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2014-04-09 23:17:24
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  1. What is genetic drift?  How is sampling error related to this evolutionary force?  Why is population size a factor when considering the effects of sampling error?
    • Genetic drift: removal of variation from a population  by causing alleles to either fix (100%) or be removed (0%) from a population
    • The genes included in any generation are a sample of the genes from the previous generation, and every sample is subject to random variation (sampling errors)
    • the percent of different alleles in each sample (generation) will differ by chance from the sample (generation) it came from
    • As population size nears infinite genetic drift (removal of diversity) is at equilibrium with mutation (addition of diversity)
  2. What does it mean when we say that human mitochondrial DNA haplotypes coalesce to a single ancestral haplotype ~200,000 years ago?
    • *note- image on p260
    • Initially (t=0) population has 15 copies of gene A
    • Each gene has 0,1,or 2 descendants
    • By time t all copies descend from (coalesce to) a single ancestral copy, because the others eventually became extinct
    • If the failure of gene copies to leave descendants is random then the gene copies at t could have descended from ANY of the original gene copies at t=0 (genetic drift)
  3. Why have the generation-by-generation effects of genetic drift been compared to a "drunkard's walk"?
    • Consider a A drunkard walking next on a raised train platform.  Trying to walk straight he inevitably moves back and forth with variable success.  Eventually he is either going to fall off the platform (fixation) or fall onto the tracks (loss)
    • Genetic drift is random, not directional, and will vary from generation to generation, but the end result will be fixation or loss
  4. Be able to draw a graph of changes in allele frequencies at multiple loci over generations, comparing random genetic drift in a large vs a small population. Label axes appropriately
    • graph-Allele frequency (p) [0-1 vs generations [0-20]
    • In a small population the graph quickly spreads from .5 @ generation 0 and ends all over the place (some lines fix at 4,6,8,15 gens, removed at 8,10,15,17 gens, some end at different frequencies)
    • In a large population we see much less apparent randomness, all lines start at .5, but none fix by the end of the twenty, although the lines are spread randomly throughout)
    • *note- the lines are FAR from straight and exhibit drunkards walk
    • *image pg 262
  5. What is the average time to fixation (in generations) of a newly arisen neutral allele?  How does population size (N) influence this time?
    • Average time to fixation of a newly arisen neutral allele is 4N generations (4 to consider each allele contributed by 2 diploid parents)
    • As population size increases the time to fixation increases.
  6. What is effective population size (Ne)? How can the mating system or sex ratio of a species influence this population metric?
    • Ne: # breeding adults in a pop
    • often smaller than total adults in pop (n)
    • EX- elephant seals and marine iguanas - a few dominant males mate with all the females
    • Ne also decreases when sex ratio differs from 1:1, generations overlap (offspring mate with previous generation - # alleles propagated is reduced, and when population size fluctuates dramatically in a given generation
  7. What is a population bottleneck?  What are some causes?  What is the result?  Discuss this process and outcome with respect to cheetahs.
    • Pop bottleneck: large population reduced to very low numbers
    • Caused by seasonal climactic change, heavy predation, disease, catastrophic events, etc
    • Results in a loss of genetic diversity (even after pop size is restored)
    • EX-cheetahs experienced bottleneck ~10-20kya and insufficient time has passed for random mutations to produce new variation
    • Lack of genetic variation led to decreased fecundity, increased cub mortality and increased sensitivity to disease (increased genetic load, increased homozygosity)
    • Selective pressure may be acting on female cheetah mating behavior, selecting for promiscuity to increase genetic variabilty of litters (females "step out" of "relationship pair")
  8. What is the founder effect?  Why do island populations exhibit founder effect?
    • Founder effect: special case of a bottleneck when a new population is established by a small # of colonists
    • If the colony remains small genetic drift alters allele frequency and erodes genetic variation
    • If the colony grows # founders (N0) and rate of pop growth (r) affect how much heterozygosity is restored after a bottleneck
