Academic journal article Genetics

Intraspecific Phylogeographic Genomics from Multiple Complete mtDNA Genomes in Atlantic Cod (Gadus Morhua): Origins of the "Codmother," Transatlantic Vicariance and Midglacial Population Expansion

Academic journal article Genetics

Intraspecific Phylogeographic Genomics from Multiple Complete mtDNA Genomes in Atlantic Cod (Gadus Morhua): Origins of the "Codmother," Transatlantic Vicariance and Midglacial Population Expansion

Article excerpt

ABSTRACT

On the basis of multiple complete mitochondrial DNA genome sequences, we describe the temporal phylogeography of Atlantic cod (Gadus morhua), a lineage that has undergone a complex pattern of vicariant evolution, postglacial demographic shifts, and historic sharp population declines due to fishing and/or environmental shifts. Each of 32 fish from four spawning aggregations from the northwest Atlantic and Norway has a unique mtDNA sequence, which differs by 6-60 substitutions. Phylogenetic analysis identifies six major haplogroups that range in age from 37 to 75 KYA. The widespread haplotype identified by previous single-locus analyses at the center of a "star phylogeny" is shown to be a paraphyletic assemblage of genome lineages. The coalescent that includes all cod occurs 162 KYA. The most basal clade comprises two fish from the western Atlantic. The most recent superclade that includes all fish examined from Norway, and which includes 84% of all fish examined, dates to 128 KYA at the Sangamon/Würm interglacial, when ocean depths on continental shelves would have favored transcontinental movement. The pairwise mismatch distribution dates population expansion of this superclade to the middle of the Wisconsinan/Weichsel glaciation 59 KYA, rather than to a postglacial emergence from a marine refugium 12 KYA, or to more recent historic events. We discuss alternative scenarios for the expansion and distribution of the descendants of the "codmother" in the North Atlantic. Mitochondrial phylogenomic analyses generate highly resolved trees that enable fine-scale tests of temporal hypotheses with an accuracy not possible with single-locus methods.

EVOLUTIONARY analysis of mitochondrial DNA (mtDNA)hasgraduatedfromRFLPmapping(Brown et al. 1979; Wilson et al. 1985) to direct sequencing of single-loci (Kocher et al. 1989; Carr and Marshall 1991) to comparisons of complete genome sequences among species (Horai et al. 1995; Inoue et al. 2001; Coulson et al. 2006). Recent intraspecific analyses of complete human mtDNA genomes have supported the "mitochondrial Eve" hypothesis and clarified the historical emergence of her daughters "out of Africa" (Ingman et al. 2000; Torroni et al. 2006).

Atlantic cod (Gadus morhua L. 1758) is another lineage that has undergone a complex pattern of phylogeographic evolution, including vicariant events and population fluctuations attributable to long-term geological events, short-term ecological history, and contemporary anthropogenic fishing and/or environmental shifts (Myers et al. 1995; Hutchings 1996; Rose et al. 2001; Rose 2004, 2007; Coulson et al. 2006; International Council for the Exploration of the Sea 2006).

We have shown (Carr et al. 1999; Coulson et al. 2006) that the basal gadine genera are endemic to the northeast Atlantic (Melanogrammus and Merluccius). The sister genera to Gadus L. 1758 are the Polar basin Arctogadus and Boreogadus. The genus Gadus comprises three nominal species, including Atlantic cod (G. morhua), its sister species walleye pollock [G. (= Theragra) chalcogrammus], and Pacific cod (G. macrocephalus) (cf. Figure 4 of Coulson et al. 2006). The latter two species are found on both Pacific coasts and north of the Bering Strait. Greenland cod, found in the Davis Strait west of Greenland and previously considered a separate species G. ogac, is a subspecies of G. macrocephalus and apparently represents a tertiary invasion of the western Atlantic via the Canadian arctic archipelago. We presented a model in which Gadus is of North Atlantic origin, and the two Pacific species derive from separate but simultaneous invaders of the Pacific through the Bering Strait 3.5 MYA. Pogson and Mesa (2004) suggested instead that the genus was of Pacific origin, with morhua reentering the North Atlantic via a polar route. Although this latter model requires only a single event and Pacific to Atlantic vicariance is more common (Vermeij 1991), we suggested that it is difficult to understand how speciation of macrocephalus and chalcogrammus and their current distribution could have arisen in sympatry. …

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