA you are comparing are truly equivalent (e.g. same gene, same region of gene, same strand, in different organisms)

Mechanism of descent with modification

Mutation Drift/ Founder Effect Migration > Natural Selection

What is a transversion

Mutation from a purine to a pyramidine and vise versa

Zhang and Gerstein 2003 study into mutation rates

Mutation patterns in humans obtained from analysing 1726 pseudogene sequences Mutation (and therefore substitution) rate are not uniform Neutral mutation rate is different for different types of mutation

What is U

Mutation rate per site per generation in neutral regions

What is the concept that relates to why deleterious alleles persist in populations?

Mutation-Selection Balance

How are new alleles formed?

Mutations create new alleles that can be inherited by carrier descendants Each new allele starts as a mutation in a single individual Higher mutation rate = higher level of polymorphism/diversity

What are silent polymorphisms

Mutations in non coding region and synonymous polymorphisms

What are non-synonymous mutations?

Mutations in the coding region that change the amino acid sequence Likely to have fitness effects as most mutations affecting the phenotype much be deleterious as it has undergone millions of years of selection to improve its performance

What are synonymous polymorphisms

Mutations in the protein coding region that do not change the amino acid sequence

In the absence of a barrier what does divergence of sub populations depend on

N = effective population size of each sub population M = proportion of subpopulation made up of migrants each generations N determines drift and gene flow depends on M

How do we calculate non synonymous diversity

NSD = 4 Ne U (1-d)

How do we calculate d

NSD/SD = 4NeU(1-d)/4NeU = cancels to 1-d SO d = 1- (NSD/SD)

Medical use example for sequencing

National cancer institute sequences 33 tumour types from 11,000 people as well as normal cells 2.5 petabytes of data collected (huge) Indentured tumour subtypes, molecular basis of some cancers and potential therapeutic targets

Darwin's logic for natural selection fact 3

Natural resources are limited. In a stable environment, they remain relatively constant

What is important in determining the efficacy of selection

How do you calculate Ne

Ne = nucleotide diversity at neutral sites / 4U

Effect of Ne on drift and polymorphism

Ne determines the rate of drift Loss of genetic variation is faster in populations with small Ne Populations with smaller Ne are less polymorphic Large Ne allows more alleles to be maintained in a population

Predictions for a SFS under neutrality

Neutral WF population with constant population size Most derived alleles will be present at low frequency We can conceptually class derived (SNPs) alleles as low/medium/high frequency

How do we calculate rate of substitution

New mutations per generation x neutral fixation probability RoS = 2nu x 1/2n = u Rate of substitution is equal to the neutral mutation rate

When drift (N) and gene flow (M) are in equilibrium, what does Fst depend on?

Nm = number of migrants each generation

3 possible outcomes each generation of Genetic drift

No change Random increase (+ Delta P) Random Decrease in allele Freq (- Delta P)

What occurs if we didnt have no mutations

No new alleles/genes and eventually no evolution

Features of histone 3 molecular evolution

No non synonymous changes between humans and mice despite 90 million years of evolution and separation

Darwin's logic for natural selection fact 4 & 5

No two individuals are exactly the same; rather, every population displays enormous variability. Much of this variation is heritable

Why do non-synonymous changes have lower nucleotide diversity than synonymous changes

Non synonymous are more deleterious than synonymous as they alter the phenotype

How do we calculate K for non synonymous changes

Non synonymous mutations are more likely to be deleterious so have lower fixation probability and lower rate of substitution Proportion C are so deleterious that there fixation probability = 0 So substitution rate = u(1-C) KA = 2TU(1-C)

Which of the following will change genotypic frequencies in a population without also changing allelic frequencies?

Non-random mating

Limitations of linkage mapping

Not as useful as GWAS for wild populations Requires crossing and inbreeding so difficult and unethical in species like humans

What is effective population size?

Number of individuals in a WF population that produce the same rate of genetic drift as seen in the natural population

What is K

Number of substitutions between 2 homologous sequences from 2 species

What was found when comparing Fst for African and European human populations

Observed proportions exceeded expected for the very lowest and very highest Fst values At low Fst genes may be kept similar by purifying selection if they are essential to survival (or maintained by balancing selection) Very highest Fst = surprise as no Fst over 0.7 was predicted, loci must be fixed in genome (likely in isolated populations with high divergence)

why is morphology important

Offers independent support for genetics. Radical genetic trees will never be believed unless they make biological sense: are consistent with certain morphological features, e.g. whales + hippos, ecdysozoa

Method for linkage mapping mice

Oldfield and deer mice crossed F1 gen back crossed with deer mouse due to evidence of dominance (100% F1 exhibited escape tunnel oldfield phenotype) and backcrossing dilutes proportion of oldfield mice in genome (0.25 of genome but 50% phenotype) 526 SNPs types in 272 backcrossed mice

Burrowing differences in mice

Oldfield mice have long entrance tunnel and escape tunnel behaviour that is consistent across different habitats and repeated in the lab = unique to this species Deer mice have short entrance tunnels and don't build escape tunnels

Typical eukaryotic mutation rates

One in a million (1x10^-6) or one in a billion (1x10^-9)

what is a rooted/unrooted tree

Outgroup rooting uses existing knowledge of relationships to place the root using an outgroup taxon: e.g. kangaroo vs placental mammals

Directional mutation

Over long periods of time, it eventually produces small changes in allele frequency

Darwin's logic for natural selection inference 3

Over the generations this process of natural selection will lead to a continuing gradual change of populations, that is, to evolution and to the production of a new species.

Probability of fixation is equal to what?

P initial

Example uses for microsatellites

Parental analysis and relatedness Forensics Inbreeding in conserved populations and genetic structure in populations and sub populations Evidence of bottlenecks, effective population size and gene flow Phylogeographic studies

How have molecular phylogenies been useful in classifying bats

Pettigrew suggested that Megachiroptera may b more closely related to primates due to similarities in retinal connections suggesting polyphyly of bats and two flight origins in mammals Molecular phylogenies confirmed Monophyly of bats as rooted and unrooted trees put mega and micro in the same clade Petrigrews suggestion requires 10 more evolutionary steps than most parsimonious suggestion

What are the 2 phases of evolution

Polymorphism and divergence Within species polymorphism leads to between species divergence

What is Tajimas D sensitive to

Population expansion and purifying selection can also cause excess of low frequency neutral variants, producing a similar SFS to positive selection and a negative D value D is less sensitive to population structure

Assumptions of the WF model

Population of N diploid hermaphroditic individuals Random mating Discreet non overlapping generations No selective differences among the loci in question (predictions under neutrality) New individuals formed by random sampling with replacement of gametes from parent

Rate of evolution by drift is inversely proportional to what?

Population size

What does genetic diversity depend on

Population size and gene flow

Bottleneck Effect

Population size is drastically reduced by a disaster causing drift, after the population crash the population may return to large size

What is Fay and Wu's H sensitive to?

Population subdivision (bottlenecks) can lead to an excess of high frequency neutral variants and a negative H value H is less sensitive to population expansion

What does a high Fst mean

Populations are distinct/ strongly differentiated Most variation is between populations with less within populations

What does a low Fst mean

Populations are not very divergent Most variation is within populations, not between

How do bottlenecks affect Ne

Populations experiencing bottlenecks are expected to have lower Ne Nucleotide diversity will be lower as loss of variation due to drift is faster in small populations and because Ne = pi/4U So as diversity decreases so does Ne Bottlenecks have significantly lower Ne

How can we track changes in distribution and glaciation example

Populations persist in southern refugia, recolonise by moving north Modern populations will show genetic similarity with source of colonists Refugia populations will have greater genetic diversity and be distinct from each other due to isolation and divergence due to gene flow

What would we expect D to be under positive, purifying and balancing selection?

Positive = <0 Purifying = <0 Balancing = >0

What would we expect H to be under positive, purifying and balancing selection

Positive = <0 Purifying = ~0 Balancing = <0

What can cause departures from molecular clock

Positive selection

Prediction for non synonymous vs synonymous diversity

Prediction that SD > NSD As NSD is likely selected against whereas SD is selectively neutral

A farmer has a herd of cows in which the milk protein content and butterfat are both desirable characteristics. The phenotypes of both characteristics are correlated with a coefficient of 0.91. The narrow-sense heritability for milk protein content is 0.76, and for milk butterfat it is 0.82. What is the most likely result regarding protein milk content in a subsequent generation, if the farmer selects for higher milk butterfat?

Protein content will increase.

quantitative trait loci regions of genes that contribute to quantitative traits mapping=> identification of chromosome regions that are likely to contain ___, association w/genetic markers described and located -SNPs= single nucleotide polymorphisms *microsatelites=tandem repeats AVG --individual vary in # of copies --highly variable present in all indiv.s/easy to use

QTLs

A flock of sheep produces on average 22kg of wool per year. Ten sheep (five female and five male) are allowed to breed among each other. These ten sheep produce on average 30kg of wool per year. Their progeny produces 28kg of wool per year. What is the narrow-sense heritability for wool production among the sheep in this flock?

R = h^2 x S (28-22) = h^2 x (30-22) h^2 = 0.75

Why might there be a departure from hardy Weinberg equilibrium in the total population when there wasn't in a sub population?

Random mating assumption is violated, sub populations mate assortatively Form of inbreeding leads to an excess of homozygotes

How is GWAS carried out

Random sample from a population and uses recombination events occurring naturally by evolution (more recombination events than linkage mapping)

What is genetic drift?

Random sampling leads to fluctuating allele frequencies across generations Once fixation occurs, variation is lost Has a greater effect in smaller populations

What determines K?

Rate of substitutions and time since divergence Therefore K is determined by T and neutral mutation rate (as rate of substitution is the same as the neutral mutation rate) K is proportional to the mutation rate so as this increases, K becomes larger

Why is read depth important

Read depth = number of times a read is sequenced Higher read depth = higher coverage If a SNP is only present in 1/2 variants it is unlikely to be a genuine difference SNPs occurring in all/majority of reads is likely to be a genuine difference

Which WF assumptions are violated in natural populations? And solution

Real populations have age structure and sex differences Genetic drift in real populations is described by WF by the concept of effective population size (Ne)

Spinal Muscular Atrophy

Recessive combination is detrimental and homozygotes usually die. The fitness for W22 is only 10%

Heterozygosity in fragmented arid plant populations

Regardless of initial allele freq p, we predict smaller populations have decreased polymorphism within populations due to random fixation

Features of non combining region on b chromosome in polygyne fire ants

Region is > half of chromosome 16 encompassing at least 616 genes (3.7%) of total genome Inversion evidence as markers are opposite to B chromosome inversion prevents recombination

What are pseudogenes

Regions that beat close resemblance to functional genes at a different locus but are rendered inactive due to mutations They are likely not subject to functional constraints and can evolve neutrally

what is rRNA

Repetitive (ie more than one copy per genome) Can be found in all eukaryotes DNA sequence based (via PCR/Sanger or NGS)

Why don't differences in Ne scale linearly with differences in census size

Result of past evolutionary events such as selection and demography

What is d

Rough measure of purifying selection Proportion of non synonymous mutations so strongly deleterious that they don't contribute to sequence variability 1-d are neutral variation

Lohmueller methods

SNP data taken from 15 African Americans and 20 European Americans 10,150 genes analyses and synonymous SNPs used as neutral reference (to determine if selection is cause of difference NSD) Classified non-synonymous as benign, weakly deleterious and strongly deleterious Theoretically should decrease in frequency the more harmful they are

What are SNP's

SNPs - single nucleotide polymorphisms Highly abundant; Genome wide distribution;

How does sex biased gene expression help to solve the problem of sexual conflict

Same trait for males and females may have different optimums so expressing gene at same level in males and females = not at optimum for either sex (compromise reduced fitness in both sexes) Differential gene expression allows both sexes to reach optimum for a trait

what is parsimony

Search for topologies that require the fewest character (nucleotide or morphology) changes Shortest tree length ⇒ most parsimonious

Ecological speciation

Selection for different ecological traits creates reproductive barriers -can lead to pre and postzygotic isolation

How does correlation cause conflict

Selection has caused dimorphism for a region Both sexes exhibiting the same trait will reduce fitness if one or both sexes

How does Ne (effective population size) affect selection

Selection is stronger in large populations

Method for innocenti and Morrow SBGE and fitness experiment

Selectively chose 15 hemiclonal lines of drosophila 3 groups, equal fitness between sexes, males fitter and females fitter Equal group was a control to see evidence of antagonism 24 males and 24 females from each line measured for gene expression Microarrays for 18,500 genes using cDNA

Effect of a barrier on 2 sub populations

Separation by a barrier will prevent gene flow and allele frequencies will drift apart due to genetic drift Populations tend to diverge and Fst will become larger with more variation between populations than within

what is the sequence alignment for RNA genes

Sequence alignment for RNA genes is more difficult Can't use codon/amino acid Can use secondary structure of mature RNA

What can tell us about long term evolution

Sequence divergence between species This is caused by substitutions We can use neutral substitution rate to identify departures from this that give insight into evolutionary/demographic factors that have affected the course of evolution

Additional disciplines involved with big data generation

Sequencing genomes results in huge data sets Data storage and indexing/searching required computer science Data reuse and mining requires maths and stats

Innocenti and Morrow conclusions about SBGE

Sex biased gene expression is very common And sometimes associated with sexual conflict (antagonism) SBGE is often a signal of resolved conflict SBGE is a way of solving sexual conflict

Short Term effects of Mutations

Sex recombination shuffles alleles in new genotypes

What maintains genetic variation for fitness in drosophila

Sexually antagonistic selection

what are some of the un-useful characters for phylogenic reconstruction

Shared primitive characters are not informative (under parsimony) Unique derived characters are not informative (under parsimony)

what are microsatellites

Short Tandem Repeats (STRs) Polymorphisms are variation in number of repeat unit (each unit is 2-6 bp) Need to be developed for each species (or groups of closely related species)

What are 2 causes of incomplete lineage sorting ?

Short internal branches and large population size

Genetic control of horn size in soay sheep

Significance peak on chromosome 10 RXFP2 explains 75% heritability

How do you distinguish homology with analogy

Similarity "test": Homologous features are expected to display detailed similarity (in position, structure, development) whereas homoplastic similarities are more likely to be superficial Congruence Test: Did the character state originate once or multiple times? DNA/amino acid sequence alignment:

How can we infer relationship without molecular studies? And limitations

Similarity and fossil evidence May be unreliable since they both rely on physical similarity which may be due to convergence Fossil record is incomplete and can be lacking as therefore is difficult to construct trees from Also fossils can only be carbon dated up until ~100k years ago

what are the principles of parsimony

Simpler hypothesis = difficult hypothesis Mot plausible tree, fewest number of nucleotide changes Can be used to separate groups of sequences Simplest with lowest changes is easiest

What are SNPs

Single nucleotide polymorphism a Changes in one base pair Can be difficult to tell direction of change between 2 sequences so we can compare to an ancestral sequence

what is informative variability

Some groups are morphologically conservative, e.g. parasites, or have little obvious morphology, e.g. bacteria

Why are trees important?

Species delimitation: Trait evolution, Species diversification, Geographic distributions, rate of evolution and speciation, anti venoms, diseases etc

What is the Wright fisher model? (1930)

Standard model for evolution in molecular genetics that makes testable predictions about patterns of polymorphism and divergence

How are results of linkage mapping presented

Statistical association of marker with trait = LOD score (measure of likelihood of a QTL) LOD on y and distance along genome on x Peaks show most likely locations of QTLs LOD of 3 = foot indication of real QTL Most chromosomes have flat profiles

What is the relative rate test?

Statistical test examining the null hypothesis from the neutral model that the amount of evolutionary change between 2 lineages is equal

Lohmueller 2008 aim

Study the prediction that deleterious variants and more common in non African populations as repeated bottlenecks have decreased Ne and diversity Reduced Ne means selection is weaker and therefore more deleterious variants are maintained

Why study Fst in heliconius

Sub species of heliconius melpomene have different wing marking These are involved in survival and mate choice so are likely under selection Well studied species so we have knowledge of control genes Background rate with Fst for most of genome

Darwin's logic for natural selection inference 2

Survival in the struggle for existence is not random but depends in part on the hereditary constitution of the surviving individuals. This unequal survival constitutes the process of natural selection

How to be calculate K for synonymous changes

Synonymous changes are likely to be neutral so substitution rate for synonymous changes is the same as the neutral rate = U Synonymous K is the same as neutral K so Ks = 2TU

Neutral markers

Synonymous polymorphism Silent polymorphism

What is Ks and how is it calculated

Synonymous substitutions per synonymous sites Likely to be neutral and under neutrality rate of substitution = mutation rate So Ks = 2TU

According to international agreements, GMOs are approved on a case-by-case basis.

Approved commercial GMOs include corn, soybean, and canola.

GMO stands for Genetically Modified Organism.

GMOs have one or more genes from another organism placed into their genome.

Horizontal and vertical gene transfer are ecological risk of GMOs that occur when genes inserted into a GMO are transferred unintentionally into a wild relative of the GMO.

One of the reasons molecular data is so useful in studies of evolution is that all organisms contain DNA and proteins, whose sequences can be analyzed and compared.

Protein variation is an underestimate of DNA sequence variation.

How do we calculate T (molecular clock)

T = K/2U

What is T, and the relationship between T and K

T = time since divergence Neutral theory predicts a linear relationship between T and K

Sawyer et al study of TRIM5a

TRIM5a sequences in 17 primates KA/KS estimates for whole gene and SPRY region alone, selection seems particularly high in hominids Most intense selection in SPRY protein domain (KA/KS = 8.8) Positively selected residues cluster in a 13 aa patch in SPRY domain Tight cluster of strong positive selection is likely to be site of interaction between proteins locked in genetic conflict

What is the Kimura 2 parameter method?

Takes into account the difference in mutation rates and transition bias when correcting for multiple hits and estimating K P = differences due to transitions and Q = differences due to transversions

What are microsatellites

Tandemly repeated DNA, 1-6bp repeats Alleles defined by number of repeats , loci have multiple alleles Mutation rate is several orders of magnitudes higher than SNP (10-3 compared to 10-8 per site per generation), slippage replication useful for delineating between close relatives

What did sewall Wright suggest

That inbreeding could be used as a measure of differentiation between sub populations

What determines the efficacy of selection

The efficacy of both positive and negative selection is determined by |NeS| This is an absolute value so as the value increase, selection is stronger

allopatric speciation

The formation of a new species as a result of an ancestral population's becoming isolated by a geographic barrier

What explains why we have Spinal Muscular Atrophy?

The high mutation rate. Its in balance with selection so evolution can never can take it out

Ne in humans

The human population is >7 billion but Ne is only 28,000 people Differences in Ne do not scale linearly with census size

Innocenti and Morrow, sex specific fitness and sexual antagonistic fitness

The majority of genes associated with sex specific fitness were also sexually antagonistic 62% for males and 66% for females Expression of 1,487 genes affected fitness antagonistically (817 to male benefit/female harm and 661 female benefit) 867 genes affect male fitness 634 genes affect female fitness

When is C largest

The more functionally important a gene is the more likely a non synonymous mutation is deleterious C is larger for important genes KA is smaller as selection acts to maintain gene function

What is the molecular clock

The neutral model predicts that rate of molecular evolution is constant over time as it only depends on the substitution (mutation) rate so we can use the neutral mutation rate to estimate how long ago lineages split (estimate divergence time)

What is the neutral theory- Kimura 1968

The neutral theory hypothesises that the fate of the bulk of mutations contributing to molecular evolution and variation is determined by drift rather than selection Assumes that most mutations are neutral or so weakly selected that they behave as if neutral This allows for positive/purifying selection but assumed contribution to diversity/divergence is negligible

What does the allele frequency of non neutral genetic variants depend on

The relative strength of selection and drift

what is metameric segmentation

The repetition of organs and tissues at intervals along the body of an animal

what is the distance method

The simplest approach to building trees. Clusters sequences in the order of the most similar to the most different. Sequence alignment -> Distance matrix

Why study patterns in evolution

The study of patterns deals with the detection of order in nature;

Why study processes in evolution

The study of processes deals with the mechanisms generating and maintaining this order.

How do we analyse sequence evolution

Theoretical models showing how factors such as selection and drift affect genome evolution Data analysis methods that measure variability or rate of evolution, detect genes need selection and reconstruct evolutionary relationships between species

what are protein coding genes

There are 20 naturally occurring amino acids that contribute to building cells, muscles, and other tissues Amin-acids are encoded by three reading frames (codons): 64 possible combinations. 3 combinations are stop codons (TAA, TAG, TGA) 61 combinations code for amino acids

Problems with DNA sequence method for constructing phylogenetic trees

There are many possible trees to consider, as the number of species in a tree increases the number of possible trees increases exponentially Genomes are huge

How do Ne and actual population census size compare?

