BIO 467 Exam 2

What are the five assumptions of Hardy-Weinberg Equilibrium?

(1) random mating (i.e, population structure is absent and matings occur in proportion to genotype frequencies) (2) the absence of natural selection (3) a very large population size (i.e., genetic drift is negligible) (4) no gene flow or migration (5) no mutation

Lenski performed the longest known study on selection/mutation in terms of number of generations studied. When a beneficial mutation occurred, what happened to the population it occurred in?

- Mutation was its only source of genetic variation. each population gets better at dealing with the limited resources (they have better relative fitness compared to the original strain. note: they do not end up with equal fitness, in fact, there is quite a lot of variation. Mutation and Selection are both involved. Source of variation: mutation. Beneficial selection carries the mutation to higher frequencies. Mutations with large effects: increases cell size. These mutations quickly sweep through populations and the population jumps in size = large change in growth efficiency.

Sex Ratio may be influenced by

-accidental death of adults before breeding - sexual selection - behaviour (harems) - genetic sex ratio distorters - male-killing elements (i.e. Wolbachia, wars)

Empirical Evidence of Drift

Allele frequency changes in populations with-out selection.

effects of Random Fixation of Alleles

At any time, the probability that an allele will become fixed is its present frequency: p The probability that an allele becomes lost is: (1-p)

neutral theory of molecular evolution

The hypothesis that most mutations that become fixed do not significantly alter fitness and have become fixed by genetic drift.

Positive Assortative Mating:

when individuals are more likely to mate with like individuals. Example: Population Bottleneck, self-fertilization.

What effect does inbreeding have on population allele frequencies?

Inbreeding causes a loss of heterozygosity with no expected change in allele frequencies.

Gene Flow

Movement of alleles from one population to another

How are deleterious alleles for diseases like muscular atrophy maintained in a population? Why are these alleles not completely removed from the population by selection?

1. Deleterious alleles may also be maintained because of linkage to beneficial alleles 2. Deleterious alleles appear more often, making individuals less fit genetically, they pass fewer copies of their genes to future generations.

s "p" the genotype or allele frequency? What about "p2"?

1. p is defined as the frequency of the dominant allele and q as the frequency of the recessive allele for a trait controlled by a pair of alleles (A and a) q = frequency of the recessive allele in the population. p2 = percentage of homozygous dominant individuals. q2 = percentage of homozygous recessive individuals. 2pq = percentage of heterozygous individuals.

Mutation of an Allele

A = functional allele, f = 0.90 a = loss of function recessive allele (not lethal), f = 0.10A is converted, by mutation, to a rate of 1 copy in 10,000 per generation (ignore back mutation)

Mutation

A random alteration in DNA, alteration of an organisms DNA.

Where do synonymous mutations produced in DNA? Are they likely to be removed from a population?

A synonymous mutation is a change in the DNA sequence that codes for amino acids in a protein sequence, but does not change the encoded amino acid. Usually occur in the third position of a codon. The neutral theory predicts that synonymous substitutions will be tolerated, but nonsynonymous substitutions will be removed by purifying selection.

If an allele is fixed:

All individuals in the population are homozygous for that allele (for example, B1 is fixed, the only allele in the population is B1, and the only genotype in the population is B1B1.

Genetic Drift

Chance fluxes in allele frequencies in a population due to non-random sampling of the gene pool Chance alterations of gene frequencies in population because of non-random sampling of the gene pool.

Is there a difference in coding and non-coding parts of the genome??

Coding = DNA sequences that result in a functional protein. Non-coding DNA. = introns, regulatory sites, pseudogenes, junk Should be neutral = no fitness consequences if they have mutations. Rate of evolution should equal the mutation rate. Silent Mutations (because of redundancy of the amino acid code) may also be neutral.

Do island populations of silvereyes (and likely many other island species) have more or less genetic variation than mainland species? Is this because of selection?

