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

Tony Kess, Paul Bentzen, Sarah J. Lehnert, Emma V.A. Sylvester, Sigbjørn Lien, Matthew P. Kent, Marion Sinclair-Waters, Corey J. Morris, Brendan Wringe, Robert Fairweather, Ian R. Bradbury

Research output: Contribution to journalArticleScientificpeer-review

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.

Original languageEnglish
JournalEcology and Evolution
Volume10
Issue number2
Pages (from-to)638–653
Number of pages16
ISSN2045-7758
DOIs
Publication statusPublished - 11 Jan 2020
MoE publication typeA1 Journal article-refereed

Fields of Science

  • 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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