There is a smaller difference between Ne than actual size

Why are pseudogenes useful

They can be used to study substitutions as they evolve neutrally

¥a1 pseudogene in humans as an example of use of pseudogenes

This genes is a pseudogene of the a1 gene and also has a homologous in mice Sequences are aligned and using parsimony principle we can infer substitutions occurring in the pseudogene lineage A -> G mutation

what are the types of trees

Three main kinds Cladogram is basic Branching relationships, horizontal cross bars Phylogram - tips don't flush, proportional to character changes on tips Chronogram (time tree) proportional to time Scale bar length of tree Length of divergence

3 reasons we construct trees

To represent inferred historical relationships between organisms To study the evolution of phenotypes and genes To test hypotheses about the cause of evolution

What does pseudoinfinitesimal mean

Trait is controlled by many genes all with tiny effects on the trait Complex control of trait with many genes effects too small to detect with GWAS Missing heritability problem

What is a phylogenetic tree

Tree representing a hypothesis about historical relationships between species Trees can be rooted or unrooted

What are some limitations to phylogenetic analysis?

Trees are hypotheses Scoring characters can be hard Homoplasy (same mutations along different branches can confound parsimony analysis) Ancient events are hard to infer Hybridisation and gene flow occur in real populations and trees are not strictly bifurcation Incomplete lineage sorting

What is TRIM5a and what can we predict about it's evolution

Tripartite motif protein isoform 5 alpha is part of primates innate immunity to the HIV retrovirus Restriction depends on the viral capsid via an unknown mechanism that involves direct interaction between TRIM5a and virus Red queen dynamics for antagonistic interactions As virus mutates there is strong selection for TRIM5a to evolve defence and then strong selection for virus to evolve again Prediction that positive selection will drive rapid amino acid replacement at site of interaction and that area with the highest KA is likely to be the site of interaction

T/F, Recessive alleles should persist when mutation is introduced more than dominant alleles

True

T/F, rate of loss of variation is faster in small populations

True

True or False: A bacterium containing a prophage is immune against infection by this type of phage

True

True or False: A diploid individual has two alleles of every gene.

True

True or False: A phenotypic ratio of 3:1 is typical for the offspring of two heterozygous parents.

True

True or False: An E. coli strain referred to as trp- requires tryptophan to grow.

True

True or False: During meiosis, homologous chromosomes pair with each other.

True

True or False: During metaphase, chromosomes align in the equatorial plane of the cell.

True

True or False: Meiosis I is also called the 'reductional division'.

True

True or False: When an F factor integrates into the bacterial chromosome, the strain becomes Hfr.

True

True or False: When bacteria exchange genetic material via bacteriophages it is called transduction.

True

Expectation for Fay and Wu's H under neutrality

Under neutral WF model H = 0 Statistically significant departures from 0 suggest evolutionary forces are acting

Expectation for Tajimas D under neutrality

Under neutral evolution and constant population size D = 0 Statistically significant departures from 0 suggests evolutionary forces are acting

Why is Fst useful

Under neutral evolution we expect Fst to be similar for all genes Fst can be used to identify more divergent regions of the genome with higher than expected Fst where selection may be acting

Features of K that make it appropriate to use for constructing phylogenetic trees

Under neutrality the mean number of substitutions between 2 homologous DNA sequences is K = 2TU Neutral model predicts linear relationship between K and T so the smaller K is the more closely related species are Calculating K for neutral sites between multiple species we can arrange them based on evolutionary distance

What can we use genetic data for

Under population history including distribution, size and gene flow

Why do we construct mathematical models for evolution

Understand how evolution ought to proceed Check if predictions are comparable to observations Make inferences about past history and identify essential loci

what is the difference between rooted and unrooted trees

Unrooted, no polarity or direction Reconstruct ancestry, need to direct BC close to AD Can't see the closest ancestors on tree in comparison to rooted

What is UPGMA

Unweighted pair group method with arithmetic mean

Two methods for constructing phylogenetic trees

Using DNA sequence data and parsimony principle Using estimated genetic distance (K)

what are some of the useful characters for phylogenic reconstruction

Variable, e.g. blue in one taxon, red in another. Heritable, e.g. not phenotypically plastic, such as growth forms in the same species of corals or plants.

Why is purifying selection strong on histone 3

Very functionally important as most amino acids interact with DNA and other cores histones directly, needs to maintain compactness and alkalinity to interact with acidic DNA Mutations are likely to impair function

Frequency of IlS across autosomes and X

We can construct statistics that show frequency of ILS across the genome Frequency of IlS is consistent across autosomes but lower on the X chromosome X has a lower Ne that autosomes as it occurs at 0.75 frequency in the population (Ne(A)/Ne(X) = 0.75) Large population size is a cause of ILS so autosomes have higher frequency

Why is phylogeography useful

We can reconstruct environmental change and changes in animal and plant distributions using genetic data

Why study Darwin's finches?

Well known case of large scale adaptive radiation over a short timescale with an unknown genetic basis GWAS to find genes behind beak shape divergence

Example of sequencing initiatives

Wellcome at the danger institute aims to sequence all 66,000 native UK animals and plant species Global effort to sequence all known 1.5 mil species in the world (animal/plant/fungi/Protozoa) Coat of sequencing genomes has decreased which has lead to many organisations wanting to collect this big data

How can we tell which alleles are derived and ancestral?

When a new variant arises at a locus where an allele was previously fixed we need to determine which is ancestral and which is derived We can infer which it is by comparing sequences to an outgroup and using the parsimony principle

How do short branches cause incomplete lineage sorting

When internal branches are short (short timeframe for divergence) there is not enough time to ensure coalescence between lineages and a distinct ancestral population Gene divergence may not be complete before populations split again especially when divergence is rapid (short branch length)

What is substitution

When one allele replaces all others at a given locus and becomes fixed in the population This is the cause of divergence

P initial is equal to what

X/2N

A DNA strand is labeled with heavy nitrogen (15N). If the conservative model of replication had been correct, what would you see after two rounds of DNA replication in medium containing 14N? a. one heavy, one light band b. one heavy, one intermediate and one light band c. one heavy, one intermediate band d. one intermediate and one light band

A certain species of mammal has 14 pairs of homologous chromosomes. What is the diploid number of this species? a. 7 b. 14 c. 28 d. 42

A family has 5 children, all boys. Mom would really like to have a girl. What are her chances? A. 1⁄2 B. 1/64 C. 63/64 D. 1/6 E. 3/4

A father with myotonic dystrophy has three daughters who are all carriers of the mutant allele and two sons who are unaffected noncarriers. The three daughters have six sons, of which four are affected and two are not, and four daughters, of which two are carriers and two are not. From this description, what type of mutation is probably responsible for myotonic dystrophy? a. X-linked recessive b. X-linked dominant c. autosomal recessive d. Y-linked

A female is diagnosed with the X-linked recessive gene disorder hemophilia. In checking her medical history, the doctor will most likely discover that __________. a. her father had hemophilia and her mother was normal b. her mother had hemophilia and her father was normal c. all siblings also have hemophilia d. there is no family history of hemophilia

A fruit fly with the genotype XO would be phenotypically a. male b. female c. both male and female d. neither male or female

A lacI- mutation is- a. constitutive. b. trans-dominant to lacI+. c. repressible d. all of the above e. none of the above

A male with one Barr body would belong to which of the following syndromes? a. Klinefelter's b. Turner's c. XYY d. Hermaphordite e. Poly X

A mother who is blood type AB has a child who is AB also. A potential father is blood type O. What would a well-informed geneticist conclude? a. He might be the father, but it is unlikely. b.He or any other man of blood type O could be the father. c. He is very likely to be the father. d. He cannot be the father.

A mutation of the operator CAP-binding site occurs such that nothing can bind to the site. Does the bacteria with this CAP-site mutation produce less or more LacZ product in the presence of lactose than non-mutant E. coli? a. less b. more c. about the same

A protein which turns transcription off is a (an)- A. repressor B. activator C. effectors

A self cross of a red hibiscus plant produces 11 red flowered plants, 2 pink with red centers, 2 white with red edge and 1 white-flowered plant. Chi square = 6.6. Is your hypothesis of two independent genes with 2 alleles each correct? a. Yes, likely within parameters of proof accepted by the scientific community b. No, highly unlikely

A sequence that is transcribed but not present in mRNA is _____ a. introns b. exons c. mutations

Acridine dyes such as proflavin and ethidium bromide are highly mutagenic because they - a. Insert between the stacked bases of DNA b. Alter the pairing behavior of bases c. Absorb UV light d. Remove base amine groups

Alkylating agents such as EMS are mutagenic because they - a. Add an alkyl group to bases which causes mispairing b. They insert or delete a base c. They cause thymine dimers d. They break the sugar-phosphate backbone of DNA

All of the alleles of the members of a population are known as __________. a. the gene pool b. genetic drift c. speciation d. phylogeny

Alternate forms of a gene on homologous chromosomes are called _________ a. Alleles b. Homologs c. Genes d. Segregants e. Pseudogenes

An E. coli nutritional mutant is described as an auxotroph, which requires minimal medium with supplementation of an organic component or inorganic ion for growth. a. True b. False

An allele of a gene that confers great athletic ability is identified in a family of ten children in which all ten children have the same genotype. However, only three of the children exhibit great athletic ability, four have slightly better than average athletic ability, and three have average athletic ability. What can be inferred about the expressivity of this gene? a. The gene shows less than 100 percent expressivity. b. The gene shows 100 percent expressivity. c. The gene shows 1 percent expressivity. d. Nothing can be inferred about the expressivity of the gene from this information.

An enhancer is likely to bind directly to -- a. Zinc finger proteins b. TBP (TATA Binding Protein) c. RNA polymerase d. DNA polymerase e. All of the above will bind to enhancers

An organism that has lost its ability to synthesize its own histidine is called: a. auxotroph b. donor cell c. prototroph d. revertant

Assume that a Robertsonian translocation occurs between two 21st chromosomes. Will the progeny of a carrier for this translocation have Down Syndrome? a. yes, all progeny will be down syndrome b. some progeny will be down syndrome c. no progeny will be down syndrom

Autotrophic mutants for inability to synthesize the amino acid arginine were selected Neurospora, mutants Arg 1- and Arg 5- were crossed to produce a dikaryon (cells have a single haploid genome from either parent). If the dikaryon is also unable to syntheisze arginine, what does that tell you about these two mutant Neurospora isolates? a. the two arginine mutants are in the same gene b. the two arginine mutants are in two different genes c. Arg 1- and Arg 5- are co-dominant d. the mutation screen did not select for arginine auxotrophs

Chromatin of eukaryotes is organized into repeating interactions with protein octamers called nucleosomes. Nucleosomes are composed of which class of molecules? a. histones b. glycoproteins c. lipids d. H1 histones e. nonhistone chromosomal proteins

Chromosomes condense during a. prophase b. metaphase c. anaphase d. telophase e. interphase

Drosophilia, a heterozygous female for the sex-linked traits a,b, and c (ABC/abc) was crossed to a male that was phenotypically abc. Offspring of this cross occurred in the following phenotypic ratios: Abc--- 460 aBC---450 abc--- 32 ABC--- 38 aBc--- 11 AbC--- 9 ABc--- 0 abC--- 0 Calculate the map distance between loci a and b? a. 7 mu b. 2 mu c. 9 mu d. 5 mu

During DNA replication, the lagging strand is synthesized _____ a. 5' to 3' b. 3' to 5'

During which stage of the cell cycle are individual chromosomes NOT visible within cells? a. S phase b. metaphase c. anaphase d. telophase

Eukaryotic chromosomes contain two general domains that relate to the degree of condensation. These two regions are ________. a. heterochromatin and euchromatin b. uniform in the genetic information they contain c. separated by large stretches of repetitive DNA d. each void of typical protein-coding sequences of DNA e. void of introns

For the following cross, what are the phenotypes of the parents? fut1/fut1 IA/IA (Mom) x Fut1/Fut1 ii (Dad) a. Mom isO,Dad is O b. Mom is A,Dad is O

Frederick Griffith's transformation experiment showed that - a. A chemical component from disrupted "smooth" bacterial cells could introduce a new, heritable trait to a cell b. DNA is the genetic material of viruses c. DNA is the genetic material of bacteria d. DNA is the genetic material of mice e. All of the above

Genes which are transcribed all the time are - A. constitutive B. inducible C. repressors D. activators E. effectors

Genes with GC or GXC sequences can be silenced by a. Cytosine methylation b. Guanine methylation c. By binding to TFIID d. By RNA polymerase binding to GC-rich regions

Geographically isolated populations may diverge genetically from each other. When divergence results in two populations that are genetically distinct and reproductively isolated, then: a. allopatric speciation has occurred b. sympatric speciation has occurred c. no speciation has occurred

Glucose is always the preferred substrate for E. coli because it enters directly into glycolysis to produce ATP. In both lac and ara operons, transcription of ara or lac is reduced in the presence of glucose by - a. CAP + cAMP failing to bind to the promoter b. CAP + cAMP binding to the promoter c. CAP + cAMP binding to the operator d. cAMP binding to the operator

Glucose present, lactose present. β- galactosidase will- a. be synthesized (low) RNA b. not be synthesized

Haplotype networks can be used to- a. describe the relationships between different haploid genotypes b. describe unique sequence of bases that is shared by several individuals c. determine if populations are interbreeding d. determine if populations in Hardy-Weinbergy equilibrium

How is a vector used in DNA cloning? a. A vector is a carrier molecule into which a specific sequence of DNA is inserted. b. A vector is a bacterial cell. c. A vector is a sequence of DNA placed into a carrier molecule for cloning. d. A vector cuts DNA at specific sequences.

How many autosomal linkage groups are there in humans? a. 22 b. 23 c. 46 d. 1

If gene A is haplosufficient, and a mutation in gene A gene creates a null allele (a), the behavior of the null allele in a heterozygote (wild- type/null) would be predicted to be a. recessive. b. dominant. c. incompletely penetrant. d. variable in expressivity. e. codominant.

If mom is a carrier for the recessive sex-linked gene for the protan defective color vision and Dad is normal, which of their children will have defective color vision? a. some sons only b. some daughters only c. some sons and some daughters d. all sons and daughters e. neither sons nor duaghters will be color blind

If two genes on the same chromosome exhibit complete linkage, what is the expected F2 phenotypic ratio from a selfed heterozygote with the genotype a+b+ ⁄ ⁄ ab? a. 3:1 b. 1:1 c. 1:1:1:1 d. 9:3:3:1

In E. coli, the genetic material is composed of ________. a. circular, double-stranded DNA b. linear, double-stranded DNA c. RNA and protein d. circular, double-stranded RNA e. polypeptide chains

In a certain human population in genetic equilibrium for the typical X-linked red-green color blindness locus, 6 males in 100 are color blind. What is the percentage of color-blind females in the population? a. 0.36 percent b. 11.3 percent c. 88.4 percent d. 94 percent

In a population of birds in Africa, it was observed that birds with small or large beaks could efficiently crack and eat small or large seeds, respectively. Birds with intermediate beaks had trouble with both types of seeds. What type of selection would be expected to occur in this population if small and large seeds were the only types of food available to these birds? a. disruptive b. stabilizing c. directional d. There would be no selection in this population.

In a three-point mapping experiment for the genes x‑y‑z, the following percentages of events are observed: NCO events: 65% SCO events between x and y: 15% SCO events between y and z: 17% DCO events: 3% What is the map distance between y and z? a. 20 map units b. 17 map units c. 15 map units d. 18 map units

In prokaryotes, eukaryotes and viruses, genes are a. arranged in linear fashion along a chromosome b. paired c. located in the nucleus

In the lac operon in e. coli, a nonsense mutation in the ________ gene will result in a loss of beta-galactosidase activity in the cell. a. lacZ b. lacI c. lacY d. both A and B e. all of the above

LacZ- = nonsense mutation in LacZ; LacI- = no repressor, LacIC = mutation in repressor operator binding site. β-galactosidase will - (Note this cell is a merozygote) a. be translated b. not be translated

Leiber's hereditary optic neuropathy (LHON) is due to a _______________ a. Mutation in the mitochondrial genome b. Duplication of part of the 18th chromosome c. Translocation between 18 and 21 d. Deletion of part of the 5th chromosome

Many scientists believe that the evolution of multigene families, such as the genes for hemoglobin, is a result of which type of genetic rearrangement? a. duplication b. deletion c. inversion d. translocation

Most of our commercial wheat varieties commonly grown in the US are a. allopolyploid b. autopolyploid c. diploid d. aneuploid

No glucose, lactose present. β-galactosidase will- a. be synthesized b. not be synthesized

Petite mutants are yeast mutants that are deficient in cellular respiration. There are three kinds of petite mutants. A petite mutant that is segregational is a _____________gene with a gene product that is critical to mitochondrial function. a. Nuclear b. Mitochondrial c. Chloroplast

Phage rII mutants cannot lyse E. coli K12 but can lyse E. coli B. E. coli B is infected with two different rII- mutants. Progeny viruses are used to infect E. coli K 12 and bacteria able to lyse K12 are found. What might have happened in E. coli B during infection? a. recombination between an insertion and a deletion b. recombination between two insertions c. recombination between two deletions

Post translational modifications of proteins include - a. Chaperon-mediated folding of the polypeptide b. Addition of a poly A tail c. Removal of intervening sequences d. Refolding proteins in prion-associated diseases

Proofreading repair - a. is carried out by DNA polymerase 3' to 5' exonuclease activity b. activates enzymes which remove purines c. excises thymine dimers

Protein bound to DNA can either turn on or turn off transcription. When transcription is turned off, the operon is under a. negative control b. positive control

Sickle cell anemia is caused by a change in the amino acid sequence of the two beta chains in the hemoglobin molecule. How many amino acids have been changed in each beta chain, compared to normal hemoglobin? a. 1 b. 3 c. hundreds d. none

Studies with sex determination in Drosophila show that sex is determined by - a. alternate splicing of the gene sxl b. alternative polyadenylation c. post-transcriptional processing d. nucleosome condensation

The DNA compoudn with two rings is: a. purine b. pyrimidine

The Hardy-Weinberg model predicts that allele frequencies remain the same in a population when all of the following assumptions are fulfilled EXCEPT __________. a. no linkage b. infinitely large population size c. no selection or mutation d. random mating within the population

The effect of Barr body formation in mammals is that: a. females are mosacis for expression of heterozygous sex-linked gnes b. females are mosacis for expression of homozygous sex-linked gnes c. Males are mosaics for expression of homozygous sex-linked genes d. males are mosaics for expression of heterozygous autosomal genes e. females are mosaics for expression of heterozygous autosomal gnes

The end result of F+ mediated conjugation- a. is that both strains can be F+ b. involves transfer of the entire bacterial chromosome c. converts the recipient strain to F+ and the donor to F- d. is that only some bacterial genes are transferred to the recipient cell

The evolution of inter sterile chromosome races (species) of Drosophilia pseudoobscura in the western United States is associated with- a. hybrid sterility due to inversions b. hybrid sterilty due to deletions c. hybrid sterilty due to translocations d. hybrid sterilty due as a consequence of accumulated mutations e. geographic region

The first breakthrough leading to "breaking the code" was by Nirenberg and Matthaei in 1961. They used which of the following techniques to determine the first codon a. In vitro synthesis of a polypeptide using UUUUU b. Labeled peptide binding to a ribosome c. Mixed co-polymer mRNA synthesis

The frequency of crossover between genes A and B is 7.5%, between genes B and C is 34.5%, and between genes A and C is 41.4%. What is the most likely order of these three genes? a. A B C b. The gene order cannot be determined from these data. c. C A B d. B C A

The genetic code is degenerate and ordered. Degenerate refers to __________, ordered refers to _______ . a. More than one codon codes for the same amino acid; a mutation may substitute an amino acid with similar properties b. Some codons are non-functional; the third base wobbles c. Three stop codons; there are 6 codons for arginine

The genotype of a cell is AaBb. What genotypes are possible after mitosis? a. AaBb only b. AB and ab only c. Aa and Bb d. AA and BB only e. Ab, aB, AB and ab

The human insulin gene contains introns. Prokaryotic systems will not excise introns. How can a functional insulin molecule be synthesized in E. coli? a. The gene can be cloned into an expression vector b. A bacterial insulin gene can be used c. A cDNA copy of the insulin gene can be cloned d. It doesn't matter if introns are present. A function gene will be produced anyway

The molecular basis for many genetic disorders is now known. Which is LEAST likely to be a possible use of this information? a. A vaccine for the disease can be made. b. A therapy can be devised knowing what the defect is. c. The genetic disorder can be diagnosed by DNA analysis. d. A model system can be created in another species for study.

