From promise to practice: pairing non-invasive sampling with genomics in conservation

PeerJ. 2015 Jul 21;3:e1106. doi: 10.7717/peerj.1106. eCollection 2015.


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-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 ng. 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.

Keywords: American pika; Biodiversity; Climate change; Genotyping-by-sequencing; Hair; NextRAD; Ochotona princeps; Restriction-site associated DNA sequencing; Single nucleotide polymorphism.

Grant support

Funding for this work was provided by the Sarah and Daniel Hrdy Fellowship in Conservation Biology (Harvard University to MR), the Natural Sciences and Engineering Research Council of Canada (Discovery Grant # 341711 to MR) and Seattle City Lights (grant # 2013-03 to MR). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.