Data from: Discovery and characterization of single nucleotide polymorphisms in coho salmon, Oncorhynchus kisutch

Molecular population genetic analyses have become an integral part of ecological investigation and population monitoring for conservation and management. Microsatellites have been the molecular marker of choice for such applications over the last several decades, but single nucleotide polymorphism (SNP) markers are rapidly expanding beyond model organisms. Coho salmon (Oncorhynchus kisutch) is native to the north Pacific Ocean and its tributaries, where it is the focus of intensive fishery and conservation activities. As it is an anadromous species, coho salmon typically migrate across multiple jurisdictional boundaries, complicating management and requiring shared data collection methods. Here, we describe the discovery and validation of a suite of novel SNPs and associated genotyping assays which can be used in the genetic analyses of this species. These assays include 91 that are polymorphic in the species and one that discriminates it from a sister species, Chinook salmon. We demonstrate the utility of these SNPs for population assignment and phylogeographic analyses, and map them against the draft trout genome. The markers constitute a large majority of all SNP markers described for coho salmon and will enable both population- and pedigree-based analyses across the southern part of the species native range

Tree file for Supplemental Figure 1

NEXML tree file for the ten validation populations genotyped with the 91 SNP markers described in the paper

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

Data from: Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha

No description availabl

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

Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding

<div><p>Molecular analysis of environmental DNA (eDNA) can be used to assess vertebrate biodiversity in aquatic systems, but limited work has applied eDNA technologies to marine waters. Further, there is limited understanding of the spatial distribution of vertebrate eDNA in marine waters. Here, we use an eDNA metabarcoding approach to target and amplify a hypervariable region of the mitochondrial 12S rRNA gene to characterize vertebrate communities at 10 oceanographic stations spanning 45 km within the Monterey Bay National Marine Sanctuary (MBNMS). In this study, we collected three biological replicates of small volume water samples (1 L) at 2 depths at each of the 10 stations. We amplified fish mitochondrial DNA using a universal primer set. We obtained 5,644,299 high quality Illumina sequence reads from the environmental samples. The sequence reads were annotated to the lowest taxonomic assignment using a bioinformatics pipeline. The eDNA survey identified, to the lowest taxonomic rank, 7 families, 3 subfamilies, 10 genera, and 72 species of vertebrates at the study sites. These 92 distinct taxa come from 33 unique marine vertebrate families. We observed significantly different vertebrate community composition between sampling depths (0 m and 20/40 m deep) across all stations and significantly different communities at stations located on the continental shelf (<200 m bottom depth) versus in the deeper waters of the canyons of Monterey Bay (>200 m bottom depth). All but 1 family identified using eDNA metabarcoding is known to occur in MBNMS. The study informs the implementation of eDNA metabarcoding for vertebrate biomonitoring.</p></div

Taxa identified using edna metabarcoding.

<p>Taxa identified using edna metabarcoding.</p

Percent of OTUs identified in 1, 2 or 3 of the biological replicates collected at each station/sampling depth.

<p>Samples are labeled with station (i.e., 1F, 2F, etc.) followed by the sampling depth (i.e., 0 m, 20 m, 40 m). 3F-0 m and 5F-0 m are not shown because they do not have complete sets of three replicates after rarefying.</p

Presence/Absence of 33 families at each station identified during the study across biological replicates and sampling depths.

<p>Presence/Absence of 33 families at each station identified during the study across biological replicates and sampling depths.</p