The offspring of two phenotypically normal people who are heterozygous for albinsim would be expected to exhibit which phenotypic ratio of normal to affected individuals? a. 3:1 b. 1:1 c. 1:2:1 d. 1:3

The β chain of adult hemoglobin is composed of 146 amino acids of a known sequence. In comparing the normal β chain with the β chain in sickle cell hemoglobin, what alteration is one likely to find? a. valine instead of glutamic acid in the sixth position b. glutamic acid replacing valine in the first position c. extensive amino acid substitutions d. trinucleotide repeats e. frameshift substitutions

Tobacco mosaic virus consists of a protein coat surrounding RNA. A TMV strain A virus was stripped of its coat and a different protein coat from strain B was reconstituted over the strain A RNA core. If this new hybrid virus (RNA from strain A and protein coat from strain B) is used to infect a tobacco leaf, which coat will be produced in the progeny viruses? A. Coat protein A B. Coat protein B

Topoisomerases a. Unwind supercoiling b. Disrupt bonds at ori sequences c. Keep helices separated d. Ligate sugar phosphate backbones

Two chocolate dogs that are genotype BbEe are crossed. What proportion of the progeny will be golden? A. 1⁄4 B. 9/16 C. 3/16 D. 1/16

Ultra violet (UV) light can damage DNA by a. causing thymine dimers b. making apyrimidinic sites. c. causing spontaneous deamination of bases. d. intercalation of molecules between stacked DNA bases

What general transcription factors play a key role in proper selection of the start site for transcription of eukaryotes transcribed by RNA polymerase II? a. TBP and TFIID b. RNA polymerase III c. TATA box e. PIC

What is the difference between forward genetics and reverse genetics? a. In forward genetics a phenotype is generated and used to identify the gene, while in reverse genetics the DNA sequence is known and a phenotype is generated. b. In forward genetics knockin technology is used to identify the gene, while reverse genetics uses knockout technology. c. In forward genetics a genotype is generated and used to identify the gene, while in reverse genetics the DNA sequence is known and a genotype is generated. d. In forward genetics a gene is known and used to identify the phenotype, while in reverse genetics the phenotype is known and used to identify a gene.

What is the study of the set of proteins present in a cell under a given set of conditions called? a. proteomics b. bioinformatics c. metabolomics d. genomics

What represents an oranism's genome? a. the haploid DNA content of an organism b. all of an organisms active genes c. the set of RNAs produced by an organism d. the set of functional proteins produced by an organism

Which of the following can serve as a postzygotic reproductive isolating mechanism? a. hybrid sterility b. geographic isolation c. physiological isolation d. mechanical isolation

Which of the following conditions is caused by a chromosomal deletion? a. Cri du chat syndrom b. Edwards syndrome c. Bar eye in Drosophilia d. alpha hemoglobin

Which of the following is a human autosome? a. chromosome 2 b. X chromosome c. Y chromosome d. all of the above

Which of the following is not an assumption of the Hardy-Weinberg equilibrium? a. mating occurs preferentially b. the population size is large c. there is no migration d. there are no mutaitons

Which of the following statements about phenylketonuria is FALSE? a. Individuals with PKY are homozygous for a defective gene, phenylalanine hydroxylase, that converts the amino acid tyrosine to phenylalanine b. People with PKU disease must remain on a special phenylalanine-deficient diet through at least their teenage years b. People with PKU disease have lighter skin than their sibs with one or more normally functioning alleles d. PKU is an inherited disease

Which stage of meiosis enhances genetic variability among gametes? a. prophase I b. metaphase II c. anaphase II d. telophase

Wood comes predominately from: a. air b. water c. soil

leu- bacteria are mixed in a flask with arg- bacteria, and prototrophs are recovered. However, if the leu- cells are on one side of a U-tube and the arg- cells are on the other with a semi-permeable membrane between them, prototrophs are not recovered. This suggests that the prototrophs were a result of- a. conjugation b. transduction c. transmission

crossing 2 homozygous strains (P gen) that are diif in multi gen. markers P->F1->F2 goal is to link QTL to ___

a known genetic marker

what is a trait

a measurable physical, biochemical, physiological, or behavioural feature of an organism

what is a character state

a set of alternative conditions that a particular character can exhibit (e.g. blue or green, GATC in DNA sequences).

These data suggest that the gene and the marker are linked. Estimate the recombination frequency from the data. Do not concern yourself with either the margin of error or the 'phasing problem'. a) 0% b) 1-10% c) 10-20% d) 20-30% e) >30%

a) 0%

The result from the previous question indicates that the darwinian (relative) fitness of the a/a genotype is a) 0.99 b) 0.95 c) 0.90 d) 0.80 e) 0

a) 0.99

A cell that was diploid during the G1 phase of the cell cycle is ready to undergo meiosis: How many sets of genetic material will be present in each one of the meiotic products? a) 1 b) 2 c) 4 d) 8 e) 0

a) 1

The fruit fly became a genetic model organism due to its adoption by: a) Thomas Hunt Morgan b) Joe DiMaggio c) Gregor Mendel d) Reginald Punnett e) Theodor Boveri

a) Thomas Hunt Morgan

A female fly heterozygous for short bristles (s/s+) and ebony body (e/e+) is testcrossed to a male homozygous for the corresponding recessive alleles, s and e. The following progeny were observed: long bristles, normal color 436 short bristles, ebony color 454 long bristles, ebony color 58 short bristles, normal color 52 Are these two genes linked? a) Yes b) No c) Cannot tell

a) Yes

Make a correct statement by completing the sentence. The Ti plasmid ... a) mediates the transfer of DNA from bacteria into the plant genome b) causes the infection of plants with a virus c) contains DNA that a bacterium acquired from its host plant d) provides resistance against T-series phages e) is unusual in that it is single-stranded

a) mediates the transfer of DNA from bacteria into the plant genome

Did non-disjunction occur during a) meiosis I b) meiosis II c) cannot tell

a) meiosis I

Name the general category that describes double-stranded, circular, extra-chromosomal DNA elements (such as F-factors). a) plasmid b) plaque c) pretzel d) phage e) capsid

a) plasmid

A female fly heterozygous for short bristles (s/s+) and ebony body (e/e+) is testcrossed to a male homozygous for the corresponding recessive alleles, s and e. The following progeny were observed: long bristles, normal color 436 short bristles, ebony color 454 long bristles, ebony color 58 short bristles, normal color 52 Which allele combination is considered 'parental' type? a) s e b) s e+ c) s+ e d) s s+ e) e e+

a) s e

Do your data fit the Null-hypothesis of independent segregation? (see below for X2-table; as the critical Chi-square value use the one for the standard P-value). a) Yes b) No

a) yes

A graduate student is studying the effect of selection in dragonflies. She uses a laboratory population in which the narrow-sense heritability of wing length is 0.7. The average wing length in this population if 5 cm. She selects the dragonflies with the largest wings to interbreed. Their average wing length is 10 cm. a. Calculate the selection differential and expected response to selection for wing length in these dragonflies. b. What should be the average wing length of the progeny of the selected dragonflies?

a. R = h^2 x S R = (0.7) x (10-5) 3.5 b. 5+3.5 8.5

Sickle cell anemia is an autosomal recessive disease. Individuals who are heterozygous for this disease are immune to malaria. In a malaria invested population under Hardy Weinberg conditions, 9% of the people have sickle cell anemia. Find the Allelic frequencies Genotypic frequencies of SS and Ss individuals How many people of a 8000 person population would you expect to have each genotype?

a. q^2 = .09 q = .3 p = .7 p+q = 1

What does PCR provide

access to any DNA Revolution in molecular biology - biomedical genetics, evolution, forensic biology, taxonomy Supplanted bacterial cloning methods

Relationships among alleles at a locus

additive: allele yields twice the phenotypic effect when two copies present dominance: dominant allele masks presence of recessive in heterozygote

can be used w/ all organisms access a large amt of data regardless of taxa; shared molecular traits like rRNA sequences quantifiable data provide info abt process of evolution

advantages of molecular techniques

what is gamma distribution

among site variations, Curves different alpha values Creates shape in gamma distribution most sites have low rates, tail ends = fast rate

what is biological evolution

any change in heritable traits of biological populations over successive generations

what is meant by character

any heritable trait that can be compared across organisms, e.g. physical characteristics (morphology), molecular data, behavioural traits

human driven mechanism select which indiv will reproduce base on desired characteristics selective breeding has produced domesticated plants (crops) and animals

artificial selection

When mapping QTLs _________.

associations with molecular markers are identified

A Florida dentist tested positive for HIV. At a later date, a female patient also tested positive for HIV. Genetic analysis determined that the dentist had infected some of his patients. What was the principle behind this analysis? a. All cases of HIV infection yield a unique strain of the virus. b. The virus isolated from an infected individual will be more similar to the infecting virus than to any other. c. All strains of HIV are identical. d. A viral strain passed from one individual to another will be identical in each person.

A careless graduate student, after a sleep-deprived night in the lab, accidentally irradiates her yeast cells, creating a ton of mutants. She thinks this is fortuitous, as she is trying to create a histone-deficient mutant yeast and may have achieved her goal this way. Do you think she can obtain histone deficient mutants? a. yes, why not?. b. No, histone-deficient yeast mutants would be unable to divide and propagate themselves c. No, histone-deficient mutants would not undergo DNA replication

A cross between a white-leafed female Mirabilis plant and a green-leafed male plant would yield - a. green progeny. b. white progeny. c. variegated progeny. d. a mixture of green and white progeny.

A gene pool represents- a. the genes that are available to a community b. the sum total of all genes of the individuals in a population c. the frequency of genotypes in a populaiton d. all genes available to a species

A male Drosophila melanogaster is genotypically e+//e-, where e (ebony) is an autosomal gene. Of the four gametes produced by a single meiosis, how many of them will carry both the e- allele and the Y chromosome? (remember the law of probability for independent events) a. None b. 1/4 c. 2/4

A male embryo with a mutation that inactivated the SRY region would a. develop normally b. develop as a female c. be an intersex d. all of the above

A possible mechanism for human gene therapy involves siRNAs. Which of the following statements is FALSE? a. The enzyme "dicer" cleaves double stranded RNA into short fragments for both miRNAs and siRNAs b. miRNAs are expressed whenever siRNAs are unable to appropriately degrade RNA sequences c. RNA induced silencing complex (RISC) binds to double-stranded and degrades one strand d. siRNAs originate from exogenous dsRNAs

A true-breeding plant __________. a. produces plants exhibiting both contrasting characteristics in a 3:1 ratio b. produces offspring that exhibit the same characteristics as the parent when self-fertilized c. produces offspring that exhibit neither of the parental characteristics when crossed with a plant exhibiting the contrasting characteristics d. produces plants exhibiting both contrasting characteristics in a 1:2:1 ratio

Albinsim in humans is ingerited as a simple recessive trait. In the Hopi Indians, albinism is considered good luck. A normally prigmented male and an albino female have 6 children, three normal and three albino. What is the genotype of the father? a. AA b. Aa c. aa

All of the following are considered model organisms for genetic studies EXCEPT __________. a. mice b. humans c. yeast d. Drosophila

All of the following are stages of mitosis EXCEPT __________. a. telophase b. S phase c. metaphase d. prophase

An organism that must be supplied with one or more amino acids in order to grow is a. prototypic. b. auxotrophic. c. autotrophic. d. prototrophic.

Based on Mendel's fourth postulate of independent assortment, if 1/4 of the F2 generation is expected to be dwarf plants and 1/4 is expected to be yellow, what is the probability that a plant will be both dwarf and yellow? a. 1/4 b. 1/16 c. 9/16 d. 3/16

Brassica oleracea (2n=18) is crossed with pollen B. nigra (2n=16) Seeds are produced. Which of the following statements is INCORRECT a. seeds will germinate and form a plant b. a plant from this cross can be self-pollinated and will produce progeny c. a plant from this cross would have phenotypic characteristics of both parents d. pollen produced by this plant will be viable

Carr's study with Scottish spontaneous abortions and newborns showed that- a. human polyploids never occur b. human polyploids occur but are aborted before birth c. only triploids occurred in aborted fetuses d. polyploids were born but died by age 3

Complications with molecular clock studies might arise because __________. a. DNA sequence analysis is not always reliable b. analyzing different genes can give different results c. nucleic acids and proteins evolve separately d. during evolution, mutation rates for a given gene have been variable

Consider a locus with two alleles, B and b, where bb is homozygous lethal and BB and Bb have identical fitness. What is the expected allele frequency of b after 10 generations, if the frequency of b is 0.1 at generation zero? a. 0 b. 0.05 c. 0.1 d. 0.5

DNA binding proteins include proteins with specific motifs. Which of the following is NOT one of the known DNA binding protein motifs? a. Zinc finger proteins b. Methionine repeats c. Helix-turn-helix proteins d. Leucine zipper proteins

DNA is double stranded, but only one strand is used as a template for transcription. How does the cellular machinery determine which strand to use as the template? a. The cellular machinery recognizes the start codon b. The cellular machinery recognizes the promoter c. The cellular machinery recognizes introns d. DNA binding proteins prevent transcription of the wrong strand e. Both sides of the helix are copied.

DNA replication occurs during a. interphase G1 b. interphase S c. methaphase d. prophase

Drosophilia, a heterozygous female for the sex-linked traits a,b, and c (ABC/abc) was crossed to a male that was phenotypically abc. Offspring of this cross occurred in the following phenotypic ratios: Abc--- 460 aBC---450 abc--- 32 ABC--- 38 aBc--- 11 AbC--- 9 ABc--- 0 abC--- 0 What is the arrangement of alleles on the X chromosome of the female? a. abc//ABC b. Abc and aBC c. ABc and abC d. aBc adn AbC

Eukaryotic messenger RNAs are synthesized by a. RNA polymerase I. b. RNA polymerase II. c. RNA polymerase III. d. all of the above e. none of the above

Evolution is the _______ of natural selection a. process b. outcome c. mechanism d. purpose

For linked genes A, B, and C, the map distance A-B is 5 map units and the map distance B-C is 25 map units. If there are 10 double crossover events out of 1000 offspring, what is the interference? a. 0.8 b. 0.2 c. 0.0125 d. 0.01

For the following cross, what are the phenotypes of the Children? fut1/fut1 IAIA (Mom) x Fut1/Fut1 ii (Dad) a. O b. A c. A and O

Founder effect and genetic bottlenecks give rise to __________. a. migration b. genetic drift c. inbreeding d. natural selection

Fourteen alleles control leaf patterns in white clover. How many alleles can any individual plant have? a. 1 b. 2 c. 6 d. 10

Gamma and x-rays induce mutations by a. forming pyrimidine dimers. b. ionizing water molecules around DNA. c. spontaneous deamination of 5-methylcytosine. d. intercalation of molecules between stacked DNA bases

Genes A and B are farther apart than genes A and C, and all three genes are linked. All EXCEPT which of the following conclusions could be drawn from this information? a. Gene C might be between genes A and B. b. Gene B might be between genes A and C. c. More crossovers will occur between genes A and B than between genes A and C. d. Gene A might be between genes B and C.

Genes A and B are linked. If A and B are in trans configuration (genotype AaBb) , what would a parental (non-crossover) chromosome look like? a. AB b. Ab c. ab

Genes that are expressed in response to the presence of a substance are considered- a. constitutive. b. inducible. c. essential. d. repressible. e. lethal.

Glucose is present but not lactose. β- galactosidase will- a. be synthesized b. not be synthesized

Helicases - a. Unwind supercoiling b. Unwind the double helix at the replication fork c. Keep helices separated d. Ligate sugar phosphate backbones

How does recombination in bacteria occur? a. Recombination does not occur in prokaryotes. b. A portion of DNA from one genome is replaced with homologous DNA from another strain of bacteria. c. Only the plasmid DNA goes through recombination in prokaryotes. d. Sister chromatids, not homologous chromosomes, exchange information during recombination.

If "A" is the active site of an enzyme, a synonymous mutaiton in A would be-- a. auxotrophic b. prototrophic c. leaky d. all of the above

If "A" is the active site of an enzyme, a synonymous mutation in A would be- (A synonymous mutation is a mutation that does not change the amino acid) a. auxotrophic b. prototrophic c. leaky

If a mouse with the genotype AaBb were testcrossed, what offspring would be expected if the two genes are 30 map units apart and the heterozygote has the dominant alleles on one chromosome and the recessive alleles on the other? a. 20% of the offspring will exhibit A and B, 20% will exhibit a and b, 30% will exhibit A and b, and 30% will exhibit a and B. b. 35% of the offspring will exhibit A and B, 35% will exhibit a and b, 15% will exhibit A and b, and 15% will exhibit a and B. c. 35% of the offspring will exhibit A and b, 35% will exhibit a and B, 15% will exhibit A and B, and 15% will exhibit a and b. d. 25% of each possible combination of traits: A and B, A and b, a and B, and a and b.

If a stretch of DNA that codes for a protein contains 12 nucleotides, how many amino acids does it code for? a. 3 b. 4 c. 6 d. 12

If two chromosomes of a species are the same length and have similar centromeres but are not homologous, what is different about them? a. they are telomeric chromosomes b. they contain different genes c. they divide at different times d. chromosome condensation is different

If two genes on the same chromosome exhibit complete linkage, what is the expected phenotypic ratio of offspring from a heterozygote testcrossed with a homozygous recessive individual? a. 3:1 b. 1:1 c. 1:1:1:1 d. 9:3:3:1

In Drosophila subobscura, a recessive gene called grandchildless (gs) causes the offspring of homozygous females to be sterile but not the offspring of homozygous males. Which of the following best explains this phenomenon? a. gs is a sex-linked gene b. gs females produces an egg cytoplasmic substance which affects the development of reproductive structures in the embryo c. gs is a mitochondrial gene d. gs is a chloroplast gene

In eukaryotes, translation is initiated by - a. binding of the Shine-Delgarno sequence to the ribosomal small subunit b. Binding of the 7-mg mRNA cap to the ribosomal small subunit c. binding of the start codon to the ribosomal small subunit d. Attaching the large and small subunits of the ribosomes together then attracting the mRNA e. Binding enhancers to the ribosomal small subunit

In many species, there are two representative of each chromosome. In such species, the characteristic number of chromosome is called ________ number. It is usually symbolized as _________. a. haploid; n b. diploid; 2n c. diploid; n

In prokaryotes, intrinsic transcription termination is achieved by - a. a poly adenylation signal sequence b. a GC-rich sequence that folds back on itself c. a rho protein

In rice, plants homozygous for the recessive allele sd1 are relatively short in stature. Plants homozygous for a dominant allele, Xa4, corresponding to a second gene located on a different chromosome are resistant to bacterial blight. If a farmer crosses a plant homozygous for sd1 with a plant homozygous for Xa4 (assume the plants are otherwise isogenic and the listed mutant alleles are the only ones present in these parent plants), which of the following statements is correct? [sd1/sd1 xa4/xa4 X Sd1/Sd1 Xa4/Xa4] a. The progeny will be monohybrids. b. The progeny will be dihybrids. c. Three-quarters of the progeny will be resistant to bacterial blight, while one-quarter will be short. d. a and c e. a and b

In the lac operon, the function of the β-galactosidase gene is to - a. bring more lactose into the cell b. convert lactose to glucose + galactose c. make a small amount of permease d. synthesize cyclic AMP e. metabolize glucose

In the moss Physcomitrella patens, mutations for antibiotic resistance were induced by UV irradiation. Following UV irradiation, moss cultures kept in the dark produced significantly more mutations than moss cultures kept in the light. What is the reason for this? a. Antibiotic mutations were not random b. Light is required for one of the repair processes c. UV irradiation damaged proofreading repair enzymes d. Antibiotic mutations affect chloroplasts and therefore are more effective in the light

Individuals with defective telomerase activity a. are phenotypically normal b. age prematurely c. accumulate mutations

Individuals with three copies of most autosomes do not survive. Individuals with an extra X chromosome, however, survive with relatively mild (compared to autosomal abnormalities) consequences. Why? a. The X chromosome contains few genes while autosomes contain a large number b. the extra X chromosome(s) are inactivated c. the X chromosome determines sex only d. the answer is unknown

LacI- = no functional repressor is made a. Inducible b. constitutive (always on) c. repressed (off)

LacIc = mutation in the repressor protein cannot bind operator. Transcription will be - a. Inducible b. constitutive (always on) c. repressed (off)

LacOc = mutation in the operator, repressor cannot bind. Transcription will be- a. Inducible b. constitutive (always on) c. repressed (off)

Mendel's work showed __________. a. that genetics and evolution are linked b. that traits in living organisms were controlled by discrete units of inheritance (genes) that existed in c. that certain genes are linked d. that pea plants had patterns of inheritance different than those of other organisms

Mendelian crosses involving alleles at two segregating loci will always produce a 9:3:3:1 phenotypic ratio. a. True b. False

Normal parents have a child with Tay-Sachs disease, a recessive condition. What is the probability that their next child will be normal? a. 0 percent b. 75 percent c. 100 percent d. 25 percent

Photoreactivation repair of ultraviolet-damaged DNA requires a. no enzymatic catalyst. b. visible blue light. c. methyltransferase. d. AP endonuclease.

