Advances in Using Non-invasive, Archival, and Environmental Samples for Population Genomic Studies

Abstract

Recent advances in DNA sequencing and genotyping technologies are rapidly building our capacity to address ecological, evolutionary, and conservation questions for wildlife species. However, a large portion of wildlife genetic research relies on samples containing low quantities and quality of DNA, such as non-invasive, archival, and environmental DNA (eDNA) samples. These samples present unique methodological challenges that are largely responsible for a lag in the adoption of new genetic technologies for many areas of wildlife research. Nonetheless, steady progress is being made as researchers test and refine laboratory protocols and bioinformatic methods tailored to low-quality samples. Here we provide an overview of the progress toward low-quality sample applications for amplicon sequencing, single nucleotide polymorphism (SNP) genotyping, DNA capture, mitogenome sequencing, restriction site-associated DNA sequencing (RADseq), and whole-genome sequencing. We also review methods for generating DNA sequence data from samples comprised of multiple individuals and species, such as eDNA or fecal samples, including metagenome sequencing, metabarcoding, metagenome skimming, and metatranscriptomics. The implementation of these approaches has provided insight into a wide range of questions such as modern and historic population genetic structure and diversity, adaptation, inbreeding, ancient hybridization, occupancy, diet composition, microbiome composition, and many more. As the development of methods tailored for low-quality DNA sources continues to advance over the coming years, we expect these samples to provide unprecedented insight into the ecology, evolution, and conservation of wildlife species.