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Data from: From promise to practice: pairing non-invasive sampling with genomics in conservation Russello, Michael A.; Waterhouse, Matthew D.; Etter, Paul D.; Johnson, Eric A.


Conservation genomics has become an increasingly popular term, yet it remains unclear whether the non-invasive sampling that is essential for many conservation-related studies is compatible with the minimum requirements for harnessing next-generation sequencing technologies. Here, we evaluated the feasibility of using genotyping-by-sequencing of non-invasively collected hair samples to simultaneously identify and genotype single nucleotide polymorphisms (SNPs) in a climate change-sensitive mammal, the American pika (Ochotona princeps). We identified and genotyped 3,803 high-confidence SNPs across eight sites distributed along two elevational transects using starting DNA amounts as low as 1 nanogram. Fifty-five outlier loci were detected as candidate gene regions under divergent selection, constituting potential targets for future validation. Genome-wide estimates of gene diversity significantly and positively correlated with elevation across both transects, with all low elevation sites exhibiting significant heterozygote deficit likely due to inbreeding. More broadly, our results highlight a range of issues that must be considered when pairing genomic data collection with non-invasive sampling, particularly related to field sampling protocols for minimizing exogenous DNA, data collection strategies and quality control steps for enhancing target organism yield, and analytical approaches for maximizing cost-effectiveness and information content of recovered genomic data.; Usage notes
SNP genotypic data from American pika in North Cascades National ParkExcel file including genotypes at 9825 SNPs for 67 American pika sampled in North Cascades National Park, Washington, USA. The first column is contig name. The second column is SNP position within the contig. Every two columns after is an individual. Each row is a locus. Sample names include the transect identifier (PP=Pyramid Peak; TL=Thornton Lake), site name (ex. 1A), and individual number (ex. 20a). Allele calls are as follows: 1=A, 2=C, 3=G, 4=T.PikaNextRAD_SNP.xlsx

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