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. 2006 Mar;172(3):1607-19.
doi: 10.1534/genetics.105.048223. Epub 2005 Nov 19.

Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster

Kevin Thornton  1 , Peter Andolfatto
Affiliations

Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster

Kevin Thornton et al. Genetics. 2006 Mar.

Abstract

Genome-wide nucleotide variation in non-African populations of Drosophila melanogaster is a subset of variation found in East sub-Saharan African populations, suggesting a bottleneck in the history of the former. We implement an approximate Bayesian approach to infer the timing, duration, and severity of this putative bottleneck and ask whether this inferred model is sufficient to account for patterns of variability observed at 115 loci scattered across the X chromosome. We estimate a recent bottleneck 0.006N(e) generations ago, somewhat further in the past than suggested by biogeographical evidence. Using various proposed statistical tests, we find that this bottleneck model is able to predict the majority of observed features of diversity and linkage disequilibrium in the data. Thus, while precise estimates of bottleneck parameters (like inferences of selection) are sensitive to model assumptions, our results imply that it may be unnecessary to invoke frequent selective sweeps associated with the dispersal of D. melanogaster from Africa to explain patterns of variability in non-African populations.

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Figures

Figure 1.
Figure 1.
A simple stepwise bottleneck model.
Figure 2.
Figure 2.
Marginal posterior distributions of θ and ρ per site in Zimbabwe (solid line) and the Netherlands (dashed line). The parameters θ and ρ were jointly estimated from the 115-locus data set in both populations, using a rejection sampling scheme (see methods). These marginal distributions are summarized in Table 3.
Figure 3.
Figure 3.
Marginal posterior distributions of bottleneck parameters with four values of formula image. The parameters are tr, the time at which the population recovered from the bottleneck, d, the duration of the bottleneck, tb, the time of the crash in population size, and f, the bottleneck severity. Time is measured in units of 4Ne generations, and smaller values of f correspond to more severe bottlenecks (see Figure 1). These marginal distributions are summarized in Table 2.
Figure 4.
Figure 4.
Timing of bottleneck in the Netherlands. Times are converted from units of 4Ne generations into years, assuming Ne = 2.4 million and 10 generations per year.
Figure 5.
Figure 5.
Distributions of P-values for the observed data under equilibrium and bottleneck models. Shown are the distributions of two-sided P-values for four summary statistics. The P-values were obtained for both the standard neutral model (solid bars) and a bottleneck model described by a posterior distribution conditional on the data (shaded bars). The value formula image is the maximum a posteriori estimate based on the Zimbabwe data (Table 3).
Figure 6.
Figure 6.
The effect of a bottleneck on Tajima's D in a derived population when the ancestral population is not at demographic equilibrium. Distributions of Tajima's D were obtained from 105 coalescent simulations with n = 12 in both populations, θ = 0.01 per site, formula image, and 1000 bp. The bottleneck parameters are based on the MAP estimates for each of the marginal distributions inferred when formula image (Figure 2). (a) The derived population is bottlenecked from an ancestor at demographic equilibrium. (b) The growth parameter in the ancestral population was set to give a mean Tajima's D close to the −0.56 observed in the Zimbabwe sample. Vertical lines indicate the median D for each population.
Figure 6.
Figure 6.
The effect of a bottleneck on Tajima's D in a derived population when the ancestral population is not at demographic equilibrium. Distributions of Tajima's D were obtained from 105 coalescent simulations with n = 12 in both populations, θ = 0.01 per site, formula image, and 1000 bp. The bottleneck parameters are based on the MAP estimates for each of the marginal distributions inferred when formula image (Figure 2). (a) The derived population is bottlenecked from an ancestor at demographic equilibrium. (b) The growth parameter in the ancestral population was set to give a mean Tajima's D close to the −0.56 observed in the Zimbabwe sample. Vertical lines indicate the median D for each population.
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