Colonization from Tasmania to New Zealand Islands and Norfolk Island. Norfolk Island populations of Silvereyes contain ½ the genetic diversity as the mainland Australian Populations. Evolution, change in allele frequencies, has happened without invoking selection

Detecting selection on DNA sequences

Compare synonymous and non-synonymous changes in a gene: Neutral: d N / dS = 1 Advantageous Selection: dN / dS > 1 (more non-synonymous than synonymous changes) Deleterious Selection: d N / dS < 1 (more synonymous than non-synonymous changes)

Implications of Sample Size on Genetic Drift:

Drift is more important in populations within populations with small numbers of breeding individuals than large numbers of breeding individuals.

What did Dawson find in his study of selection in Tribolium? Is a population's response to selection stronger when a deleterious allele is higher in frequency or lower?

False option: as predicted by thr GSM, the rate at which selection was able to remove a lethal recessive allele from experimental populations showed over successive genertation. In 1970 Dawson conducted an experiment with Tribolium castaneum (Flour beetle) he began the population with all the individuals heterozygous for a lethal allele and tracked the frequency of the allele for 12 generations.They found that the level of mortality in the population dropped over a 15 month period.

In species with mating systems under frequency dependent selection is it better (in terms of relative fitness) to be common or rare?

Frequency dependent selection occurs when the fitness of a genotype or phenotype in a population is related to its frequency in the population Positive frequency dependent selection occurs when the more common a variant is in a population, the higher its fitness, while negative frequency dependent selection occurs when a variant has higher fitness the less common it is.

Does gene flow between two population make the allele frequencies of a population more or less similar?

Gene flow does not change allele frequencies for a species as a whole, it can alter allele frequencies in local populations.

Calculating Genotype and Allele Frequencies:

Gene: A segment of DNA (RNA) that transcribes proteins, or regulatory signals. Allele: One of alternative forms of a gene. Genotype: the genetic make-up of an organism. The frequency of genotype AA is determined by squaring the allele frequency A. The frequency of genotype Aa is determined by multiplying 2 times the frequency of A times the frequency of a.

How can heterosis affect allele frequencies?

Heterosis refers to the phenomenon that progeny of diverse varieties of a species or crosses between species exhibit greater biomass, speed of development, and fertility than both parents. Various models have been posited to explain heterosis, including dominance, overdominance, and pseudo-overdominance.

migration-selection balance

Homogenizes allele frequencies. The two populations are more similar if there is migration.

What effect does inbreeding have on population genotype frequencies?

Inbreeding increases the frequency of homozygous genotypes and decreases the frequency of heterozygous genotypes in the population.

hat did Mukai and Burdick find in Drosophila melanogaster?

In experiments with laboratory populations of Drosophila melanogaster, Mukai and Burdick (1959) observed that a lethal allele maintained a higher than expected frequency

What can happen when heterozygosity is lost?

Loss of heterozygosity (LOH) refers to a specific type of genetic mutation during which there is a loss of one normal copy of a gene/ a group of genes. In some cases, loss of heterozygosity can contribute to the development of cancer.

Migration

MOVEMENT OF ALLELES BETWEEN POPULATIONS "immigration and emigration" -not in the ecological sense of seasonal movement of individuals. Migration can cause allele frequencies to change, and not be in Hardy Weinberg Eq.. Migration homogenizes different populations, preventing evolutionary divergence.

The ultimate source of genetic variation

Mutation Before: as the ultimate source of variation. Now: as a force in evolution.

What assumption of H-W is violated by assortative mating?

Non-random mating leads to departures from Hardy-Weinberg proportions. ... By contrast, negative assortative mating (where opposites attract and individuals prefer to mate with phenotypically different individuals) results in excess of heterozygotes. Selection, mutation, migration, and genetic drift are the mechanisms that effect changes in allele frequencies, and when one or more of these forces are acting, the population violates Hardy-Weinberg assumptions, and evolution occurs.

non-random mating

Not all individuals in a population have equal probabilities of mating than would be predicted by random chance one member of a population is not equally likely to mate with another as would be expected by chance encounters. (positive or negative assortative mating).

Natural Selection

Organisms better adapted to their environment are more likely to survive and reproduce than those without the adaptations

What is the difference between positive and negative assortative mating?