Pretend there is a segment of the E. coli genome with the sequence: 5′ CTGAATCGGGTTGGG 3′ 3′ GACTTAGCCCAACCC 5′ In order for the top DNA strand to be replicated, which of the following primers is needed? a. A primer with the sequence 5′ CTGAAT 3′ b. A primer with the sequence 5′ CCCAAC 3′ c. A primer with the sequence 5′ GGGTTG 3′ d. A primer with the sequence 5′ GGGUUG 3′ e. A primer with the sequence GACUUA

Roan color in horses is due to a mixture of white and colored hair. It is a codominant trait (Rn1//Rn2 = roan) The Belgium Registar of Horse Breeding was examined to determine the frequency of roan and non-roan foals from roan x roan matings. Roan x roan matings resulted in 122 non-roan foals and 249 roan foals. How can this result be explained? a. Roan is dominat to non-roan b. One homozygous class is lethal c. epistatis d. expressivity e. penetrance

Round (W) seed shape is dominant to wrinkled (w) seed shape in pea plants. If a WW plant is crossed with a wwplant, what is the frequency of phenotypes in the F2 generation? a. all wrinkled seeds b. three round seeds, one wrinkled seed c. 1/4 WW, 1/2 Ww, 1/4 ww

Some cancers are caued by translocations including Burkitt lymphoma and actue lymphocytic leukemia. The underlying cause of these cancers is thought to be due to- a. distrubance of chromosome segregation mitosis b. a structural gene is moved under the control of a different promoter c. loss of a piece of genetic material d. gain of a piece of genetic material

The N-terminal ends of histone proteins are modified after assembly into nucleosomes. Histones associated with active genes are_____ while histones associated with inactive genes are ______. a. methylated, acetylated b. hyperacetylated, hypoacetylated c. carboxylated, decarboxylated

The antibiotic, streptomycin inactivates prokaryotic organisms by binding to a ribosomal protein. Streptomycin does not affect eukaryotic cells. A mutation to streptomycin-resistance was found in Chlamydomonas (green algae). Where is this mutation located? a. In the nucleus b. In the chloroplast

The color pattern of a Himalayan rabbit is an example of __________. a. a nutritional mutant b. the effect of temperature on gene expression c. genetic anticipation d. epigenetics

The evolution of antibiotic resistant E. coli is due to 5 specific mutations, each conferring some level of antibiotic resistance. This is-- a. stabilizing selection b. directional selection c. disruptive selection

The evolution of antibiotic resistant E.coli is due to 5 specific mutations, each conferring some level of antibiotic resistance. This is - a. stabilizing selection b. directional selection c. disruptive selection

The following interactions are found in mice. The albino allele, b, eliminates all color in homozygotes and is recessive to the normal pigment allele, B, which yields a black color. A second allele, A, allows the black pigment to be converted to agouti, whereas this does not occur in the homozygous recessive condition in which the mouse is homozygous for the null, a allele. A mouse of genotype Aabb will __________. a. have an agouti coat b. be an albino c. have a black coat d. have a spotted pattern

The following is a list of components that are involved in transcription. Which function only in prokaryotes. a. TATA box b. Sigma subunit c. Promoter d. RNA polymerase II

The location of the BRCA1gene 17q21. This means that- a. it is located on the short arm of the chromosome 17 b. it is located on the long arm of chromosome 17 c. it is located on the long arm of chromosome 21 d. it is found only as a translocation between 17 and 21

The nitrogenous base that is present only in RNA and NOT in DNA is __________. a. thymine b. uracil c. cytosine d. guanine

The null hypothesis states that __________. a. the observed values deviate from the expected values b. there is no real difference between observed values and measured values in an experiment c. an observed deviation from predicted values occurs by chance d. differences of the observed values from the predicted values occurred due to experimental error

The percentage of tuskless elephants (or elephants with tiny tusks) in Zambia's South Luangwa National Park increased from 10.5% in 1969 to 38.2 percent in 1989—the peak of the ivory wars. The appearance of tuskless elephants was due to - a. Increased mutation rate of the tusk gene to tuskless due to hunting pressure b. Random mutation of the tusk gene and selective survival of tuskless elephants.

The sequence of a template strand of DNA is: 3'-C A T T A C G C T T-5' Which of the following is the sequence of the corresponding mRNA? a. 5'-C A U U A C G C U U-3' b. 5'-G U A A U G C G A A-3' c. 3'-A A G C G T A A T G-5' d. 5'-G T A A T G C G A A-3'

Trp attenuation occurs when - a. RNA polymerase reads a trp codon b. The ribosome reads a trp codon

What animal was the first to be cloned using the nucleus of a differentiated adult cell? a. mouse b. sheep c. pig d. rat

What is a merozygote? a. the result of sexual reproduction between two bacterial cells b. a partially diploid bacterial cell c. a zygote formed from a bacteriophage and a bacterial cell d. a haploid bacterial cell

What is the difference between the theory of preformation and the theory of epigenesis? a. Epigenesis states that sex cells already contain a complete miniature adult, whereas the theory of preformation states that an adult organism develops because of a series of events that form de novo structures from substances present in the egg. b. Preformation states that sex cells already contain a complete miniature adult, whereas the theory of epigenesis states that an adult organism develops because of a series of events that form de novo structures from substances present in the egg. c. Preformation states that all species on Earth have remained unchanged since they appeared; epigenesis states that adult structures of an organism develop de novo from substances in the egg. d. Epigenesis means that living organisms can arise from nonliving organisms, whereas preformation states that sex cells contain a complete, miniature adult.

When the translation machinery encounters a "stop" codon a. special "stop" tRNAs are recruited that bind to stop codons by complementary anticodons. b. translation is terminated by release factors (proteins) that are recruited in response to the stop codon. c. translation terminates because the small ribosomal subunit dissociates and is targeted for proteolytic destruction d. it triggers addition of a poly(A) tail to the mRNA. e. the 5' cap is removed, destabilizing the translation complex.

When there is no glucose and no lactose, β- galactosidase will- a. be synthesized b. not be synthesized

When tryptophan levels in the E. coli cell are low - a. formation of a rho-like terminator occurs b. The ribosome stalls c. mRNA synthesis is terminated

Which character of DNA fragments allows their separation by gel electrophoresis? a. charge density b. length of fragment c. base sequence d. prokaryote vs eukaryote DNA

Which of the following are characteristics of an E. coli strain of genotype F- gal+ lac- pur+ lie- str^s? a. it has the ability to form a pilus b. it can act only as a recipient in conjugation c. it is prototrophic for lactose d. it is resistent to streptomycin e. it can grow on minimal media + lactose

Which of the following factors is most likely to contribute to a gene flow between populations? a. random mating b. migration c. mutation d. genetic drift

Which of the following is a decription of generalized transduction? a. inaccurate excision of prophage can occasionally remove a small portion of the bacterial chromosome b. random pieces of bacterial DNA can become incorporated into a phage coat c. Pieces of bacterial DNA may be released into the culture medium when a cell is lysed d. all of these

Which of the following is an incorrect step in cloning eukaryotic DNA into a bacterial plasmid? a. The eukaryotic DNA must be digested with a restriction enzyme b. A cloning site on the plasmid must be opened with a different restriction enzyme. c. The eukaryotic DNA must be ligated into the plasmid cloning site d. The recombinant plasmid must be inserted into a bacterial host e. There must be a selection step for bacterial hosts that contain a recombinant plasmid

Which of the following proteins' primary function is unwinding the double-stranded DNA at the replication fork? a. Single-stranded binding protein b. Helicase c. DNA polymerase d. RNA primase e. DNA ligase

Which of the following statements about homologous chromosomes is true? a. They have identical sequences of base pairs. b. They contain all of the same genes, but not necessarily the same alleles. c. In each cell, there are two pairs of homologous chromosomes—one pair from each parent. d. Homologous pairs of chromosomes can be observed in haploid cells.

Which of the following statements about inbreeding in a natural population is true? a. It increases the genetic variation in a population. b. It can increase the frequency of homozygotes. c. It is likely to occur as population size increases. d. It occurs in all populations that are not in Hardy-Weinberg equilibrium.

Which of the following statements is correct regarding DNA and RNA? a. The nucleotides in both DNA and RNA contain ribose. b. RNA is generally single stranded, whereas DNA is usually double stranded. c. DNA is generally single stranded, whereas RNA is usually double stranded. d. The nitrogenous bases in the nucleotides of both DNA and RNA are adenine, guanine, uracil, and cytosine.

Which of the following statements is true of an X-linked disorder that is normally lethal before the onset of reproduction? a. Males are always heterozygous carriers, but they do not express the disorder. b. The disorder occurs only in males. c. The disorder occurs only in females. d. Heterozygous females pass the disorder to half of their daughters, all of which express the trait.b

Which of the following statements is true regarding a sporophyte? a. It is haploid. b. It is diploid. c. It is a product of meiosis. d. Flowering plants do not have the sporophyte stage.

Which of the following statements regarding Hfr bacteria is FALSE? a. They function as the donor in crosses with F− bacteria. b. They frequently convert recipient bacteria to F+ cells. c. They function as the donor only in crosses with F− bacteria and are so called because they result in high-frequency recombination. d. They are derived from F+ bacteria.

Which statement does NOT describe both eukaryotic and prokaryotic transcription? a. DNA Promoter elements are required for polymerase binding b. Transcription factors bind to promoter sequences and then recruit RNA polymerase c. RNA polymerase opens a double stranded DNA to expose the template strand d. RNA polymerase catalyzes nascent RNA synthesis 5' to 3'.

Which term describes the entire haploid content of DNA contained within an organism? a. gene b. genome c. transgenic d. clone

Why does a dideoxy nucleotide terminate transcription? a. It can't add a nucleotide at its 5' position b. It can't add a nucleotide at its 3' position c. It can't be added to the growing 5'->3' DNA d. It can't be added to the growing 3'->5' DNA

Yellow seeds (Y) dominant to green seeds (y) Round seeds (R) dominant to wrinkled seeds (r) A plant with round seeds is crossed to a plant with wrinkled seeds. 50% of the progeny have wrinkled seeds. Is the plant with round seeds homozygous or heterozygous for the "round" gene? a. homozygous b. heteozygous

Yellow seeds (Y) dominant to green seeds (y) Round seeds (R) dominant to wrinkled seeds (r) Two heterzygous plants are crossed (YyRr x YyRr). What proportion of the progeny will be yellow and have wrinkled seeds? a. 9/16 b. 3/16 c. 1/16 d. 100%

You construct a genetic linkage map by following allele combinations of three genes—X, Y, and Z. You determine that X and Y are 3 cM apart, X and Z are 3 cM apart, and Y and Z are 6 cM apart. These cM numbers are most likely based on a. DNA sequencing of the region in question. b. recombination frequencies. c. measuring the distance in a scanning EM micrograph. d. independent assortment. e. none of the above.

You isolate cells from two different patients, both with Xeroderma pigmentosum (XP). After growing these cells in culture, you fuse them together and test for DNA repair ability. You find that the fused cell has normal DNA repair ability. What does this tell you about the genes causing XP in the two patients? a. The mutations affect the same DNA repair component b. The mutations affect two different DNA repair components c. Something other than DNA repair is causing XP

Use the Chi square test to judge whether the results fit the ratio expected for 'independent segregation' of the two genes. (Note: Use proper fractions, instead of decimal fractions for ease of calculation). What is the Chi-Square value? a) between 0 and 1.0 b) 1.1 to 2.0 c) 2.1 to 3.0 d) 3.1 to 4.0 e) over 4.1

b) 1.1 to 2.0

Among Alfred Sturtevant's (Thomas Morgan's student) first crosses demonstrating the phenomenon of 'genetic linkage' the following data were obtained after crossing a double-heterozygous female fly (v/v+; r/r+) to a male carrying the recessive alleles, vermilion (v) and rudimentary wings (r): Class 1 vermilion eye, normal wings 290 2 red eye, rudimentary wings283 3 vermilion eye, rudimentary wings 7 4 red eye, normal wings 10 Before you think about the actual numbers he obtained, think: what phenotypic ratio would you have expected according to standard Mendelian genetics? a) 9:3:3:1 b) 1:1:1:1 c) 1:2:2:1 d) 3:1 e) 9:3:4

b) 1:1:1:1

In Drosophila males there is no crossing over during meiosis. How many different gamete genotypes will there be in a male (still assuming all three genes are on the same chromosome)? a) 1 b) 2 c) 4 d) 8 e) 16

b) 2

Next, let's assume that the three genes reside on the X chromosome of the male fly. This male fly will make this many different gametes (don't 'overthink'). a) 1 b) 2 c) 4 d) 8 e) 16

b) 2

What would have been the recombination frequency according to Mendel? a) 25% b) 50% c) 75% d) 3% e) 0%

b) 50%

A good example for 'co-dominant alleles' is given by the gene for a) pattern baldness b) ABO blood type c) sex d) polydactyly e) Down syndrome

b) ABO blood type

In humans, monosomy of any one chromosome, even the smallest (Chr 22), causes early death and abortion of the embryo, with one exception. Monosomy of the X chromosome is viable. Which of the following sentences is false? a)These monosomic individuals have Turner syndrome (X0). b)Monosomy of the X is tolerated because the X contains very few genes. c)X_ is tolerated because in XX individuals (females) only one X is expressed anyway. d)The Barr body is a condensed X chromosome. e)In X_ individuals, no Barr body forms.

b) Monosomy of the X is tolerated because the X contains very few genes

Critical data for the determination of the structure of DNA were provided by a) Salvador Luria b) Rosalind Franklin c) Beadle & Tatum d) Charlie Parker e) Hershey & Chase

b) Rosalind Franklin

A similar phenomenon as with the Curly gene in fruit flies is observed for this gene: a) Black-body mutations in the fruit fly b) The Agouti-yellow coat color allele in the mouse c) Mendel's wrinkled pea d) Coat color in dogs e) Sickle cell allele of hemoglobin

b) The Agouti-yellow coat color allele in the mouse

The disease known as phenylketonuria is due to a defect in the gene for phenylalanine hydroxylase. The defect is inherited in a(n) ___(47)____ fashion. Mutations in this gene have been identified in many different ethnic groups. Actually, the specific mutation causing the disease is _____(48)____ . This finding suggests that the mutation arose ______(49)_____. If 7left untreated, the condition causes _____(50)______ . Fortunately, there is a treatment that can prevent the worst symptoms of the disease; it is ______(51)______ . 47. a) autosomal dominant b) autosomal recessive c) X-linked recessive d) X-linked dominant e) maternal

b) autosomal recessive

During his summer job at a nursery in Michigan, Peyton discovers a single chrysanthemum with orange blossoms. After test-crossing it to a true-breeding white plant, he germinates 40 seeds and finds 21 orange and 19 white progeny. Therefore 'orange' is a) recessive b) dominant

b) dominant

This rule is known as Chargaff's rule, and it applies to a) single stranded DNA b) double stranded DNA c) RNA d) all DNA e) all nucleic acids

b) double stranded DNA

In the fruit fly Drosophila, XXY would result in a fly that is a) male b) female c) in between d) there is no Y in flies

b) female

With his precious find, Peyton relocates to Tennessee to start his own nursery business. He crosses the orange parent plant with a true-breeding, white, male-sterile plant (male sterility is recessive). To obtain any progeny at all, he must have used the male-sterile parent as a a) male b) female c) doesn't matter

b) female

The extra chromosome is the product of non-disjunction in one of the parents. Two X-chromosomal, genes, A and B, were used to determine the pattern of inheritance of the X chromosome in a family with three children, one of which has Klinefelter. All family members were checked for their 'A' genotype (3 possible alleles) and their 'B' genotype (2 alleles). The results are shown below. In which parent did the non-disjunction event occur? a) in the father b) in the mother c) cannot tell

b) in the mother

A gene is considered pleiotropic if a) it is inherited in a sex-linked fashion b) it affects more than one phenotypic trait c) there exist many different alleles of the gene d) it is present in many copies in the genome e) it causes lethality

b) it affects more than one phenotypic trait

The subunits/monomers of DNA are a) nucleosides b) nucleotides c) amino acids d) bases e) deoxynucleosidetriphosphates

b) nucleotides

In evolution, a new allele of a gene arises from a change in the DNA sequence called a ____(43)_____. The wild type allele of a gene usually encodes a functional ____(44)____. A recessive allele usually corresponds to a loss of function. A partial loss of function is called a ___(45)_____ . A mutation causing mis-splicing of the mRNA is usually a ____(46)____ . a) neomorph b) null allele c) hypomorph d) protein e) mutation 46?

b) null allele

In sweet peas, the synthesis of the purple anthocyanin pigment in the petals is controlled by two genes, B and D. The pathway is: gene B white intermediate -> blue gene D intermediate -> anthocyanin (purple) If plants from the preceding two questions are crossed, what color petals are expected in the F1? a) red b) purple c) blue d) white e) light blue

b) purple

This is because in fruit flies sex is determined by a) the XY system b) the X/A rule c) the ZW system d) the environment

b) the X/A rule

In Drosophila, the eye-color gene 'white' is X-linked. Red eye is dominant over white. The 'miniature' gene is X-linked also. miniature (m) is recessive, wild type (m+) is dominant. A homozygous white-eyed and normal-sized female is mated with a red-eyed, miniature male. What is the phenotype of the male progeny? a) white, miniature b) white, normal c) red, miniature d) red, normal e) pink-eyed, intermediate size

b) white, normal

A new student in the lab is getting ready to perform PCR. He programs the followingtemperature cycle on the thermocycler machine: a. 2 minutes at 95ºC b. 1 minute at 55ºC -> 1 minute at 95ºC -> 1 minute at 72ºC c. The three-step cycle in part (b) is repeated 30 times d. 3 minutes at 72ºC e. Cooling down to 4ºC To his disappointment, the reaction failed; no PCR product appeared. Which of the steps was programmed incorrectly?

b. 1 minute at 55ºC -> 1 minute at 95ºC -> 1 minute at 72ºC

The _____________ hypothesis for protein variation posits that natural selection is important in maintaining variation.

balance

role of natural selection is more important to maintain genetic diversity overdominance=> heterozygote indiv.s have higher fitness than either homozygous

balancing selection

Prezygotic Barriers

before mating occurs (isolation- behavioral, mechanical, ecological -habitat, temporal, pollinator)

A drosophilia that has three sets of autosomes (AAA), and three sex chromosomes (XXY) is- a. male b. female c. intersex d. metafemale e. metamale

A major difference in the events of mitosis between plant and animal cells occurs during which stage? a. prophase b. anaphase c. telophase d. metaphase

A red-eyed male Drosophila is crossed with a white-eyed female. What ratio of white to red offspring is likely?. a. 1002redfemales,315redmales b. 1060redfemales,998redmales c. 1020redfemales,1001white males d. 1036redfemales,302whitemales

A researcher would like to map the location of galE and trpA genes in new species of bacterium that appears to be closely related to E. coli. She decides to use cotransformation, and tries transforming an appropriate auxotrophic recipient strain (galE- , trpA-) with fragmented DNA from her prototrophic bacteria. She is disappointed when prototrophs are not recovered in this experiment. What is the most reasonable explanation for this situation? a. her new bacterial species does not have galE or trpA genes b. her new bacterial species canot survive a galE or trpA mutation c. these two genes are too far apart to be mapped by cotransformation d. these two genes are too close together to be mapped by cotransformation e. transformation cannot between different species of bacteria

A sample of DNA is 27% guanine. What percent thymine is in the sample? a. 46% b. 27% c. 23% d. 18%

A strain of bacteria can synthesize tryptophan at 37C but not at 40C. This mutant is a - a. conditional mutant b. temperate sensitive mutant c. both of the above d. none of the above

A trisomic human cell would contain how many chromosomes? a. 45 b. 46 c. 47 d. 48

A woman is heterozygous for the recessive X-linked gene for Lesch-Nyhan syndrome. What proportion of her daughters will be carriers for the trait if their father is NOT affected? a. 0 percent b. 25 percent c. 50 percent d. 75 percent

A yeast strain harboring a conditional allele has a wild-type phenotype at the permissive temperature and a mutant phenotype at the restrictive temperature. This is an example of a. codominance. b. incomplete dominance. c. environmental influence on penetrance. d. pleiotropy. e. dominant inheritance.

All members of an isolated village were genotyped for a particular RFLP. Of the 1000 individuals, 200 were homozygous for the presence of the restriction site, 700 were heterozygous, and 100 were homozygous for its absence. What is the frequency of the "restriction site present" allele, p? a. 0.2 b. 0.45 c. 0.55 d. 0.90

An operon is a group of structural genes that a. encode separate parts of a single protein. b. only function in the presence of an inducer substance. c. are under the control of a single promoter. d. only function in the presence of CAP.

