Abstract
The relative role of natural selection and genetic drift in evolution is a major topic of debate in evolutionary biology. Most knowledge spring from a small group of organisms and originate from before it was possible to generate genome-wide data on genetic variation. Hence, it is necessary to extend to a larger number of taxonomic groups, descriptive and hypothesis-based research aiming at understanding the proximate and ultimate mechanisms underlying both levels of genetic polymorphism and the efficiency of natural selection. In this study, we used data from 60 whole-genome resequenced individuals of three cryptic butterfly species (Leptidea sp.), together with novel gene annotation information and population recombination data. We characterized the overall prevalence of natural selection and investigated the effects of mutation and linked selection on regional variation in nucleotide diversity. Our analyses showed that genome-wide diversity and rate of adaptive substitutions were comparatively low, whereas nonsynonymous to synonymous polymorphism and substitution levels were comparatively high in Leptidea, suggesting small long-term effective population sizes. Still, negative selection on linked sites (background selection) has resulted in reduced nucleotide diversity in regions with relatively high gene density and low recombination rate. We also found a significant effect of mutation rate variation on levels of polymorphism. Finally, there were considerable population differences in levels of genetic diversity and pervasiveness of selection against slightly deleterious alleles, in line with expectations from differences in estimated effective population sizes.
Highlights
Theory predicts that both the level of genetic diversity (Kimura and Crow 1964; Kimura 1983) and the rate of adaptive change (Gillespie 2001; Eyre-Walker and Keightley 2007; Leffler et al 2012; Lanfear et al 2014; Galtier 2016) can vary across populations and species as a consequence of differences in effective population size (Ne)
It is necessary to extend to a larger number of taxonomic groups, descriptive and hypothesis-based research aiming at understanding the proximate and ultimate mechanisms underlying both levels of genetic polymorphism and the efficiency of natural selection
Our analyses showed that genome-wide diversity and rate of adaptive substitutions were comparatively low, whereas nonsynonymous to synonymous polymorphism and substitution levels were comparatively high in Leptidea, suggesting small long-term effective population sizes
Summary
Theory predicts that both the level of genetic diversity (Kimura and Crow 1964; Kimura 1983) and the rate of adaptive change (Gillespie 2001; Eyre-Walker and Keightley 2007; Leffler et al 2012; Lanfear et al 2014; Galtier 2016) can vary across populations and species as a consequence of differences in effective population size (Ne). The level of neutral genetic diversity in a population is determined by the mutation rate (l) and the loss of genetic variants due to genetic drift (Kimura and Crow 1964; Kimura 1983). Both the total number of novel mutations entering a population and the effect of genetic drift are dependent on Ne, resulting in an equilibrium genetic diversity level which is a product of l and Ne (4  Ne  l in diploids), which translates to a higher expected level of genetic diversity in larger populations (Charlesworth 2009).
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