Map of the proportions of identified rockfish samples from six assemblages from four archaeological sites in the Broken Group Island archipelago.

<p>Map of the proportions of identified rockfish samples from six assemblages from four archaeological sites in the Broken Group Island archipelago.</p

Species accumulation curve for all rockfish species analyzed.

<p>Species accumulation curve for all rockfish species analyzed.</p

Overview of study area from which rockfish bones were recovered and analyzed.

<p>Overview of study area from which rockfish bones were recovered and analyzed.</p

Map of the proportions of rockfish ecotypes identified at each archaeological site.

<p>Mid-water schooling species include black, blue, widow, and yellowtail rockfish. Demersal solitary species include canary, china, copper, quillback, redstripe, silvergray, tiger, and yelloweye rockfish [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192716#pone.0192716.ref001" target="_blank">1</a>].</p

Multidimensional scaling plot of <i>Φ_ST</i> between samples.

<p>A) D-loop (<i>r²</i> = 0.999) and B) cytb (<i>r²</i> = 0.985). YB is Yakutat Bay (southeast Alaska), KI is Knight Inlet (northern Georgia Strait), PI is Portage Inlet (southeastern Georgia Strait), NO is Nootka Sound (west coast of Vancouver Island), AK is Southeast Alaska, BI is Burrard Inlet, GS is northern Georgia Strait, VI is West Coast of Vancouver Island.</p

Median-joining network displaying ancient and modern D-loop haplotypes.

<p>Median-joining network displaying the relationships between the ancient D-loop haplotypes and modern herring populations from different geographical regions (modern datasets are those listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051122#pone.0051122.s005" target="_blank">Table S2</a> from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051122#pone.0051122-Liu1" target="_blank">[19]</a>). The majority of the ancient samples cluster with modern herring in the two lineages from the northeast Pacific (lineages B and C). Lineage A is distinguished by 3 polymorphisms (15682C, 15841C, 15838G, coordinates based on Genbank accession NC009578); Lineages B and C are distinguished by three polymorphisms: lineage B resembles NC009578, while lineage C is defined by 15670C, 15823G, 15831T.</p

Plots of genetic diversity.

<p>Graphs displaying genetic diversity (nucleotide diversity and haplotype diversity) of samples from the two major phylogeographic groups described in Liu et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051122#pone.0051122-Liu1" target="_blank">[19]</a>, and the ancient DNA samples from British Columbia and Alaska, for A) D-loop (above) and B) cytb (below). Note the lower diversity of the northwest Pacific group and the close clustering of ancient samples with the modern samples from the northeast Pacific. The one outlying sample with low D-loop haplotype diversity is from Portage Inlet (southern Georgia Strait), which shows similar cytb diversity to the other samples.</p

Power to detect significant genetic differentiation between two populations with a sample size of 48 individuals each with different marker sets.

<p>We compared data from 12 empirical microsatellites <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051122#pone.0051122-Mitchell1" target="_blank">[21]</a>, empirical mtDNA haplotypes from the present study and three and one simulated biallelic SNP loci (3 SNPs, 1 SNP) with even allele frequencies. For comparison, the empirical microsatellite <i>F_ST</i> values found in Puget Sound herring (PS-MS, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051122#pone.0051122-Mitchell1" target="_blank">[21]</a>) and the empirical <i>F_ST</i> of an outlier SNP found between Prince William Sound and Kodiak Island (PWS/KI SNP, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051122#pone.0051122-Roberts1" target="_blank">[64]</a>) are shown.</p

Results of a hierarchical AMOVA.

<p>Results of hierarchical AMOVA on each mtDNA region, with ancient and modern samples as the two groups. Modern samples <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0051122#pone.0051122-Liu1" target="_blank">[19]</a> included were Portage Inlet, Knight Inlet, Yakutat Bay for cytb, and Portage Inlet, Knight Inlet, Nootka Sound and Yakutat Bay for D-loop. Portage Inlet (PI) was an outlier for all analyses, so AMOVAs are presented with and without that sample.</p