Vicki Funk: The Age of Tree Thinking

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In the last post, I began my discussion of Vicki Funk’s (2018) recent article on “Collections-Based Science in the 21st Century” that I’ll continue here.  In this review, she terms the first 15 years of the 21st century “An Age of Tree Thinking,” in other words a time of investigating evolutionary relationships and the use of phylogenies.  This is a major interest of Pam and Douglas Soltis of the University of Florida, two other leaders in the field of collections-based research (Allen et al., 2019).   Funk gives examples of what she means by this term, beginning with evolutionary medicine.  This field’s work includes tracing changes in viruses as they are transmitted through a population and even within one body over time.  Funk notes that museum specimens of woodrats have been found to harbor viruses similar to those causing Chagas disease.  She also touches on food safety, beginning with GenomeTrakr a pathogen database set up by the Food and Drug Administration.  It hosts whole genome sequences for pathogens, mostly those implicated in food poisoning.  When an outbreak occurs, the pathogen involved can now be quickly sequenced, and then compared to sequences in the database; this helps to identify the source of contamination and speed control of the outbreak.

Moving on to evolutionary ecology, Funk cites a number of examples of how phylogenetics can illuminate ecological questions.  For example, DNA was sequenced from ragweed (Ambrosia artemisiifolia) specimens collected through time, both before and after deforestation in particular areas.  Pollen core data suggest that ragweed, an aggressive weed, was uncommon before deforestation.  The DNA sequencing data indicates that there was a hybridization before deforestation that may have permitted the hybrid to grow more aggressively when trees were removed.  This is a good example of pairing historical data with molecular analysis.

Funk’s paper also explores the idea of DNA barcoding, a technique that her colleague John Kress at the Smithsonian has fostered.  For plants, it involves sequencing two regions of the chloroplast genome that serve as a fingerprint for species identification.  Kress and his colleagues (2009) barcoded all tree species growing in a plot on Barro Colorado Island in Panama, a long-term Smithsonian study site.  The resulting phylogenies are being employed to investigate the relationship between habitat and community structure.  Barcodes are also used to monitor illegal traffic in endangered species, for example, as a way to identify illegal shipments of rare woods.  Since her article’s title, “Collections-Based Science in the 21st Century,” doesn’t limit Funk to only plants, she slips in a reference to molecular phylogenetics in human evolution studies, noting how DNA extracts from fossils of Neandertals and of a hominin population called the Denisovans found in the Siberian Altai Mountains, as well as from present-day humans, were employed to work out the relationship among them, with Neanderthals and today’s humans more closely related to each other than to Denisovans.  In an example relevant to botany, medically important plants have been barcoded over the past ten years, and molecular phylogenetics can be used to test the purity of ingredients in herbal medicines.  This is a perennial problem due to varying levels of quality control for these materials, resulting in impure or ineffective products.

What these examples of tree thinking have in common is that they involve DNA sequencing and the storage of that information so it can be used in future studies.  In other words, there is a summative process going on here, and these databases, if properly maintained and utilized will only become more and more valuable and effective.  In the next section of her article, Funk deals with the future, and calls it “An Age of Thinking Big.”  This theme is also taken up by a group of European researchers (Besnard et al., 2018).  Funk discusses not only collections of DNA sequences, and the voucher specimens that back them up, but also the increasing availability of online data about natural history specimens as well as images of them.  Digitization has been going on for years, especially since the development of BISON, which is a database for specimens from US government facilities such as the Smithsonian, and iDigBio, for private research and educational collections.  While more and more information is coming online, there is still a great deal to do.  To date, less than half of all plant specimens are databased, and that percentage is even lower for animals—there are an awful lot of insects out there, which were relatively easy to collect, but not so easy to image, to say nothing of jellyfish, etc.

Funk considers some of the questions that could be tackled if all specimen data were available to researchers:  “What parts of the world need additional collecting expeditions?  How many species are rare?  How many species have not been collected in the last 50 years and may be extinct?  Are there certain areas that have a lot of rarely collected species and are these areas endangered ecosystems?  How fast have invasive species moved into new areas?  How has community composition changed through time?” (p. 182).  This list is reminiscent of Funk’s “100 Uses for an Herbarium.”  With her vast experience she is very good at thinking about why collections are valuable as research tools, and this analysis is especially useful today as many collections are facing uncertain futures.  In an earlier post I cited one example of Funk’s writing on this topic.  Here I’ll end with another citation, a review article she wrote with several of her colleagues on what collection based systematics should look like in 2050 (Wen et al., 2015).  Her answers to this question will be covered in the next and last post in these series.

References

Allen, J. M., Folk, R. A., Soltis, P. S., Soltis, D. E., & Guralnick, R. P. (2019). Biodiversity synthesis across the green branches of the tree of life. Nature Plants, 5(1), 11–13.

Besnard, G., Gaudeul, M., Lavergne, S., Muller, S., Rouhan, G., Sukhorukov, A. P., … Jabbour, F. (2018). Herbarium-based science in the twenty-first century. Botany Letters, 165(3–4), 323–327.

Kress, W. J., Erickson, D. L., Jones, F. A., Swenson, N. G., Perez, R., Sanjur, O., & Bermingham, E. (2009). Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proceedings of the National Academy of Sciences, 106(44), 18621–18626.

Wen, J., Ickert‐Bond, S. M., Appelhans, M. S., Dorr, L. J., & Funk, V. A. (2015). Collections-based systematics: Opportunities and outlook for 2050. Journal of Systematics and Evolution, 53(6), 477–488.

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