Analyses of sucrose non-fermenting mutants of yeast that also repress mating type switch processes (swi-snf mutants) show that this particular mutant type - a. is a point mutation in the TATA site b. is a frameshift mutation in the sucrase gene c. cannot re-position nucleosomes d. may be repressed by DNA methylation e. cannot bind TBP (TATA binding protein)

Anthony Bourdain (CNN) and Eric Ripert produce some of the world's finest chocolate based on beans from the mountains of Peru ($18/bar). In searching for the best beans, they came across groves of Cacao trees that produced a mixture of colored and white beans in the same pod. Higher in the Peruvian mountains, they found groves of trees that produced only white seeds in the same pod. What is NOT a possible genetic explanation based only on these data? a. The white pods are from homozygous plants that self pollinated or crossed with other homozygous white-seeded plants b. The pods with both pigmented and white seeds came from heterozygous plants that self-pollinated or crossed with other heterzygous plants c. the pods with both white and pigmented seeds are the result of a cross between homozygous white-seeded patent and a homozygous pigmented-seeded plant d. podds with white and pigmented beans are the result of epistasits showing a 9:7 raitio

Assume that A A is lethal. What is the expected ratio of yellow to agouti in the following cross? Ay A x Ay A (Yellow x Yellow) A y A = Yellow AA = Wild type (agouti) a. 3⁄4 yellow to 1⁄4 agouti b. 3⁄4 agouti to 1⁄4 yellow c. 2/3 yellow to 1/3 agouti

By their experimentation using the Neurospora fungus, Beadle and Tatum were able to propose the far-reaching hypothesis that ________. a. prototrophs will grow only if provided with nutritional supplements b. several different enzymes may be involved in the same step in a biochemical pathway c. the role of a specific gene is to produce a specific enzyme d. genetic recombination occurred in Neurospora e. more than one codon can specify a given amino acid

Chromatids separate from each other in - a. anaphase I of meiosis b. prphase II of meiosis c. anaphase II of meiosis and anaphase of mitosis d. interphase of meiosis and mitosis

Chromosomes regions are numbered - a. from the top to the bottom b. from the bottom to the top c. based on Giemsa staining patterns d. based on the location of genes e. based on the location of repetitive elements

Color blindness is a recessive X-linked gene. Predict the outcome of a color blind mother and normal father. a. All children color blind b. Only female children colorblind c. Only male children colorblind d. No colorblind children

Creating an appropriate probe to find a gene of interest in a genomic may be the most difficult part of the gene isolation process. Which of the following cannot be used as a probe? a. DNA synthesized from a consensus sequence of similar genes from other organisms b. A gene isolated from a related (sometimes not closely related) species c. the antibiotic-resistance gene from the cloning vector d. Antibody against the protein product of the gene e. cDNA from a cell line or tissue that over-produces the gene in question

Crossing over normally occurs between all of the following EXCEPT _______. a. sister chromatids b. chromosomes in haploid organisms c. nonhomologous chromosomes d. homologous chromosomes

During _______ of cell division, there are _____ which signal termination of further division process if the cell is damaged. a. prophase; cyclins b. pophse; cell division factors c. interphase; cyclins d. telophase; P53 proteins

Eukaryotic genes are often - a. found in operons. b. polycistronic. c. under coordinated control. d. all of the above e. none of the above

Even though sickle-cell anemia is usually fatal to homozygous individuals, the disease persists because: a. gene therapy has alleviated the condition b. the disease is carried on a dominant allele c. individuals with one allele for sickle-cell anemia are resistant to malaria d. a combination of all of the above

Examine the information flow from gene to phenotype on the next page. Process (DNA--> mRNA) is called a. Transformation b. Transfection c. Transcription d. Transduction e. Translation

Exons and introns are best described by the fact that exons are ______ and introns are ______. a. long; vary in size b. short; long c. relatively short; variable in size and oftern very large d. vary in size; relatively long

For three linked genes, the fraction of single crossovers between genes 1 and 2 and genes 2 and 3 are both 0.11 and the double‑crossover fraction is 0.0121. Which of the following statements is true about these genes? a. There is total interference of one crossover on the other. b. There is evidence of substantial positive interference. c. There is no interference of one crossover on another. d. There is evidence of substantial negative interference.

Francis Crick demonstrated that the genetic code involved three bases and suggested that the code was degenerate. What experimental technique did he use? a. Gel electrophoresis b. Density gradient centrifugation c. Frameshift mutagenesis d. Restriction digests of the rII phage gene

Genes for Xeroderma pigmentosum are defective in - a. DNA polymerase self-repair processes b. Repair by homologous recombination c. Excision repair d. Photoreactivation repair

If a cell has two different alleles, A and a, at the same locus on a pair of homologous chromosomes, what alleles will be in each cell at the end of meiosis? a. A and A b. A and a c. A or a

If a population is in Hardy-Weinberg equilibrium for the multiple alleles A+, A, and a, whose frequencies are p = 0.60 for A+, q = 0.20 for A, and r = 0.20 for a, what percentage of the population is expected to be heterozygous? a. 42 percent b. 50 percent c. 56 percent d. 67 percent

If a recessive disease is found in 50 out of 100,000 individuals, what is the frequency of the heterozygote carriers for this disease? a. 0.0005 b. 0.022 c. 0.043 d. 0.956

In incomplete dominance, heterozygotes have a phenotype that is __________. a. characteristic of both homozygous phenotypes b. indistinguishable from one of the homozygous phenotypes c. intermediate between the two homozygous phenotypes d. more environmentally influenced than the phenotypes of the homozygotes

In prokaryotes, transcription starts at - a. the start codon b. the promoter c. immediately after the promoter

In the ABO blood types, all of the following offspring are commonly possible EXCEPT__________. a. an individual with type B blood from a mother with type A and a father with type AB b. an individual with type A blood from a mother with type O and a father with type AB c. an individual with type O blood from a mother with type A and a father with type AB d. an individual with type AB blood from a mother with type B and a father with type AB

In the galactose utilization system of yeast, the GAL4 protein is a(n)- a. effector. b. promoter. c. activator. d. repressor. e. enhancer.

Individuals homozygous recessive for the bombay factor (fut1 gene) a. produce A and B antigens which reside on the surface of the red blood cell b. produce only the O carbohydrate on the surface of the red blood cell c. cannot add the sguar fucose to the precursor disaccharide to make A or B antigens d. produce A B and O carbohydrates on the surface of the red blood cell

LacIs = mutation in the repressor protein cannot bind allolactose. Transcription will be - a. Inducible b. constitutive (always on) c. repressed (off)

Live pathogenic strain of bacteria--> bacteria Bacterias: 1. potease 2. RNAse 3. DNAse Which bacteria will be transformed to pathogenic bacteria? a. 1 only b. 2 only c. 1 and 2 d. 3 e. 1, 2, and 3

One source of variegation in plants is- a. A deletion in the mitochondrial genome b. Kappa particles which kill the chloroplasts c. Segregation of normal and defective chloroplasts from a cell with a mixture of the two

Parents are each heterozygous for Tay-Sach's disease a recessive lethal neurodegenerative disease. If they have three children, what is the probability that all three will be normal? A. 3/4 B. 9/16 C. 27/64 D. 16/64

Regulation of the tryptophan operon by a repressor molecule is inefficient and a second level of regulation called attenuation has evolved. Which of the following occurs with attenuation? a. Binding of tryptophan to the ribosomes causes translation to proceed b. Binding of tryptophan to the DNA causes transcription to proceed c. Tryptophan tRNA pairing with the mRNA att locus causes transcription to halt d. The repressor molecule produced by R binds to tryptophan e. Tryptophan binds to RNA polymerase

Removal of introns is mediated by: a. the carboxyl tail domain of the ribosome b. the splicesome c. a and b

Sex-influenced inheritance differs from sex-limited inheritance in which of the following ways? a. Sex-limited traits occur only in males. b. These are both terms for the same thing. c. Expression of the phenotype occurs only in one sex in sex-limited inheritance, but not in sex-influenced inheritance. d. Sex-influenced inheritance is X-linked, but sex-limited inheritance is not.

Sickle-cell anemia is an autosomal recessive disease. A man whose father had sickle-cell anemia, but who does not himself have the disease, marries a woman whose mother had sickle-cell anemia, but who does not herself have the disease. Which of the following statements is FALSE? a. They can produce offspring that are neither carriers of the trait nor affected with sickle-cell anemia. b. About three-fourths of their offspring, on average, can be expected to have at least one sickle-cell allele. c. All of their offspring must be carriers of the sickle-cell allele. d. If their first two children do not have sickle-cell anemia, the chances of the third having the disease are one in four.

Structure required to initiate DNA synthesis by a DNA polymerase is - a. an Okazaki fragment b. a telomere c. an RNA primer d. ligase e. topoisomerase

Suppose that in another world, DNA does not undergo semiconservative replication, but instead a conservative mechanism is used. In a repeat of the Meselson and Stahl experiment, bacterial cells that are grown in 15N medium for many generations then transferred to 14N medium for two generations will have the following distribution of DNA molecules in a CsCl gradient: a. 1⁄2 heavy, 1⁄2 light b. 1⁄4 heavy, 1⁄2 intermediate, 1⁄4 light c. 1⁄4 heavy, 3⁄4 light d. 3⁄4 heavy, 1⁄4 light e. Impossible to predict

The Ames test for environmental mutagens uses several His- auxotrophs. What auxotrophs are used? a. Point mutation b. Insertion or deletion frameshift c. Both of the above are used in testing for environmental mutagens

The DNA polymerase in bacteria which is responsible for DNA synthesis is- a. Polymerase I b. Polymerase II c. Polymerase III

The Trp operon - a. is regulated by tryptophan alone b. is regulated by a repressor protein alone c. is regulated by a repressor protein + tryptophan d. Is an example of positive regulation

The centromere of a submetacentric chromosome is located __________. a. in the middle of the chromosome b. close to the end of the chromosome c. midway between the middle and the end of the chromosome d. at the end of the chromosome

The genetic code is __________. a. a series of tRNA molecules b. an enzyme c. a series of triplet nucleotide sequences d. a linear series of amino acids

The gross physical structure of a chromosome can be described by a. The location of a centromere b. Chromosome staining or fluorescence patterns c. Either of the above

The most important DNA sequence ("element") in the promoter region of eukaryotic genes transcribed by RNA polymerase II machinery is known as the a. TFIIB Recognition Element (BRE). b. Downstream Promoter Element (DPE). c. TATA box. d. TFIIH Recruiting Element (HRE). e. Preinitiation Center (PIC).

The results of a three-point linkage test cross are given below. What is the order of the genes on the chromosome? AXv/axv = 100 axV/axv = 100 AxV/avx = 50 aXv/avx = 50 aXv/avx = 30 AxV/avx = 30 axv/axv = 1 AXV/axv = 2 a. AXV b. VAX c.AVX

The secondary structure of a protein includes ________. a. gamma and delta b. alpha and gamma c. α-helix and β-pleated sheet d. hydrophobic clusters e. disulfide bridges

Through the study of mitochondrial disorders, scientists have suggested a link between the decline of mitochondrial function and aging. What process appears to be involved in this suspected phenomenon? a. accumulation of sporadic mutations in the nuclear genome b. decline of mutations in the nuclear genome c. accumulation of mutations in the mtDNA d. recombination of mtDNA and nuclear DNA e. recombination among mtDNAs of different mitochondria

Transduction is a form of recombination in bacteria that involves ______. a. the mutagen 5-bromouracil b. plasmids c. bacteriophages d. fertility factors

Two alleles determine coat color in mice. For a population in Hardy-Weinberg equilibrium, if the frequency of individuals exhibiting the recessive coat color, brown (b), is 0.16, what is the frequency of the b allele? a. 0.16 b. 0.36 c. 0.4 d. 0.48

Two curly-winged Drosophila are mated and produce 973 curly and 464 wild-type offspring. What is the genetic basis for these results? a. incomplete dominance—the mutant allele is dominant to the wild-type allele b. X-linkage c. a lethal allele d. simple dominance—the mutant allele is dominant to the wild-type allele

Two genes, A and B, are located on the same chromosome. Which of the following represents the genotype of an individual who is heterozygous for both genes (chromosomes indicated by //) a. Aa//bB b. Ab//Ab c. Ab//aB d. AB//AB e. AA//bb

What are the different types of gametes that can be formed by individuals with the genotype AaBbcc? a. ABc, Abc, aBc b. ABc, Abc c. ABc, Abc, aBc, abc d. AaBbcc

When mating between a specific Hfr strain and F- strain was interrupted at varying times, the following was observed Time after mating --------- Genes transferred to F- cell 1 min Z 30 min H and Z 50 min H, O, and Z 70 min H, O, Z, and T 90 min H, O, Z, and T What is the order of genes on the bacterial chromosome? a. H, O, Z, T b. H, Z, O, T c. Z, H, O, T d. O, Z, T, H

When nutrients become limiting, what happens to a population of bacteria? a. It enters lag phase. b. It enters log phase. c. It enters stationary phase. d. None of the answers given.

When the "lac I" gene product is NOT bound to the operator region of the lactose operon- a. RNA polymerase cannot bind to the P site b. Attenuation is used as a contol c. β-galactosidase is transcribed d. repressor cannot bind to allolactose

Which of the following errors is a source of heritable genetic variation? a. changes in the three-dimensional structure of proteins that are not caused by mutation b. errors in transcription c. changes in the nitrogenous base sequence of DNA d. errors in translation

Which of the following gametes could be produced by a plant that is RrYy (F1 hybrid)? a. RrYy b. Rr c. RY d. Yy

Which of the following statements about three linked genes that are spaced very close together along a chromosome is most likely to be true? a. Interference is not likely to affect the number of crossovers observed. b. The number of hidden double crossovers will be very large. c. Interference will be a significant factor in the number of crossovers observed. d. Interference and the number of hidden double crossovers will significantly affect the number of crossovers observed.

Which of the following statements best represents variable expressivity and incomplete penetrance? a. How much of a gene is expressed is a measure of its expressivity; the effect it has on phenotype is a measure of its penetrance. b. If expressivity is variable, penetrance must be complete. c. Polydactyly, a dominant trait in humans, does not develop to the same degree in different heterozygous individuals and provides an example of variable expressivity; the extreme case, where a heterozygote does not develop polydactyly, is an example of incomplete penetrance. d. Incomplete penetrance can occur only if expressivity is variable. e. An allele showing strong penetrance has a severe effect on phenotype and the large amount of protein product made correlates with high expressivity.

Which of the following statements regarding the behavior of Mendel's unit factors (genes) and chromosomes is true? a. Alternative forms of a gene are found on sister chromatids. b. During prophase I of meiosis, sister chromatids with identical alleles synapse. c. Alternative forms of a gene are found on homologous chromosomes. d. A diploid organism receives two copies of a gene from the maternal parent and two copies from the paternal parent.

Which of the following type (s) of genetic transfer lead to incorporation of new DNA into the bacterial chromosome? I. conjugation mediated by F factor II. Hfr mediated conjugation III. transduction IV. transformation a. I and II only b. III and IV only c. II, III, and IV d. I, II, III, and IV e. none of these

Which organelle is responsible for generating cellular energy in the form of ATP in plant and animal cells? a. endoplasmic reticulum b. nucleus c. mitochondrion d. chloroplast

Why are enzymes crucial to living organisms? a. They transport amino acids to the ribosome during translation. b. They compose codons. c. They act as biological catalysts. d. They are the subunits of DNA.

Wild cats (Felis silvestris) and common mice (Mus musculus) are diploid. In wild cats 2n = 38, while in common mice 2n = 40. Based on this information, we can conclude that wild cat cells have - a. less DNA than common mouse cells. b. smaller genomes than common mouse cells. c. fewer DNA molecules than common mouse cells. d. fewer genes than common mouse cells. e. fewer haploid sets of chromosomes than common mouse cells

Without telomerase - a. chromosomes could not attach to the spindle b. chromosomes could not replicate c. chromosomes would get shorter

Women with the BRAC 1 gene have a higher risk for breast cancer but may never develop breast cancer. This is an example of - a. incomplete dominance b. epistasis c. incomplete penetrance d. phenotype switching e. anticipation

Yellow seeds (Y) dominant to green seeds (y) Round seeds (R) dominant to wrinkled seeds (r) Two heterozygous plants are crossed (YyRr x YyRr). What proportion of green-seeded plants will there be in the progeny of this cross? a. 75% b. 50% c. 25% d. 0%

You are testing a drug for a drug company to determine if experimental drug X245 is mutagenic using the Ames test. You add the drug to two paper disks, A and B. To disk A, you add liver enzymes and nothing to disk B. Both disks are placed on a lawn of His- bacteria. His + revertants were found surrounding disk A but not B. You report to the drug company that - a. The drug is not mutagenic b. The drug is mutagenic c. The drug is not mutagenic but metabolic byproducts of the drug are mutagenic.

You wish to amplify the region in BOLD CAPS below using PCR. Select the correct set of primers. Assume, for the purposes of this question, that an octamer primer is sufficient. (Usually, primers 18-20 nucleotides in length are required). 5'gagatcaggacttaGATTACAGATTACAGATTACAGATTACAggccaagtc3' a. 5'AGGACTTA3' and 5'GGCCAAGT3' b. 5'TAAGTCCT3' and 5'ACTTGGCC3' c. 5'AGGACTTA3' and 5'ACTTGGCC3' d. 5'AGGACTTA3' and 5'TGAACCGG3'

As Watson and Crick pondered the structure of DNA, they learned that the molarratios of the four bases of DNA in nature obey the following rule a) (A+G)/(C+T) = 0.5 b) (A+T)/(C+G) = 1.0 c) (A+G)/(C+T) = 1.0 d) (A+T)/(A+C+G+T) = 0.5 e) C=T and A=G

c) (A+G)/(C+T) = 1.0

In a Hopi Indian population of 10,000 people 25 are phenotypic albinos. Albinism is recessive. Apply the Hardy-Weinberg law to estimate: what is the frequency (q) of the albinism allele in the Hopi population? a) 0.0025 b) 0.01 c) 0.05 d) 0.10 e) 0.25

c) 0.05

A healthy couple requests genetic counseling to determine the chances that their first child will have cystic fibrosis, an autosomal recessive disease affecting the lung and other organs. In the wife's family, one out of her three siblings died of the disease. In the husband's family, his two siblings were healthy, but one first cousin had the disease.(space to draw the pedigree) 5Please advise the couple. The chance that the couple's first child has the disease is a) 1/256 b) 1/64 c) 1/24 d) 1/16 e) 1/8

c) 1/24

One form of hemophilia is caused by an X-linked recessive gene. Assume that a man with hemophilia marries a phenotypically normal woman whose father had hemophilia. What is the probability that they will have a daughter who also has hemophilia? a) none b) 1/8 c) 1/4 d) 1/2 e) 3/4

c) 1/4

Can you calculate a LOD score for linkage for this family? The LOD score is between ... a) 0 and 1 b) 1 and 2 c) 2 and 3 d) 3 and 4 e) >4

c) 2 and 3

What is the fraction of recombinants? a) <1% b) 1-2% c) 2-4% d) 4-8% e) >8%

c) 2-4%

How many 'degrees of freedom' are there in this dataset? a) 1 b) 2 c) 3 d) 4 e) 5

c) 3

The parents of the female fly that Sturtevant used were v/v; r+/r+ and v+/v+; r/r. That means, their phenotypes were as follows: ______________ x ________________ (no point for this) . With this information, now consider this question: Of the phenotypic Classes 1-4 that Sturtevant obtained, which ones represent new, 'recombinant' phenotypes and which represent original, 'parental' phenotypes? These following classes are recombinant: a) 1 and 2 b) all c) 3 and 4 d) 1 and 4 e) 2 and 3

c) 3 and 4

A diploid cell is presently in the G1 phase of the cell cycle. How many sets of genetic material will be present in the G2 phase? a) 1 b) 2 c) 4 d) 8 e) 0

c) 4

The meiotic recombination frequency between two unlinked genes is: a) 100% b) 75% c) 50% d) 25% e) 0%

c) 50%

The recombination frequency between two unlinked genes is: a) 100% b) 75% c) 50% d) 25% e) 0%

c) 50%

However, if the two mutations were in different genes then the F2 would yield this many purple-eyed flies a) 3/4 b) 1/2 c) 7/16 d) 3/8 e) all

c) 7/16

A female fly heterozygous for short bristles (s/s+) and ebony body (e/e+) is testcrossed to a male homozygous for the corresponding recessive alleles, s and e. The following progeny were observed: long bristles, normal color 436 short bristles, ebony color 454 long bristles, ebony color 58 short bristles, normal color 52 What is the recombination frequency between them? a) 0-4% b) 4-8% c) 8-12% d) 12-16% e) >16%

c) 8-12%

A man and a woman are each heterozygous for both cystic fibrosis and phenylketonuria. Both conditions are autosomal recessive, and they assort independently. What is the probability for a child of this couple to have neither CF nor PKU. a) 1/16 b) 6/16 c) 9/16 d) 12/16 e) 15/16

c) 9/16

The dominant allele Curly (Cy) results in curly wings in fruit flies. The cross betweenCy/+ and Cy/+ (where + stands for the wild type allele) results in a ratio in the progeny of 2 curly to 1 wild-type. When these curly progeny are intercrossed the ratio of curly to wild type is again 2:1. How can this result be explained most easily? a) The Curly gene is sex linked. b) The curly phenotype is converted to wild-type by the epistatic effect of a second gene c) The Cy/Cy genotype is lethal and therefore not recovered. d) The two Cy alleles in the parent generation are actually mutations in two different genes. e) This is the standard result expected for a monohybrid cross.

c) The Cy/Cy genotype is lethal and therefore not recovered.

