Using Digitized Herbarium Data in Research: A Virtual Botany 2020 Workshop

Fri, 2020-09-04 12:57 -- maphillips


iDigBio and BiotaPhy, an NSF-funded project to link iDigBio data, the Open Tree of Life, and Lifemapper and other analytical platforms to enable biodiversity research, held a training workshop at Botany 2020 – Virtual! on July 31.  The full-day online workshop, entitled, “Using Digitized Herbarium Data in Research: Applications for Ecology, Phylogenetics, and Biogeography,” attracted over 100 participants.   

Emerging cyberinfrastructure and new data sources provide unparalleled opportunities for mobilizing and integrating massive amounts of information from organismal biology, ecology, genetics, climatology, and other disciplines.  Key among these data sources is the rapidly growing volume of digitized specimen records from natural history collections. With nearly 125 million specimen records available online (nearly half of which are herbarium records), these data provide excellent information on species distributions, changes in distributions over time, phenology, morphology, and more. Particularly powerful is the integration of phylogenies with specimen data, enabling analyses of phylogenetic diversity in a spatio-temporal context, the evolution of niche space, and more.  Ongoing efforts to link and analyze diverse data are yielding new platforms for comparative analyses of biodiversity data. However, the inundation of data and methods can be overwhelming for potential users of these data.

To help users navigate both the data and the methods, iDigBio and BiotaPhy adapted their popular annual workshop to an online format. In addition to training on the use of various software packages, the assumptions of the analyses and interpretations of results were presented. Participants learned how to access and download digitized herbarium data (from iDigBio, GBIF, and other aggregators) and prepare cleaned data sets for analysis.  Modules on using georeferencing software (GEOLocate), applying Maxent software to construct ecological niche models, conducting statistical analyses of Maxent output, and performing phylogenetic diversity analyses were also presented. Participants were introduced to new integrative software tools developed by the BiotaPhy Project that link occurrence data (through iDigBio), niche models, and ecological statistics calculated from the models, applying these to large trees in a desktop geospatial environment.

Materials from the workshop are being assembled into online packages for future webinars and public use.

The workshop was led by Pam Soltis (iDigBio Director of Research and BiotaPhy Co-PI), Doug Soltis (BiotaPhy Co-PI), iDigBio Research Assistant Shelly Gaynor, and University of Florida graduate students Andre Naranjo, Maria Cortez, and Lauren Whitehurst.