Getting the Most Out of Herbaria: The Environment

A major argument used for preserving and digitizing natural history collections is that they contain critical information useful for researchers attempting to understand climate change.  This idea is now so much a part of the herbarium communities’ thinking that I hesitate to mention it, but there are some interesting examples worth noting on how botanists are mining collections.  Phenological research on specimens have been going on for years and its success in documenting changes in flowering, fruiting, and other points in plant life cycles have bred more such work.  This has gotten to the point where digitization efforts have become more focused on carefully documenting the phenological status of plants in a rigorous and systematic way, so this information can be mined from databases.  The NSF is sponsoring a project of the California Herbarium Consortium to do just this, including training citizen scientists to identify phenological status and record it in the online specimen records (Yost et al., 2020).

However, there isn’t a clear cause and effect relationship between increasing temperature and phenology.  Some species seem more affected than others, and some show little effect, with many factors involved in these differences.  Also, phenological changes can lead to more than just a habitat too warm for a particular species.  For certain orchid species, flowering times have not changed, but the emergence their pollinators have been pushed earlier.  This means that the pollinators will not find the resources they need from these orchids, and when the flowers do bloom, the insects they rely on may no longer be around or may have moved on to other species.  It’s a complicated dynamic, which is why a variety of species in many different habitats need to be investigated.

One cause of climate change—carbon dioxide (CO2) increases in the atmosphere—can have effects on plant physiology and morphology.  Not surprisingly these include an impact on the apparatus for the process that uses the gas, namely photosynthesis.  Researchers in New Zealand measured stomatal density on leaves in specimens from their national herbarium.  Since stomata are the leaf structures that allow in CO2, their number indicates how much of the gas a leaf can absorb at one time.  Some material in the study dated back to Captain James Cook’s first voyage to New Zealand in 1769-1790.  Since the specimens were so old and fragile, the botanists employed an indirect technique to examine the leaves.  After painting the leaves with gel that was allowed to harden, they gently removed the film, which had an impression of the stomata from the leaf surface.  Karaka tree leaves (Corynocarpus laevigatus) gave particularly good prints.  Fortunately, specimens of this species had been collected at several sites.  The researchers also counted stomata on Karaka leaves collected in the late 19th century, as well as modern specimens and fresh material.  There was little difference in stomata density between the 18th and 19th century, but the modern-day leaves had about 50% fewer pores, suggesting that increased CO2 concentrations in the air meant that the plant could absorb the same amount of gas while expending less energy creating these structures.  I went into this example in some detail to show the thinking and work involved in any one study to provide a single piece of information about the climate change puzzle.

While fungi are not technically plants, historically they have been treated as such, remain in many herbarium collections, and are studied by those who call themselves botanists.  Researchers at the University of Arizona have created a collection of 7,000 specimens of endophytic and endolichenic fungi, that is, those that live inside the cells of healthy plants and lichens respectively.  This team emphasizes that they are dealing with healthy organisms, since the fungi are beneficial rather than harmful to their hosts.  These fungi are receiving a great deal of attention because of their importance in moving nutrients between plants and the environment.  What makes this particular collection significant is that it is not historical.  It was created in the digital age, with all the information entered directly into a database with extensive metadata on location and host, as well as genetic sequencing data, namely DNA barcodes.  The latter provide a way to identify many fungi that are otherwise difficult to distinguish from one another.  The organisms were collected from a variety of plant and lichen hosts at 50 locations throughout Arizona, representing a range of habitats.   Because the resulting database is so sophisticated, researchers were able to analyze the data and “highlight the relevance of biogeography, climate, hosts, and geographic separation in endophyte community composition” (Huang et al., 2018, p. 47).

Another Arizona study was done by a student at Arizona State University who collected weedy plants from alleyways in Tempe, Arizona.  He used the SEINet database of southwestern plant specimens to attempt tracking the first occurrence of these weeds in the area.  He collected specimens from 83 species, but was only able to trace a portion of these back to early introduction.  However, the study serves as a baseline for future work on urban weeds, a topic gaining more attention.  A small but useful study done in Mexico showed that the measure of weediness among a group of related species was about the same when based on field observations versus herbarium specimens.  They employed a recognized scale of synanthropy, that is, the “degree to which a species associates with human-caused disturbance” (Hanan-A et al., 2016, p. 1).  They found that the index generated comparable weediness ratios from field observations and herbarium specimens, indicating that specimens could be used to measure weediness.

References

Hanan-A., A. M., Vibrans, H., Cacho, N. I., Villaseñor, J. L., Ortiz, E., & Gómez-G., V. A. (2016). Use of herbarium data to evaluate weediness in five congeners. Annals of Botany Plants, 8.