To investigate allelism between the two different purple mutations, a complementation test was set up. If the two purple mutations are in the same gene (allelic), the F1 is expected to be ... a) all red b) all orange c) all purple d) all white e) 50% red

c) all purple

In sweet peas, the synthesis of the purple anthocyanin pigment in the petals is controlled by two genes, B and D. The pathway is: gene B white intermediate -> blue gene D intermediate -> anthocyanin (purple) What color petals would you expect in a homozygous plant unable to catalyze the second reaction? a) red b) purple c) blue d) white e) light blue

c) blue

In a small population, changes in allele frequency from one generation to the next occur just by chance. This is called: a) assortative mating b) positive selection c) genetic drift d) migration e) mutation

c) genetic drift

c) hypomorph

The disease known as phenylketonuria is due to a defect in the gene for phenylalanine hydroxylase. The defect is inherited in a(n) ___(47)____ fashion. Mutations in this gene have been identified in many different ethnic groups. Actually, the specific mutation causing the disease is _____(48)____ . This finding suggests that the mutation arose ______(49)_____. If 7left untreated, the condition causes _____(50)______ . Fortunately, there is a treatment that can prevent the worst symptoms of the disease; it is ______(51)______ . 50. a) tooth decay b) arthritis c) mental retardation d) muscle weakness e) anemia

c) mental retardation

Locus Z is analyzed for a population of sloths. Long claws (Z1) is dominant to short claws (Z2) and the following numbers were observed: Number of individuals Genotype 74 Z1/Z1 120 Z1/Z2 46 Z2/Z2 Calculate the genotypic frequency. Calculate the allelic frequency. In a population of 130 sloths, how many would you expect to have long claws?

c. Z1Z1 or Z1Z2 f(Z1Z1) = p^2 = (.558)^2 = .311 x 130 = 40 f(Z1Z2) = 2pq) = 2(.558)(.442) = .493 x 130 = 64 104 total

h^2 = R/s A= pop. mean before selection B= pop. mean after selection C= mean of mating indiv R = B-A s = C-A

calculating h^2 from response to selection

what is meant by the term heritable

capable of being transmitted genetically from parent to offspring

founder effect

causes genetic drift

What is small scale "micro" evolution

changes in gene frequency in a population from one generation to the next

what are some of the disadvantages of molecular data over morphological data

character state space is relatively low: amino acids = 20, DNA = 4 (A,T,G,C), so there is a high probability of homoplasy: convergence, parallelism, and reversal. - molecular data can still be functional (herbivory, aquatic life).

what are homologous characters

characters in different organisms that are similar because they were inherited from a common ancestor

Vg = Va + Vd + Vi -Va=additive variance: due to additive effects of genes on phenotype -Vd=dominance genetic variance: alleles are not additive/phenotype is result of interaction of alleles gene T- T,t=> TT, Tt have same phenotype vs tt -Vi=gene interaction variance: alleles of diff loci interact w/each other ex. epistasis/ no additive effects Vp = Vg + Ve + Vgxe Vp = Va + Vd + Vi + Ve + Vgxe

components of genetic variance

A bacterial cell can transfer chromosomal genes F- cells but rarely caues the F- cell to become F+. The bacterial cell is- a. auxotrophic b. prototrophic c. lysogenic d. Hfr e. lytic

A loss-of-function mutation __________. a. is a neutral mutation b. results in an increased quantity of the normal gene product c. is the wild-type allele d. results in reduced or no production of the gene product

A mutation is more likely to be silent if it is found in- a. an intron. b. intergenic regions. c. the wobble position of a codon. d. All of the above are true.

A plasmid used as a cloning vector in E. coli must have a. an ori sequence. b. a selectable marker such as an antibiotic resistance gene. c. unique restriction sites. d. all of the above e. none of the above

A pleiotropic mutation __________. a. is also known as a conditional mutation b. is expressed more frequently in males than in females c. is expressed only in the homozygous recessive condition d. is a mutation that causes multiple phenotypic effects on the organism

A single nucleotide polymorphism is a. most often found in noncoding genic DNA. b. variable in length. c. detectable by DNA sequencing only. d. a single base mutation. e. most often caused by replication slippage.

A standard eukaryotic chromosome is composed of a. a single strand of DNA b. histone proteins c. regulatory proteins d. all of the above

A testcross is designed to determine the genotype of a parent with the dominant, tall phenotype. Half of the resulting progeny are tall and half are dwarf. What is the genotype of the parent? a. dd b. DD c. D d. Dd

A transgenic organism __________. a. has been changed from one species into another b. has been cloned from an adult cell c. is found only in crop plants d. has a gene from another species inserted in its DNA

All EXCEPT which of the following are directly related to linkage groups? a. The number of haploid chromosomes in an organism's genome b. Lod scores c. A group of genes found on the same chromosome d. Members of the same family expressing the same trait

Arabidopsis is a model organism for the study of ______. a. fruit flies b. fungi c. prokaryotes d. plants

Birds and mammals diverged million of years ago, each developing a chromosome mechanism of sex determination. Which of the following statements are correct? a. in both birds and mammals, females are the heterogametic sex b. in both birds and males, females are the homogametic sex c. birds have XO chromosomal system and lack a Y chromosome d. in birds, females are the heterogametic sex and males are homogametic sex e. sex determination in birds is due to a balance of autosomes and the X chromosome

Codons are nucleotide triplets. How many different codons can be formed? a. 3 b. 16 c. 20 d. 64

Complementation tests are used to determine whether a. a new mutant phenotype of interest is dominant or recessive to another mutant phenotype. b. two phenotypically identical mutants carry mutations in the same or in different genes. c. two or more mutants are allelic to each other. d. a and b are correct.

Crossing over refers to __________. a. the formation of lateral elements between paired homologs during zygonema b. the onset of homology search in the leptotene stage of meiosis I c. the random segregation of dyads in metaphase I of meiosis d. genetic exchange between nonsister chromatids during the pachytene stage of meiosis I

DNA replication in prokaryotes and eukaryotes differs in fundamental ways. Pick the INCORRECT statement from the following statement. a. The primer is RNA in bacteria and RNA+DNA in eukaryotes b. There is one origin of replication in prokaryotes, many in eukaryotes c. Okazaki fragments are shorter in prokaryotes (100-150 nucleotides long) d. The speed of polymerization is faster in eukaryotes e. The direction of polymerization is 5' to 3' in both prokaryotes and eukaryotes

During the elongation phase of translation, the aminoacyl-tRNA carrying the next amino acid to be added to a growing polypeptide chain a. first binds the A site of the ribosome. b. first binds the P site of the ribosome. c. binds the ribosome so that its anticodon is positioned in the ribosomal small subunit to base pair with the matching codon of the mRNA. d. both a and c. e. both b and c.

During the elongation phase of translation, the aminoacyl-tRNA carrying the next amino acid to be added to a growing polypeptide chain - a. first binds the A site of the ribosome. b. first binds the P site of the ribosome. c. binds the ribosome so that its anticodon is positioned in the ribosome to base pair with the matching codon of the mRNA. d. both a and c. e. both b and c.

Enhancers are thought to act on promoters to enhance transcription of a gene. This requires a. DNA bending proteins b. promoter binding proteins c. enhancer binding proteins d. all of the above

Exchange of genetic material between two homologous chromatids occurs during what stage of cell division? a. prophase I of meiosis b. prophase II of meiosis c. prophase of mitosis d. interphase of both meiosis and mitosis e. metaphase of mitosis

Genes X, Y, and Z are linked. Crossover gametes between genes X and Y are observed with a frequency of 25%, and crossover gametes between genes Y and Z are observed with a frequency of 5%. What is the expected frequency of double crossover gametes among these genes? a. 30% b. 5% c. 50% d. 1.25%

Human disease associated with dysfunctional mitochondria which results from mutation in a single gene locuse in nuclear DNA, is most likely to: a. be inherited from the mother, because mitochondria are not inherited from the father. b. show heteroplasmy in the progeny of affected individuals, depending on chance events during meiosis. c. show a non-Mendelian inheritance pattern, because the number of mitochondria varies from cell to cell. d. show a Mendelian inheritance pattern. e. none of the above.

If two nuclear genes in a diploid eukaryote are physically linked by DNA sequence data, but we have no additional data other than this, we can say with confidence that they a. are homologs. b. are genetically linked and would cosegregate during meiosis. c. are separated by no more than 1 cM (centiMorgan-a unit of chromosome distance). d. are located on the same chromosome. e. are located on separate chromosomes.

In a population in Hardy-Weinberg equilibrium, the frequency of allele A is 0.9 and the frequency of allele a is 0.1. What proportion of individuals exhibits the dominant phenotype? a. 0.01 b. 0.09 c. 0.18 d. 0.99

In a population of red (dominant alleles) or white flowers, the frequency of red flowers is 91%. What is the frequency of the red allele? a. 9% b. 30% c. 91% d. 70%

In addition to highly repetitive and unique DNA sequences, a third category of DNA sequences exists. What is it called, and what types of elements are involved in it? a. composite DNA; telomeres and heterochromatin b. dominant DNA; euchromatin and heterochromatin c. multiple gene family DNA; hemoglobin and 5.0S RNA d. moderately repetitive DNA; SINEs, LINEs, and VNTRs e. permissive DNA; centromeres and heterochromatin

In an experiment by Hershey and Chase, phage were labeled with either radioactive P32 or S35 and the fate of the two labels was followed. These experiments DEMONSTRATED that a. S35 was transmitted to the next generation of phage. b. P32 was incorporated into proteins. c. DNA was packaged into phage heads. d. the P32 labeled material was the genetic material. e. That some phage have an RNA genome

In an individual that is XX, if non-disjunction for the X chromosome occurs during meiosis anaphase I and the second meiotic division is normal, what gametes are produced? a. X, Y, O, O (O indicates the gamete does not carry this type of chromosome). b. X, X, X, X c. X, XX, X, O d. XX, XX, O, O e. None of the answers given above are correct

In humans, red-green colorblindness is a sex-linked recessive trait. A colorblind male has the genotype XbY and a normal male has a genotype XBY. If the frequency of a red-green colorblind males in a population is 0.20, what is the frequency of re-green colorblind females in this population? a. 0.2 b. 0.8 c. 0.36 d. 0.04

In which of the following organisms is gender determination influenced by environment? a. humans b. birds c. butterflies d. turtles

Lightly stained areas of the chromosome are called ____ and are believed to be genetically _____ a. heterochromatin, inactive b. euchromatin, inactive c. Heterochromatin, active d. euchromatin, active

Nucleosomes a. Are distributed randomly to newly synthesized DNA b. Are composed of a mix of old histone proteins and new histone proteins c. Are completely removed from the entire chromosome before replication d. a and b are correct

Over time, the lethal load (lethal genes carried by an individual) has increased from 4-5 to 6-7. The underlying cause is thought to be- a. improved medical care keeps genes in the population past reproductive age b. changing populaiton demographics changes the level of populaiton inbredding c. mutation rates have increased d. both a and b

Pick the INCORRECT statement. Telomeres in eukaryotes - a. are repetitive sequences b. in cells without functional telomerase, get progressively shorter with each cell division c. are affected by stress and illness d. are capped and protected with the protein/RNA complex 'telomerase'

Prokaryotic chromosomes are- a. Found in the nucleus b. a single naked strand of DNA c. complexed with histone proteins d. circular

Select the INCORRECT statement from the following: a. Bar eye in drosophilia is a duplication b. DNA sequence analysis suggests that gene families arose by duplication c. duplications can result from unequal crossing over d. duplications form a characteristic cross-like shape when seen in heterozygous during meiosis e. ribosomal genes represent a duplicated region

Sickle-cell anemia results from __________. a. an error during transcription of the hemoglobin gene b. the deletion of a chromosome c. a mutation that causes no production of hemoglobin d. a single nucleotide change in the DNA resulting in the substitution of a valine for a glutamic acid in the protein

Silent alleles (alleles with no phenotypic effect) - a. Occur but don't affect detectable gene function b. Are always harmful c. May occur in introns d. both a and c

Specific promoter sequences may- a. be required to initiate transcription. b. bind specific regulatory proteins. c. bind directly to enhancer DNA sequences. d. both A and B e. all of the above

Suppose an animal with genotype AaBb were crossed to one with the genotype aabb. The offspring include: 442 AaBb, 458 aabb, 46 Aabb, and 54 aaBb. What can be deduced about the location of the genes? a. The genes are on separate chromosomes. b. The genes A and B are linked and are 20 units apart. c. The genes A and B are linked and are 5 units apart. d. The genes A and B are linked and 10 units apart.

Suppose that protein had been found to be the hereditary material instead of DNA. How would the results of the Hershey- Chase experiment with T2 infection of E coli have differed? a. Most of the radioactive sulfur (35S) would have been found inside the infected cells. b. Most of the radioactive phosphorus (32P) would have been found associated with the phage ghosts outside the infected cells. c. Radioactive phosphorus (32P) would have been found equally distributed between the phage ghosts and the infected cells. d. Both a and b would have been observed.

The first step in eukaryotic transcription of genes with discrete promoters is binding of____ to the _____. a. RNA polymerase, promoter b. Transcription factors IIA-IIJ, CAAT box c. Methyl groups, GC repeats d. Transcription factor IID, TATA box e. Polymerase II, TATA box

The majority of calico cats are female. However, a few rare males are observed. What is the genotype of a male calico cat? a. XBXb b. XBY c. XbYY d. XBXbY

The necessary information to control cell and organism function is encoded in- a. the sequence of DNA bases b. the sequence of mRNA bases c. the sequence of amino acids d. all of the above

The nuclear genome of a mouse nerve cell is compared to that of a mouse skin cell. What differences can we expect to see between these two cells' nuclear genomes? a. the two cells have almost identical genomes, but the nerve cell has more nerve-specific genes b. the two cells ahve almost identidcal genomes, but the skin cell has more skin-specific genes c. the two cells have similar genomes, but the nerve cell has more nerve-specific genes and the skin cell has more skin-specific genes d. the two cells have the same genome; there will be no differences

Two genes that show recombination between them more than 50% of the time are probably a. far apart on the same chromosome b. on different chromosomes c. close together on the same chromosome d. either a or b

Unlike DNA polymerase during replication,......... a. RNA polymerase can initiate synthesis without a primer. b. The nascent RNA strand is displaced as synthesis proceeds, so that the template DNA and newly synthesized RNA do not remain base-paired. c. RNA polymerase copies only one of the two DNA strands for any given gene. d. all of the above. e. none of the above.

What amino acid(s) are coded by a single codon? a. tryptophan b. methionone c. thymine d. a and b

What are the two monohybrid crosses that together make up the dihybrid cross AaBb x AaBb? a. AB x AB and ab x ab b. Ab x aB and aB x Ab c. AA x AA and BB x BB d. Aa x Aa and Bb x Bb

What is Mendel's law of independent assortment? a. Each gamete receives only one allele for each trait. b. Only if individuals mate randomly can inheritance patterns be predicted. c. The frequency that a trait appears in a population is unrelated to that allele's frequency in the population. d. The pattern of inheritance of one trait does not influence the inheritance pattern of another trait.

What is the likely effect of a mutation from CAU to CGU in a protein's active site? a. auxotrophic b. leaky c. prototrophic d. any of the above are possible

What is the probability of a family with six children having three boys and three girls? a. 1/64 b. 6/64 c. 15/64 d. 20/64

What is the probability of getting exactly 2 girls and 2 boys in a family of 4? a. 1/16 b. 3/16 c. 4/16 d. 6/16

What lines of evidence suggest that organelles are endosymbionts? a. Organelles have prokaryotic ribosomes b. Organelles have gene sequences more closely related to prokaryotes than eukaryotes c. Organelles have a prokaryotic-type of translation d. All of the above

When do sister chromatids separate during meiosis? a. anaphase II b. metaphase I c. anaphase I d. metaphase II

When is DNA duplicated for cell division? a. during prophase of mitosis and meiosis b. during G1 and G2 of interphase c. during metaphase of mitosis and meiosis d. during the S phase of interphase

When mating between a specific Hfr strain and F- strain was interrupted at varying times, the following was observed Time after mating --------- Genes transferred to F- cell 1 min Z 30 min H and Z 50 min H, O, and Z 70 min H, O, Z, and T 90 min H, O, Z, and T Where did F integrate in the bacterial chromosome? a. between Z and H b. between O and H c. between H and T d. between T and Z e. between O and T

Where does your fat go when you lose weight a. CO2 b. water c. O2 d. a and b

Which DNA marker is generated by restriction enzymes? a. Microsatellites b. SNPs c. Chiasmata d. RFLPs

Which condition is evaluated at the G2/M checkpoint? a. adequate cell size b. proper spindle assembly c. proper spindle formation d. precise replication of DNA

Which of the following is NOT necessary for evolution by natural selection for a particular trait to occur? a. Some variants are more successful at surviving and reproducing than others. b. More offspring are born than can survive. c. The trait is heritable. d. All of these conditions are necessary for evolution by natural selection to occur.

Which of the following statements about cell division is FALSE? a. In meiosis, but not mitosis, there is a reduction in the amount of genetic material in the daughter cells. b. Gametes are formed by meiosis. c. In mitosis, but not meiosis, the daughter cells are identical copies of the mother cell. d. After mitosis the daughter cells are haploid, whereas after meiosis the daughter cells are diploid.

Which of the following statements about the children of first-cousin matings is true? a. They contain more unique alleles than other children. b. They exhibit greater levels of heterozygosity. c. They contain more dominant alleles. d. They exhibit decreased levels of heterozygosity.

