Genetics Exam 3
After doing whole genome sequencing on 120 birds from all putative species from all major islands, they calculated FST in a sliding window for pairs of species—where one member of the pair had a pointy beak and the other had a blunt beak. what was Fst used for there? That is, what were they looking for in this calculation? They discovered 15 significant regions in this process and argue in the concluding paragraph of their paper for a "polygenic basis for beak diversity". What does that phrase mean? They then focus in on one gene: ALX1. What kind of gene is this? Is the same gene found in humans? How does this illustrate the theme that evolution often makes regulatory changes to drive changes in phenotypes?
-Fst was measured between species with different beaks to measure population differentiation between them by looking for regions of the genome that differed from most, and reasoned that they might have caused the divergence of beaks. -Polygenic means from many genes -ALX1 is a transcription factor that binds to DNA and regulates expression of other genes -Yes but it is disrupted by regulatory changes, which shows that evolution can more easily drive changes in phenotypes by activating regions of DNA if there is a change in environment.
You can think of the infecting phage as having one of two basic strategies: (1) make progeny fast and lyse open the cell ASAP so the progeny can go off and infect more cells or (2) delay lysis and thereby make more progeny in the cell it's already in. When the host cells are scarce, which strategy is favored? In our experiment, where did most of the mutations occur? How does this again reinforce the idea that evolution often proceeds by regulating gene expression?
-the second strategy -in the promoter region -Promoters control how much a gene is transcirpted and, therefore, how much it is expressed. Thus strategy 2 was pursued not by changing the lysis protein, but by turning down it's expression.
What are the basic types of natural selection that can occur at one locus?
1. Balancing selection 2. Overdominance 3. Frequency dependent selection 4. Spatial and Temporal heterogeneity 5. Neutral Theory 6. Epistasis and dominance
What are 2 reasons why named species are not found to be monophyletic?
1. Gene flow 2. Not enough time for the monophyly to develop
Which of these species are monophyletic? (ch. 26 Part c) 1. C. olivacea 2. C. fusca_L 3. C. fusca_E 4. C. fusca 5. G. difficilis 6. G. conirostris
1. yes 2. yes 3. yes 4. yes 5. no 6. no
How many hotspots are there in the human genome? If the genome is 3 billion bases long, what proportion of sites in the genome are hotspots?
25,000-50,000 hotspots in human genome and 60% of all crossovers happen in these spots .00001 are hot spots or .001%
Here is a generic chromosome map with three loci: A, B, and C. The map units between the A-B pair, and the B-C pair is given. Give the approximate recombination frequency you expect between loci A and C. A to B mu B to C mu Recombination frequency 2 1.5 3 5 10 10 50 50 100 100
3.5 8 20 approx 16 approx 42 approx 48
To the right is the molecular clock applied to the finch phylogeny. The x-axis is in thousands of years. What is the estimated time of the divergence of all the extant Darwin's finches? What is the estimated time since C. fusca_E and C. fusca _L diverged?
901,000 years ago. 291,000 years ago.
What are the fitness values for selection against a recessive trait> A1A1 A1A2 A2A2
A1A1= 1 A1A2= 1 A2A2= 1-s (s measures the intensity that selection is acting against the trait)
What are the fitness values for selection against a trait with no dominance> A1A1 A1A2 A2A2
A1A1= 1 A1A2= 1-1/2s A2A2= 1-s (like incomplete dominance)
What are the fitness values for selection against a dominant trait> A1A1 A1A2 A2A2
A1A1= 1-s A1A2= 1-s A2A2= 1
What is it called when a large number of species originate from the same common ancestor in a relatively short period of geologic time? Why would the process of speciation be more readily observed in this type of scenario than say when comparing the species of different continents?
Adaptive Radiation is when a large number of species originate from the same common ancestor. 1. islands have speciation in replicate form (so we can see it over and over) 2. Hard to see speciation on continents 3. Continents are old and islands are young, and speciation has happened more recently and common ancestry is more apparent 3. Islands have open ecological niches that new species can colonize
Do we yet know how exactly recombination works?
Although considerable evidence supports the double-strand-break model in yeast, the extent to which it applies to other organisms is not yet known
What is T. bicolor in the phylogeny?
An outgroup.
What is the difference between anagenesis and cladogenesis?
