Botany Today: Herbaria

Global map of biodiversity from GBIF occurrce data, showing continued bias in records from the Northern Hemisphere

While the articles I discussed in the last post on important questions facing plant research hardly mentioned herbaria, they are front and center in Charles Davis’s (2023) article: “The Herbarium of the Future.”  It’s an opinion piece in Trends in Ecology and Evolution, so it perhaps takes a broader view of the uses of herbaria than might be found in a systematics journal.  It is also written with a vitality, a lively pace, as if Davis is trying to fit in as much as possible about the promising future of herbaria—and plants—before a reader’s interest might flag.  But this is unlikely since he does a good job of introducing, one after another, aspects of the world of plant collections and how they can be used now and in the future in researching many questions that appeared in the lists of critical issues in the field (see last post).

Davis employs terms that connote change and growth.  His first heading is “A Revolution in Herbarium Use” where he outlines changes in herbaria and in how they are used.  One is what he terms the development of the global metaherbarium:  the growing collection of herbarium specimen data and images available on the internet, in most cases without paywalls.  The Global Biodiversity Information Facility (GBIF) is the largest of these portals, but there are many others including DiSSCo for European herbaria and iDigBio for those in the United States.  The data in these repositories overlap, and yet there really is no “metaherbarium” which harvests information from all other sources.  And there may never be, or at least it will take a long time to get there.

Davis is presenting what the plant science question group calls “horizon scanning,” peering into the future of what might be (Armstrong et al., 2023).  However, there are enormous technical difficulties in linking even collections that are using similar hardware and software.  The plus side is that as these problems have come to light so has the realization that they must be dealt with on a global level (Manzano & Julier, 2021).  The Alliance for Biodiversity Knowledge and other organizations such as the long-standing Biodiversity Information Standards (TDWG) are important forces in moving these goals forward.  The reason for urgency in effectively mobilizing data for all natural history collections is the crying need to use them for research on biodiversity and its conservation, or as Davis puts it: “Innovating Traditional Applications of Herbaria to Speed Discovery.” 

Writing of innovation and speed are rhetorical devices Davis uses to emphasize how critical the situation is.  There are still new species to be discovered, many of these already sitting in herbarium cabinets.  Could AI help to recognize some of them?  Here again, we are still in the early stages, but there have been significant advances in training machine learning systems to identify specimens.  The same is even more true of improvements in “herbariomics,” that is, extracting and sequencing DNA from herbarium specimens, even in cases where they are hundreds of years old.  Davis writes that:  “The metaherbarium soon will become the central resource for such [phylogenomic] investigations spanning populations, communities, and whole continents (p. 4).”  This is definitely on the far horizon.  If collection databases are often difficult to link together, how much more challenging will it be to extract DNA from far-flung collections?  Still, such forward thinking is essential so that possibilities feed into the groundwork now being laid for this bright future.  It includes training individuals worldwide in the skills needed to bring such work to fruition. 

The final section before the conclusion is entitled:  “Breathing New Life into Herbaria: Expanding Users and Novel Applications.”  This doesn’t require as much stretching to see the horizon because much has already happened here.  Ecologists are becoming more aware of herbaria as sources of information on life cycle traits and how they may change over time (Heberling, 2022).  Fifteen years ago phenological studies of the effect of climate change on flowering times were novel; now they have increased to the point of indicating the complexity and variety of species responses, on both small and large geographical scales.  Insect herbivory, fungal relationships, and pollinator interactions can be investigated, often by using more than one kind of natural history collection. 

Herbaria are also important in conservation work, in comparing past plant distributions with those of the present, and in studying how the genetics of populations may have changed over time.  There are really just too many ways herbaria can be used to list them all here or in Davis’s article (Funk, 2003).  However he does give a rather extensive list of uses, including devoting a full-page spread of photos from an exhibit at his home institution, Harvard University.  The Harvard Museum of Natural History opened “In Search of Thoreau’s Flowers: An Exploration of Change and Loss” in June 2022.  I’ve written about it before (see earlier post), but I want to mention it again here in the context of Davis’s article.  All 600 Thoreau herbarium specimens held at Harvard have been digitized.  These images are in the exhibit, presented through the work of several artists.  Davis is highlighting a trend that has become much more common in the 21^st century:  the use of herbarium specimens as inspiration for artists.  The great thing about this exhibit is that it remained up for almost a year, was at a popular museum, and highlighted the work of a well-known figure.  It was a wonderful way to introduce herbaria to a wider audience, while also highlighting the changes in the environment in which Thoreau collected.

References

Armstrong, E. M., Larson, E. R., Harper, H., Webb, C. R., Dohleman, F., Araya, Y., Meade, C., Feng, X., Mukoye, B., Levin, M. J., Lacombe, B., Bakirbas, A., Cardoso, A. A., Fleury, D., Gessler, A., Jaiswal, D., Onkokesung, N., Pathare, V. S., Phartyal, S. S., … Grierson, C. S. (2023). One hundred important questions facing plant science: An international perspective. New Phytologist, 238(2), 470–481. https://doi.org/10.1111/nph.18771

Davis, C. C. (2023). The herbarium of the future. Trends in Ecology & Evolution, 38(5), 412–423. https://doi.org/10.1016/j.tree.2022.11.015

Funk, V. A. (2003). 100 uses for a herbarium. American Society of Plant Taxonomists Newsletter, 17(2), 17–19.

Heberling, J. M. (2022). Herbaria as big data sources of plant traits. International Journal of Plant Sciences, 183(2), 87–118. https://doi.org/10.1086/717623

Manzano, S., & Julier, A. C. M. (2021). How FAIR are plant sciences in the twenty-first century? The pressing need for reproducibility in plant ecology and evolution. Proceedings of the Royal Society B: Biological Sciences, 288(1944), 20202597. https://doi.org/10.1098/rspb.2020.2597