Sequences for loci in Genepop file

This fasta file contains the consensus sequences for all of the loci in the genepop file. The locus name in this file corresponds to locus names in the genepop file, which also gives the position of the SNP

Individual barcodes of RAD sequences used in Stacks

This text file is a combination of the barcodes file and the "population map" file for the program stacks. Each line consists of (1) the individual barcode, (2) the sample ID, and (3) a numeric designation for the sampling site (putative population) to which the individuals belongs. Copying the first two columns into a separate text file will provide the barcodes.txt file used in stacks to demultiplex raw data. Copying the second two columns into a separate text file will provide the population map file used in the stacks function `populations` to call genotypes

Genepop file of RAD SNP genotypes

Genepop file of RAD SNP genotype

Pacific cod scripts

Scripts for Stacks, Perl and R. Details within the fil

Role of oceanography in shaping the genetic structure in the North Pacific hake <i>Merluccius productus</i>

<div><p>Determining the relative influence of biotic and abiotic factors on genetic connectivity among populations remains a major challenge in evolutionary biology and in the management and conservation of species. North Pacific hake (<i>Merluccius productus</i>) inhabits upwelling regions in the California Current ecosystem from the Gulf of California to the Gulf of Alaska. In this study, we examined mitochondrial DNA (mtDNA) and microsatellite variation to estimate levels of genetic differentiation of <i>M</i>. <i>productus</i> in relation to the role of oceanographic features as potential barriers to gene flow. Samples were obtained from nine sites spanning a large part of the geographic range of the species, from Puget Sound, Washington to Costa Rica. The microsatellite results revealed three genetically discrete populations: one spanning the eastern Pacific coast, and two apparently resident populations circumscribed to the Puget Sound and the northern Gulf of California (F_ST = 0.032, p = 0.036). Cytochrome b sequence data indicated that isolation between the Puget Sound and northern Gulf of California populations from the coastal Pacific were recent phenomena (18.5 kyr for Puget Sound and 40 kyr for the northern Gulf of California). Oceanographic data obtained from the Gulf of California support the hypothesis that permanent fronts within the region, and strong gradients at the entrance to the Gulf of California act as barriers to gene flow. A seascape genetics approach found significant genetic–environment associations, where the daytime sea surface temperature and chlorophyll concentrations were the best predictive variables for the observed genetic differentiation. Considering the potential causes of genetic isolation among the three populations, e.g. spawning areas in different latitudes associated with upwelling processes, oceanographic barriers, asymmetric migration and specialized diet, oceanographic barriers appear to be a likely mechanism restricting gene flow.</p></div

Relaxed Bayesian topology with the estimated divergence times based on CYTB sequences for populations of <i>Merluccius productus</i> obtained with BEAST [65].

<p>Numbers at nodes indicate divergence time in millions of years. Blue bars correspond to the 95% highest posterior density (HPD) intervals. For clarity, samples from the NGC, PC and PS were collapsed into triangles.</p

Hierarchical analysis of molecular variance (AMOVA) of genetic variation of <i>Merluccius productus</i> for mitochondrial DNA (mtDNA) and microsatellite loci (M).

<p>Hierarchical analysis of molecular variance (AMOVA) of genetic variation of <i>Merluccius productus</i> for mitochondrial DNA (mtDNA) and microsatellite loci (M).</p

Satellite and hydrographic data.

<p>Climatology of February of the Gulf of California (2002–2010) from the MODIS-Aqua satellites: sea surface temperature (SST) °C. Midriff archipelago region (MAR), northern Gulf of California (NGC), south of the Gulf of California (SGC), and entrance of Gulf of California (EGC).</p

Pairwise F_<i>ST</i> values (below diagonal) and ϕ_<i>ST</i> (above diagonal) for <i>Merluccius productus</i>.

<p>Location abbreviations as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194646#pone.0194646.t001" target="_blank">Table 1</a>.</p

Role of oceanography in shaping the genetic structure in the North Pacific hake <i>Merluccius productus</i> - Fig 4

<p><b>Genetic barriers detected using pairwise population differentiation indices for <i>Merluccius productus</i>: a) mtDNA and b) microsatellite data.</b> Red lines indicate genetic barriers. Voronoï tessellation shown in blue and the corresponding Delaunay triangulation of samples in green. Numbers in parentheses indicate bootstrap percentages. Abbreviations are as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194646#pone.0194646.t001" target="_blank">Table 1</a>.</p