Anagenesis is the evolution that takes place in a single lineage within a population Cladogenesis is the splitting of one lineage into two, how species originate
In the case of the apple maggot fly example from our textbook, how might sympatric speciation be occurring?
Apples ripen several weeks before hawthorns. So When flies lay their eggs on ripening fruit, there is a sympatric selection for flies to synchronize their reproduction to match apples. Therefore, the peak mating period of apple flies is 3 weeks before hawthornes. Reduced gene flow
what is reinforcement?
Assertive mating is mating within the same species. Selection favors this because the offspring are more viable. REINFORCEMENT of the zygotes because the hybrids have reduced fitness
What is horizontal gene transfer? How does horizontal differ from vertical? ? Is it more common among prokaryotes or eukaryotes?
Bacteria and bacteriophage pick up DNA from their environment and incorporate it into their genome. bacteria use plasmids. more common in prokaryotes Vertical is parent to offspring
In short, many bacterial infections that were readily treatable with antibiotics, are much harder to treat b/c the infecting bacteria are resistant to many different antibiotic drugs. What does this have to do with horizontal gene transfer?**
Bacteria use HGT to incorporate the drugs into their DNA so that they can become resistant to antibiotics
Huntington disease declines by approximately q per generation. Recall recessive lethal alleles decline by q2. Based on Hardy-Weinberg proportions, why do you think autosomal dominant lethal alleles decline much faster than recessives do?
Because selection "sees" all the dominant alleles. They never hide from selection. This makes selection very efficient.
Suppose a bird species eats a certain species of moths and the moths come in dark and light morphs (forms), where the color morph is controlled by genetic variation at a single locus. Most predators develop a "search image", where they key into one pattern and look for it. Why would this type of scenario generate frequency-dependent selection?
Because the predators have developed a search image trait that searches for the most common color. If a moth has a color that is rare, they will not be hunted and will therefore be more fit. 1. But the predation driven change in allele frequencies turns the tables and eventually what was common becomes rare and then enjoys the benefits of being rare.
Who were the two people who independently proposed the theory of evolution by natural selection?
Charles Darwin and Alfred Russell Wallace
What is a famous example of sympatric speciation in fish in Africa?
Cichild fishes in lake victoria and lake malawi have generated more than 1000 species in less than 1 million years. Driven by ecological niches and reinforcement on nuptial coloration
What is true about evolution? A. It only requires phenotypic variation—even when none of it is genetic in basis B. It occurs within individuals C. It occurs within each generation D. It occurs in the gene pool, as it changes across generations
D. It occurs in the gene pool, as it changes across generations
What allows us to estimate the times of divergence events on phylogenetic trees?
DNA substitutions occur at approximate a constant rate, especially at synonymous sites
What has happened to horn length since? Why do think the rate of increase is not as fast as the decline was? Can you think of any reason why the trait may not quickly return to pre-hunting horn size?*
Dereased 30% and then increased 13%. The sow increase might be because the gene pool after the large decrease had very little large horns, so they were less frequent in the population and therefore not able to produce as much offspring
What is directional selection? Why do you think directional selection doesn't go on forever and why would balancing selection tend to emerge once directional selection slows down
Directional selection is when one trait or allele is favored over the other and eventually leads to fixation of the favored allele. It doesn't go on forever because there are tradeoffs when having an extreme phenotype which might render it less fit (cost and benefit that would make being in the middle better)
Which of the following types of sites in the genome undergo relatively rapid evolution and which undergo much slower change: synonymous mutations in exons, nonsynonymous changes in exons, introns, pseudogenes?
Evolve fast: Neutral mutations- synonymous mutations in exons, non coding and non regulatory sites like intros and pseudogenes Evolve slow: sites that affect stress- nonsynonymoous changes in exons
Still, if we wait thousands or thousands of generations, it seems like selections should eventually remove these lethal alleles. Yet I told you in class that, on average, every one of us is walking around with between 1 to several lethal recessive alleles in our genome. Given that humans have indeed been around hundreds of thousands of generations (or more), how can it be that selection hasn't purged such alleles?
For rare deleterious recessive alleles, selection becomes so weak that the force of mutation becomes its equal. Mutation constantly generates new copies of the recessive allele and reintroducing them into the population. Almost always arises in heterozygote form and rare and selection doesn't remove it. Removal of harmful recessive alleles has hardly any effect on frequency of the disease bc nearly all copies are hidden in heterozygotes
If you read the paper, you will see that the authors argue that one named species, in particular, has undergone extensive hybridization with other finches. Based on the phylogeny, which one do you think this is?
