Herbarium specimens have always been important for taxonomy, but in recent years there has been a resurgence in the use of herbaria for various avenues of biological research. Herbarium research touches on everything from ancient DNA sequencing to machine learning for species identification to climate change, making your contributions to herbaria more important than ever! While physical specimens provide the most research opportunity, digital documentation of biodiversity helps enrich global species distribution databases that can be utilized by researchers as well.

Taxonomy and Morphometrics

Herbarium specimens are indispensable for species identification. Identifying organisms to species can be extremely challenging and labor-intensive, especially when researchers need to identify all species found within a community or ecosystem. Herbaria act as an essential repository for species identification, allowing researchers to compare their specimens to those whose ID’s have been confirmed by expert taxonomists. Despite the hard work of taxonomists, thousands of herbarium specimens remain unidentified or require review after taxonomic revision. In an example of modern techniques applied to herbarium research, Carranza-Rojas et al (2017) used machine-learning technology to help identify thousands of unidentified plant specimens.

Classically, herbarium specimens are known to be extremely useful to traditional taxonomists. Just like the organisms on this planet, taxonomy is ever-evolving, with species constantly being renamed, split apart, or grouped together. Many areas do not have regional taxonomic keys, and many groups are poorly described or in need of revision. For example, Jamie Fenneman devoted the majority of his PhD thesis at UBC (2019) to the taxonomic revision of Antennaria and Symphyotrichum, two very complicated plant genera in the Asteraceae family. His research would not have been possible without the hundreds of specimens available at the UBC herbarium and associated institutions.

Herbarium specimens have also been used in the field of morphometrics – the quantitative analysis of physical forms (size and shape). In taxonomy, morphometrics can be used to delineate closely related species that may differ in several morphological traits that are difficult to categorize by the human eye. Traditionally, morphometric analysis is conducted by measuring a variety of traits using physical specimens, but now that many herbarium specimens have become digitized (check out the UBC herbarium’s database!), samples can be processed much more efficiently than before. For any specimen with a high quality digital scan is available, programs like ImageJ can be used to make standardized measurements by computer! In another example from researchers at UBC, Groh et al (2019) used multivariate morphometric analysis (as well as DNA sequencing) to characterize a hybrid population of Aquilegia flavescens and A. formosa in British Columbia.

DNA Sequencing

Since the advent of DNA sequencing technology, herbaria have been recognized as vital storehouses of DNA samples, allowing researchers to reconstruct phylogenetic trees of now-extinct lineages and examine genetic changes through time, in some cases analyzing specimens that are hundreds or thousands of years old. Unfortunately, DNA degrades over time, which initially made it quite difficult to generate high quality sequences from old specimens. Over the past 30 years, however, researchers have made great strides in DNA extraction methods that can work with old specimens (Särkinen et al 2012). DNA from herbaria has now been utilized to settle many biological mysteries, including the origins of the European potato from South American cultivars (Ames and Spooner 2008) and the recovery of the genome of the potato blight pathogen Phytopthora infestans (Yoshida et al 2014).

Biogeography

Documenting biodiversity is extremely important for research in biogeography, which is concerned with present and past species distributions and their underlying causes (environmental and historical). Researchers and policy makers need to know where species occur in order to describe their ranges and understand their movements over time.  Despite their usefulness, herbarium specimens have so-far been under-utilized for biogeography research, with the majority of studies being published in the last 20 years and only a small percentage of world’s specimens being used (Lavoie 2012). This means that herbaria provide huge untapped potential for future studies!

Biogeography is a huge field in itself that touches on several other fields within biology, so herbaria have been used in biogeographical research in a variety of ways. Dolan et al (2011) used herbarium records to investigate the effects of urbanization on the flora of Indianapolis, finding significant species turnover and a decrease in native plant species over the past several decades. Loiselle et al (2008) used over 300,000 georeferenced herbarium collections and several climate variables to predict species predictions and evaluate the accuracy of biogeographic models. Wollan et al (2008) used over 1000 herbarium collections and 75 climate variables to perform a similar study, but focused on predicting the distribution patterns of fungi in Norway.