Huang, Y.-L., Bowman, E. A., Massimo, N. C., Garber, N. P., U’Ren, J. M., Sandberg, D. C., & Arnold, A. E. (2018). Using collections data to infer biogeographic, environmental, and host structure in communities of endophytic fungi. Mycologia, 110(1), 47–62.

Yost, J. M.et al. (2020). The California Phenological Collections Network: Using digital images to investigate phenological change in a biodiversity hotspot. Madroño, 66(4), 130–141.

On the Road, Learning about Herbaria: The ESN

Diagram of an Extended Specimen Network (ESN) from Extending U.S. Biodiversity Collections to Promote Research and Education

This post continues my report on the Digital Data Biodiversity Research Conference held at Yale University in June (see 1,2).  Digitizing the nation’s millions of natural history specimens is a massive undertaking.  iDigBio is the National Resource for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation.  As the iDigBio website notes:  “Through ADBC, data and images for millions of biological specimens are being made available in electronic format for the research community, government agencies, students, educators, and the general public.”  Under this umbrella there have been a number of other projects including the TCNs or Thematic Collection Networks, through which particular types of collections were digitized with a focus on research questions that could be answered by the digitized data.  For example, there was one on insect herbivores, their parasitoids, and their host plants.

Another related project just being completed is the Biodiversity Collections Network (BCoN) “to support the development of a new, sustainable community of practice that will ensure that all U.S. biodiversity collections are digitally available for research, education, informed decision-making, and other scholarly and creative activities.”  This spring, BCoN released a report along with an informative summary.  The report develops the concept of yet another acronym, the ESN or Extended Specimen Network.  Now that information on a substantial number of natural history specimens has been digitized, the biodiversity science community is looking at ways to maximize use of this data, as well as opening it to new user communities.

The ESN is an exciting idea with specimens as the focus.  There are three layers of extensions out from the specimen (figure above).  First, the digital specimen record and an accompanying specimen image, or in some cases, a 3-D image file.  Second would be links to field notes and images, gene sequences, morphometrics, and isotope data.  The third includes phylogenies, species descriptions, ecological interactions, distribution maps, and protection status locations.  The report envisions that a user could enter the name of a species into a portal and from that one portal be able to access all these types of information for that species.  This would be a dream come true for biologists and might be a way to counteract the increasing specialization that has so changed the discipline over the past 200 years:  geneticists being able to easily call up information on the source species for a gene sequence and ecologists finding phylogenies for related species in an ecosystem.

Right now the ESN is more a concept than a reality.  Yes, at least some of the circles in this diagram are connected to each other for at least some species or for some geographic areas.  As I discussed in an earlier post, projects such as NEON and the Map of Life (MOL) are moving in the direction of integrating at least some of these pieces, but also as mentioned in that post, the problems of integration are massive.  It is as if iDigBio and other projects have amassed the building blocks for an intricate structure, most of which remains unbuilt, with even the plans in a rudimentary stage, and with developers trying to devise tools that will allow the building to continue.  Still, I find the ESN an exciting idea and can’t wait to see it evolve.  In the two years since the first Digital Data conference, projects such as MOL have made amazing strides, and so the next conference scheduled for Indiana University in 2020 will surely show significant progress on the ESN.

At the end of two days of presentations, there was a reception and poster session in the great hall of Yale’s Peabody Museum of Natural History.  This venue is noteworthy because of The Age of Reptiles, a massive mural depicting the history of dinosaurs on earth (Volpe, 2007).  It was created by Rudolph Zallinger in the 1940s and covers one long wall of the main gallery.  My poster stood under it and presented the argument that the ESN should be extended even further to include more historical material, and that biodiversity digitization projects should be linked to such large-scale digital humanities projects as the Darwin Correspondence Project and the website for the Dumbarton Oaks exhibit on the Botany of Empire in the Long Eighteenth Century.  In fact, JSTOR, the digital library database, and Dumbarton Oaks Research Library hosted a workshop in late 2017 in which they brought together historians of science, librarians, and technical experts to brainstorm and come up with ideas for future work in connecting biodiversity studies and the humanities.  There they developed ideas for linking different resources that are reminiscent of the ESN, including one where the focus would be on taxa.  Other possible points of entry could be through a geographic area, an expedition, and a collector or taxonomist.  There is an interesting video on the workshop that gives a good recap of its work.

My dream is that those involved in the ESN would meet with a group similar to the one convened at Dumbarton Oakes Library, and that they would explore where their various inquiries intersect.  A couple of years ago, E.O. Wilson (2017) published The Origins of Creativity, in which he argues that the sciences and humanities are much more intertwined than is usually assumed.  It would be a fitting tribute to the person who made the word biodiversity so central in present-day biology, to work toward interconnectivity between these two great accomplishments of the human species.