G. difficilis.
the Tay Sachs allele is way more common in Ashkenazi Jews than can be explained by mutation-selection equilibrium . What is the likely explanation of how it got relatively common in the first place?
Genetic drift
What riddle was Charles Darwin trying to solve?
He was trying to understand how species originate, he thought this was the key to explaining all of the variation we see in nature.
Let's suppose the double-stand-break model is closer to reality. What is the name of the pretzel-like junctions where the strands from different homolog DNA molecules cross over to the other homolog?
Holliday Junction
Many alleles that cause Huntington disease have 36-40 repeats and, for these, the age of onset is usually not before 50. Yet the allele is ultimately lethal. Do you think the selection coefficient for such alleles is nearer 0 or 1? Why? How might this relate to answering the question: why has selection not eliminated the disease?
In this case, s will be nearer 0. Dying at 60 from a disease has little effect on fitness b/c the person has already either passed their genes on or they have not. Ever wondered why there are so many diseases that afflict the old? It's b/c selection doesn't "care" nearly as much about these diseases.
What does the neutral theory say about why there is so much genetic variation in real populations?
It says the reason for genetic variation is due to neutral mutations that cause molecular variation and individuals with different molecular variants have equal fitness
a hybrid with six chromosomes (ABCGHI) is created. Does chromosome A in species 1 have a homolog in species 2? What about chromsomes B or C, do they have homologs? Why is speciation from this hybridization event much more likely the chromosomes don't have homologs? ***
No there is no homologs for the chromosomes between species. If none of the chromosomes are homologous, and if there is a mitotic nondisjunction event in the hybrid plant, then you get a clean case of all chromosomes in two copies—so that, going forward, meiosis can proceed normally.
What is the difference between synonymous and non-synonymous changes?
Non-synonymous nucleotide changes alter the amino acid sequence and synonymous do not.
What about when selection is actively selecting for changes in a protein—say because the species is adapting to a new environment—what type of mutations will be observed then?
Nonsynonymous mutations will be observed more often than expected (where expectation is based on assumption of neutrality).
Go to the monopyletic tree in ch. 26 Part C and differentiate between mammals and lizards, snakes, and turtles as monophyletic groups
Notice that snakes and lizards share a more recent common ancestor with crocodiles and birds than they do with turtles. So going back to the definition: the clade that includes lizards, snakes and turles, also includes crocs and birds—so turles+snkaes+ lizares is not a monophyletic group.
What is overdominance? How is sickle-cell disease an example of this? How does this provide a second explanation (see question 9 above) for how a disease-causing allele can become relatively common in a population despite its deleterious effect?
Overdominance is when the heterozygote has a higher fitness than either of the homozygotes. Sickle cell is an example of over dominance because people that are homozygous for the mutation only produce sickle cell hemoglobin and have severe anemia. Heterozygotes have a normal copy and have enough to prevent anemia as well as have a higher fitness against malaria. It becomes common because more in a population will be carriers and likely to pass on the trait.
What is the reason sickle-cell anemia occurs at a high frequency in people from Africa?
Overdominance: the heterozygote genotype Aa is actually more fit than the homozygote AA—so selection maintains the allele that causes the disease.
When selection tolerates very little change in a protein—________—what type of mutations in the genes coding sequence will be observed?
Purifying selection, synonymous
I said at the beginning of the lecture that, very roughly, recombination rate is 1 crossing over event per 1 million bases (1 Mb). But at the end of the lecture I said the frequency of crossing varies a lot. What are some things it depends on? Is it the same for all species? Is it the same for all chromosomes within a species? Is it the same for all locations within a given chromosome? Is it the same for both sexes?
Recombination rates vary between species, between chromosomes, within chromosomes and between sexes Not the same for species, sexes, or chromosomes within a species. Recombination rates on autosomes in human females 1.5x human males There are certain spots on chromosomes that have elevated variation rates
what type of mating does reinforcement promote? Does reinforcement accelerate or halt the speciation process?
