The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.

Martinez Barrio A, Lamichhaney S, Fan G, Rafati N, Pettersson M, Zhang H, Dainat J, Ekman D, Höppner M, Jern P, Martin M, Nystedt B, Liu X, Chen W, Liang X, Shi C, Fu Y, Ma K, Zhan X, Feng C, Gustafson U, Rubin CJ, Sällman Almén M, Blass M, Casini M, Folkvord A, Laikre L, Ryman N, Ming-Yuen Lee S, Xu X, Andersson L

Elife 5 (-) - [2016-05-03; online 2016-05-03]

Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.

Bioinformatics Compute and Storage [Service]

Bioinformatics Long-term Support WABI [Collaborative]

Bioinformatics Support and Infrastructure [Collaborative]

NGI Uppsala (SNP&SEQ Technology Platform) [Service]

QC bibliography QC xrefs

PubMed 27138043

DOI 10.7554/eLife.12081

Crossref 10.7554/eLife.12081

pmc PMC4854517

Dryad 10.5061/dryad.5r774 [Gene annotation and genetic variants]

GCA_000966335.1 [Genome assembly]

SRA SRP017094 [Population sequencing reads, set 1]

SRA SRP017095 [Population sequencing reads, set 2]

SRA SRP056617 [Population sequencing reads, set 3]