References

Volpe, R. (2007). The Age of Reptiles: The Art and Science of Rudolph Zallinger’s Great Dinosaur Mural at Yale. New Haven, CT: Peabody Museum of Natural History.

Wilson, E. O. (2017). The Origins of Creativity. New York, NY: Norton.

On the Road, Learning about Herbaria: Education and Citizen Science

BLUE Port: Biodiversity Literacy in Undergraduate Education

In the last post, I described sessions I attended at the Digital Data Biodiversity Research Conference at Yale University.  Besides presentations on portals that integrate various kinds of data and on projects to create and analyze 3-D images of specimens, there was an emphasis on education.  Now that so much specimen data and other biodiversity information is available digitally, one of the major goals of iDigBio, the National Resource for Advancing Digitization of Biodiversity Collections (ADBC) funded by the National Science Foundation, is to have this data used widely.  This requires education, both of the present research community and of its future members.  For several years, iDigBio has been holding workshops and conferences, like the one at Yale.  These have resulted in a major upswing in the number of studies and publications employing biodiversity data.  Now that many professionals are trained in how to access and analyze the available information, it’s time to leverage this knowledge.  The task is to help these experts teach the next generation.

As every teacher realizes, knowing something is very different from teaching about it.  The subject matter has to be analyzed and organized; ways into the basics have to be found; a learning structure has to be created.  For many years, I was involved with the BioQUEST Curriculum Consortium and attended a number of workshops dealing with using genomic data in teaching genetics and bioinformatics.  The portals for gene sequence data are extremely powerful, but they were built for researchers who committed a great deal of time to learning to use them effectively.  Teachers, and even more so students, do not have the time, the technical support, nor the expertise to make effective use of these portals.  That’s where BioQUEST and other initiatives came into play.  At the workshops I attended, we learned enough about the available resources to “tame” them, to download data and present it to students in a way they could understand and use.  We became part of an education community committed to bringing students into the genetic sequencing research space in a way that would make sense for them.

Now the same kinds of initiatives are being developed for biodiversity research using powerful tools like iDigBio, GBIF, NEON, and MOL discussed at the conference (see last post).  Anna Monfils of Central Michigan University is the principle investigator for an NSF-funded project called BLUE: Biodiversity Literacy in Undergraduate Education that includes participation from BioQUEST.  Monfils and members of her team led a lively session at the conference on the question of what biodiversity literacy means and how to achieve it.  As the conversation developed, it became clear that these are not easy issues to resolve.  However, the BLUE project is a great first step in defining what a biology student needs to have in terms of conceptual understanding and technical skill to tackle the vast ocean of biodiversity data now available to them.  What didn’t arise as strongly is an issue that is dear to my heart:  how do you make biodiversity data understandable and accessible to students who are not majoring in biology or environmental science?  One of iDigBio’s aims has been to broaden the community of biodiversity data users, and non-scientists make up a huge audience.  Taming data for them is very different than for those interested in science, but everyone encounters organisms in their lives every day, so why not make it easier to learn more about them?

One way into such learning is through an area that has burgeoned in the last few years and that had a larger presence at the conference than in the past:  citizen science.  The field has many different aspects from political advocacy to volunteer data entry.  Examples of the latter include the development of portals such as Notes from Nature, where many institutions with natural history collections post well-defined projects such as digitizing specimen data.  The Smithsonian has an online transcription center where notebooks, journals, and letters are posted.  All these sites have sophisticated digital architectures that allow data managers to have confidence in the input, such as by having the same data entered by more than one user and then compared.  Many of those involved have commented on how fast the projects are completed.  Sometimes thousands of individuals participate, with a number being very committed and doing a great deal of data input.  In cases like this, citizen science is another name for unpaid help or volunteering.  With an increasing number of retirees looking for something interesting to do, these projects are very attractive because there is no commute involved and fascinating things to learn.

Still another type of citizen science work is done by those who use portals such as iNaturalist to record field observations and phenological information.  These data ultimately are uploaded into GBIF, a global biodiversity portal, and the citizen science input has grown to the point where it is having a significant impact on biodiversity research.  Walter Jetz of Yale University and principle investigator for the Map of Life (MOL) project, commented on the importance of citizen science several times in his presentation.  Not surprisingly, this is particularly true in ornithological research where amateurs have always been especially welcomed by the scientific community.

