Editorial: Recent advances in museomics: revolutionizing biodiversity research

Museomics, a term coined by Drs. Stephan Schuster and Webb Miller in ~2009, refers to “the large-scale analysis of the DNA content of museum collections” (http://mammoth.psu.edu/museomics.html). Although such DNA studies existed before the term was first used, “museomics” highlighted the importance of specimens in biological studies.

Specimens in natural history collections (NHCs) have been collected for hundreds of years to document the spatial and temporal occurrences of species. It is estimated that NHCs worldwide house 3 billion specimens (Soberon, 1999). These specimens preserve a wealth of information, such as morphological and genetic data on the identity and phylogenetics of species, biogeographic and ecological data, and even biographical information of the collectors, and the contributions of NHCs extend well-beyond organismal biology research to fields such as public health (Suarez and Tsutsui, 2004; Cook et al., 2020) and education (Ellwood et al., 2020; Lendemer et al., 2020; National Academies of Sciences Engineering and Medicine, 2020). NHCs are valuable resources with unknown future potential, and there are countless examples of research made possible that was not the goal of the original collector (Heberling et al., 2019; Miller et al., 2020). We provide three examples. First, Moritz et al. (2008) compared modern specimens of small mammals to those collected ~100 years prior to document how climate change caused the distributions of some species to shift in elevation. Second, bird egg collections in museums were instrumental in showing the role of DDT in causing egg-shell thinning that adversely affected raptor and pelican populations (Ratcliffe, 1967; Hickey and Anderson, 1968). Lastly, Freelance et al. (2022) stress the importance of properly designing captive breeding programs, since the sensory organs of the endangered Lord Howe Island stick insect (Dryococelus australis) differed between wild specimens (>100 years old) and individuals bred in captivity. Given the accelerated rate of biodiversity loss, the role of NHCs will increase in prominence by being an archive of genetic and phenotypic diversity across space and time for many species that have gone extinct or where populations have vanished.

Similarly in terms of unexpected potential, the advent of DNA sequencing technology opened up new avenues for specimen-based research. Modern specimen preparation now includes special steps to preserve DNA/RNA in tissues (e.g., freezing or placing tissues in ethanol or other storage media) for genetic studies, while previously there were no special efforts to preserve the DNA. There are challenges working with these materials, such as DNA naturally degrading over time and the DNA of formalin-fixed specimens being cross-linked with proteins and other DNA (Raxworthy and Smith, 2021). Advances in laboratory methods and new sequencing technologies (e.g., high throughput short-read sequencing) have facilitated improvements in our ability to recover and sequence DNA from museum specimens.

There are four primary sources of DNA that we discuss here: ancient DNA (aDNA), historical DNA (hDNA), modern DNA, and archival DNA (Raxworthy and Smith, 2021). DNA extracted from samples that died under natural circumstances and were later recovered from the field are referred to as aDNA. Familiar examples of aDNA include samples obtained from species such as mammoths and cave bears, which can be quite old and are often >200 years in age. In contrast, DNA extracted from formalin-fixed or ethanol-fixed specimens that were preserved and stored in museum collections is referred to as hDNA (these specimens are usually <200 years old). DNA extracted from tissue samples specifically prepared with genetic analysis in mind is referred to as modern DNA and is usually <40 years old. Archival DNA refers to hDNA and modern DNA stored in museum specimens. The first studies from researchers using the word “museomics” sequenced mitochondrial genomes from the aDNA in hair of the extinct Siberian mammoth (Gilbert et al., 2008) and Tasmanian tiger (Miller et al., 2009).

This Research Topic is a collection of studies highlighting advances in museomics, both in demonstrating applications and refining methodologies. Some applications demonstrated in this Research Topic include using DNA barcoding of a degraded whale sample to identify it to subspecies (Ren et al.), obtaining data from a holotype to verify the existence of an undescribed rodent genus (Castañeda-Rico et al.), obtaining DNA from hundreds of herbarium specimens to elucidate the phylogeography of the genus Dalbergia (Sotuyo et al.), and using target capture to understand the phylogenetic placement of two rare shark species (Agne, Naylor et al.). These studies are diverse in the DNA type used (hDNA and modern DNA), taxa studied, objectives, and approaches. A variety of factors have been identified that affect the performance of sequencing DNA from specimens, and a major goal of museomics is to develop a set of best practices to maximize success (Raxworthy and Smith, 2021). Efforts are being made to document and understand these factors (e.g., Irestedt et al., 2022), and this Research Topic was initiated to further this cause. As an overview of this Research Topic, we identify several factors being addressed across the articles (Figure 1). Following the terminology of Roycroft et al., we organize these factors temporally in the research process as pre-sequencing and post-sequencing (Figure 1). This list of factors is not exhaustive, but rather highlights those that are addressed in this Research Topic. We note that findings in different studies may contradict each other, highlighting the dynamic state of the field and the need for more exhaustive research on this topic.