DOI: 10.5061/dryad.q31f8
title: Data from: Phylogeography of amphi-boreal fish: tracing the history of the Pacific herring Clupea pallasii in North-East European seas

description: Background: The relationships between North Atlantic and North Pacific
 faunas through times have been controlled by the variation of hydrographic
 circumstances in the intervening Arctic Ocean and Bering Strait. We
 address the history of trans-Arctic connections in a clade of amphi-boreal
 pelagic fishes using genealogical information from mitochondrial DNA
 sequence data. The Pacific and Atlantic herrings (Clupea pallasii and C.
 harengus) have basically vicarious distributions in the two oceans since
 pre-Pleistocene times. However, remote populations of C. pallasii are also
 present in the border waters of the North-East Atlantic in Europe. These
 populations show considerable regional and life history differentiation
 and have been recognized in subspecies classification. The chronology of
 the inter-oceanic invasions and genetic basis of the phenotypic
 structuring however remain unclear. Results: The Atlantic and Pacific
 herrings both feature high mtDNA diversities (large long-term population
 sizes) in their native basins, but an ocean-wide homogeneity of C.
 harengus is contrasted by deep east-west Pacific subdivision within
 Pacific C. pallasii. The outpost populations of C. pallasii in NE Europe
 are identified as members of the western Pacific C. pallasii clade, with
 some retained inter-oceanic haplotype sharing. They have lost diversity in
 colonization bottlenecks, but have also thereafter accumulated abundant
 new variation. The data delineate three phylogeographic groups within the
 European C. pallasii: herring from the inner White Sea; herring from the
 Mezen and Chesha Bays; and a strongly bottlenecked peripheral population
 in Balsfjord of the Norwegian Sea. Conclusions: The NE European outposts
 of C. pallasii are judged to be early post-glacial colonists from the NW
 Pacific. A strong regional substructure has evolved since that time, in
 contrast to the apparent broad-scale uniformity maintained by herrings in
 their native basins. The structure only partly matches the previous
 biological concepts based on seasonal breeding stocks or geographical
 subspecies designations. The trans-Arctic herring phylogeography is
 notably similar to those of the amphi-boreal mollusk taxa Macoma and
 Mytilus, suggesting similar histories of inter-oceanic connections. We
 also considered the time dependency of molecular rates, critical for
 interpreting timing of relatively recent biogeographical events, by
 comparing the estimates from coding and non-coding mitochondrial regions
 of presumably different mutation dynamics.
description: SampleID_listList of individual samples with sampling locations and Genbank accession numbers for cytochrome-b and control region.Arlq_cytb_populationsArlequin input files with population grouping for cytochrome-b data.Arlq_cr_populationsArlequin input files with population grouping for control region data.Arlq_trans_Arctic_populations_concatArlequin input files with population grouping for concatenated data.IM_CYTB_NWP_MEZCHEIM input file for comparing NW Pacific lineage with Mezen-Chesha populations.IM_CYTB_NWP_WSIIM input file for comparing NW Pacific lineage with White Sea (and Pechora Indiga) populations.IM_CYTB_NWP_BLSIM input file for comparing NW Pacific lineage with Balsfjord population.Distance matrix for the MDS ordinationPairwise interpopulation ΦST distance matrix of trans-Arctic lineage populations for MDS ordination.