title: Multiple ice-age refugia in Pacific cod, Gadus macrocephalus.
abstract: Pleistocene ice-ages greatly influenced the historical abundances of Pacific cod, Gadus macrocephalus, in the North Pacific and its marginal seas. We surveyed genetic variation at 11 microsatellite loci and mitochondrial (mt) DNA in samples from twelve locations from the Sea of Japan to Washington State. Both microsatellite (mean H = 0.868) and mtDNA haplotype (mean h = 0.958) diversities were large and did not show any geographical trends. Genetic differentiation between samples was significantly correlated with geographical distance between samples for both microsatellites (FST = 0.028, r(2) = 0.33) and mtDNA (FST = 0.027, r(2) = 0.18). Both marker classes showed a strong genetic discontinuity between northwestern and northeastern Pacific populations that likely represents groups previously isolated during glaciations that are now in secondary contact. Significant differences appeared between samples from the Sea of Japan and Okhotsk Sea that may reflect ice-age isolations in the northwest Pacific. In the northeast Pacific, a microsatellite and mtDNA partition was detected between coastal and Georgia Basin populations. The presence of two major coastal mtDNA lineages on either side of the Pacific Ocean basin implies at least two ice-age refugia and separate postglacial population expansions facilitated by different glacial histories. Northward expansions into the Gulf of Alaska were possible 14-15 kyr ago, but deglaciation and colonization of the Georgia Basin probably occurred somewhat later. Population expansions were evident in mtDNA mismatch distributions and in Bayesian skyline plots of the three major lineages, but the start of expansions appeared to pre-date the last glacial maximum.
authors.affiliation: NOAA Fisheries, Alaska Fisheries Science Center, 7600 Sand Point Way NE, Seattle, WA 98115, USASchool of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105, USADepartment of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USAAlaska Department of Fish and Game, 333 Raspberry Road, Anchorage, AK 99518, USA.
authors.forename: Michael F
authors.initials: MF
authors.lastname: Canino
authors.forename: Ingrid B
authors.initials: IB
authors.lastname: Spies
authors.forename: Kathryn M
authors.initials: KM
authors.lastname: Cunningham
authors.forename: Lorenz
authors.initials: L
authors.lastname: Hauser
authors.forename: W Stewart
authors.initials: WS
authors.lastname: Grant
mesh_terms: D000818:Animals; D005075:Biological Evolution; D004272:DNA, Mitochondrial / Q000235:genetics; D048388:Gadiformes / Q000235:genetics*; D014644:Genetic Variation; D005828:Genetics, Population; D006239:Haplotypes; D018895:Microsatellite Repeats; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010140:Pacific Ocean; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial