Museum genomics: low‐cost and high‐accuracy genetic data from historical specimens

Abstract

Natural history collections are unparalleled repositories of geographical and temporal variation in faunal conditions. Molecular studies offer an opportunity to uncover much of this variation; however, genetic studies of historical museum specimens typically rely on extracting highly degraded and chemically modified DNA samples from skins, skulls or other dried samples. Despite this limitation, obtaining short fragments of DNA sequences using traditional PCR amplification of DNA has been the primary method for genetic study of historical specimens. Few laboratories have succeeded in obtaining genome-scale sequences from historical specimens and then only with considerable effort and cost. Here, we describe a low-cost approach using high-throughput next-generation sequencing to obtain reliable genome-scale sequence data from a traditionally preserved mammal skin and skull using a simple extraction protocol. We show that single-nucleotide polymorphisms (SNPs) from the genome sequences obtained independently from the skin and from the skull are highly repeatable compared to a reference genome.

Herbarium genomics: skimming and plastomics from archival specimens

“…Where in the pre-NGS, polymerase chain reaction (PCR), era fragmented template DNA represented a major roadblock to successful amplification, the opposite is now true. Indeed next-generation sequencing has opened up tremendous possibilities for sequencing museum specimens, not only because of its increased output and power, but also because of the ever-decreasing costs (Millar et al 2008;Metzker 2010;Glenn 2011;Rowe et al 2011;Buerki and Baker 2016).…”

Reticulation, divergence, and the phylogeography–phylogenetics continuum

“…Another comparison (102) found similar phylogeographic resolution between exons (drawn randomly from transcriptomes) vs. anchored hybrid enrichment (AHE) loci, which mostly target conserved exons (96,97). Exon capture has been effectively used to study diverging lineages of both vertebrates and invertebrates (e.g., 12, 98, 103) and is particularly appropriate for retrieving genomic data from museum specimens (80,104,105). Arguably, most UCE, AHE, or exon capture loci that have been used thus far for next-generation phylogeography are under mild or even strong purifying selection.…”

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

“…While the degraded nature of historical DNA poses a particular set of challenges and requires stringent data quality control and validation, a number of different methods can be used to obtain reliable high-throughput sequence or genotype data from ancient and historical samples (see Rizzi et al, 2012). We now have the technology to fully sequence the entire genome of samples that are thousands of years old (e.g., Rasmussen et al, 2010;Prüfer et al, 2014), and recent studies with archived fish samples or other museum specimens have generated high-quality data through minor methodological modifications using standard genotyping assays of 100s or 1000s of SNPs (e.g., Johnston et al, 2013;Therkildsen et al, 2013a, b), sequence capture methodology (Bi et al, 2012;Carpenter et al, 2013), or whole-genome sequencing (Rowe et al, 2011;Staats et al, 2013).…”