On the Road, Learning about Herbaria: Digitization

iDigBio Portal

I recently went north, to Yale University, for the third annual Digital Data Biodiversity Research Conference, sponsored by iDigBio, the NSF-sponsored project to digitize natural history specimens.  I attended the first of these conferences two years ago at the University of Michigan (see earlier post).  Both were fascinating and informative, but also different from each other, in that the focus of attention in this field has moved beyond digitizing collections to using digitized collections.  This seems a healthy trend, but as Katherine LeVan of National Ecological Observatory Network (NEON) mentioned, only 6% of insect collections have been even partially digitized, and Anna Monfils of Central Michigan University noted that iDigBio has information from 624 of 1600 natural history collections in the United States.  Admittedly, it’s mostly small collections that aren’t represented, but Monfils went on to show that smaller collections hold larger than expected numbers of local specimens, providing finer grained information on biodiversity.

Despite the caveat about coverage, the results of the NSF funding is impressive and is leading to an explosion in the use of this data.  It is difficult to keep up with the number of publications employing herbarium specimens as sources of information for studies on phenological changes, tracking invasive species, and monitoring herbivore damage.  While the earlier conference included sessions on using data for niche modeling, the meeting at Yale also had presentations on how to integrate such data with other kinds of information.  Integration was definitely a major theme, and two large-scale projects are front and center in this work.  Nico Franz of Arizona State University is principle investigator in NEON, a massive NSF-funded project that includes 22 observatories collecting ecological data, including specimens, and then using that data in studies on environmental change.  Franz noted that while other projects might collect data over short periods of time, NEON plans for the long-term and for building strong communities sharing and using that data.

Another large sale project, one headed by Yale professor Walter Jetz, is called Map of Life (MOL).  Here again, integration is central to this endeavor that invites researchers to upload their biodiversity data and also to take advantage of the wealth of data and tools available through its portal.  As the name implies, biogeography is an important focus, and users can search for distribution maps for species and create species lists for particular areas .  As with many digital projects, this one still has a long way to go in terms of living up to its name, which implies a much broader species representation than is now available.  In a session led by MOL developers, it became clear that the issue of how different kinds of data can be integrated is still extremely fraught.  Even databases for different groups of organisms, vertebrates versus invertebrates for example, are difficult to integrate because important data fields are not consistent:  what is essential in one field, might not be noteworthy at all in another or might be handled in a different way.  Progress is being made, but as Roderick Page of the University of Glasgow notes, even linking to scientific literature is hardly a trivial task, to say nothing of more sophisticated linking.

While this may seem discouraging, there were also many bright points in the presentations.  The massive Global Biodiversity Information Facility (GBIF) has, as I write, 1,330,535,865 occurrence records, that is, data on specimens and observations.  Last year, GBIF launched an impressive new website and often adds new features.  While the tools available through GBIF are not as sophisticated as with some other portals, it is still an incredible resource since iDigBio data is fed into GBIF as well as data from projects around the world.  For example, data from the University of South Carolina, Columbia A.C. Moore Herbarium where I volunteer, which was fed into SERNEC and iDigBio, is now also available in GBIF, so researchers worldwide can access data on this collection that is particularly rich in South Carolina plants.  This was not an easy undertaking—nothing in the digital world is—and it’s important to always keep that in mind as developers have flights of fancy about could be possible in the future.

Another conference highlight for me involved the use of sophisticated neural network software, such as that coming out of the Center for Brain Science at Harvard University.  James Hanken, Professor of Zoology and Director of the Museum of Comparative Zoology at Harvard, reported on a project to scan slides of embryological sections and then use the neural network software to create 3-D reconstructions of the embryos.  Caroline Strömberg of the University of Washington discussed a project to build a 3-D index of shapes for phytoliths, microfossils from grass leaves that can be more accurate for identifying species than pollen grains.  Her lab has studied 200 species and has quantified 3-D shapes, even printing them in 3-D to literally get a feel for them.  They used this information in a study of phytoliths from a dinosaur digestive track suggesting that grasses are older than previously thought.  Others have questioned these results, so Strömberg’s group is now refining the identification process, measuring more points on the phytolith surface.  Reporting on another paleontological study, Rose Aubery of the University of Illinois described image analysis done with Surangi W. Punyasena on plant fossil cuticle specimens to obtain taxonomic information about ancient ecosystems.  What all these presentations had in common was the use of massive computational power to analyze 3-D images.  At the first conference, reports of 3-D imaging were impressive, but now it is the analysis that has taken center stage.  This is a good sign:  all that data is proving valuable.

