Genomics of natural history collections for understanding evolution in the wild

Abstract

A long‐standing question in biology is how organisms change through time and space in response to their environment. This knowledge is of particular relevance to predicting how organisms might respond to future environmental changes caused by human‐induced global change. Usually researchers make inferences about past events based on an understanding of current static genetic patterns, but these are limited in their capacity to inform on underlying past processes. Natural history collections (NHCs) represent a unique and critical source of information to provide temporally deep and spatially broad time‐series of samples. By using NHC samples, researchers can directly observe genetic changes over time and space and link those changes with specific ecological/evolutionary events. Until recently, such genetic studies were hindered by the intrinsic challenges of NHC samples (i.e. low yield of highly fragmented DNA). However, recent methodological and technological developments have revolutionized the possibilities in the novel field of NHC genomics. In this Special Feature, we compile a range of studies spanning from methodological aspects to particular case studies which demonstrate the enormous potential of NHC samples for accessing large genomic data sets from the past to advance our knowledge on how populations and species respond to global change at multiple spatial–temporal scales. We also highlight possible limitations, recommendations and a few opportunities for future researchers aiming to study NHC genomics.

Mining museums for historical DNA: advances and challenges in museomics

“…The potential of natural history museums and herbariums to serve as a vast source of DNA has long been recognized [1][2][3][4][5][6]. The growing genomic field of museomics (see Glossary) [7], initially yielded short fragments of historical DNA (hDNA) that was often from mitochondrial genes, but has since expanded to sequence the entire genome (e.g., [8,9]).…”

Brown trout phylogenetics: A persistent mirage towards (too) many species

“…Few studies have considered museum specimens, only using mtDNA (Levin et al, 2018;Splendiani et al, 2016Splendiani et al, , 2017Tougard et al, 2018). The study of nuclear ancient DNA is challenging, but may improve knowledge (Chassaing et al, 2016;Lopez et al, 2020).…”

The utility of formalin-fixed tissues and allozyme supernatant for population genomics and considerations for combining capture- and RADseq-based SNP datasets

“…Some museum collections house large series of allozyme supernatants (Table 1) that serve as valuable records of biodiversity but have not been fully leveraged in the genomic age. These collections may serve similar purposes as other hDNA samples, such as filling sampling gaps, or evaluating genomic variation through time (Wandeler, Hoeck, & Keller, 2007;Lopez, Turner, Bellis, & Lasky, 2020).…”