Which structure is missing from some mitotic cells? a. kinetochore b. spindle fibers c. sister chromatids d. centriole

Why are SNPs used to map and locate unknown disease loci? Why don't we just sequence the DNA from diseased individuals and compare it to "normal" individuals? a. It is too invasive to obtain DNA from individuals for DNA sequencing. b. A SNP always causes a phenotypic change, and is therefore ideally suited for mapping purposes. c. A SNP is always linked to a disease allele and so positional mapping is easy. d. Detecting SNPs is faster and more economical than genome-wide sequencing. e. Both b and c

Yellow seeds (Y) dominant to green seeds (y) Round seeds (R) dominant to wrinkled seeds (r) Which of the following gametes could a plant that is heterozygous for seed color and seed appearance (YyRr) produce? a. Yy b. YyRr c. RR d, YR

______________ are reversible changes in the position of protons in DNA purine and pyrimidine bases. a. transversions b. transitions c. point mutations d. tautomeric shifts

And how many of the F2 progeny will be white and male-sterile? a) 1/2 b) 1/4 c) 3/16 d) 1/16 e) 1/64

d) 1/16

Peyton hopes to increase the fraction of orange, male-sterile, plants from his crosses. You can probably suggest to Peyton which two genotypes he should generate and cross with each other to derive a larger fraction of orange, male-sterile, plants... The maximal fraction of orange, male sterile progeny possible is a) all b) 3/4 c) 1/3 d) 1/2 e) 1/4

d) 1/2

Two organisms, AABBCCDDEE and aabbccddee, are mated to produce an F1 that is then self-fertilized. If the capital letters represent dominant, independently assorting alleles: 53. How many different phenotypes will occur in the F2? a) 1 b) 5 c) 8 d) 32 e) 243

d) 243

Two organisms, AABBCCDDEE and aabbccddee, are mated to produce an F1 that is then self-fertilized. If the capital letters represent dominant, independently assorting alleles: 54. How many different gamete genotypes will be produced by the F1? a) 1 b) 5 c) 8 d) 32 e) 243

d) 32

Two organisms, AABBCCDDEE and aabbccddee, are mated to produce an F1 that is then self-fertilized. If the capital letters represent dominant, independently assorting alleles: How many different gamete genotypes will be produced by the F1? a) 1 b) 5 c) 8 d) 32 e) 243

d) 32

Assume you have a fruit fly that is heterozygous for three genes... All genes are on different chromosomes. How many different genotypes do you expect to find among the gametes? a) 1 b) 2 c) 4 d) 8 e) 16

d) 8

Now, let's assume the three genes all reside on the same chromosome (not the X). Assuming there are crossovers in each interval, how many different genotypes will appear among the gametes of a female fly? a) 1 b) 2 c) 4 d) 8 e) 16

d) 8

If the first child of the couple is healthy, calculate the probability that the child is a carrier for either or both conditions. a) 1/9 b) 6/16 c) 4/9 d) 8/9 e) 1 (certain)

d) 8/9

In sweet peas, the synthesis of the purple anthocyanin pigment in the petals is controlled by two genes, B and D. The pathway is: gene B white intermediate -> blue gene D intermediate -> anthocyanin (purple) What ratio of purple:blue:white plants would be expected in the F2 (intercross of F1 plants)? a) 12:1:3 b) 9:0:7 c) 9:7:0 d) 9:3:4 e) 9:4:3

d) 9:3:4

The disease known as phenylketonuria is due to a defect in the gene for phenylalanine hydroxylase. The defect is inherited in a(n) ___(47)____ fashion. Mutations in this gene have been identified in many different ethnic groups. Actually, the specific mutation causing the disease is _____(48)____ . This finding suggests that the mutation arose ______(49)_____. If 7left untreated, the condition causes _____(50)______ . Fortunately, there is a treatment that can prevent the worst symptoms of the disease; it is ______(51)______ . 48. a) always the same in every patient b) always a splice site mutation c) always an amino acid substitution d) any one of over 30 different basepair changes e) generally unknown

d) any one of over 30 different basepair changes

The disease known as phenylketonuria is due to a defect in the gene for phenylalanine hydroxylase. The defect is inherited in a(n) ___(47)____ fashion. Mutations in this gene have been identified in many different ethnic groups. Actually, the specific mutation causing the disease is _____(48)____ . This finding suggests that the mutation arose ______(49)_____. If 7left untreated, the condition causes _____(50)______ . Fortunately, there is a treatment that can prevent the worst symptoms of the disease; it is ______(51)______ . 51. a) Gene therapy b) blood transfusion c) kidney transplant d) dietary restrictions e) amniocentesis

d) dietary restrictions

A combination of linked alleles is also called a a) hap-map b) haploid c) hapless d) haplotype e) haploinsufficiency

d) haploinsufficiency

d) protein

In sweet peas, the synthesis of the purple anthocyanin pigment in the petals is controlled by two genes, B and D. The pathway is: gene B white intermediate -> blue gene D intermediate -> anthocyanin (purple) What color petals would you expect in a homozygous plant unable to catalyze the first reaction? a) red b) purple c) blue d) white e) light blue

d) white

Drosophila eyes are normally red. You have isolated two independent purple-eyed mutant strains. The purple phenotype is inherited as an autosomal recessive trait in each case. 11. In genetic parlance the red eye phenotype is commonly referred to as a) epistatic b) pretty c) regular d) wild-type e) normal

d) wild-type

what are substitution parameters

describe the rate that one base replaces another during evolution

what is an invariant sites parameter

doesn't change

A nullisomic human cell would contain a. 23 pairs b. 22 chromosomes c. 45 chromosomes d. 22 pairs e. both d and c

A purpose of using a test cross in linkage anaylses is to- a. examine crossovers derived from only a single parent b. allow identification of progeny genotype from progeny phenotype c. simplify the analysis of sex linked genes d. reduce double crossovers e. both a and b above

A short segment of an mRNA molecule is shown below. The polypeptide it codes for is also shown: 5′-AUGGUGCUGAAG-3′: methionine-valine-leucine-lysine Assume that a mutation in the DNA occurs so that the fourth base (counting from the 5′ end) of the messenger RNA now reads A rather than G. What sequence of amino acids will the mRNA now code for? a. methionine-valine-leucine-lysine b. methionine-lysine-leucine-lysine c. methionine-leucine-leucine-lysine d. methionine-valine-methionine-lysine e. methionine-methionine-leucine-lysine

If a wild-type allele is haploinsufficient, the behavior of a null allele in a heterozygote (wild-type/null) would be predicted to be - a. recessive. b. dominant. c. incompletely penetrant. d. variable in expressivity. e. Incompletely dominant

If mom is blood type A and Dad is blood type B, which of the following children are possible? a. A blood type b. B blood type c. O blood type d. AB blood type e. All are possible

If two different auxotrophic strains are placed in liquid medium in a culture tube, prototrophic strains can sometimes be subsequently recovered. Name a mechanism by which this is possible a. reverse mutation b. conjugation c. transformation d. transduction e. all of the above

In an individual that is XY, if non-disjunction for the X chromosome occurs during meiosis anaphase I and the second meiotic division is normal, what gametes are produced? a. X, Y, O, O (O indicates the gamete does not carry this type of chromosome). b. X, X, Y, Y c. X, XY, Y, O d. XX, YY, O, O e. XY, XY, O, O

Place the following steps for making a plant DNA library in pUC19 in correct order. a. digest pUC19 with Bam HI b. mix digested DNAs c. transform pUC19 into E. coli d. ligate sugar phosphate backbone e. digest plant DNA with Bam HI a. abced b. acbde c. debac d. cdbae e. aebdc

Poly-X syndome is characterized by - a. most spontaneously aborted b. epicanthal fold c. webbed neck d. 1 barr body e. occasional slight retardation

Restriction enzymes - a. Protect bacteria from viral infection b. Cut DNA in a staggered fashion c. Cut DNAs producing a blunt end d. Cut DNA at Palendromic sequences e. All of the above are correct

The genotype of a cell is AaBb. What genotypes are possible after meiosis? a. AaBb only b. AB and ab only c. Aa and Bb d. AA and BB only e. Ab, aB, AB and ab

Turner's syndrome is characterized by a. unusually tall b. severely retarded c. epicanthal fold d. intersex characterisitics e. most spontaneously aborted

What information is absent from a cDNA library? a. intron sequences b. promoter sequences c. sequences coding for amino acids d. start and stop codons e. a and b

Which of the following correctly states a difference between the functions of DNA Polymerase III and DNA Polymerase I in E. coli? a. DNA Polymerase III synthesizes the leading strand, whereas DNA Polymerase I is used for synthesis of the lagging strand (Okazaki fragments). b. DNA Polymerase III does not require an RNA primer, whereas DNA Polymerase I does. c. DNA Polymerase III synthesizes new DNA strands in the 5' to 3' direction only, whereas DNA Polymerase I also can synthesize DNA in the 3' to 5' direction. d. DNA Polymerase III has a 3' to 5' exonuclease activity that serves a proofreading function, whereas DNA Polymerase I lacks this activity. e. DNA Polymerase III is the main polymerase of the replisome, whereas DNA Polymerase I removes primers and fills in the gaps that are left.

Which of the following is NOT a feature of Drosophila polytene chromosomes? a. ~ 1500 copies of each chromosome b. homologous chromosomes paired c. chromosomes held together at a chromocenter d. found in Drosophila salivary gland chromosomes e. Genetically inactive

Which of the following will result in modifications to the expected Mendelian ratios? a. epistatis b. incomplete dominance c. incomplete penetrance d. gene interaction e. all of the above

A/A and A/a individuals are equally fertile. The mutation rate from allele A to a is 10-5per generation. The genotype frequency of (a/a) in the population is 0.001. Calculate the selection coefficient (s) for a/a. a) 1 b) 0.2 c) 0.1 d) 0.05 e) 0.01

e) 0.01

Two organisms, AABBCCDDEE and aabbccddee, are mated to produce an F1 that is then self-fertilized. If the capital letters represent dominant, independently assorting alleles 55. How many different genotypes will occur in the F2? a) 1 b) 5 c) 8 d) 32 e) 243

e) 243

He derives a number of F1 progeny that are now heterozygous for both the color and the sterility traits. He plans to intercross the double-heterozygous plants and sell only those (F2) progeny that are orange and male-sterile. That way his customers will always come back for more. How many of the progeny will be suitable for sale?a) 3/4 b) 1/2 c) 3/8 d) 1/4 e) 3/16

e) 3/16

Which of the following reagents does NOT belong into a polymerase chain reaction. a) template DNA b) dexoynucleotides c) DNA polymerase d) oligonucleotide primer e) ATP

e) ATP

X-ray diffraction data were crucial to determine the structure of DNA. These dataprovided information about most of the following features, except one that does not belong into this list: a) DNA is a helix b) DNA has a diameter of 2nm c) DNA has a periodicity of ~3.5nm d) DNA has a steps size of about 0.34nm e) The two strands in double stranded DNA are oriented antiparallel to each other.

e) The two strands in double stranded DNA are oriented antiparallel to each other.

Proposing the chromosome theory of inheritance is attributed to: a) Reginald Punnett b) Thomas Hunt Morgan c) Charles Darwin d) Gregor Mendel e) Theodor Boveri and Walter Sutton

e) Theodor Boveri and Walter Sutton

In the allelic case, intercrossing of F1 flies would probably yield this many purple progeny a) 3/4 b) 1/2 c) 7/16 d) 3/8 e) all

e) all

The precise term to refer to different versions of a gene is a) clones b) genotypes c) varieties d) forms e) alleles

e) alleles

Which one of the following characteristics is not true for DNA polymerase? a) is recruited to the origin of replication which is marked by DnaA protein (in bacteria) b) copies the template strand c) proofreads by virtue of a 3'->5' exonuclease activity d) uses dATP, dCTP, dGTP and dTTP as substrates e) attaches a new deoxynucleotide to a 5' phosphate group

e) attaches a new deoxynucleotide to a 5' phosphate group

Many organisms use a chromosomal mechanism for determining sex. In most cases, the female is the homogametic sex. In which of the following is the female the heterogametic sex? a) humans b) fruit flies c) corn d) round worms e) birds

e) birds

The substrate molecules for DNA synthesis are a) nucleosides b) nucleotides c) amino acids d) basepairs e) deoxynucleosidetriphosphates

e) deoxynucleosidetriphosphates

In maize, 'A' specifies purple seeds, as opposed to colorless seeds (a). A second, unlinked, gene specifies properties of the starch: Normal (Wx) versus waxy (wx). Give relative frequencies of the phenotypes in the progeny when a plant with genotype A/a; Wx/wx is crossed to a plant that is homozygous for the recessive alleles. a) all seeds purple and with normal starch b) two phenotypes: 1:1 c) two phenotypes: 3:1 d) four phenotypes: 9:3:3:1 e) four phenotypes: 1:1:1:1

e) four phenotypes: 1:1:1:1

The disease known as phenylketonuria is due to a defect in the gene for phenylalanine hydroxylase. The defect is inherited in a(n) ___(47)____ fashion. Mutations in this gene have been identified in many different ethnic groups. Actually, the specific mutation causing the disease is _____(48)____ . This finding suggests that the mutation arose ______(49)_____. If 7left untreated, the condition causes _____(50)______ . Fortunately, there is a treatment that can prevent the worst symptoms of the disease; it is ______(51)______ . 49. a) once, early in human evolution b) only recently c) in Yemen d) in space aliens e) multiple times, independently

e) multiple times, independently

e) mutation

Individuals who are heterozygous for one defective allele of the Rb gene are at high risk for developing retinoblastoma, a cancer of the retina. However, not all individuals who inherit this defective allele develop the disease. The Rb allele shows: a) maternal effect b) variable expressivity c) pleiotropy d) epistasis e) reduced penetrance

e) reduced penetrance

Calvin Bridges eventually produced the final, incontrovertible evidence for the chromosome theory of inheritance. His argument was based on four of the following five elements. Which of the five does not belong here? a) non-disjunction of X-chromosomes b) unexpected phenotypes among offspring of an X-linked trait c) the XO genotype specifies a male fly d) the XXY genotype specifies a female fly e) the white-eye gene is a Y-linked trait

e) the white-eye gene is a Y-linked trait

genetic change in pop. over time

evolution

What makes us human

evolution & fixation on lineage leading to AMH evidence for selection in humans duplication or deletion changes in expression pathogenic effect on traits unique to humans

mechanisms of evolution=> needs genetic variation to occur -mutation -gene flow(migration) -genetic drift -natural selection

evolutionary forces

proportion of indiv. expect to be heterozygous @ locus under HW conditions ex: 60 MM 120 MN 20 NN 200 total genotype freq.s: f(MM) = 60/200 = .3 f(MN) = 120/200 = .6 f(NN) = 20/200 = .1 allele freq.s: p = f(M) = 2(60)+120 / 2(200) = .6 q = f(N) = 2(20) + 120 / 2(200) = .4 expected heterozygosity: 2 pq = 2(.6)(.4) = .48 He ->1 He->0

expected heterozygosity

when a new pop. is established by a few "random" indivs whose allele freq. are not representative of the pop. they cam from

founder effect

Postmating-prezygotic barriers

gametic incompatibility: sperm or pollen from one species fails to penetrate and fertilize the egg of another species

pop. undergoes drastic dec in size, recovering pop. contains only alleles of survivors of bottle=> effects of genetic drift: leads to loss of genetic variation, changes in allele freq. causes pop. to become genetically diff

genetic bottleneck

genes are associated inherited together or exhibit pleiotropy (gene(s) has(ve) multiple effects)

genetic correlation

can cause an allele to become fixated or loss

genetic drift

You examine a SNP locus that has a C/T polymorphism. You obtain the following number of individuals per genotype: Calculate the genotype frequencies and the allele frequencies in the sample. Calculate the value for expected heterozygosity. Genotype Number of individuals CC 42 CT 16 TT 32

genotype freq: CC= p^2=> f(CC) = 42/90 = .467 CT= pq => f(CT) = 16/90 = .178 TT = q^2=> f(TT) = 32/90 = .356 allele freq: C: f(p) = 42(2)+16 / 180 = .556 T: f(q) = 32(2)+16 / 180 = .444 expected heterozygosity = 2pq 2(.556)(.444) = .493

A second locus has three alleles: A, C, T. Genotype Number of individuals AA 10 AC 10 AT 5 CC 20 CT 5 TT 20 Calculate the genotype frequencies and the allele frequencies in the sample.Find the expected homozygosity and the expected heterozygosity, given the observed allele frequencies.

genotype: f(AA) = 10/70 = .142 f(AC) = 10/70 = .142 f(AT) = 5/10 = .071 f(CC) = 20/70 = .286 f(CT) = 5/70 = .071 f(TT) = 20/70 = .286 allele: f(A) = 2(10)+10+5 / 140 = .25 f(C) = 10+20(2)+5 / 140 = .393 f(T) = 20(2)+5+5 / 140 = .357 homozygosity: q^2 = (.25)^2 = .0625 p^2 = (.393)^2 = .1521 r^2 = (.357)^2 = /1296 heterozygosity: 2pq = 2(.25)(.393) = .195 2pr = 2(.25)(.357) = .18 2qr = 2(.393)(.357)= .28

An apple farmer determines that the average weight of apples produced by trees in his garden is 80g. He selects trees that produce the largest apricots with an average weight of 90g and interbreeds these trees. The progeny trees produce apples that weigh 86g. What is the narrow sense heritability?

h^2 = R/S = 6/10 = .6

The father of a child with Down Syndrome was found to have one 21st chromosome and an unusually large chromosome 18. Chromosome painting determined that a second 21st chromosome was present and had been translocated to the 18th chromosome. Assume that the mother is normal (phenotypically and has a normal chromosome configuration). What kinds of children can this couple have? a. Down syndrom only b. Down + Edward c. Down + normal d. Down + Edward + normal

her answer guide- d accepted- c

What is character construction

how different expressions of a character is subdivided into character states (e.g. blue/green, blue/blue-green/green), homology / alignment, how to analyses characters,

Postzygotic barriers

hybrids are produced but have low fitness, after zygotes develop -hybrid inviability -hybrid sterility -ecological inviability -behavioral sterility

increases the frequency of homozygous individuals

inbreeding

Genetic Drift

isolates small amounts of variation; under-representation of genetic variability results from random sampling error

Which of the following is NOT true of biological evolution?

it can include non-genetic changes in an organism, if the organism is complex enough

Look at 18 on test 3

look at 18 on test 3

look at 19&20 on test 1

Look at 31 on test 1

look at 31 on test 1

look at 45 & 46 on test 4

look at number 10 test 1

gene flow consequences alter allele freq.s a. causes gene pools bt pop. to become more similar b. inc genetic variation w/in pop. 2 alleles: A,a qi = .2, qii = .7 size pop. ii=5> after ____ size pop. ii 50 m = 5/50 = .1 proportion of ____ qii = qiim + qii(1-m) qii(.2)(.2)+(.7)(.9) = .65

migration

what is gene flow?

migration = movement of individuals from one population to another

Migration

movement of genetic variation to new locations

What is the source of genetic variation

mutation

main source of genetic variation in a population

mutation

no diff. in fitness bt molecular variants-> molecular variation is adaptively neutral selection is directional- 1 variant is favored=> selection leads to less genetic variation

neutral mutation (mutation theory)

2 theories of types of molecular variation

neutral mutation (mutation theory) balancing selection

assortative mating if like mates w/ like =>(+) assortative mating if like mates w/ unlike=> (-) assortative mating inbreeding=> related indiv.s preferentially mate w/ each other, inc freq of homozygous and dec heterozygous -can lead to desired trait, to diseases (recessive) F=inbreeding coefficient (prob. of having 2 alleles that come from a common ancestor) 0<F<1; 0-random mating; 1-all alleles are identical bc they came from common ancestor -alters genotype freq. => locus A,a --f(AA) = p^2 +Fpq --f(Aa) = 2pq - 2Fpq --f(aa) = q^2 + Fpq ---total = 1 *ex. AA = .36, Aa = .48, aa = .16 q = .4, p + q = 1 q = .6 genotypic frequencies in next gen, F = .7 f(AA) = 2(.6)(.4) + (.7)(.6)(.4) = .528 f(Aa) = 2pq - 2Fpq = 2(.6)(.4) - (.7)(.6)(.4) = .144 f(aa) = q^2 + Fpq = .16 + (.7)(.6)(.4) = .328

non-random mating

The short arm of a chromosome is designated by what letter? a. s b. q c. g d. p

what is a parsimony, maximum likelihood and Bayesian approach

parsimony: Retain sequence data Search plausible tree, how evolution occurs and evolves Simple model Max like and bayesian are trickier

selection on one phenotype/trait also changes phenotype in a second trait

phenotypic correlation

organisms of same species vary in their appearance

phenotypically

how is genetic variation described?

phenotypically crosses; artificial selection genetic variation is phenotypic variation was heritable

How to calculate nucleotide diversity from sequence data

pi = Ndiff/NPc x L Ndiff = total number of differences between all possible pair wise comparisons NPc = number of pair wise comparisons (n(n-1)/2) L = sequence length n = sample size

proportion of examined loci in which at least 2 diff alleles are observed in pop. ex: 50 loci examined-> 25 have 1 allele: monomorphic loci, all indivs are homozygous for allel-> 25 have 2+ allleles in pop. %____=25/50 x 100 = 50%

proportion of polymorphic loci

how is genetic variation quantified in natural pop.?

proportion of polymorphic loci expected heterozygosity

protein electrophile-> separated based on size or charge

protein variation

what are the types of molecular variation

protein variation DNA molecular variation

what are some other model parameters

rate variation among sites in the alignment rate variation among different branches; the tree itself (topology)

sympatric speciation

reproductive isolation evolves without geographic isolation -requires nonrandom mating based on genetic or phenotypic factors

estimate of potential response to selection measures the diff bt the pop. mean value for a trait and mean trait value for the mating portion of the pop. ex. plant height s= 42 cm - 37.5 cm = 4.5 cm

selection differential (s)

What is a symplesiomorph

shared ancestral character (shared primitive characters) are also not phylogenetically informative. They were just retained from the common ancestor of all taxa in the tree

what is a synapomorph

shared derived character (derived characters shared by 2 or more taxa) are highly phylogenetically informative.

