Locally Adaptive Inversions Modulate Genetic Variation at Different Geographic Scales in a Seaweed Fly.
Claire Mérot,Emma L. Berdan,Hugo Cayuela,Hugo Cayuela,Haig Djambazian,Anne-Laure Ferchaud,Martin Laporte,Eric Normandeau,Jiannis Ragoussis,Maren Wellenreuther,Maren Wellenreuther,Louis Bernatchez +11 more
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TLDR
In this article, the authors examined how chromosomal inversions shape genetic variation across a species range, and ask how their contribution to adaptation in the face of gene flow varies across geographic scales.Abstract:
Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes of selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation may reside in the heterogeneity of recombination along the genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci at a potentially massive scale. In this study, we examined how chromosomal inversions shape genetic variation across a species range, and ask how their contribution to adaptation in the face of gene flow varies across geographic scales. We sampled the seaweed fly Coelopa frigida along a bioclimatic gradient stretching across 10° of latitude, a salinity gradient and a range of heterogeneous, patchy habitats. We generated a chromosome-level genome assembly to analyse 1,446 low-coverage whole genomes collected along those gradients. We found several large non-recombining genomic regions, including putative inversions. In contrast to the collinear regions, inversions and low recombining regions differentiated populations more strongly, either along an ecogeographic cline or at a fine-grained scale. These genomic regions were associated with environmental factors and adaptive phenotypes, albeit with contrasting patterns. Altogether, our results highlight the importance of recombination in shaping adaptation to environmental heterogeneity at local and large scales.read more
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A beginner's guide to low-coverage whole genome sequencing for population genomics.
TL;DR: An overview of software packages that explicitly account for genotype uncertainty in different types of population genomic inference is provided, and the potential for using imputation to bolster inference from lcWGS data in non-model species is assessed.
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A chromosomal inversion contributes to divergence in multiple traits between deer mouse ecotypes
Emily Hager,Olivia S. Harringmeyer,Tyler Wooldridge,Shunn Theingi,Jacob T. Gable,S. McFadden,Beverly I. Neugeboren,Kyle M. Turner,Jeffrey D. Jensen,Hopi E. Hoekstra +9 more
TL;DR: A key role for a large, previously uncharacterized inversion is uncovered in the evolution and maintenance of classic mammalian ecotypes and fitness benefits that arise from suppressed recombination within the inversion.
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Chromosomal inversion polymorphisms shape the genomic landscape of deer mice
TL;DR: In this article , a single species of deer mouse (Peromyscus maniculatus) was found to have 21 polymorphic inversions that are large (1.5-43.8 Mb) and cause near-complete suppression of recombination when heterozygous (0.03 cM Mb −1 ).
Journal ArticleDOI
A supergene underlies linked variation in color and morphology in a Holarctic songbird
Erik R. Funk,Nicholas A. Mason,Snæbjörn Pálsson,Tomáš Albrecht,Tomáš Albrecht,Jeffrey A. Johnson,Scott A. Taylor +6 more
TL;DR: Acanthis et al. as mentioned in this paper used genome sequences to investigate the genetic basis of phenotypic variation in redpoll finches and found that variation in the redpoll phenotype is broadly controlled by a ~55-Mb chromosomal inversion.
Journal ArticleDOI
Repeated genetic adaptation to altitude in two tropical butterflies
Gabriela Montejo-Kovacevich,Joana I. Meier,Caroline Bacquet,Ian A. Warren,Yingguang Frank Chan,Marek Kucka,Camilo Salazar,Nicol Rueda-M,Stephen H. Montgomery,W. Owen McMillan,Krzysztof M. Kozak,Nicola J. Nadeau,Simon H. Martin,Chris D. Jiggins +13 more
TL;DR: In this article , the authors study adaptation to altitude in two tropical butterflies, Heliconius erato and H. melpomene , which have repeatedly and independently adapted to montane habitats on either side of the Andes.
References
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