Positive assortative mating, or homogamy, exists when people choose to mate with persons similar to themselves (this type of selection is very common). Negative assortative mating is the opposite case, when people avoid mating with persons similar to themselves.

Be able to calculate through the population genetics matrix- that is: if you are given p, can you calculate the frequency of individuals that express the allele (q2)?

Practice this

Another level where we see randomness:

Production of genotypes of zygotes are random.

Population Size and Genetic Drift

Random Error is reduced as population i i size increases.

Mooto KimuraMasatoshi Nei

Selection might not be important at all! Evolution can happen by stochastic processes. Non-adaptive.

examples of heterozygote advantage.

Sickle cell anemia is the best-known example of heterozygote advantage and balanced polymorphism in humans.

If we add w (relative fitness) to the H-W equation, what assumption are we likely to be breaking?

Small mutations that confer a large increase in the relative fitness of an organism can shape the trajectory of its evolution

Is genetic drift more important in small or large populations? Why?

Small populations tend to lose genetic diversity more quickly than large populations due to stochastic sampling error (i.e., genetic drift). This is because some versions of a gene can be lost due to random chance, and this is more likely to occur when populations are small.

What are different ways that species ensure outbreeding?

Species cross - Crossing of animals of different species. Crossbreeding - Mating of animals of different established breeds. Outcrossing - Mating of unrelated animals within the same breed.

Effective Population Size: Ne

The average number of individuals in a population that contribute genes equally to the next generation. Usually smaller than the actual (census) population size Different from the census size: N Bases on the population size of mating adults. Sensitive to the sex ratio of breeding adults.

What does a chi-square test compare in H-W? What does a chi-square statistic over 5.99 indicate?

The larger the Chi-square value, the greater the probability that there really is a significant difference. There is a significant difference between the groups we are studying.

Are most mutations beneficial?

The majority of mutations are neutral in their effects on the organisms in which they occur. most mutations are not beneficial. - Consider deleterious mutation-selection acts to eliminate these mutations.

What is the probability that an allele will become fixed in a population? Lost? What implication does this have on heterozygosity?

The probability that a new allele in a population will eventually become fixed is 1/2N, the frequency of the allele in the population at the time it arose. If the allele is to become fixed in the population, the average time to fixation is approximately 4N generations. As alleles became fixed, heterozygosity was lost!

how to determine if a population is in Hardy-Weinberg Equilibrium.

To know if a population is in Hardy-Weinberg Equilibrium scientists have to observe at least two generations. If the allele frequencies are the same for both generations then the population is in Hardy-Weinberg Equilibrium.

If an allele is lost:

all individuals in the population no individuals in the population have that allele.

FOUNDER EFFECT

change in allele frequencies as a result of the migration of a small subgroup of a population New populations, recent colonization: Allele frequencies are likely, by chance, to be different in new (founder) populations than in the source populations

Using dN/dS, how can you determine if selection for mutation is advantageous, neutral, or deleterious? What are some examples of positive selection for mutation?

dN/dS ratio quantifies the mode and strength of selection by comparing synonymous substitution rates (dS)—assumed to be neutral—with nonsynonymous substitution rates (dN), which are exposed to selection as they change the amino acid composition of a protein

Heterozygosity

having different alleles at a gene locus As one allele becomes higher in frequency, heterozygosity for that gene is lost.

What factors can lead to inbreeding in populations?

inbreeding due to genetic drift and inbreeding due to non-random mating.

General Binomial Distribution

k = proposed outcome p = probability n = sample size

Are synonymous mutations always neutral? Why or why not?

synonymous changes are not always neutral is the fact that exon sequences close to exon-intron borders function as RNA splicing signals.

What is frequency dependent selection?

the fitness of a phenotype depends on how common it is in the population.

Negative Assortative Mating:

when individuals are more likely to mate with different individuals. Example: out-Breeding because of Self - Incompatibility, Out-Breeding because of dispersal

Balance between mutation and selection?

ų = the mutation rate s = selection coefficient = the strength of selection against the mutation.

Two major tenants of Molecular Evolution

•Most changes in DNA are neutral in effects on fitness of the individual that carries them. •DNA sequence evolution is influenced more by Genetic Drift than Selection.