Vicki Funk: Thinking Big about Collections

4 ala

This is a last in a series of posts [1,2,3] on the plant systematist Vicky Funk and her recent review article on collections-based research.  Since Funk is a research scientist and curator in the National Museum of Natural History’s (NMNH) Botany Department, it isn’t surprising that she begins a section on the future use of collections with stats on herbaria.  The NMNH, part of the Smithsonian Institution, is home to the U.S. National Herbarium, with a collection of over five million specimens.  The goal there and at many herbaria is to digitize the data for all specimens and in some cases to also image them.  If this could be done at every herbarium, the data would serve as a potent research tool not only for taxonomists but for ecologists, conservationists, and researchers in other fields who never before considered using the information about plants available in herbaria.

One burgeoning field based on the availability of digital specimen images is computer vision and machine learning techniques that make automated plant identification possible.  It is sort of face recognition for plants and is developing to the point that herbarium specimens can be sorted rather well, though the processes are hardly at the point where identification is as good as that done by taxonomists.  However, machine sorting could be employed as a way to narrow down the number of specimens a researcher would have to look at in hunting for new species.  One recent report the computer was able to distinguish between moss groups better than the human eye could.

Funk cites several successful digitization projects, noting that the Atlas of Living Australia is a particularly comprehensive one that has resulted in online access to all records of Australian plant specimens held in the country’s national herbaria.  Australia is also at the forefront in developing software tools to assist researchers in extracting as much information as possible and in the most effective ways.  However, Funk sees the future as going beyond national or even regional databases:  “A Central Portal so all resources are available to everyone is critical.  It is particularly important that these efforts are making the data and images available to researchers in the countries where the specimens were collected, thereby supporting research in those countries” (p. 185).  She is referring to the fact that the bulk of specimens collected in developing countries, particularly during their colonial pasts, are held in European and North American herbaria.  A first attempt to make these specimens broadly available was the Andrew W. Mellon Foundation funding of type specimen digitization, the results now accessible through JSTOR Global Plants along with a great deal of supporting botanical literature.

But what Funk visualizes is something more comprehensive, and as an example, she describes a project funded by the Powell Center of the US Geological Service.  It focuses on the approximately 2500 species of North American Compositae (Asteraceae) and the location data on hundreds of thousands of specimens aggregated from GBIF (includes information from institutions outside the US), BISON (from US government institutions) and iDigBio (US private institutions).  Funk notes that this data is not only aggregated but “cleaned” to make sure it is of high quality, an issue that critics of aggregation emphasize.  The data is then integrated with environmental and geophysical data on geochemistry, climate, topography, etc., as well as phylogenetics—including gene sequences from GenBank.  Think of the power of this:  linking specimens with sequence and environmental data.   This is truly a harbinger of a new age in collections-based research.  It is amazing that ten years ago, just digitizing data and imaging specimens was considered a feat, with the Paris Herbarium’s plan to digitize most of its specimens considered daring.  Now the assembly line method they used has become relatively common, and other large herbaria have substantial percentages of their collections digitized and imaged.

Linking natural history collections to genetic data banks means uniting the two great arms of bioinformatics.  It is a biologist’s dream come true, and this connection will become even more powerful when environmental data is brought into the mix—a much more complex process.  But Funk has seen the digital world burgeon and has been one of the forces behind making it applicable to systematics.  She has also helped make systematics valuable to other fields such as phylogenetics and the growing discipline of phylogenomic—being able to sequence and compare entire genomes.  This is the result of new sequencing techniques that utilize fragmented DNA, just the type available in herbarium specimens.  Drawing on an example from the Asteraceae, Funk cites a study in which the entire genomes of 93 of 95 Solidago, goldenrod, herbarium specimens were sequenced with the plants ranging in age from 5-45 years (Beck & Simple, 2015).

In closing Funk notes:  “One exciting trend is the developing field of Integrative Systematics where collections-based systematics is combined with extensive field studies, phylogenetics, phylogenomics, detailed morphological studies, biogeographic inferences and diversification analysis to present a more comprehensive global” (p. 187).  She also argues for the maintenance of collections in educational institutions to insure the instruction of future generations of systematists; the digitization of cleared leaf slides, anatomy slides, pollen images, chromosome count images, and illustrations to fill out the information available to researches; and finally a series of symposia on the Tree of Life where systematists can map out a research agenda for the rest of the 21st century.

References

Beck, J. B., & Semple, J. C. (2015). Next-Generation Sampling: Pairing Genomics with Herbarium Specimens Provides Species-Level Signal in Solidago (Asteraceae). Applications in Plant Sciences, 3(6), 1500014.

Vicki Funk: The Age of Tree Thinking

3 idigbio

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.

