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Genome architecture enables local adaptation of Atlantic cod despite high connectivity

Journal article
Authors Julia M.I. Barth
Paul R. Berg
Per R. Jonsson
Sara Bonanomi
Hanna Corell
Jakob Hemmer-Hansen
Kjetill S. Jakobsen
Kerstin Johannesson
Per Erik Jorde
Halvor Knutsen
Per-Olav Moksnes
Bastiaan Star
Nils Chr Stenseth
Henrik Svedäng
Sissel Jentoft
Carl André
Published in Molecular Ecology
Volume 26
Issue 17
Pages 4452–4466
ISSN 0962-1083
Publication year 2017
Published at Department of marine sciences
Pages 4452–4466
Language en
Keywords Chromosomal inversion, Ecological adaptation, Gadus morhua, Gene flow, Population divergence
Subject categories Evolutionary Biology, Marine ecology, Genetics, Biological Sciences


Adaptation to local conditions is a fundamental process in evolution; however, mechanisms maintaining local adaptation despite high gene flow are still poorly understood. Marine ecosystems provide a wide array of diverse habitats that frequently promote ecological adaptation even in species characterized by strong levels of gene flow. As one example, populations of the marine fish Atlantic cod (Gadus morhua) are highly connected due to immense dispersal capabilities but nevertheless show local adaptation in several key traits. By combining population genomic analyses based on 12K single nucleotide polymorphisms with larval dispersal patterns inferred using a biophysical ocean model, we show that Atlantic cod individuals residing in sheltered estuarine habitats of Scandinavian fjords mainly belong to offshore oceanic populations with considerable connectivity between these diverse ecosystems. Nevertheless, we also find evidence for discrete fjord populations that are genetically differentiated from offshore populations, indicative of local adaptation, the degree of which appears to be influenced by connectivity. Analyses of the genomic architecture reveal a significant overrepresentation of a large ~5 Mb chromosomal rearrangement in fjord cod, previously proposed to comprise genes critical for the survival at low salinities. This suggests that despite considerable connectivity with offshore populations, local adaptation to fjord environments may be enabled by suppression of recombination in the rearranged region. Our study provides new insights into the potential of local adaptation in high gene flow species within fine geographical scales and highlights the importance of genome architecture in analyses of ecological adaptation.

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