Digitization: A Boost to Circulation

Portal of the Global Biodiversity Information Facility

In the last two (1,2) posts, I’ve discussed how herbarium specimens have circulated since they were first created, and also how sometimes specimens get stuck in a limbo of uncurated collections.  Now I want to discuss how circulation has changed thanks to the massive digitization projects of the 21^st century.  This is a familiar story to those in the herbarium world, but I’ll quickly review it for those who aren’t lucky enough hang around herbaria.  The upshot of digitization is that now everyone can hang around them, at least virtually. 

Digitization is very much tied to the development of computer technologies, but also to globalization that has brought an awareness that the planet we live on is a shared asset and a shared responsibility.  Over the years there have been a number of international conferences and agreements that articulated this vision and made it actionable.  The 1993 international  Convention on Biological Diversity gave each nation sovereignty over its biological wealth, which implies knowledge of that wealth.  This led to the 2002 Global Strategy for Plant Conservation with later updates and goals including a global flora of all known plants with online access, the best way to make the information widely available.  While this goal has yet to be met in full, there have been significant advances toward it.  

In the early 21^st century, the Andrew W. Mellon Foundation spearheaded the digitization of type specimens so that researchers around the world could access the plants that were used in describing species.  Because of the way many specimens circulated—collected in the species-rich tropics and transported to botanist-rich Europe and North America—researchers in developing nations did not have ready access to these materials.  Botanical literature was also relatively unavailable so the project digitized many publications of the past as well.  This project morphed into the portal JSTOR Global Plants and also set the stage for other large-scale digitization projects such as ADBC (Advancing Digitization of Biodiversity Collections) in the United States with its massive iDigBio portal and what ultimately became DiSSCo (Distributed System of Biodiversity Collections) in Europe.  Meanwhile GBIF (Global Biodiversity Information Facility) has aggregated data from these projects and others worldwide to create the largest portal for natural history collections along with observational data. 

While an amazing achievement, digitization has not totally solved access problems for those in developing nations.  They often do not have the hardware, software, and internet connections to make good use of these resources.  Still, digitization has broadened availability in other ways.  It was difficult for those not involved in botanical research to visit herbaria, if for no other reason than specimens’ fragility; each use opens the possibility of damage.  This is not a problem with a digital collection, so students can study specimens on the web as can curious gardeners and artists looking for new forms of inspiration, leading to greater plant awareness, a positive counter to what has been called plant blindness. 

Digital collections have already had a major impact on the ways specimens are used in research (Heberling et al., 2021).  For phenological work, botanists can now search GBIF for a particular species and by checking a specimen’s flowering or fruiting status against the date it was collected, they can see if there is a pattern of change in the dates over a period of 100 years or more.  They may check hundreds or even thousands of specimens, something that wouldn’t be possible for physical examination.  Niche or species distribution modeling, determining areas that might provide suitable habitat for a species based on what is known about its range, is another area where digital specimens are pivotal:  geographic coordinate data on where plants were collected are used to create a model of the environmental conditions that meet a species’ habitat requirements.  This research is helpful in identifying possible collection areas and also where a species might be able to grow as the climate changes. 

There’s also an increase in the use of artificial intelligence (AI) tools to recognize traits like leaf shape and even to identify species.  This work requires a great deal of computer power and sophisticated neural networking techniques, so it’s costly in both technology and human input.  However the field is advancing rapidly in exciting ways.  Botanists foresee being able to rapidly analyzing large numbers of specimens and at least sorting them into families or genera if not species.  However, at the moment even the identification of leaf shapes is still in its infancy.  When deep learning AI techniques are tested in identifying specimens, this is done on carefully selected specimen sets.  It requires a great deal of computer capacity, but the increasing frequency with which AI projects presented at conferences on digital specimens suggests that these tools will soon become widely used in biodiversity research.             

I should add that there are obviously many research areas where digital specimens cannot possibly replace the real thing.  There is no DNA in a data file.  Specimens have proved to be goldmines for those working on plant genetics.  As sequencing techniques become more sophisticated, even the rather short degraded DNA fragments found in specimens, hundreds if not thousands of years old, can provide substantial information on a plant’s relationship to other species.  But this isn’t the only reason why physical specimens need to be retained.  They can give clues on chemical changes in plants under siege from herbivores (Zangerl & Berenbaum, 2005), and more than one entomologist has found new insect species hidden away on plant specimens (Whitehead, 2016).  Each specimen is unique:  a particular plant collected at a particular place and time, and therefore irreplaceable.

References

Heberling, J. M., Miller, J. T., Noesgaard, D., Weingart, S. B., & Schigel, D. (2021). Data integration enables global biodiversity synthesis. Proceedings of the National Academy of Sciences, 118(6). https://doi.org/10.1073/pnas.2018093118

Whitehead, D. R. (1976). Collecting Beetles in Exotic Places: The Herbarium. The Coleopterists Bulletin, 30(3), 249–250.

Zangerl, A., & Berenbaum, M. (2005). Increase in toxicity of an invasive weed after reassociation with its coevolved herbivore. Proceedings of the National Academy of Sciences, 102(43), 15529–15532. https://doi.org/10.1073/pnas.0507805102