Vicki Funk: The History of Collections-Based Science

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In the last post, I introduced Vicki Funk, a plant systematist who is a research scientist and curator at the U.S. National Herbarium, part of the Smithsonian Institution’s National Museum of Natural History.  There I mentioned that Funk had recently published a review article called “Collections-Based Science in the 21 Century,” published in the May 2018 issue of the Journal of Systematics and Evolution.  As with most review articles, it begins with a historical perspective.  The first sentence is a bold claim:  “Major revolutions in scientific thought have occurred because of collections-based research” (p. 175).  Funk is in a position to know both because she works in an institution with a premier natural history collection, and because she herself has contributed to today’s revolution in how collections are accessed and utilized.

Funk begins with the age of classification and Carl Linnaeus’s heavy reliance on natural history collections in creating his artificial system of classification and nomenclatural reform.  Michel Adanson and Antoine Laurent de Jussieu, working at the botanical garden in Paris with its notable herbarium, devised natural classification schemes that in various forms eventually replaced the Linnaean artificial system.  The 19th century, Funk notes, began with Alexander von Humboldt’s expedition to Latin America that gave him the perspective to develop the field of biological and physical geography, along with ecology and meteorology.  He and his traveling partner Aimée Bonpland collected 50,000 specimens, documenting many new genera and species as well as the relationship between geography and species distributions.  Later, Charles Darwin, Joseph Dalton Hooker, and Alfred Russel Wallace not only collected specimens but used them to build on Humboldt’s work and to document the concept of species change.  With examples like this Funk makes clear the connection between collection and theory building, as well as the importance of great natural history museum collections, many of which were built in the 19th century.

Funk terms the 20th century the “Age of Synthesis” in reference to the evolutionary synthesis that developed at mid-century and to “four collection-based ideas and methods that changed . . . the way we do science” (p. 178).  The first was the concept of continental drift and with it the idea that land bridges between continents had existed in the past.  Both Humboldt and J.D. Hooker argued for these from the similarities among organisms in areas that are now separated by great distances.  Second was the development of phylogenetic systematics or cladistics, a field to which Funk has contributed a good deal both theoretically (1991) and in terms of her research, especially on the Asteraceae.  Cladistics deals with using derived characters to objectively construct relationships, then grouping taxa so all are descended from a single common ancestor without omitting any of its descendants.  This is a complex field, and as a recent issue of the American Journal of Botany (August 2018) on fossil plants reveals, there are problems that arise when only living species are used in creating monophyletic groups, so fossil collections are crucial to the process.

Under the third 20th-century trend, Funk lists databasing collections, biodiversity science, and niche modeling.  This is a huge triumvirate, but with its parts closely tied together.  Databasing collection data—specimen identification as well as place and time of collection—makes it possible to more easily assess data on the biodiversity of a region as well as on how it may be changing over time.  It also allows rigorous niche modeling, a term for techniques employing occurrence data to model the possible spatial extent of a species based on geographical and climatic data.  Ecology has always been a field using sophisticated mathematical models but the availability of digital data and high-speed computing have caused an explosion in research.  And this is really only the beginning, as more collection data and analytic tools come online.

The final concept Funk cites as developing in the 20th century is molecular phylogenetics, the analysis of gene sequences as a way to discover phylogenetic relationships.  She writes:  “Collections are an excellent source of material for the extraction of DNA, but they are also important because they provide the vouchers of the DNA sequences, and their presence allows us to check the identification of samples and to gather the data needed to ask questions about character evolution and modes of speciation” (p. 180).  These vouchers usually contain at least some geographic information, bringing in the biogeography she mentioned earlier.  Molecular systematics helped to clear up some arguments about derived characters used in cladistics and resulted in a major reorganization of plant phylogenetics.  As will become apparent in the next two posts, sequencing techniques have changed rapidly during the latter part of the 20th and into the 21st century, increasing the efficacy of DNA analysis with herbarium specimens.  These tools now allow sequencing of species for which no fresh material is available because the species are rare, inaccessible, or even extinct.  If historical material is available, they also enable work on how the genetics of a species may have changed over the last few hundred years.

Vicki Funk and the Uses for a Herbarium

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Montanoa hibiscifolia, photo by Forest & Kim Starr.

Early in my romance with herbaria I came across an article by Vicki Funk called “100 Uses for an Herbarium (Well at Least 72).”  Learning about the many ways plant collections can be utilized got me even more excited about them.  I also felt I had met a friendly member of the herbarium community, someone with a sense of humor.  She came up with a great title for her piece and then stuck with it even though she didn’t quite get to the magic number her title promised.  In the piece, Funk lists herbarium functions from verifying plant Latin names in issues of nomenclature, to serving as a repository for voucher specimens, to making specimens available to students and interested members of the public.  This article was written in 2004, and I am sure that Funk could come up with many more roles today.  She in fact does move in that direction in a major review article she recently published on “Collections-Based Science in the 21st Century” (2018).  I plan to use that article as the basis for this series of posts, but first I’ll say a little more about Vicky Funk, who seems to me to be the epitome of a plant systematist in the 21st century.

