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

Area of Science:

• Ecology
• Genetics
• Conservation Biology

Background:

• Conservation genomics relies on non-invasive sampling, but its compatibility with next-generation sequencing (NGS) is uncertain.
• The American pika (Ochotona princeps) is a climate-sensitive mammal, making it a key species for conservation studies.

Purpose of the Study:

• To assess the feasibility of genotyping-by-sequencing (GBS) using non-invasively collected hair samples for SNP identification and genotyping in the American pika.
• To explore the relationship between genetic diversity, elevation, and potential selection pressures in this species.

Main Methods:

• Utilized GBS on hair samples from eight sites across two elevational transects.
• Identified and genotyped high-confidence single nucleotide polymorphisms (SNPs) with low starting DNA amounts (as low as 1 ng).
• Analyzed outlier loci for divergent selection and correlated genome-wide gene diversity with elevation.

Main Results:

• Successfully identified and genotyped 3,803 high-confidence SNPs.
• Detected 55 outlier loci potentially under divergent selection.
• Found a significant positive correlation between genome-wide gene diversity and elevation, with low elevation sites showing heterozygote deficit indicative of inbreeding.

Conclusions:

• Non-invasive GBS is a viable method for conservation genomics in the American pika.
• Genetic diversity is influenced by elevation, suggesting adaptation to different climate conditions.
• Highlights critical considerations for non-invasive sampling in genomics, including field protocols, data quality control, and cost-effective analysis.