Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish

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http://hdl.handle.net/10138/313848

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Kess , T , Bentzen , P , Lehnert , S J , Sylvester , E V A , Lien , S , Kent , M P , Sinclair-Waters , M , Morris , C J , Wringe , B , Fairweather , R & Bradbury , I R 2020 , ' Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish ' , Ecology and Evolution , vol. 10 , no. 2 , pp. 638–653 . https://doi.org/10.1002/ece3.5828

Title: Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish
Author: Kess, Tony; Bentzen, Paul; Lehnert, Sarah J.; Sylvester, Emma V.A.; Lien, Sigbjørn; Kent, Matthew P.; Sinclair-Waters, Marion; Morris, Corey J.; Wringe, Brendan; Fairweather, Robert; Bradbury, Ian R.
Contributor: University of Helsinki, Evolution, Conservation, and Genomics
Date: 2020-01-11
Language: eng
Number of pages: 16
Belongs to series: Ecology and Evolution
ISSN: 2045-7758
URI: http://hdl.handle.net/10138/313848
Abstract: Genomic architecture and standing variation can play a key role in ecological adaptation and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behavior in regional analyses. However, the degree of parallelism, the extent of independent inheritance, and functional distinctiveness of these rearrangements remain poorly understood. Here, we use a 12K single nucleotide polymorphism (SNP) array to demonstrate extensive individual variation in rearrangement genotype within populations across the species range, suggesting that local adaptation to fine-scale ecological variation is enabled by rearrangements with independent inheritance. Our results demonstrate significant association of rearrangements with migration phenotype and environmental gradients across the species range. Individual rearrangements exhibit functional modularity, but also contain loci showing multiple environmental associations. Clustering in genetic distance trees and reduced differentiation within rearrangements across the species range are consistent with shared variation as a source of contemporary adaptive diversity in Atlantic cod. Conversely, we also find that haplotypes in the LG12 and LG1 rearranged region have diverged across the Atlantic, despite consistent environmental associations. Exchange of these structurally variable genomic regions, as well as local selective pressures, has likely facilitated individual diversity within Atlantic cod stocks. Our results highlight the importance of genomic architecture and standing variation in enabling fine-scale adaptation in marine species.
Subject: 1181 Ecology, evolutionary biology
Atlantic cod
environmental association
genomic architecture
marine
migration
parallel evolution
ATLANTIC COD ECOTYPES
LOCAL ADAPTATION
GENOMIC ARCHITECTURE
ADAPTIVE EVOLUTION
POPULATION-GENETICS
R PACKAGE
INVERSIONS
DIVERGENCE
SPECIATION
SELECTION
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