Focusing on Funk’s work right now is particularly timely because she has won the 2018 Asa Gray Award, the American Society of Plant Taxonomists’ highest honor.  The fact that her nomination was accompanied by 18 letters of support suggests just how deserved this recognition is.  Funk is a research scientist and curator at the U.S. National Herbarium in the Department of Botany at the National Museum of Natural History, part of the Smithsonian Institution.  She is an expert on the Asteraceae or Compositae and is lead editor for the 2009 Compositae: Systematics, Evolution, and Biogeography of the Compositae.  This is a massive work in every sense of the term because it treats one of the largest flowering plant families.  She has also been involved in the creation of the digital Global Compositae Checklist.

Funk received her Ph.D. from Ohio State University for work on Montanoa, a genus of plants with daisy-like flowers in the Heliantheae or sunflower tribe of the Asteraceae.  They are native to Central and South America, but since then Funk has worked in Hawaii, Guyana, and a number of other places, and perhaps most importantly in the developing field of phylogenetics.  She has also been an important figure in the development of plant cladistics and is coauthor of the classic, The Compleat Cladist.  While doing all this research, she has been a good citizen of the plant systematics community as president of both the American Society of Plant Taxonomists and the International Association of Plant Taxonomists.  I have yet to meet Funk, in part because I am in awe of her.  However I have heard her speak; her passion, intelligence, and good sense come through along with her deep and comprehensive knowledge of the field.

Funk has also been a hard working member of the Smithsonian scientific community.  I keep up with her through the pages of the U.S. National Herbarium’s newsletter that has the great title The Plant Press and is available online.  The first issue I read was from 2007 when she had the lead article on the 20-year project of the National Museum of Natural History called the Biological Diversity of the Guiana Shield program.  As Funk describes it, the shield is a geological formation of igneous and metamorphic rock that underlies the northeast corner of South America and includes parts of Venezuela, Guyana, Surinam, French Guiana, Brazil, and Columbia.   At the point when she was writing, the Shield plants checklist, of which she was an editor, was in press.  It has proven to be an important resource since its publication in 2007.  I should note that her article includes a photo of herself and two colleagues doing what is stated to be their “best” imitation of a jacana, a South American marsh bird, standing on one leg.  In a later issue of The Plant Press, (April-June 2011), she is pictured more sedately with the University of the District of Columbia students she was mentoring.  In most photos Funk is wearing Hawaiian patterned shirts replete with large tropical blooms, seemingly to remind herself of her work on Hawaiian plants and to provide others with a pleasant aesthetic experience.

But while Funk can be light-hearted, she can also be deadly serious, as she was in the October 2014 issue of The Plant Press with the opening lead article:  “The Erosion of Collections-Based Science: Alarming Trend or Coincidence?”  She unfortunately sides with the first alternative, citing a number of disturbing cases over the prior years, including elimination of the science program at the Milwaukee Public Museum, dwindling support for scientific research at Fairchild Tropical Botanic Garden in Florida, closing of the science program at the Brooklyn Botanic Garden, and diminishment of programs and staff at the California Academy of Sciences, the Field Museum in Chicago, and the Royal Botanic Gardens, Kew.  Funk then goes on to outline the results of these cuts:  less projects in developing nations to assist in their scientific and economic development, weakening of education programs in the life sciences, and reduction in research on such crucial topics as climate change.  As the following posts will illustrate, these were hardly Funk’s last words on these topics.  She is in the forefront of the effort to support the future of systematics and environmental studies.

References

Funk, V. A., & International Association for Plant Taxonomy. (2009). Systematics, evolution, and biogeography of Compositae. Vienna, Austria: International Association for Plant Taxonomy, Institute of Botany, University of Vienna.

Seeking Plants in Seattle: Burke Herbarium

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Sign from the A.C. Moore Herbarium, University of Carolina, Columbia on a cabinet in the Burke Herbarium, University of Washington.

Last month, I went to the History of Science meeting in Seattle.  I was only there for a few days, but I did manage to visit a herbarium.  It’s part of the Burke Museum of Natural History and Culture at the University of Washington’s (UW) campus, but it’s located at some distance from the museum on UW’s sprawling campus.  I was greeted by the herbarium collections manager, David Giblin, and felt right at home.  Though with 660,000 specimens it is five times larger than the A. C. Moore Herbarium at the University of South Carolina where I volunteer, it is as packed with metal cases of different vintages and also stuffed with books, posters, mounting tables, and all the other trappings of an active collection.