  9. What two factors influence how average heterozygosity is reduced in populations after bottlenecks?
    • # founders (N0) [linked to initial loss of heterozygosity] and rate of pop growth (r)
    • graph- avg heterozygosity [0-15%] vs # generations [0-108]
    • r=1, N0=10: line starts at 15% slightly dips then returns to 15%
    • r=1, N0=2: line starts at 15%, dips to ~8% then returns to 15%
    • r=.1, N0=2: line starts at 15%, dips to ~1% then returns to 15%
    • note- graph 3/25 in notes
  10. Describe the two groundbreaking studies that demonstrated the effects of genetic drift in laboratory pops.
    • Buri (1956): genetic drift in Drosophila
    • Established 107 pops (8M,8F in each), all heterozygous for 2 alleles that affect eye color (bw and bw75)
    • after gen 1, # of bw75 copies ranged from 7 (q=.22) to 22 (q=.69)
    • after gen 19, 30 pops lost bw75 and 28 were fixed
    • McCommes and Bryant (1990): Drift in house flies
    • established 4 replicate pops @ 3 bottleneck sizes (1,4, and 16 pairs) and after the pops grew back to ~1000 they caused another bottleneck
    • Average heterozygosity fell steadily after each bottleneck episode
    • smaller bottlenecks resulted in a more rapid decline (1>4>16)
  11. Describe the Selander 1970 study of house mice in barns across Texas.  What were the results, and what occurred in the past to produce these results?
    • Studied allozyme variation at 2 loci in pops from widely scattered barns in TX
    • there was low overall heterozygosity, but more variance in allele frequency among smaller populations than larger populations
    • This is consistent with the genetic drift theory
    • It is likely that each barn represents an instance of the founder effect (perhaps coupled with an overall bottleneck due to human invasion of land), and thus larger population sizes have undergone reduced drift
  12. How does the example of the Argentine ant (CA vs native Argentina pops) provide the exception to the "rule" that low genetic variation is bad for a population?
    • Small colonies defend territories against non-specific colonies
    • In CA populations there is a high genetic similarity between all individuals (founder effect decreased variation)
    • Since CA colonies differ very little in "colony odor" they are not aggressive toward each other and tend to fuse into supercolonies which competitively exclude other ant species through numbers.
  13. What is the neutralist-selectionist debate? How did the revolution in genetic technology spark this controversy?  What is the current belief?
    • neutral theory of molecular evolution: the great majority of those mutations that are fixed are effectively neutral with respect to fitness and are fixed by genetic drift
    • If NS and drift act to reduce variation, what maintains it?
    • Genetic technology revealed 2 lines of evidence-
    • 1. some of the variation appeared to be selectively neutral
    • 2. proteins evolved at similar rates in different lineages ("constancy")
    • Today most geneticists agree that variation at different loci is a result of...
    • 1. purifying selection @ conserved loci
    • 2. natural selection @ loci where variation is adaptive
    • 3. neutral drift @ loci which are selectively neutral
  14. Why would the neutral mutation rate (μ0) be more properly called the neutral mutation retention rate?
    • The rate depends on the gene's function
    • If changing the AA sequence seriously affect protein function, then majority of mutations at that locus are deleterious
    • this locus has many functional constraints and experience purifying selection
    • If the protein can function well despite many AA changes then the locus is less constrained and may only experience neutral drift
    • *note-we can only measure the mutations which have persisted throughout generations
  15. In what parts of the genome is the neutral mutation rate (μ0) high, and in what parts is it low?  Why?
    • Substitution rates low in coding regions (especially non-degenerate sites)
    • Rate increases at degenerate sites (especially 4 fold degenerate sites)
    • Rate highly increases in introns, pseudogenes, and untranslated regions
    • *note- slowest evolving genes are very functionally constrained
  16. What does the equation 2Neμ0 x 1/(2Ne) = μ0 refer to?  Why is this the basis for the molecular clock?
    • 2Neμ0: probability of new mutations
    • 1/2Ne: probability of fixation
    • therefore rate of fixation and mutation is theoretically constant (μ0)
    • much DNA sequence evolution is neutral, and the rate appears to be nearly constant EXCEPT when NS is acting
  17. Describe homoplasy
    • homoplasy: identity in state, but not identity by descent
    • As time since divergence increases the # of differences plateus due to reverse mutations
    • ex- image pg 271
    • #bp differences increase for 5-10my, but then level off around 40my.  
    • Data from taxa on the plateau region cannot be used to estimate substitution rate (it is likely undergoing reverse mutation), we must use data from the initial slope of the line

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