What is moulting

shed old feathers, hair, or skin to make way for a new growth.

what is homology

similarity resulting from shared common ancestry

Darwin's logic for natural selection inference 1

since more individuals are produced than can be supported by the available resources but population size remains stable, it means that there must be a fierce struggle for existence among the individuals of a population, resulting in the survival of only a part, often a very small part or the progeny of each generation

Balancing selection

some forms of selection maintain diversity in populations -negative frequency-dependent selection -heterozygote advantage

What is Analogy

superficial similarity that has evolved independently in different lineages. Some analogous characters are the result of convergent evolution via natural selection, some are due to random chance (e.g. DNA sequences).

protein DNA fragment electrophiles micro satellite analysis PCR DNA sequencing protein sequencing

techniques of genetic variation

What is large scale "macro" evolution

the descent of different species from a common ancestor over many generations

All of the alleles of the members of a population are known as __________.

the gene pool

what is a retain character based method

the sequence data and model the substitutions that have occurred to explain divergence

What is the study of phylogenetics

the study of evolutionary relationships among biological entities - major groups of organisms (e.g. mammals, vertebrates, eukaryotes), species, individuals or genes

which tree is best for all 6 characters

the tree the best fits the majority

what is a distance method?

throw out the original data and replace these with a simple matrix usually wrong one.

what are the pros and cons of distance methods

throw out the original data and replace these with a simple matrix • Fast. Useful for 'quick and dirty' check that data are behaving as expected Cons: But often returns an incorrect tree. •Fails to account for multiple hits and unequal rates of change across lineages (will come back to this)

what is a autapomorph

unique derived character unique derived characters) are not phylogenetically informative

what are some of the advantages of molecular data over morphological data

universality of the character types and states (yielding a more objective selection of character states and homology e.g. A,T,G,C). - the high number of characters available .- the high degree of variation in the substitution rates among genes and gene regions

what is meant by outgroup

uses existing knowledge of relationships to place the root using a outgroup taxon

What are the three ingredients for evolution

variation for a trait within a population; trait must be heritable variation in reproductive success amongst individuals random (= genetic drift) • non-random (= natural selection)

the environmental wheel of fortune

well adapted: top of wheel partially adapted: sides poorly adapted: bottom

Habitat Fragmentation

when the size of an organism's natural habitat is reduced, or when development occurs that isolates a habitat.. Has Low to moderate genetic drift

A population of green beetles has a narrow-sense heritability of 0.8 for wing length and of 0.9 for body length. The genetic correlation between wing length and head width is −0.7. If a geneticist selects for increased body length in these beetles, what will happen to wing length?

wing length would decrease since there is a negative correlation

What are the axis on a site frequency spectra

x = i, i can be between 1 and (n-1) and it is the amount of times a SNP is present in a population it can't = i as this allele is fixed and the site isn't polymorphic y = proportion of polymorphic sites when SNPs are present i times

Conserved regions in the human genome

~5% of the human genome (140Mb) is significantly more conserved than underlying neutral substitution rate would suggest Likely under purifying selection for essential biological functions Only ~1% of the human genome is protein coding which makes up less than half of the conserved regions, therefore many functional elements in non coding regions must be conserved

what are character based methods

• Huge number of possible trees that could explain the data • Rely on computer algorithms to successively generate and score trees until the tree

In the population above, the forward mutation rate is 4 x 10-5 (M → N) and the reverse mutation rate is 1 x 10-5 (N → M). What is the expected change Δq?

∆q = Mp - rq (4x10^-5)(.6) - (1x10^-5)(.4) 2x10^-5

The MN blood group is examined in a population, and the following numbers of genotypes are observed: 5 MM 25 MN 20 NN Assuming Hardy-Weinberg conditions, what is the expected frequency of MM individuals in the next generation?

0.123

The MN blood group is examined in a population, and the following numbers of genotypes are observed: 5 MM 25 MN 20 NN What is the frequency of the M allele in the population?

0.35

In a species, the phenotypic and additive variances are measured. Calculate the narrow sense heritability, h^2? VP = 22.97 VA = 9.27

0.40

0.455

0.485

The MN blood group is examined in a population, and the following numbers of genotypes are observed: 5 MM 25 MN 20 NN What is the frequency of the MN genotype in this population?

0.50

On average, each chicken in a population produces 5 eggs a week. A farmer selects for increased egg production, whereby only chickens producing more than 8 eggs per week are allowed to reproduce (average egg production per chicken in the reproducing chickens is 9). The next generation of chickens produces an average of 8 eggs per week per chicken. What is the realized heritability?

0.75

increases genetic similarities between populations

migration - gene flow

Match the statement with the method for finding QTLs. Crosses are made between two strains that have different alleles for multiple markers Scans the whole genome in search for associations between markers and specific phenotypes tests two alleles that differ between the twoparents of the mapping population may sample a large number of individuals for the trait

A. QTL mapping B. GWAs C. Both C. Both

assumes no changes in allele or genotype frequencies across gen.s pop. is evolving 5 conditions violate random mating=>changes in genotypic frequencies violate the other 4 conditions => changes in allelic frequencies

Hardy Weinberg

What is the difference between broad-sense heritability and narrow-sense heritability?

Narrow-sense heritability considers additive (not total) genotypic variance.

Locus A is analyzed for a population of rats. The following numbers were observed: Calculate the allelic frequencies for this population. Number of individuals genotype A1/A1: 384 A2/A2: 260 A1/A2: 210

P(A1) = total # A1 alleles / 2 x total # of alleles 384(2) + 210(1) / 1708 0.573 P(A2) = total # A2 alleles / 2 x total # of alleles 260(2) + 210(1) / 1708 0.427

Correlations among traits can be positive or negative, and are often due to pleiotropy.

Evolution is the change in allele frequency in a population.

Inbreeding decreases heterozygosity in a population.

Mutation and migration both tend to increase genetic variation within a population.

What are good qualities of genetic markers used in QTL mapping? Mark all that apply.

The are relatively easy to use. They can modify native DNA sequences. They are highly variable. They are present in all individuals.

In a population of chickens, body weight and egg weight exhibit a genetic correlation of 0.42. If higher-body-weight chickens are selected in this population, what will be the effect on egg weight?

The egg weight will increase.

A rancher determines that the average amount of wool produced by sheep in her flock is 15 kg per year. In an attempt to increase the wool production in the flock, she picks 5 male and 5 female sheep with the highest wool production; the average amount of wool produced per sheep by those selected is 25 kg per year. She interbreeds these selected sheep and finds that the average wool production among the progeny of the selected sheep is 22 kg per year. After multiple generations of selection for increased wool production in her flock, in generations 20 and 21 of selection the rancher notices that there is no response to selection. She is getting tired of shearing sheep, anyway, so she decides to try two generations of selection for decreased wool production ("reverse selection"). She is surprised when she does not see a response to this reverse selection. What is the most likely explanation for the lack of response to selection for either increased or decreased wool production?

There is no genetic variation remaining for wool production in the flock

Phenotypic variation in two traits in mice have the following components: For each trait, calculate the phenotypic and genetic variance as well as the narrow-sense heritability. Variance Trait 1 Trait 2 Additive genetic variance (VA) 248.1 73.0 Dominance genetic variance (VD) 15.6 365.2 Gene interaction variance (VI) 0 10.3 Environmental variance (VE) 275.1 292.2 Genetic-environmental interaction variance (VGxE) 0.0 0.0

Trait 1 Vp=Va+Vd+Vi+Ve+Vexg Vp=248.1+15.6+0+275.1+0 Vp=538.8 h^2=Va/Vp 248.1/568.8 h^2 =0.46 Trait 2 Vp=Va+Vd+Vi+Ve+Vexg Vp= 73.0+365.2+10.3+292.2+0 Vp=740.7 h^2=Va/Vp 73.0/740.7 h^2 =0.0986 9.86%

Two independent chicken breeders, Jim and Paul, want to increase the mean number of eggs laid per hen in a month and they each ask for your advice. The average for both populations is 28 and the variance is 5 eggs2. Jim has consulted previously with a geneticist who estimated the narrow-sense heritability for number of eggs/hen/month to be 0.8. Paul consulted with his cousin who estimated the broad-sense heritability for the same trait to be also 0.8. Given this information, can Jim expect that his population of chickens will respond to selection for an increase in the number of eggs per hen in the next generation? What can Paul expect regarding his chickens?

Yes, Jim can expect that his population of chickens will respond to selection for an increase in the number of eggs per hen in the next generation. Paul should expect similar results. Jim = h^2 = .8 Paul = h^2 = .8 if Va inc then they would respond to selection if Vd+Vi inc then they wouldn't Vg = Va+Vd+Vi, no assurances

In QTL mapping a correlation with a genetic marker indicates that the marker and the locus of interest are found ________.

close by in the same chromosome

more than one trait changes 1. phenotypic correlation: selection on one phenotype/trait also changes phenotype in a second trait due to: -2. environmental correlation: 2 or more characteristics are influenced by the same environmental factor -3. genetic correlation: genes are associated inherited together or exhibit pleiotropy (gene(s) has(ve) multiple effects)

correlated responses to selection

2 or more characteristics are influenced by the same environmental factor

environmental correlation

An autosomal gene has two alleles, A and a. If the frequency of the A allele is 0.7 and the frequency a allele is 0.3 in a given population, what would the frequency be of Aa individuals in the population? (Assume the population is in Hardy-Weinberg equilibrium.)

.42

.216

What is the predicted response to selection (R) if the narrow-sense heritability is 0.6 and the selection difference is 1.9?

1.1

10 kg

7 kg

The alcohol dehydrogenase gene in Drosophila melanogaster has two alleles designated F (fast) and S (slow). A population has allelic frequencies of Adh-F is 0.75 and Adh-S is 0.25. If this population has 480 flies, what are the genotypic frequencies under Hardy-Weinberg equilibrium?

Adh-F at p = 0.75 and that of Adh-S at q = 0.25 F/F = p2 = 0.752 = 0.5625(480) = 270 F/S = 2pq = 2 × 0.75 × 0.25 = 0.375 (480) = 180 S/S = q2 = 0.252 = 0.0625(480) = 30

A plant species is chosen to study QTLs has a diploid number of 8 (2n = 8). A large number of genetic markers have been studied and developed in this species. You are given the task to design an experiment using crosses to determine the location of QTLs for plant height. Describe your experiment. What is the least number of markers you should use? Where in the genome should these markers be located? Show the genotypes for the P and F1 generations. What do you expect to find in the F2? (You do not have to write the genotypes) Explain your reasoning.

Alleles at the T locus influence plant height. The A, B, C, and D loci are genetic markers. Cross 2 homozygous strains that differ in alleles at many loci. This is the P generation. AABBCCDD x aabbccdd Intercross the F1 to allow genes to recombine. AaBbCcDd x AaBbCcDd Many different combinations of alleles appear in the F2

In the human MN blood type systems, alleles M and N are codominant. The frequency for N is 0.4 in a population of a remote South Pacific island. a. If the population is under HW equilibrium, calculate the genotype frequencies. b. If the inbreeding coefficient for this population is 0.1, what are the genotype frequencies under inbreeding?

a. f(N) = .4 f(NN) = .16 f(M) = .6 f(MM) = .36 f(MN) = .48 b. F = .1 f(MM) = .36 + (.1)(.4)(.6) = .384 f(NN) = .16 + (.1)(.4)(.6) = .184 f(MN) = 2(.4)(.6) - 2(.1)(.4)(.6) = .432

A population of mice is found on two populations: one on the North Rim and a second on the South Rim of the Grand Canyon. The tail of the mice can be banded or unbanded, where banding is recessive to no bands. The frequency of mice with banded tails is 0.4 in the South Rim and of 0.81 in the North Rim. One year a large number of South Rim mice use a log as a raft and cross to the North side of the canyon. After this migration, 10% of the North Rim population is made of mice that came from the South Rim. a. If the both populations are assumed to be under HW equilibrium. What are the allele frequencies for banded tails in both populations before migration? b. After migration has taken place, what is the frequency of the banded allele in the North Rim?

a. f(bb) in South Rim = .4 f(b) = 2sqrt(.4) = .632 f(bb) in North Rim = .81 f(b) = 2sqrt(.81) = .9 b. m = .1 = proportion of migration qii = qiim + qii(1-m) (.63)(.1) + (1-.1)(.9) = .873

The frequency for a rare allele s is 0.03 in a large, randomly mating population. The average number of offspring for each genotype in this locus is shown on the table below: What is the fitness value for each genotype? What is the selection coefficient for each genotype? Genotype Average number of offspring produced SS 5 Ss 6 ss 0

a. fitness = W SS = 5/6 = .833 Ss = 6/6 = 1 ss = 0/6 = 0 S = 1-W SS = 1 - .833 = .167 Ss = 1 - 1 = 0 ss = 1 - 0 = 1

5. The following numbers were observed in a population for a locus with three alleles: A1, A2, A3. Calculate the genotypic and allelic frequencies for this population. What would the expected numbers of genotypes be if the population were in Hardy-Weinberg equilibrium? Genotype Number A1 A1: 15 A1 A2: 50 A2 A2: 37 A1 A3: 9 A2 A3: 12 A3 A3: 2 Total 125

a. genotypic: F(A1A1) = 15/125 = .12 F(A1A2) = 50/125 = .4 F(A2A2) = 37/125 = .296 F(A1A3) = 9/125 = .072 F(A2A3) = 12/125 = .096 F(A3A3) = 2/125 = .016 allelic: A1 = p = 15(2) + 50 + 9 / 250 = .356 A2 = q = 50 + 37 (2) + 12 / 250 = .544 A3 = r = 9 + 12 + 2(2) / 250 = .1 b. A1 = p = .356 A2 = q = .544 A3 = r = .1 p^2 = (.356)^2 = .127 2pq = 2(.356)(.544) = .387 q^2 = (.544)^2) = .296 r^2 = (.1)^2 = .01 2pr = 2(.356)(.1) = .0712 2qr = 2(.544)(.1) = .109 in a population of 100 P(A1A1) = .127 x 125 = 16 P(A1A2) = .387 x 125 = 48 P(A2A2) = .296x125 = 37 P(A1A3) = .0712x125 = 9 P(A2A3) = .109x125 = 14 P(A3A3) = .01x125 = 1

Three quantitative characteristics are measured in a population of pigs. The variance values for each are shown in the table below. a. Calculate the narrow-sense heritability for each character. b. In the population of animals studied, which character would respond best to selection? Why? c. A project is undertaken to decrease mean fat content in the herd. The mean fat content is currently 10.5 percent. Animals with a mean of 6.5 percent fat content are interbred as parents of the next generation. What mean fat content can be expected in the descendants of these animals? Characters Variance Loin length Shoulder length Fat content Phenotypic 533.7 730.4 106.0 Gene Interaction 0 15.7 2.4 Additive genetic 75.8 100.8 42.4 Dominance genetic 32.5 265.2 10.6

a. narrow-sense heritability: h^2=Va/Vp loin length= 75.8/533.7= 0.142 shoulder length= 100.8/730.4= 0.138 fat content= 42.4/106.0= 0.40 b. fat content would respond best to selection because the larger the value of narrow sense heritability, the greater the difference between selected parents and the population, the more the characteristic will respond to selection. c. R= h^2 x S (0.40)(0.105 - 0.065) = 0.016 mean fat content = .105 - .016 8.9%

p = f(M) q = f(N) p+q=1 total # of x alleles/2(total number of alleles) f(M) = 14(2) + 80x1 / 200 = .54 f(N) = 2(6) + 80x1 / 200 = .46 -1 locus w/ 3 alleles A1, A2, A3 1 1: 40 1 2: 90 1 3: 8 2 2: 84 2 3: 16 3 3: 12 total = 250 A1 p = 2(40) + 90 + 8 /2(250) = .356 A2 q = (84)2 + 90 + 16 = .548 A3 r = 2(12) + 8 + 16 = .096

allele frequencies

In Drosophila body color can be black (determined by allele b) or brown (determined by the dominant allele B). A population of flies is observed and 96% of the individuals have brown bodies while 4% of the flies have black bodies. Calculate the allele frequencies of B and b and the genotypic frequencies of B/B and B/b?

allele frequencies: q^2 = .04 p^2 + 2pq = .96, so q = .2 and p = .8 frequency B = p = .8 frequency b = q = .2 genotypic frequencies: B/B = p^2 = .64 B/b = 2pq = .32

Hardy Weinberg Equilibrium: model used to help determine whether evolution is occurring in a pop. assumptions: -no new mutations -no migration -large pop. -random mating bt genotypes -all genotypes have same fitness = no natural selection p = f(M) = .54 q = f(N) = .46 MM = p^2 = .29 MN = 2pq = .50 NN = q^2 = .21 p^2 + 2pq + q^2 = 1 (p+q)^2 = 1 for a locus w/ 3 alleles: (p+q+r)^2 = p^2 + 2pq + 2pr + q^2 + 2qr + r^2 = 1

expected genotypic frequencies in next gen.

effect of change more intense in smaller pop.s=>sampling error by change alleles present in one gen. will not be represented in gametes that form offspring=> may cause an allele to inc or dec in freq. in next gen => cause allele to become fixated or 2 disappear -small pop.s may occur a. founder effect b. genetic bottleneck

genetic drift

increases the genetic differences between populations

genetic drift

can be described in terms of: 1. genotypic frequencies 2. allele frequencies: diploid- total # of alleles in a pop. = 2(total # of indiv.) 3. expected genotypic frequencies in next gen.

genetic structure of a population

wide association studies (GWAs) whole-____ sequencing methods SNPs goal: tie presence of a DNA marker to a QTL in a pop. looks for non-random associations bt the presence of a trait (phenotype) and markers (alleles) across ____ *does not use crosses humans to study disease susceptibility: obesity, intelligence, height

genome

An autosomal recessive condition has an occurrence of 1/569 live births in a population. If this population is under Hardy- Weinberg equilibrium, what is the frequency of carriers of the disease allele?

genotype frequency (aa) = q^2 = 1/569 carriers (Aa) = 2pq q = sqrt(1/569) = .042 p = 1-q = .958 2pq = 2 x .958 x .042 = .08

1 locus w/2 alleles and 3 possible genotypes MN blood in humans: M and N alleles are codominant 100 indiv.s total 14 MM: f(MM) = 14/100= .14 80 MN: f(MN)= 80/100 = .80 6 NN: f(NN)= 6/100 = .06 *total = 1

genotypic frequencies

The average height of a population of corn plants is 1.8 m tall. A breeder selects plants that are 10 cm taller on average than the population mean to produce the next generation, and the breeder continues applying this level of selection for eight generations. What will the average height of the plants be after eight generations of selection? Narrow-sense heritability for plant height in this population is 0.5. Assume that h2 remains 0.5 over the course of the experiment.

h^2 = 1/2 the height diff bt generations is heritable 10 cm/2 = (5cm)(8) = 40 cm taller

The narrow-sense heritability of ear length in Reno rabbits is 0.4. The phenotypic variance (VP) is 0.8, and the environmental variance (VE) is 0.2. What is the additive genetic variance (VA) for ear length in these rabbits?

h^2=0.4 Vp=0.8 Ve=0.2 Va=? h^2=Va/Vp 0.4=Va/0.8 Va=0.32

reduces the number of heterozygous individuals in a population

inbreeding

related indiv.s preferentially mate w/ each other, inc freq of homozygous and dec heterozygous -can lead to desired trait, to diseases (recessive) F=_____ coefficient (prob. of having 2 alleles that come from a common ancestor)

inbreeding

increases the appearance of recessive lethal or deleterious alleles

inbreeding depression

Narrow sense heritability (h^2) measures the proportion of the phenotypic variance due to __________ variance.

interactive

main source of genetic variation rate of ____ is very slow => becomes significant over evolutionary time locus w/2 alleles, G1 and G2 forward _____=> G1->G2 M=rate of forward ____ reverse _____=> G2->G1 r = rate of reverse _____ ∆q = Mp - rq alters allele freq.s

mutations

more precise than broad-sense heritability representation of the proportion of Vp that is due to genetic variance passed from parents to offspring varies bt 0-1: high is closer to 1 (offspring resemble parents), low is closer to 0 (offspring do not resemble parents) used to calculate response to selection: important in selective breeding h^2 = Va/Vp

narrow-sense heritability

changes allele frequencies based on the fitness of the genotypes in a population

natural selection

mechanism of evolution- differential reproduction and survival of indiv.s w/ diff genotypes

natural selection

one genotype (adaptive traits) produce more offspring than others fitness=W, measure of how reproductively successful a genotype is relative to others in the pop. 0<W<1........offspring..............W MM.............20..........................20/20 = 1 MN.............15...........................15/20 = .75 NN...............10............................10/20 = .5 s = selection coefficient=> how strongly a genotype is selected against S = 1-W MM: 1-1 = 0 MN: 1-.75 = .25 NN: 1-.5 = .5 effect of ____-changes allele freq.s=> depend on fitness of genotypes

natural selection

group of indiv.s of same species that live in same place and time interbreeding sexually reproducing have a common set of genes (gene pool)

population

study of genetic make-up of a pop. how genetic composition changes over time (evolution) studies evolutionary forces that shape evolution of a population

population genetics

A gene has two alleles A and a. What is the Hardy-Weinberg genotypic frequency of a?

q^2

genetic variation can change over time

quantitative trait

how much a characteristic submitted to selection changes in 1 gen influenced by: - h^2: degree of resemblance bt parents and offspring -amt of selection: intensity R= h^2 x s depends on extent to which the diff bt mating trait mean and pop. mean value can be passed down onto progeny ex. plant height h^2 = .70 s = 4.5cm R = 3.15 cm expect progeny to have a height that is equal to pop. mean and R 37.5 cm + 3.15 cm = 40.65 cm

BIO 240 FINAL

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