Abstract
Atlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic adaptation due to minute genetic differentiation at selectively neutral loci. Here, we report hundreds of loci underlying ecological adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying ecological adaptation in herring deviates from expectation under a classical infinitesimal model for complex traits because of large shifts in allele frequencies at hundreds of loci under selection.
Highlights
Atlantic herring (Clupea harengus) constitutes the basis for one of the world’s most important commercial fisheries (Food and Agriculture Organization of the United Nations Statistics Division, 2013) and has been a valuable food resource throughout human history in North Europe
It is likely that genetic draft (Walsh and Lynch, 2018) that is purging of neutral genetic variation linked to polymorphisms under positive or negative selection, contributes to restricting nucleotide diversity in the herring
Whole-genome sequencing has completely changed the picture, we find striking genetic differentiation but at a limited number of loci (Figures 3– 5)
Summary
Atlantic herring (Clupea harengus) constitutes the basis for one of the world’s most important commercial fisheries (Food and Agriculture Organization of the United Nations Statistics Division, 2013) and has been a valuable food resource throughout human history in North Europe. It is one of the most abundant vertebrates on earth with a total estimated breeding stock of one trillion individuals (Feng et al, 2017).
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