The mitogenomic structure of Atlantic cod investigated using ancient DNA

Atlantic cod is an economically important species distributed in the North Atlantic Ocean and adjacent seas. Although this species has a fundamental ecological role in marine ecosystems, continuous large-scale fishing activities have led to the decline and collapse of several populations during the last century. The genomic consequences of such declines, however, remain unclear. Here, we compare 48 ancient Atlantic cod mitogenomes dated up to 6500 BC to 496 modern mitogenomes sampled across the North Atlantic. We investigate whether any population bottlenecks or loss of mitogenomic variation can be associated with historical or recent demographic fluctuations. Our results reveal a high genetic mtDNA diversity with a low genetic spatial structure across large geographical scales. Furthermore, our temporal comparisons did not detect a significant loss of mitogenomic variation during the last millennia. Instead, mitogenomic variation in Atlantic cod reflects past demographic processes, such as population expansions driven by the interglacial and warming periods experienced during the last glaciations, rather than contemporary fluctuations in stock abundance. Our results indicate that recent anthropogenic impacts such as fisheries, have had little impact on ancient mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. Finally, our observations show that conservation management measures aimed towards demographic recovery will not be constrained by irreversible loss of mitogenomic variation.