The Type Locality Project: collecting genomic-quality, topotypic vouchers and training the next generation of specimen-based researchers

Abstract

DNA evidence is often critical for taxonomic studies; however, many historical type specimens lack corresponding genetic samples, which limits contemporary molecular research questions and may restrict conservation and management decisions. We conducted a pilot Type Locality Project to collect voucher specimens and genomic-grade samples from amphibian type localities in the state of Virginia, USA. These samples can serve as proxies for cases in which obtaining genomic data from the type specimen is not possible. Undergraduate students participated in all aspects of the project including fieldwork, DNA barcoding, and incorporating specimens into the Smithsonian Institution's National Museum of Natural History research collection. The Type Locality Project is an excellent platform for providing undergraduate students with hands-on research experience and training in taxonomy and systematics. Other institutions could easily adapt our approach to obtain genomic-quality, topotypic vouchers for other taxa and simultaneously create authentic undergraduate research experiences in field, laboratory, and natural history museum settings.

Evolution in the Model Genus Antirrhinum Based on Phylogenomics of Topotypic Material

“…This has also prevented the accurate naming of some Antirrhinum populations. In contrast, our study offers a new phylogenetic hypothesis that helps to elucidate systematics and evolution thanks to a high number of phylogenetically informative nucleotide characters (>50,000 bp) taken from genome-wide (GBS) sequences, together with DNA sequences that are anchored to original Antirrhinum names (Bell et al, 2020).…”

“…The hypothesis of an evolutionary radiation of Antirrhinum based on ITS and plastid sequences (Vargas et al, 2009) is supported by our phylogenetic analysis based on GBS data, which found a high rate of diversification (0.54 spp. Myr −1 ) into at least 26 species (Valente et al, 2010;Bell et al, 2012) since the Pliocene (Vargas et al, 2009). The combination of terrain complexity and eco-climatic novelty seems to explain why the Mediterranean basin contains numerous examples of explosive radiations in the angiosperms (Valente et al, 2010).…”

DNA barcoding of the National Museum of Natural History reptile tissue holdings raises concerns about the use of natural history collections and the responsibilities of scientists in the molecular age

“…Several other sequences from that study [41] appear to have resulted from PCR contamination: one identified in BOLD and GenBank as a skink (Plestiodon) is a 97% match to a copepod, and several others identified as three distantly related lizard species are 98-99% identical to sequences from one salamander species. Many of the amphibian sequences in that study were also associated with mis-identified specimens or outdated taxonomies (see Bell et al [68]). The lesson here is that all specimen identifications should be checked before publishing, making sure that the vouchers are identified correctly and the taxonomy is up to date.…”

Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network

“…Through mutual sharing of best practices in a virtual community of practice, biorepository personnel can standardize and prioritize the types of materials and preservations most useful to EID research. Likewise, the EID community can better integrate biorepository data standards into specimen collection and sampling procedures [5,21,[76][77][78]. Darwin Core (dwc.…”

“…Through mutual sharing of best practices in a virtual community of practice, biorepository personnel can standardize and prioritize the types of materials and preservations most useful to EID research. Likewise, the EID community can better integrate biorepository data standards into specimen collection and sampling procedures [ 5 , 21 , 76 – 78 ]. Darwin Core ( dwc.tdwg.org ) stable identifiers, for example, represent a common vocabulary intended to facilitate the sharing of information about biological diversity and specimens [ 79 ].…”