On the Designation of Voucher Specimens for Molecular Phylogenetics

1. On the Designation of Voucher Specimens for Molecular Phylogenetics Mariel Campbell Biology 446/546 Dept. of Biology, University of New Mexico Fall 2018

2. What is a Voucher Specimen? • “A voucher can be broadly defined as a representative sample of an expertly identified organism that is deposited and stored at a facility from which researchers may later obtain the specimen for examination and further study “(Culley, 2013). • In a traditional natural history context, a voucher is: • An individual organism, which can provide a morphological reference for identification • A lot (group) of organisms of the same species • The data associated with this organism: • Where collected • When collected • Who collected • Any additional data on habitat, collecting method, associated species, etc.

3. Less-traditional vouchers or parts of vouchers: • Blood, saliva, fecal, hair samples • Frozen tissues • DNA, RNA extractions • Cultures • Environmental samples • soil, water, microbiome • may contain many species • Tumor biopsy • Formalin-fixed, paraffin-embedded tissues (FFPE) • Frequently maintained in Biobanks rather than natural history collections

4. Where are voucher specimens archived? • Natural History Research Collections • Depends on relevant taxonomic group • Museum of Southwestern Biology http://msb.unm.edu/ • Vertebrates, plants, arthropods, parasites • MSB Biobank = natural history genomics collection • Biobanks • Typically human-focused • Also veterinary, environmental • >600 in US • e.g. National Cancer Institute https://biospecimens.cancer.gov/about/cahub/default.asp

6. Why Provide Voucher Specimens for Molecular Work? • Identification/Taxonomic changes • What species was it, really? • A physical voucher can be re-examined, re-analyzed as taxonomy changes • Replicability of current studies • Hallmark of good science – can others duplicate your results with the same samples and similar or different methods? • Baseline for future studies • New questions can be addressed with the same samples • New technology can be used on the same samples • Specimen-based research builds over time • Same specimens can be used over the lifetimes of many individual researchers • Value of original research effort increases over time • Individual researchers do not have to manage their own specimen and data archives • A voucher documents the existence of a unique individual or species at a particular place at a particular time. • Voucher specimens allow researchers to travel back in time to ask questions about species or the environment • E.g. Pathogen or parasite prevalence, environmental contaminants, genetic changes in populations

7. “Most journals publishing molecular phylogenies, require that the sequences be deposited in accessible repositories, such as GenBank. However, as more molecular data become available, there is a growing concern about the taxonomic origin of these data . . . “Although some taxa appear to be well delineated and easy enough to recognize, others still can only be identified by a handful of specialists. . . Today there is a large number of sequences deposited at GenBank that are incorrectly labeled and, unless remedied, these will continuously be associated with the wrong taxa. Vouchers constitute an essential link between data and taxa, and provide a means to verify the taxonomic identity of the specimens sequenced..” From: “Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies”, F. Pleijel et al. / Molecular Phylogenetics and Evolution 48 (2008) 369–371

8. Searchable, Online Databases for Vouchered Natural History Genomic Samples • Arctos Collection Management System: https://arctos.database.museum/ • Multi-collections portal for Museum of Southwestern Biology, University of Alaska Museum of the North, Museum of Vertebrate Zoology, Berkeley; Denver Museum of Nature and Science genomics collections • MCZbase: Harvard University: https://mczbase.mcz.harvard.edu/SpecimenSearch.cfm • Global Genome Biodiversity Network (GGBN): http://www.ggbn.org/ggbn_portal/ • New aggregator coordinated by Smithsonian Institution • GenBank – look for “specimen voucher” fields and also in External Resources link at right

10. https://arctos.database.museum/guid/MSB:Mamm:55245

12. MSB:Host:15386 MSB:Para:18716 http://arctos.database.museum/guid/MSB:Host:15385 http://arctos.database.museum/guid/MSB:Para:18715 Kraus, T. J., Brant, S. V., & Adema, C. M. (2014). Characterization of trematode cercariae from Physellaacuta in the Middle Rio Grande. Comparative Parasitology, 81(1), 105-109.

14. References Astrin, J. J., Zhou, X., & Misof, B. (2013). The importance of biobanking in molecular taxonomy, with proposed definitions for vouchers in a molecular context. ZooKeys, (365), 67-70. doi:10.3897/zookeys.365.5875 Culley, T. M. Why Vouchers Matter in Botanical Science. Applications in Plant Sciences 2013 1 ( 11 ): 1300076 Turney, S., Cameron, E. R., Cloutier, C. A., & Buddle, C. M. (2015). Non-repeatable science: assessing the frequency of voucher specimen deposition reveals that most arthropod research cannot be verified. PeerJ, 3, e1168. doi:10.7717/peerj.1168