Enhancing DNA barcode reference libraries by harvesting terrestrial arthropods at the National Museum of Natural History

ARPHA Preprints, doi: 10.3897/arphapreprints.e84305

Bernardo Santos^‡§, Meredith E. Miller^|, Margarita Miklasevskaja^|, Jaclyn T.A. McKeown^|, Niamh E. Redmond^¶, Jonathan A. Coddington^¶, Jessica Bird^¶, Scott E. Miller^¶, Ashton Smith^¶, Seán G. Brady^¶, Matthew L. Buffington^#, M. Lourdes Chamorro^#, Torsten Dikow^¶, Michael W. Gates^#, Paul Goldstein^#, Alexander Konstantinov^#, Robert Kula^#, Nicholas D. Silverson^¶, M. Alma Solis^#, Stephanie L. deWaard^|, Suresh Naik^|¤, Nadya Nikolova^|, Mikko Pentinsaari^|, Sean W.J. Prosser^|, Jayme E. Sones^|, Evgeny V. Zakharov^|¤, Jeremy R. deWaard^|¶«

‡ UFES, Brazil§ American Museum of Natural History, New York, United States of America| Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada¶ National Museum of Natural History, Smithsonian Institution, Washington, United States of America# Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Washington, United States of America¤ Department of Integrative Biology, University of Guelph, Guelph, Canada« School of Environmental Sciences, University of Guelph, Guelph, Canada

Corresponding author: Bernardo Santos ( bernardofsantos@gmail.com )

© Bernardo Santos, Meredith Miller, Margarita Miklasevskaja, Jaclyn McKeown, Niamh Redmond, Jonathan Coddington, Jessica Bird, Scott Miller, Ashton Smith, Seán Brady, Matthew Buffington, M. Lourdes Chamorro, Torsten Dikow, Michael Gates, Paul Goldstein, Alexander Konstantinov, Robert Kula, Nicholas Silverson, M. Alma Solis, Stephanie deWaard, Suresh Naik, Nadya Nikolova, Mikko Pentinsaari, Sean Prosser, Jayme Sones, Evgeny Zakharov, Jeremy deWaard.

This is an open access preprint distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Citation: Santos B, Miller ME, Miklasevskaja M, McKeown JT.A, Redmond NE, Coddington JA, Bird J, Miller SE, Smith A, Brady SG, Buffington ML, Chamorro ML, Dikow T, Gates MW, Goldstein P, Konstantinov A, Kula R, Silverson ND, Solis MA, deWaard SL, Naik S, Nikolova N, Pentinsaari M, Prosser SW.J, Sones JE, Zakharov EV, deWaard JR (2022) Enhancing DNA barcode reference libraries by harvesting terrestrial arthropods at the National Museum of Natural History. ARPHA Preprints. https://doi.org/10.3897/arphapreprints.e84305

Abstract

The use of DNA barcoding has revolutionized biodiversity science, but its application depends on the existence of comprehensive and reliable reference libraries. For many poorly known taxa, such reference sequences are missing even at higher-level taxonomic scales. We harvested the collections of the Smithsonian’s National Museum of Natural History (USNM) to generate DNA barcoding sequences for genera of terrestrial arthropods previously not recorded in one or more major public sequence databases. Our workflow used a mix of Sanger and Next-Generation Sequencing (NGS) approaches to maximize sequence recovery while ensuring affordable cost. In total, COI sequences were obtained for 5,686 specimens belonging to 3,888 genera and 202 families. Success rates varied widely according to collection data and focal taxon. NGS helped recover sequences of specimens that failed a previous run of Sanger sequencing. Success rates and the optimal balance between Sanger and NGS are the most important drivers to maximize output and minimize cost in future projects. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, the Global Genome Biodiversity Network Data Portal and the NMNH data portal.

Keywords

COI, cox1, dark taxa, OTUs, BINs, natural history collection, museum harvesting