Abstract
Using the data provided by the Drosophila Population Genomics Project, we investigate factors that affect the genetic differentiation between Rwandan and French populations of D. melanogaster. By examining within-population polymorphisms, we show that sites in long introns (especially those >2000 bp) have significantly lower π (nucleotide diversity) and more low-frequency variants (as measured by Tajima's D, minor allele frequencies, and prevalence of variants that are private to one of the two populations) than short introns, suggesting a positive relationship between intron length and selective constraint. A similar analysis of protein-coding polymorphisms shows that 0-fold (degenerate) sites in more conserved genes are under stronger purifying selection than those in less conserved genes. There is limited evidence that selection on codon bias has an effect on differentiation (as measured by FST) at 4-fold (degenerate) sites, and 4-fold sites and sites in 8–30 bp of short introns ⩽65 bp have comparable FST values. Consistent with the expected effect of purifying selection, sites in long introns and 0-fold sites in conserved genes are less differentiated than those in short introns and less conserved genes, respectively. Genes in non-crossover regions (for example, the fourth chromosome) have very high FST values at both 0-fold and 4-fold degenerate sites, which is probably because of the large reduction in within-population diversity caused by tight linkage between many selected sites. Our analyses also reveal subtle statistical properties of FST, which arise when information from multiple single nucleotide polymorphisms is combined and can lead to the masking of important signals of selection.
Highlights
Natural populations are often divided into subpopulations
Insights into fundamental processes such as historical demographic changes, adaptation and speciation can be obtained by comparing patterns of genetic differentiation across different genomic regions (Wu, 2001; Weir and Hill, 2002; Charlesworth et al, 2003; Hey and Machado, 2003; Beaumont, 2005; Holsinger and Weir, 2009)
In a study comparing African and non-African humans, it was found that the X chromosome was substantially more diverged than the autosomes, over and above the null expectation based on the fact that there are four copies of each autosome for every three copies of the X chromosome, which in turn suggests that dispersal in humans may be sex-biased or that the X chromosome may have experienced repeated selection after the divergence of African and non-African populations (Keinan et al, 2009)
Summary
Natural populations are often divided into subpopulations. Studying the extent to which different subpopulations are genetically differentiated has been of paramount importance in evolutionary genetics, as it provides a way to examine how different evolutionary forces such as genetic drift, natural selection and migration drive changes in the genome (reviewed in Chapter 7 of Charlesworth and Charlesworth, 2010).insights into fundamental processes such as historical demographic changes, (local) adaptation and speciation can be obtained by comparing patterns of genetic differentiation across different genomic regions (Wu, 2001; Weir and Hill, 2002; Charlesworth et al, 2003; Hey and Machado, 2003; Beaumont, 2005; Holsinger and Weir, 2009). By scanning for loci that show unusually high levels of differentiation relative to the rest of the genome, we can detect loci that are under diversifying selection, whereby different alleles are favoured in different subpopulations (Beaumont and Nichols, 1996; Beaumont and Balding, 2004; Foll and Gaggiotti, 2008; Excoffier et al, 2009) As another example, in a study comparing African and non-African humans, it was found that the X chromosome was substantially more diverged than the autosomes, over and above the null expectation based on the fact that there are four copies of each autosome for every three copies of the X chromosome, which in turn suggests that dispersal in humans may be sex-biased or that the X chromosome may have experienced repeated selection after the divergence of African and non-African populations (Keinan et al, 2009). For example, single nucleotide polymorphisms (SNPs) and microsatellites, can be used to estimate F, but using statistical procedures that take into account biological properties of the data under consideration (for example, high versus low mutation rate) is vital for acquiring accurate estimates (Weir and Cockerham, 1984; Excoffier et al, 1992; Slatkin, 1995; Nagylaki, 1998; Holsinger and Weir, 2009)
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