Reinforcement promotes assertive mating. This is because individuals that rate at random can waste their reproductive opportunity since hybrids are less viable. Accelerates the speciation process
What are Darwin's key driving forces?*
Reproduction, Inheritance, Variance, and a ratio of increase so high that leads to the struggle of life as a consequence of natural selection. Entails divergence of character and extinction.
Remaining distinct depends on what?
Reproductive Isolation mechanisms Either PREZYGOTIC mechanisms have evolved- ecological, mechanical, gametic, behavioral OR POSTZYGOTIC mechanisms have evolved - hybrid inviability, hybrid sterility, and hybrid breakdown
What is the biological species concept? What does this definition highlight must evolve if two groups of organisms are going to become distinct species?
Says that each group of species has members that can interbreed with each other but are reproductively isolated from other species. each species must evolve INDEPENDENTLY
What do we call it when the heterozygote is more fit than either homozygote? If the two semi-species were both small and somewhat inbred, why do you think hybrids might very well have higher fitness than non-hybrids (assuming that co-adapted gene complexes had not developed during isolation)
Since inbreeding can reduce fitness (consanguineous matings can cause problems and surface occurrence of diseases). So if two individuals from each semi-species that is small and somewhat inbred mate with each other, they would have higher fitness because the offspring will be heterozygotes across many loci and have higher fitness 1. (if deleterious autosomal recessive alleles are causing inbreeding depression).
I also showed a plot of the distribution of dN/dS values for the rhodopsin (RH1s) paralogs. Here is that plot and the legend from the paper. What does it tell you? That is, would it be fair to say that all of these rhodopsin paralogs have simply been evolving neutrally? Or that they've been under strong purifying selection? Or have at least some of them been under positive selection?
Since many of the values are above 1, selection has favored mutations that change the amino acid sequence (nonsym) and allow the fish to see at a different absorption, helping them survive (positive selection). However, some of the parallels show a score of 0, which is purifying selection
In general, which type of substitution is observed more often and, roughly speaking, how much more often?When a protein is under purifying selection—in other words, when virtually all amino acid changes reduce fitness—which type of substitutions predominate?
Synonymous substitutions occur roughly 5 times as often as nonsynonymous Synonymous (b/c nonsynonymous are not tolerated and don't survive.).
In cucumbers, T=warty while t=smooth and D=dull color while d=shiny. We start by doing the usual TTDD x ttdd à TtDd (F1s). Are the T and D alleles in the cis or trans configuration in the F1s? We then cross this F1 back to the homozygous recessive individual: TtDd x ttdd. What is the name of this type of cross?
T and D are in cis testcross
Suppose that someone gives you heterozygote seeds (TtDd) where the T and D alleles are in repulsion. What would that look like?
T_____d t-----D
Notice that the mutation originally arose in the 11100 haplotype. What happens over generations to the association of the disease-causing allele in yellow and that 11100 combination of SNP alleles? Which allele of which SNP is the association going to last the longest in?
The association (often called the linkage) with the haplotype of the chromosome it arose in will decay. The b1 allele is where it will last the longest.
The tPA gene is the example given in our textbook on exon shuffling. Where do the different exons in that gene come from?
The gene for TPA is believed to have acquired its exons from other genes that encode different proteins: the kringle exon came from the plasminogen gene, the growth-factor exon came from the epidermal growth factor gene, and the finger exon came from the fibronectin gene.
If the two loci are completely linked (so there is essentially 0 distance between the two), what will the haplotypes of the gametes produced by each parent be? Under this scenario, what are the expected genotype (and phenotype) frequencies of the offspring? (ch. 7 SQ)
The heterozygote will make gametes Pl and pl homozygote will make gametes pl ½ the offspring will be PpLl (from PL + pl), and the other ½ will be ppll (from pl + pl) (treat the 2 loci as 1 because they are tightly linked)
In deep sea teleost fish, what gene has undergone many rounds of duplication in the Diretmidae branch of the teleost phylogeny?
The rhodopsin gene
Applying the molecular clock to rabies virus outbreak in Pune city indicates what?
The sampled viruses diverged 1-3 decades ago—inconsistent with a single immigrant rabid dog triggering the outbreak
What did the silver spinyfish do with all these duplicated copes of the rhodopsin protein?what is the type of light down there that (presumably) selection is acting to change the perception of?