Phenology and Climate Change

An exciting new direction in herbarium research is focused on using herbarium specimens to examine how global change might be affecting plant species’ morphology and life-history. In particular, many recent studies have focused on how plants experience shifts in phenology (the seasonal timing of life-history events such as leafing-out and flowering) in response to climate change (Willis et al 2017). Because phenological data is difficult to collect in the field, requiring long-term field observations and manipulation experiments, herbarium specimens again provide an alternative wealth of information for researchers to collect. In another example of UBC research, Kopp et al (2020) used over 8000 flowering specimens to examine how bloom-time is affected by temperature across the Pacific Northwest, and found that early-season bloomers were more sensitive to temperature than late-season bloomers.

 

References

Ames, M., & Spooner, D. M. (2008). DNA from herbarium specimens settles a controversy about origins of the European potato. American Journal of Botany, 95(2), 252–257. https://doi.org/10.3732/ajb.95.2.252

Carranza-Rojas, J., Goeau, H., Bonnet, P., Mata-Montero, E., & Joly, A. (2017). Going deeper in the automated identification of Herbarium specimens. BMC Evolutionary Biology, 17(1), 181. https://doi.org/10.1186/s12862-017-1014-z

Dolan, R. W., Moore, M. E., & Stephens, J. D. (2011). Documenting effects of urbanization on flora using herbarium records. Journal of Ecology, 99(4), 1055–1062. https://doi.org/10.1111/j.1365-2745.2011.01820.x

Fenneman, J.D.A. A taxonomic revision of the genera Antennaria and Symphyotrichum (Asteraceae) in British Columbia, Canada, with additional perspectives on the role of taxonomy within the biological sciences. PhD Thesis, University of British Columbia, 2019.

Groh, J. S., Percy, D. M., Björk, C. R., & Cronk, Q. C. B. (2019). On the origin of orphan hybrids between Aquilegia formosa and Aquilegia flavescens. AoB PLANTS, 11(1). https://doi.org/10.1093/aobpla/ply071

Kopp, C. W., Neto-Bradley, B. M., Lipsen, L. P. J., Sandhar, J., & Smith, S. (2020). Herbarium records indicate variation in bloom-time sensitivity to temperature across a geographically diverse region. International Journal of Biometeorology, 64(5), 873–880. https://doi.org/10.1007/s00484-020-01877-1

Lavoie, C. (2013, February 20). Biological collections in an ever changing world: Herbaria as tools for biogeographical and environmental studies. Perspectives in Plant Ecology, Evolution and Systematics. https://doi.org/10.1016/j.ppees.2012.10.002

Loiselle, B. A., Jørgensen, P. M., Consiglio, T., Jiménez, I., Blake, J. G., Lohmann, L. G., & Montiel, O. M. (2008). Predicting species distributions from herbarium collections: Does climate bias in collection sampling influence model outcomes? Journal of Biogeography, 35(1), 105–116. https://doi.org/10.1111/j.1365-2699.2007.01779.x

Särkinen, T., Staats, M., Richardson, J. E., Cowan, R. S., & Bakker, F. T. (2012). How to Open the Treasure Chest? Optimising DNA Extraction from Herbarium Specimens. PLoS ONE, 7(8). https://doi.org/10.1371/journal.pone.0043808

Willis, C. G., Ellwood, E. R., Primack, R. B., Davis, C. C., Pearson, K. D., Gallinat, A. S., … Soltis, P. S. (2017, July 1). Old Plants, New Tricks: Phenological Research Using Herbarium Specimens. Trends in Ecology and Evolution. Elsevier Ltd. https://doi.org/10.1016/j.tree.2017.03.015

Wollan, A. K., Bakkestuen, V., Kauserud, H., Gulden, G., & Halvorsen, R. (2008). Modelling and predicting fungal distribution patterns using herbarium data. Journal of Biogeography, 35(12), 2298–2310. https://doi.org/10.1111/j.1365-2699.2008.01965.x

Yoshida, K., Burbano, H. A., Krause, J., Thines, M., Weigel, D., & Kamoun, S. (2014). Mining Herbaria for Plant Pathogen Genomes: Back to the Future. PLoS Pathogens, 10(4). https://doi.org/10.1371/journal.ppat.1004028