DOI: 10.5061/dryad.g79cnp5pk
title: Gila Trout neutral and outlier SNP genotype matrices

description: Many salmonid species exist in highly structured and isolated populations,
 and are susceptible to habitat fragmentation and disturbances. Gila Trout
 (Oncorhynchus gilae) is a threatened species found in the Southwestern
 United States, and is managed to preserve relict populations (i.e.,
 lineages) distributed across a fragmented landscape. We evaluated genomic
 variation within and among remaining lineages of Gila Trout using RADseq
 to assess how drift and selection have structured populations using
 neutral and outlier loci. We also examined whether a signature of
 hybridization was evident in relict populations. Gila Trout lineages were
 significantly differentiated from one another and were characterized by
 low effective population sizes. However, most lineages maintained genomic
 diversity and are potentially adapted to local conditions. Hybridization
 with non-native Rainbow Trout (O. mykiss) was not detected in any lineage.
 All lineages have experienced population bottlenecks associated with
 mortality from drought and severe wildfires. Current management strategies
 should be reevaluated and adapted to better account for long-term effects
 of climate change. Specifically, we suggest reconnecting some populations
 via dendritic stream networks to facilitate natural dispersal in a
 metapopulation context. This would allow natural genetic mixing on the
 landscape and potentially increase adaptive potential. Furthermore,
 genetic rescue should be implemented to preserve integrity of the unique
 Spruce Creek lineage that is currently compromised by extremely low
 diversity.
description: Gila Trout fin clips were obtained through the Museum of
 Southwestern Biology (MSB) at the University of New Mexico (https://msb.unm.edu).
 Gila Trout samples (n=154) representing all five wild-origin, relict
 lineages were assessed, and total genomic DNA was isolated from fin clip
 samples. Genomic DNA was submitted to SNPsaurus (http://snpsaurus.com)
 where genomic libraries were prepared and a reduced-representation nextRAD
 sequencing method was applied to amplify genomic loci and build RAD tag
 libraries (150 bp reads and average 20X depth). Raw reads
 were trimmed and mapped to an annotated Rainbow Trout genome (https://www.ncbi.nlm.nih.gov/genome/?term=rainbow+trout), and genotype genetic variants. Resulting SNP loci were filtered for sequencing errors, genotyping errors, linkage disequilibrium, and paralogs. Only biallelic SNPs were considered. Outlier loci were removed from the neutral dataset and retained for the outlier dataset. Outliers were assessed with two methods (Bayescan and PCAdapt) and estimated outliers were annotated. Only outliers annotated to Rainbow Trout genome were considered. Genotypes were assessed with VCFtools.
description: Genotypes are coded as 0, 1, or 2 depending on the number of alternate alleles each individual is contained (0 = homozygous reference allele, 1 = heterozygotes, 2 = homozygous alternate allele). CHROM ID's refer to RefSeq sequence ID's of Oncorhynchus gilae (Rainbow Trout) found at https://www.ncbi.nlm.nih.gov/assembly/GCF_002163495.1