Digitization of herbaria enables novel research

Abstract

As botanists, we recognize that herbarium specimens document spatial and temporal patterns of plant diversity. But they may also tell stories beyond the plants themselves—about how a specimen may have languished for decades in obscurity until a botanist with a keen eye recognized it as a new species (Ziziphus celata; see, e.g., Judd and Hall, 1984; for image, see https://www.floridamuseum.ufl.edu/scripts/dbs/herbs_project/herbsproject/herbs_pub_proc.asp?accno=136888&FamSys=A&output_style=Report_type&trys=2) or of the heroics required to relocate a species in nature (e.g., Shortia galacifolia; https://www.idigbio.org/content/portal-curiosities-asa-gray-and-quest-shortia-galacifolia-%E2%80%93-case-study-importance) or of the metamorphosing nature of collections themselves, with specimens yielding data undreamt of when they were collected (e.g., Inga umbellifera; Hart et al., 2016; for image, see http://elmer.rbge.org.uk/bgbase/vherb/bgbasevherb.php?cfg=bgbase/vherb/fulldetails.cfg&specimens_specimen__num=369514). These specimens of Ziziphus (or Pseudoziziphus!), Shortia, and Inga represent just a handful of the estimated 350,000,000 herbarium specimens deposited in the world's 3400 herbaria (Index Herbariorum, http://sciweb.nybg.org/Science2/IndexHerbariorum.asp). Collected over the past four centuries, herbarium specimens document the world's vegetation, including how it has changed in response to human activities and population expansion, and provide the basis for scientific names in the form of type specimens. Until recently, the world's herbarium specimens were under lock and key and accessible to only a small number of scientific specialists, but digitization of herbaria is now a global enterprise, and specimen data and images are emerging in digital form from herbaria around the world. Digitization—that is, electronic capture of data, including images—began decades ago in some herbaria with databasing of basic information about a specimen (scientific name, collector, date of collection, locality, etc.). Through innovations in database design and usability, application of global standards for natural history collections (e.g., DarwinCore; Wieczorek et al., 2012), improved methods for imaging herbarium specimens (e.g., Tegelberg et al., 2014), and the development of high-throughput workflows (as implemented, for example, in the Paris Herbarium; https://www.idigbio.org/sites/default/files/workshop-presentations/spnhc2014/02_SPNHC2014_chagnoux.pdf), the pace of digitization has increased dramatically. The Global Plants Initiative (GPI; https://plants.jstor.org/), a push to digitize the world's botanical type specimens, demonstrated both the global will and collaborative spirit of herbarium leaders from around the world and the feasibility of large-scale, international, collaborative digitization efforts. In many ways, GPI set the stage for the remarkable digital herbarium resources available today. Data aggregators—such as the Global Biodiversity Information Facility (GBIF), the Atlas of Living Australia (ALA), the U. S. Geological Survey's portal (Biodiversity Information Serving Our Nation; BISON), and iDigBio (Integrated Digitized Biocollections, funded by the U. S. National Science Foundation (NSF); see below)—provide digital biodiversity data, including information from herbarium specimens, to the public using standardized terminology as specified in DarwinCore. Other national and regional aggregators also serve biodiversity information, and collectively these aggregators provide data that allow visualization and analysis of patterns of biodiversity in novel and exciting ways. Although decades have passed since the first herbarium records were databased and made available via the internet, it is only within the past few years that sufficient numbers of specimen records have become available for large-scale, innovative research. We are just now at the brink of new opportunities for synthetic analyses that connect digitized specimen data with other resources (phylogenetic, climatological, genomic, etc.; e.g., Soltis and Soltis, 2016) to address both novel questions in plant biology and longstanding questions from new perspectives and larger scales. iDigBio (www.idigbio.org) was founded in 2011 to collect and share the rapidly increasing volume of digitized specimen data flowing from new investments in digitization technology and workflows funded by NSF. As of this writing, iDigBio currently serves over 105 million specimen records from US and international natural history collections. Of these, approximately 50 million are herbarium records. Moreover, iDigBio serves over 22 million media records, most of which are images, with nearly 20 million representing herbarium specimens. What a resource for botanical research and education—and many more millions are in the digitization pipeline! When NSF began funding for the Advancing Digitization of Biodiversity Collections Program in 2011, the botanical communi