New publication: Supergene origin and maintenance in Atlantic cod

By Michael Matschiner, Julia Maria Isis Barth, Ole Kristian Tørresen, Bastiaan Star, Helle Tessand Baalsrud, Marine Servane Ono Brieuc, Christophe Pampoulie, Ian Bradbury, Kjetill Sigurd Jakobsen & Sissel Jentoft in Nature Ecology and Evolution


See also the commentary "Evolution of cod supergenes" in News & Views by Anna Tigano.


Supergenes are sets of genes that are inherited as a single marker and encode complex phenotypes through their joint action. They are identified in an increasing number of organisms, yet their origins and evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been identified and linked to migratory lifestyle and environmental adaptations. Here we investigate the origin and maintenance of these four supergenes through analysis of whole-genome-sequencing data, including a new long-read-based genome assembly for a non-migratory Atlantic cod individual. We corroborate the finding that chromosomal inversions underlie all four supergenes, and we show that they originated at different times between 0.40 and 1.66 million years ago. We reveal gene flux between supergene haplotypes where migratory and stationary Atlantic cod co-occur and conclude that this gene flux is driven by gene conversion, on the basis of an increase in GC content in exchanged sites. Additionally, we find evidence for double crossover between supergene haplotypes, leading to the exchange of an ~275 kilobase fragment with genes potentially involved in adaptation to low salinity in the Baltic Sea. Our results suggest that supergenes can be maintained over long timescales in the same way as hybridizing species, through the selective purging of introduced genetic variation.

Publication details

Nature Ecology and Evolution
Published: 17 February 2022
DOI: s41559-022-01661-x
Publication webpage.

Authors with CEES affiliation

Michael Matschiner (webpage at, Ole Kristian Tørresen, Bastiaan Star, Helle Tessand Baalsrud, Marine Servane Ono Brieuc (webpage at, Kjetill Sigurd Jakobsen & Sissel Jentoft

Published Feb. 25, 2022 10:34 AM - Last modified Feb. 25, 2022 10:41 AM