In the Light of Evolution Volume X: Comparative Phylogeography (2017) / Chapter Skim
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5 Effects of the Population Pedigree on Genetic Signatures of Historical Demographic Events - John Wakeley, Landra King, and Peter R. Wilton
5 Effects of the Population Pedigree on Genetic Signatures of Historical Demographic Events - John Wakeley, Landra King, and Peter R. Wilton
Pages 91-112
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From page 91... ...
We explore the con sequences of this for patterns of variation at unlinked loci for two kinds of demographic events: the occurrence of a very large family or a strong selective sweep that occurred in the recent past. The results indicate that only rather extreme versions of such events can be expected to structure population pedigrees in such a way that unlinked loci will show devia tions from the standard predictions of population genetics, which average over population pedigrees.
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From page 92... ...
First, whereas in phylogeography the focus has been on the undesirable effects of making inferences conditional on a single gene genealogy estimated from data, here it is on the validity of inferences based on standard population-genetic models that average over population pedigrees when in fact there is only one. It turns out that in relatively large wellmixed populations with constant demography over time, the predictions of standard models are generally quite accurate even though they involve this conceptual error (Ball et al., 1990; Wakeley et al., 2012)
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From page 93... ...
Chang (1999) explored two key aspects of ancestry within population pedigrees analytically, proving for a population of N individuals that (i)
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From page 94... ...
. Here, we use simulations to assess the potential for two kinds of demographic events to alter the shape of population pedigrees so dramatically that they have marked signatures on genetic variation across the genome, specifically among independently segregating loci without intralocus recombination.
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From page 95... ...
In each generation, the proportion for each allele frequency is the fraction of the total 107 populations that showed that particular frequency. Generation 0 is not depicted but would have allele frequency equal to 16 and proportion equal to 1.
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From page 96... ...
In one experiment, Buri recorded allele frequencies of a selectively neutral mutation (bw75) at the brown (eyecolor)
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From page 97... ...
(2001) and co alescent expectations fitted to have the same average number of SNP differences (0.394)
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From page 98... ...
. Spanish Hapsburg King Charles II, who is not shown but would be three generations below, is inferred to have had an inbreeding coefficient of F = 0.254 and could neither rule effectively nor continue the family line.
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From page 99... ...
The results are from simulations of population pedigrees and coalescence of alleles from sampled individuals within pedigrees. In large part, our findings provide further support of the robustness of standard models that average over pedigrees but also suggest that some demographic events might leave signatures detectable in large samples of loci and individuals.
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From page 100... ...
B 0.14 0.12 Proportion of loci 0.10 0.08 0.06 0.04 0.02 N 2N 3N ≥4N Coalescence time (in generations) FIGURE 5.4 Simulated distributions of coalescence times conditional on a population pedigree for the case of a large family described in the text, in which the children comprise 8% of the population in generation 27.
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From page 101... ...
Fig. 5.5B compares a simulated distribution of pairwise SNP differences among loci on a single population pedigree for this case to a simulated distribution for a pedigree with the same demography but without any special demographic event.
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From page 102... ...
B without "Genghis Khan" 0.6 with "Genghis Khan" Proportion of loci 0.4 0.2 0 1 2 3 4 5 Number of differences (SNPs) FIGURE 5.5 Simulated distributions of pairwise coalescence conditional on a population pedigree in which the children in generation 27 comprise 68% of the population.
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From page 103... ...
PEDIGREE EFFECTS OF A SELECTIVE SWEEP We also investigated the potential of a strong selective sweep to structure the population pedigree in such a way that a genomewide deviation from the predictions of the standard neutral model would be observed. Whereas the genetic effects of selective sweeps are known to be dramatic for loci linked to a locus under selection (Smith and Haigh, 1974; Kaplan et al., 1989; Kim and Stephan, 2002)
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From page 104... ...
104 / John Wakeley et al. A 0.1000 0.0500 Proportion of polymorphic sites 0.0100 0.0050 0.0010 0.0005 0.0001 0 200 400 600 800 1000 Sample count of mutant base B 0.1000 0.0500 Proportion of polymorphic sites 0.0100 0.0050 0.0010 0.0005 0.0001 0 200 400 600 800 1000 Sample count of mutant base
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From page 105... ...
5.4A) , and analogously we may infer that even this exceedingly strong selective sweep should have little impact on patterns of genetic variation.
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From page 106... ...
. Each panel is based on a single population pedigree and single pair of sampled individuals.
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From page 107... ...
A 0.0025 1.0 Coalescence probability 0.0020 0.8 Allele frequency 0.0015 0.6 0.0010 0.4 0.0005 0.2 0.0000 0.0 10 20 30 40 50 Generation in the past B 0.00010 1.0 Coalescence probability 0.00008 0.8 Allele frequency 0.00006 0.6 0.00004 0.4 0.00002 0.2 0.00000 0.0 10 20 30 40 50 Generation in the past FIGURE 5.8 Distributions of pairwise coalescence times and trajectories of selective sweeps for 10 different replicate populations.
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From page 108... ...
, so the potential is there to generate similar data for more geographically localized populations and for species other than humans to investigate the detailed effects of population pedigrees. Finally, the genetic signatures of recent demographic events that we have uncovered apply marginally to single sites -- they do not take linkage and recombination into account -- and we note that the pedigree effects of such events might be relatively strong for multilocus measures such as the length distribution of blocks of identity by descent (Chapman and Thompson, 2003; Palamara et al., 2012)
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From page 109... ...
When considering sample frequencies of mutations, or site frequencies, we sampled 1,000 individuals. With multiple lineages, multiple coalescent events can occur in single generations, either in different individuals or within single individuals.
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From page 110... ...
5.6B. Pedigree-Coalescent Simulations of Strong Selective Sweeps We assumed that a selectively favored allele A was introduced as a mutant in a single copy in the population in generation 50 in the past, into a background of wild-type alleles a.
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From page 111... ...
Effects of the Population Pedigree on Genetic Signatures / 111 size was held constant at N = 10,000. Here, starting with a single pair of sampled individuals, we computed probabilities of coalescence in each generation in the past numerically (e.g., see equation 3 in Wakeley et al., 2012)
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