They used the duplicated copies of the rhodopsin proteins to create a new function for them. The new function was being able to see with impeccable vision in the deep sea using bioluminescence
Three loci (A, B and C) are located as follows, each 20 map units apart. What do we expect the recombinaHon rate between the most separated loci—A and C—to be
To be less than additive (< 20+20)
What happened to horn length on Ram Mountain in the beginning in the early 1970s and what drove the change? What type of molecular marker did David Coltman and his colleagues use to construct a pedigree of sheep? What did they estimate the heritability of horn length in males? In females?
Trophy hunters selectively shoot rams with large horns, often before they are able to reproduce, producing artificial selection for smaller horns in rams. -They extracted DNA from the samples and used PCR to amplify it. The DNA revealed variation at 20 microsatellite loci. The researchers used this variation to determine paternity in the sheep and created a detailed pedigree for the population - horn size in rams (as well as in females, or ewes) had moderate heritability.
At what level in this diagram does selection act upon variation? Where does this variation come from?
Variation in the gene pool causes variation in a population. Selection then acts on the variance at the population level, to create changes in the gene pool
Now, suppose that the recombination frequency is 8% between these two loci (yes, different than what you calculated in problem 4) and you conduct another test cross: TtDd x ttdd. Given the trans configuration, what do you expect the frequency of the following 4 phenotypes to be? Phenotype Frequency Warty dull Warty shiny Smooth dull Smooth shiny
Warty dull (TtDd)= .04 Warty shiny (Ttdd)= .46 Smooth dull (ttDd)= .46 Smooth shiny (ttdd)= .04 .08 is recombinant x 2 so each is .04 1-.08= .92 is nonrecombinant x2 so each is .46
What is exon shuffling?
When exons from different genes are combined in new ways. New genes have repeatedly evolved when exons of different genes are exchanged, creating genes that are mosaics of other genes
What is gene duplication? When a gene undergoes duplication, what might be the consequences?What do we call the different copies of a duplicated gene in the genome?
When recombinations and transposons result in duplications of genes. Consequences are 1. change in gene expression 2. 1 copy evolves a new function 3. 1 copy loses function (pseudogene) -paralogs
If you were a strong proponent of the phylogenetic species concept, what do you think you would do with C. fusca_E and C. fusca_L?
You would call them each a distinct species—since they appear to have their own unique evolutionary history as reflected by each morning their own monophyletic group.
Now, suppose that the P-locus and the L-locus are 10 cM (or map units) apart. What is a cM or a map unit? For the heterozygote (PpLl), what haplotype will the recombinant gametes have? (By contrast, what haplotypes will the nonrecombinant gametes have?) Now, what is the expected frequency of each of the possible phenotypes from our cross in this scenario: purple long, purple round, red long, and red round?
a cM (map unit) is a unit of measurement for the distance on a genetic map. a 10 coming!! means there is a 10% recombination rate -Pl and pL recombinant gametes -PL and pl gametes Nonrecombinants: 45% PpLl (purple long) and 45% ppll (red round); recombinants: 5% Ppll (purple round) and 5% ppLl (red long).
What is a monophyletic group?
a common ancestor and all of it's descendants. A species is monophyletic when every individual fall into their own called and no other individuals fall into that clade
Here are a few examples of isolating mechanisms. Indicate which category each falls into: (a) in isolation, each semi-species has shifted their seasonal breeding season and they don't overlap; (b) In isolation, the mating behaviors such as song diverged between the two semi-species so they no longer seek to mate with each other; (c) In isolation, the genitalia of the two semi-species diverged so copulation no longer works very well;
a) Prezygotic isolation: temporal b) Prezygotic isolation: Behavioral c) Prezygotic isolation: mechanical
Based on the values in that table 26.3, which of the following genes have likely been under strong purifying selection since humans and rodents diverged? (a) ⍺-actin, (b) histone, (c) apoprotein E, (d) interferon ⍺1, (e) somatostatin-28, (f) luteinizing hormone.
a-actin: .01 histone: 0 apoprotein: .98 interferon a1: 1.41 somatostatin-28: 0 luteinizing hormone: 1.02 a, b, and e all have virtually nonexistent non synonymous mutations, and still have synonymous substitutions
What is the name of the mode of speciation that involves geographic isolation for an extended period of time?
allopatric isolation
Circle the 2 haplotypes in the bottom of the figure where you expect the disease causing allele might still occur after many generations?
any haplotype with the b1 mutation will have the disease causing allele
What are exons?
