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Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species

Talla, Venkat ; Soler, Lucile ; Kawakami, Takeshi ; Dincă, Vlad ; Vila, Roger ; Friberg, Magne LU ; Wiklund, Christer and Backström, Niclas (2019) In Genome Biology and Evolution 11(10). p.2875-2886
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... (More)

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.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Animals, Base Composition, Butterflies/genetics, Genetic Variation, Molecular Sequence Annotation, Mutation, Recombination, Genetic, Selection, Genetic
in
Genome Biology and Evolution
volume
11
issue
10
pages
2875 - 2886
publisher
Oxford University Press
external identifiers
  • scopus:85073309199
  • pmid:31580421
ISSN
1759-6653
DOI
10.1093/gbe/evz212
language
English
LU publication?
yes
additional info
© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
id
7287e56d-aeef-4f61-8317-c5a61d74fdd6
date added to LUP
2021-01-28 13:25:22
date last changed
2021-06-23 03:29:00
@article{7287e56d-aeef-4f61-8317-c5a61d74fdd6,
  abstract     = {<p>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.</p>},
  author       = {Talla, Venkat and Soler, Lucile and Kawakami, Takeshi and Dincă, Vlad and Vila, Roger and Friberg, Magne and Wiklund, Christer and Backström, Niclas},
  issn         = {1759-6653},
  language     = {eng},
  month        = {10},
  number       = {10},
  pages        = {2875--2886},
  publisher    = {Oxford University Press},
  series       = {Genome Biology and Evolution},
  title        = {Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species},
  url          = {http://dx.doi.org/10.1093/gbe/evz212},
  doi          = {10.1093/gbe/evz212},
  volume       = {11},
  year         = {2019},
}