Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

Abstract

The historical phylogeography, biogeography, and ecology of Atlantic cod (Gadus morhua) have been impacted by cyclic Pleistocene glaciations, where drops in sea temperatures led to sequestering of water in ice sheets, emergence of continental shelves, and changes to ocean currents. High‐resolution, whole‐genome mitogenomic phylogeography can help to elucidate this history. We identified eight major haplogroups among 153 fish from 14 populations by Bayesian, parsimony, and distance methods, including one that extends the species coalescent back to ca. 330 kya. Fish from the Barents and Baltic Seas tend to occur in basal haplogroups versus more recent distribution of fish in the Northwest Atlantic. There was significant differentiation in the majority of trans‐Atlantic comparisons (ΦST = .029–.180), but little or none in pairwise comparisons within the Northwest Atlantic of individual populations (ΦST = .000–.060) or defined management stocks (ΦST = .000–.023). Monte Carlo randomization tests of population phylogeography showed significantly nonrandom trans‐Atlantic phylogeography versus absence of such structure within various partitions of trans‐Laurentian, Northern cod (NAFO 2J3KL) and other management stocks, and Flemish Cap populations. A landlocked meromictic fjord on Baffin Island comprised multiple identical or near‐identical mitogenomes in two major polyphyletic clades, and was significantly differentiated from all other populations (ΦST = .153–.340). The phylogeography supports a hypothesis of an eastern origin of genetic diversity ca. 200–250 kya, rapid expansion of a western superhaplogroup comprising four haplogroups ca. 150 kya, and recent postglacial founder populations.

Range‐wide genomic data synthesis reveals transatlantic vicariance and secondary contact in Atlantic cod

“…The resident populations occurring in Ogac and Tariujarusiq were established 5 to 8 kya following a period of comparatively warm climate, rising sea levels, and isostatic rebound that enabled cod to inhabit the then fully marine sites (Hardie, Gillett, & Hutchings, ). Westward colonization following glacial retreat supports the hypothesis of at least some colonization from Europe (Lait et al, ; Therkildsen et al, ). However, our results concerning these populations were inconclusive.…”

“…Where previous studies supporting transatlantic vicariance may have been confounded by the possibility of IBD due to large geographic distances between samples (Pampoulie, Stefánsson, Jörundsdóttir, Danilowicz, & Danielsdottir, ; Pogson et al, ), our higher resolution of sampling sites suggests greater differentiation between North American and European populations than within those regions, even when shelf sea distance is controlled for. Similar patterns are observed by Lait et al (), who, using analysis of the mitogenome, observe significant differentiation between many European and North American samples and an absence of population structure or IBD within regions. The role of glacial refugia in contemporary population structure is supported by East–West structure in other North Atlantic shelf species.…”

“…One of the most remarkable examples of putative secondary contact is the Flemish Cap, a shallow (125–700 m) remote bank off the easternmost tip of the Newfoundland Shelf (Stein, ). The link between the Flemish Cap and European populations is evident from Bentzen, Taggart, Ruzzante, and Cook () and Bradbury et al (), who find affiliations with several East Atlantic populations, although purely North American haplotypes are found using the mitochondrial genome (Lait et al, ). Using DAPC and structure on a wider range of European data, we find that the Flemish Cap population is dominated by a Greenlandic cluster found at no other North American locations, implying that the Flemish Cap population represents an offshoot of Greenlandic ancestry in North America.…”

“…Strong European influence has also previously been found among cod in meromictic lakes on Baffin Island, including Lake Ogac and Lake Tariujarusiq (Bradbury et al, ; Carr & Marshall, ; Lait et al, ). The resident populations occurring in Ogac and Tariujarusiq were established 5 to 8 kya following a period of comparatively warm climate, rising sea levels, and isostatic rebound that enabled cod to inhabit the then fully marine sites (Hardie, Gillett, & Hutchings, ).…”

An environmental (pre)history of European fishing: past and future archaeological contributions to sustainable fisheries

“…For example, shifts in the genetic structure of G. morhua in Icelandic waters during the 15th and 16th centuries CE have been attributed to climatic cooling (Ólafsdóttir et al, ). The power of this kind of analysis will only increase as temperature‐selective single nucleotide polymorphisms (SNP) and other genomic signatures of cold‐water ecotypes continue to be identified in modern fish populations (Bradbury et al, ; Lait et al, ; Star et al, ). Changing salinities may also be traceable based on analysis of adaptive genomic architecture (Barth et al, ; Berg et al, ).…”