are coding regions on DNA that specify protein domains and are separated by introns
What geographic feature inspired both of them to come up with the theory? What specific place was each of them working when they observed the patterns that lead to the theory? Why is speciation relatively common on this type of geographic feature?
both of them studied island and the isolation they generate. Charles darwin studied species on the galapagos islands Wallace studied species in the Malaysian Archipelago (what is now Indonesia). they studied isolated populations which makes speciation common to this feature because the geographic barrier between them interrupts gene flow (exchange of genes) so that it causes evolution of species
the allele that causes a serious, often lethal, autosomal recessive disease is very rare—say at 0.001. How will the frequency of allele change in the next generations? Absent mutation A. It will not change at all B. It will decline by 0.001 thats rightdownin the zonewhere C. It will decline by 0.001^2 = 0.000001
c
2 alleles on the same chromosome are in 2 alleles on the opposite chromosomes are in
coupled in cis configuration repulsion in trans configuration
(d) the proteins on the surface of the gametes have diverged so that fertilization no longer occurs, even when sperm and eggs come into contact; (e) fertilization occurs, but the genes controlling developmental in the two species have diverged so that zygotes abort early in pregnancy; (f) hybrids are produced, but because the semi-species differ in their number of chromosomes, they hybrids are themselves not fertile; (g) hybrids are produced, but because each semi-species has evolved sets of co-adapted gene complexes that don't work well together, hybrids are less fit.
d) Prezygotic: Gametic e) Postzygotic: hybrid inviability f) Postzygotic: hybrid sterility g) postzygotic: hybrid breakdown
The third scenario is where selection is ambivalent—not favoring amino acid changes but not removing them either. This is neutral evolution. How do these scenarios relate to the dN/dS ratio?
dN/dS ratio is the ratio that divides non synonymous to synonymous mutations. The third scenario which is neutral has a ratio of 1. Purifying selection has a ratio of 0, and positive selection has a ratio higher than 1
What is meant by evolution by evolution through regulatory changes? Why do regulatory changes often have more profound effects for evolution than changes in many "building block" genes (structural proteins and enzymes)?
evolution by regulatory changes are not changes in the DNA sequence or amino acids, but regulatory changes in gene expression. Changing gene expression alters phenotype in fewer mutational steps than is possible by altering proteins
A mutation arises in a poisonous frog species that blocks production of the toxin and saves the individual energy. The allele is favored and becomes common—until predators discover eating the frog doesn't make them sick—at which point the poison producing allele is favored. What type of selection is this?
frequency dependent selection
What does it mean to say 2 loci are linked or show linkage?
genes that are located close to each other on the same chromosome. linked genes travel together during meiosis and do not assort independently
What does GWAS stand for?
genome-wide association study
Phylogenetic analysis requires that we compare "apples to apples". That is, we must align sequences so that we are looking at the same genes, and even within genes, we must be comparing the same sites. What do we call these types of comparable DNA sequences—comparable because they evolved from a single sequence found in an ancestor?
homogolous sites
Do you think sexual dimporhism is more or less pronounced in monogamous species—where both sexes have closer to equal investment in offspring?
in monogamous species, where the males invest more in the offspring, it is LESS pronounced
How does polyploidy speciation work? In what group of organisms is it especially common?What is it called when polyploid speciation arises from the hybridization of two different species?
instant reproductive isolation from an increase in the ploidy. Common in flowering plants. Allopolyploidy is when two different species hybridize and It occurs when two diploid species mate and nondisjunction causes 4n species that has two copies of each chromosome. It is usually fertile and reproductively distinct from the parents.
How does balancing selection maintain genetic variation? If we (or nature) selected individuals in one tail to reproduce (directional selection; see next question), what do you think would happen to heterozygosity (and therefore genetic variation)?
it maintains genetic variation because it acts on the concept that heterozygotes have intermediate phenotypes and therefore more fit to adapt to an environment. If you select a tail end of the distribution, it would reduce heterozygosity and therefore reduce genetic variation
We talked about the rate of change for lethal recessive alleles like this in class. Roughly, how much will the frequency of the allele decline per generation (see the approximation slide from lecture #20)? How does this explain the apparent paradox that even though serious autosomal recessive diseases have the most severe fitness cost possible (e.g. Tay Sachs is lethal), selection does not remove them?
it will decline by -q^2 as q gets small, q^2 gets even smaller. So the rarer and rarer the allele becomes, the less able selection is able to remove it. This is because the only time it can remove it is when its in its homozygous recessive form.
