Getting the Most Out of Herbaria

1 Dig 2.0

Representation of Digitization 2.0 from “Digitization and the Future of Natural History Collections,” Hedrick, et al., BioScience, February 2020.

In our culture there is a direct connection between usefulness and value, so it’s not surprising that the arguments for preserving natural history collections entail how useful they are in many scientific endeavors.  The late Smithsonian taxonomist, Vicki Funk, is well-known for her 2003 commentary, “100 Uses for an Herbarium (Well at Least 72).”  More recently there have been articles on how collections have been utilized in the past and on how they could be employed in the future.  These studies take into account how specimen digitization is opening new ways of employing specimens in biological inquiry.  This series of posts will deal with some of these avenues, beginning with the general overview presented here.

Last fall, Heberling, Prather, and Tonsor published an article (2019) that reported on a computational text analysis of over 13,000 journal articles published between 1923 to 2017 and dealing with plant collections.  Investigation of the abstracts categorized the research into 22 topics ranging from taxonomic monographs and revisions as the most common, to morphology and anatomy ranking twenty-second.  Taxonomic work rated as most frequent throughout the study period and for most subtopics in this area the output was relatively steady over time.  However, the authors found that more recently, there have been a wider variety of topics employing herbarium specimens.  These include DNA sequencing of specimen samples and investigations of shifts in phenology over time, along with other measures of environmental change.

While there is nothing particularly shocking about the findings, this is still an important study.  First, it is broad in terms of both the time span and the number of articles covered.  Also, the authors used a rigorous methodology to come up with categories and to apply these to the texts.  Finally, this publication gives those in the natural history collection community a good citation in bolstering their case for the increasing importance of their work:  its increasing breadth promises to grow in the future if properly supported.  Another interesting, though narrower, survey in the same vein was conducted by researchers at the herbarium of the Natural History Museum, London (Carine et al., 2018).  They used 12 categories condensed from Funk’s longer list, analyzed articles published between 2013-2016 by means of the Web of Science, and then compared these results with a survey of researchers who visited NHM to use the herbarium.  In both approaches, taxonomic work ranked highest, but coming in second among the herbarium visitors was historical research.  This is in light of the herbarium’s large and rich historic collection including the herbaria of Hans Sloane and Joseph Banks.  The authors note that this number also reflects their recent work to encourage historical research.

While the studies just cited looked at past work, several publications highlight the bright promise of natural history collections in the digital age.  The author of one of these articles, “Collections-based science in the 21st Century,” is Vicki Funk (2018).  She notes that it is not only the great increase in specimen data now available on line that renders specimens so useful, but also the fact that what is called “next generation” DNA sequencing makes it more feasible and easier to sequence partially degraded DNA, the type found in most specimens.  This opens all kinds of possibilities for phylogenies based in part on specimen data as well as work in evolutionary medicine and ecology.  Georeferencing specimens also opens the way for several kinds of studies including niche modeling and climate change forecasts.

Shelley James and her coworkers give a long list of research projects using herbarium data:  “The addition of non‐traditional digitized data fields, user annotation capability, and born‐digital field data collection enables the rapid access of rich, digitally available data sets for research, education, informed decision‐making, and other scholarly and creative activities” (p. 1).  However, this bright future will only come about through investment of resources that go beyond just getting data online.  The information has to be properly coded so it can be easily retrieved in many different ways and integrated with a variety of other systems so that specimen data is tied to DNA sequences, as well as to ecological evidence and the taxonomic literature.  These are examples of what is coming to be called Digitization 2.0, that is, building on the initial digitization of label data and imaging by integrating this input with genetic and ecological data and by augmenting it with more sophisticated forms of visualization.

European researchers are coming to similar conclusions.  Besnard et al. list many of the same uses mentioned above, noting that this data can be helpful in managing genetic crop resources and monitoring crop pathogens.  Lang and her coauthors provide a good review of employing specimen data to study global environmental change with an emphasis on tracking climate change, the spread of invasive species, and on the effects of pollution and habitat change.  And while I don’t want to put a damper on these bold plans, Bingham et al. have written a comprehensive article on the large number of portals and other digital projects at various levels from the local to the international.  Many of these are not closely tied to or integrated with other projects, and some closely duplicate the efforts of others, so there seem to be too many cooks in the kitchen.  This doesn’t make sense in light of the limited financial and human resources available and the vast job to be done.  Despite this, there are some very interesting projects successfully using herbarium data, and I will touch on them in the next several posts.

References

Carine, M. A., Cesar, E. A., Ellis, L., Hunnex, J., Paul, A. M., Prakash, R., Rumsey, F. J., Wajer, J., Wilbraham, J., & Yesilyurt, J. C. (2018). Examining the spectra of herbarium uses and users. Botany Letters, 0(0), 1–9.

Funk, V. A. (2018). Collections-based science in the 21st Century. Journal of Systematics and Evolution, 56(3), 175–193.

Heberling, M., Prather, L. A., & Tonsor, S. (2019). The changing uses of herbarium data in an era of global change. BioScience, 69(10), 812–822.

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