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

Abstract

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.

Figure 1. Sites in North Cascades National Park, Washington, USA where America pika hair samples were non-invasively collected.

Topographic lines represent 100 m elevation. Inset shows a Structure bar plot depicting the model-based clustering results for all sites within the Pyramid Peak (PP) and Thornton Lake (TL) elevational transects based on 3,748 neutral single nucleotide polymorphisms.

Figure 2. Elevational patterns of genetic diversity within American pika in the North Cascade National Park.

Solid line shows the correlation between proportions of polymorphic loci (P; circles) with elevation (r² = 0.557 p = 0.034). Dashed line shows the correlation between gene diversity (N_g; squares) with elevation (r² = 0.738 p = 0.006).

Figure 3. Structure bar plots depicting the model-based clustering results for Thornton Lake (TL) and Pyramid Peak (PP) sites based on outlier loci (above) and neutral loci (below).

Analyses for the TL transect revealed evidence for both K = 2 (ΔK = 473.3) and K = 3 (ΔK = 314.6; plot shown) based on 37 outlier loci, and K = 1 (K = 2 plot shown for display purposes) based on 3,748 neutral loci. Analyses for the PP transect revealed evidence for K = 2 (=123.1) based on 18 outlier loci, and K = 2 (ΔK = 33.1) based on 3,748 neutral loci.