What are the fitness values for selection against both homozygotes (over dominance) A1A1 A1A2 A2A2
over dominance is when the heterozygote has a higher fitness than either homozygote where s11 represents the selection coefficient of the A1A1 homozygote and s22 represents the selection coefficient of the A2A2 homozygote. A1A1= 1-s11 A1A2= 1 A2A2= 1-s22
Except in rare cases, populations display a lot of phenotypic variation and much, though certainly not all, of this is genetic in origin. This is perhaps surprising b/c, if you think about selection at a single locus, only one type of selection actually maintains variation (see Table 25.6). Which one does?
overdominance
Suppose that the rate that an essential gene mutates to a non-functional version is 3x10-5 per generation. The mutant allele is lethal in homozygous form (i.e. it's autosomal recessive)—so s = 1. At mutation-selection equilibrium, what is the expected frequency of the allele in the population? (I covered this in lecture #20, but you can also find the equation in the textbook, 25.19). Assuming HW proportions, what is the expected frequency of offspring born with the lethal condition?*
q(eq)= squre root of u/s u= 3x10-5 q= .00547 children born with lethal condition= .00003
In the Ashkenazi Jewish population, Tay Sachs disease (which is autosomal recessive) affects about 1/3500 births. Assuming Hardy-Weinberg proportions, what is the frequency of the allele that causes it? Since the disease is lethal, what is the selection coefficient of the recessive allele?
q= .0169 s= .983 s= 1
Calculate s11, s12 and the expected equilibrium frequency of the a allele. Genotype W s AA 3.5 Aa 4 Aa 3
q_eq=s_11/(s_11+s_22 ) AA- W= .875 s=.125 Aa =1 s= 0 aa- W=.75 s=.25 .125/.125+ .25 = 1/3 q p= 1-1/3= 2/3 at equilibrium
What is sexual selection? Why does it tend to produce sexual dimorphism?
selection that operates on who is doing the reproducing, if there are traits that increase reproductive success, they will increase in the gene pool (even if they decrease survival) it produces sexual dimorphism because if the female has more infested in the reproduction process , they will be choosier about who they mate with. Leads to males that need traits that will increase their chances of being chosen
What is sympatric speciation? Is it as common as allopatric speciation?
speciation that occurs without a geographic barrier to gene flow. It is not as common as allopatric speciation
Suppose you are studying influenza virus. You measure the reproductive capacity of 3 different strains: a, b, and c. In cell culture, you estimate the number of viruses produced per infected cell at be 100, 150, and 200. Calculate the fitness (W) and the selection coefficient for each strain. Use the most-fit strain as you reference. Strain #viral progeny W s a 100 b 150 c 200
term-5Waa= 100/200 =.5 s= 1-.5= .5 Wbb= 150/200= .75 s=1-.75= .25 Wcc= 200/200= 1 s=1-1= 0
What do you think "ratio of increase" refers to? *
the ratio of increase is the capacity for exponential growth among all living things. However, a population cannot exponentially grow forever because of finite resources. When more offspring are born that can survive and reproduce. There is variation within the offspring. different success among the offspring lead to changes in gene pool
When you do this, you observed the following frequencies. What do you estimate the number of map units (cM) these two loci are apart? Phenotype Frequency Warty dull 0.40 Warty shiny 0.10 Smooth dull 0.10 Smooth shiny 0.40
the recombinant phenotype frequency is 2(.10)= 20% so the cM= is 20 apart
What is meant by the term secondary contact?
two populations that once diverged come into contact with each other because there is not geographic isolation anymore. the semi species may or may become distinct.
What is frequency dependent selection?
when selection favors rarity. When a allele becomes rare, it's fitness goes up
Is it true that you need a formal model of sequence evolution to find the maximum likelihood tree?
yes Need to consider every possible tree and then calculae the probability of the data for each and take the three where the probability of the data is the greatest
three loci (A, B and C) are located as follows, each 30 map units apart. Do you expect loci A and C to show linkage?
yes they will be weakly linked (60 cM part have a 30% recombination frequency). However around 100-150 cM apart they start having a 50% recombination frequency, meaning that they assort independently