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.
Highlights
An understanding of population genetic structure, in species threatened with extinction, is critical to conservation and preservation of biodiversity
We present here a mitogenomic analysis of population genetic structure in Atlantic cod
The Flemish Cap sample does not differ significantly from any Northwest Atlantic or trans-Laurentian population (ΦST = .000–.023, p > .15; Table 3a). These data suggest that the Flemish Cap likely either did not act as a refugium for Atlantic cod, or that any refugial distinctiveness has since been eliminated by gene flow
Summary
An understanding of population genetic structure, in species threatened with extinction, is critical to conservation and preservation of biodiversity. Atlantic cod previously supported one of the most important commercial fisheries in the world (Halliday & Pinhorn, 1996) Heavy fishing in the latter half of the 20th century led to severe population declines, first in Europe and in North America. Based on distinctions in meristic analysis of vertebral counts (Templeman, 1979, 1981), cod in the waters off Newfoundland and Labrador have traditionally been managed as five stock divisions designated by the North Atlantic Fisheries Organization (NAFO; see Table 1). We expand the data to a total of 153 mitogenomes by inclusion of 10 new populations from north and south of the Laurentian Channel in the Northwest Atlantic, the Baltic Sea, and a landlocked Arctic fjord at Lake Qasigialiminiq, Baffin Island (see Table S1)
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