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

Microsatellite genotypes

Genotypes of 22 microsatellites from 837 northern elephant seals

Russian River 2007-2011 SNPPITinput

Russian River 2007-2011 SNPPITinpu

Genotype data for Chinook salmon from California and Oregon

The file contains genotype data at 117 SNP loci for 337 Chinook salmon from the following Chinook salmon populations: Feather River spring-run (FRHsp, N=94); Butte Creek spring-run (ButteSp, N=54); Central Valley fall-run (MokBattle, N=94); Klamath/Trinity River fall-run (N=48); Lower Columbia River spring-run (KalCow, N=47). Data is in a text file in the Genepop 2-digit format

SNP genotypes Russian River 2007-2011

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

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

Data Archiving- Metadata

Metadata associated to the genotypes data fil

Principal components analysis of allele frequencies.

<p>Each plot includes populations from four hatchery rainbow trout stocks raised in California (Coleman, Kamloops, Eagle Lake, and Mount Shasta) and a) all Río Yaqui-Río Bavispe and Río Casas Grandes populations, and samples from “Truchas La Presita” and “Arroyo Yenquin” hatcheries; b) all Río Fuerte populations, samples from an abandoned hatchery located on the Río Fuerte-Arroyo Aparique, and samples from Centro Acuícola Guachochi; c) all Río San Lorenzo populations and samples from “Piscicultura Vencedores” hatchery; d) populations from the three southernmost basins, ríos Presidio, Baluarte, and Acaponeta. The difference in color (red, blue and green) between clusters indicates divergence using the first three principal components.</p

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