Species_diagnostic_Suppl_table

SNP calls for all samples. C: homozygous O. clarki diagnostic; M: homozygous O. mykiss diagnostic; H: heterozygote; NC: no call; nr: assay not run or failed over entire Fluidigm plate

Genotypic data for the ten validation populations of coho salmon

Genotypes for 91 novel SNPs from ten populations of coho salmon from the West Coast of North America in standard GENEPOP format (two-digit). Data were generated using TaqMan assays (Applied Biosystems) and a Fluidigm EP1

Chinook salmon SNP baseline 2014

Included here are baseline genotypes at 95 SNPs (species diagnostic marker has been excluded) for 7984 Chinook salmon from 68 distinct populations, ranging from California to Alaska. Genotypes are also included for a single sample (n=47) of California coho salmon. Data were collected on a Fluidigm EP1 platform using 96.96 Dynamic Arrays. The archive contains three files: 1) 2010_Baseline_SNPset.txt is the genotype data in gsi_sim format (very similar to GENEPOP) with a header indicating the number of samples and loci, a list of assay names, population blocks denoted with "POP", and tab-delimited genotypes with one allele per column; 2) ReportingUnits_SNPset_2010.txt indicates which populations are included in each reporting unit; 3) SNP_names.txt is simply a list of assay names. In order to these data with the software gsi_sim, all three files should be present in the Baseline directory

SNP genotypes Russian River 2007-2011

Two column format SNP genotypes from two hatcheries (WSH and CVFF) in the Russian River

Russian River 2007-2011 SNPPITinput

Russian River 2007-2011 SNPPITinpu

Data Archiving- Genotypes

Genotypes from microsatellite and Single Nucleotide Polymorphism loci from all populations and specie

Genetic Structure of Pacific Trout at the Extreme Southern End of Their Native Range

<div><p>Salmonid fishes are cold water piscivores with a native distribution spanning nearly the entire temperate and subarctic northern hemisphere. Trout in the genus <i>Oncorhynchus</i> are the most widespread salmonid fishes and are among the most important fish species in the world, due to their extensive use in aquaculture and valuable fisheries. Trout that inhabit northwestern Mexico are the southernmost native salmonid populations in the world, and the least studied in North America. They are unfortunately also facing threats to their continued existence. Previous work has described one endemic species, the Mexican golden trout (<i>O</i>. <i>chrysogaster</i>), and one endemic subspecies, Nelson’s trout (<i>O</i>. <i>mykiss nelsoni</i>), in Mexico, but previous work indicated that there is vastly more biodiversity in this group than formally described. Here we conducted a comprehensive genetic analysis of this important group of fishes using novel genetic markers and techniques to elucidate the biodiversity of trout inhabiting northwestern Mexico, examine genetic population structure of Mexican trout and their relationships to other species of Pacific trout, and measure introgression from non-native hatchery rainbow trout. We confirmed substantial genetic diversity and extremely strong genetic differentiation present in the Mexican trout complex, not only between basins but also between some locations within basins, with at least four species-level taxa present. We also revealed significant divergence between Mexican trout and other trout species and found that introgression from non-native rainbow trout is present but limited, and that the genetic integrity of native trout is still maintained in most locations. This information will help to guide effective conservation strategies for this important group of fishes.</p></div

STRUCTURE analysis.

<p>Estimated membership fraction (represented by color proportions) of 1,932 individual fish from 18 <i>O</i>. <i>mykiss</i> populations, 42 trout populations from northwestern Mexico, one <i>O</i>. <i>gilae</i> and one <i>O</i>. <i>apache</i> population, five <i>O</i>. <i>clarkii</i> subspecies, and five Mexican and four U.S. hatchery rainbow trout stocks, using data from 18 microsatellites and 93 SNPs. Horizontal plots represent individual ancestry estimates. Each thin, colored, vertical line represents one individual. Vertical black lines separate collection localities. A summary of the 20 runs for each <i>K</i> value (<i>K</i> = 2–7) is shown. The right column indicates the number of observations for that general pattern. NSMO: Northern Sierra Madre Occidental; SSMO: Southern Sierra Madre Occidental. Numbers on top represent the “Population number” in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141775#pone.0141775.s003" target="_blank">S1 Table</a>.</p

Data Archiving- Metadata

Metadata associated to the genotypes data fil

Unrooted neighbor-joining dendrograms.

<p>a) using data from both 12 microsatellites and 85 SNPs combined and b) using data from 12 microsatellite markers. The dendrogram was constructed with pairwise chord distances and bootstrap values are from 1,000 distance matrices constructed from bootstrap samples of the data from 18 <i>O</i>. <i>mykiss</i>, 19 NSMO, 10 <i>O</i>. <i>chrysogaster</i>, and 12 SSMO natural-origin populations, four <i>O</i>. <i>clarkii</i> subspecies, and five Mexican and four U.S. hatchery stocks. Bootstrap support > 50% percent is indicated for Mexican trout groupings (for <i>O</i>. <i>mykiss</i> see Garza <i>et al</i>. 2014). DPS affiliations of California <i>O</i>. <i>mykiss</i> populations (creeks) are highlighted in colors. Mexican natural-origin populations are indicated with branches and names colored.</p