I arrived at a good time because Giblin, and the curator of the herbarium, Richard Olmstead, also a professor of botany at UW, were celebrating the publication of the new edition of Flora of the Pacific Northwest: An Illustrated Manual, updating the 1973 volume by C. Leo Hitchcock and Arthur Cronquist.  This was a massive revision involving two other editors, Ben Legler and Peter Zika.  Over 1000 new illustrations were added, and Giblin and his colleagues would now like to see a companion volume of illustrations, including both these and all those from the first edition.  Considering images as particularly important to botanists, he thinks this would be a valuable resource.

Over the 16 years Giblin has been at the herbarium, he has worked on several NSF-funded projects to digitize portions of the collection, including specimens collected in the 1990s on the Russian-owned Kuril Islands as part of a collaborative project of US, Russian, and Japanese scientists.  Portions of the herbarium were databased and imaged through NSF’s Thematic Collection Networks, including one on macroalgae and the other on macrofungi.  The herbarium also works on state and federal contracts, and augments its income with the publication of plant guides:  one on the Alpine Flowers of Mount Rainier and another on the plants of the Olympic Mountains.  With Seattle’s large population including many avid hikers, these have sold well.  In addition, the herbarium staff has produced a Washington Wildflowers app available for both iOS and Android.  It has excellent photographs of the plants, and more of these are available on Burke’s Image Collection website with over 68,000 photographs.  They are organized into three categories:  vascular plants, macrofungi, and lichenized fungi, but this is much more than an image gallery.  For each species there’s information on its characteristics and range.  Even if you aren’t living in Washington, it’s fun to see what plants call it home.

These initiatives indicate the dynamism of the herbarium.  Sure there are the constraints of space and funding that almost all collections face.  More than half of the specimens still need to be digitized, and Giblin and I discussed the time-consuming task of georeferencing older sheets.  Still, he is excited about the possibilities opened up by technology such as the cell phone and Google maps to lure new users to herbarium data, and new contributors to it as well through citizen science initiatives.  I enjoyed our discussion because Giblin, though cautious about the future, seemed to be looking forward to working on new projects and keeping Burke vibrant.  As I was leaving, I saw something else that reminded me of my herbarium home at USC:  one of its bumper stickers pasted to a cabinet (see above).  It’s a reminder of how prescient the USC curator John Nelson was in procuring the herbarium.org URL during the very early days of the internet.

After leaving the herbarium, I headed further into the UW campus.  Giblin suggested I visit the graduate library, which is a beautiful neo-gothic building with a lovely reading room decorated with botanical carvings (see below).  I found a cafeteria for lunch, then visited the art museum, the Henry Art Gallery, and the campus bookstore.  Finally I headed to the Burke Museum of Natural History and Culture, to see if any of the herbarium collection was on view—and it was.  Of course, many of the exhibits deal with animals: dioramas and dinosaur fossils.  Since this is also a cultural collection, they have impressive exhibits on the indigenous peoples of the Pacific Northwest, with particularly striking wood carvings.  But close to the entrance there is an interesting display of plant specimens, with information on where they were collected and why they are so important.   The exhibit focuses on plants collected on an expedition to Argentina, suggesting the breadth of the Burke Collection.  On their website there’s also a post on a graduate of the UW botany Ph.D. program, Ana Bedoya Ovalle, who returned to Columbia to collect more specimens and continue her research.

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Wood carving in the graduate library reading room at the University of Washington.

From the museum, I walked toward the Seattle Light Rail station so I could get back to my hotel.  I hardly need to add that it was raining at the time.  I passed Rainier Vista, where on a clear day you can see that mountain in the distance.  This is a very nice campus feature, but one I could only imagine.  I also crossed what is termed “Red Square” because of its red brick work, and down a mall lined on both sides with a variety of gymnosperms.  I had had a great visit to UW, and on my next trip to Seattle, I hope to venture further, and perhaps get a little closer to Mount Rainier.

References

Hitchcock, C. L., & Cronquist, A. (1973). Flora of the Pacific Northwest: An Illustrated Manual (1st ed.). Seattle, WA: University of Washington Press.

Hitchcock, C. L., & Cronquist, A. (2018). Flora of the Pacific Northwest: An Illustrated Manual. (D. Giblin, B. Legler, P. Zika, & R. Olmstead, Eds.) (2nd ed.). Seattle, WA: University of Washington Press.

Libraries and Botany: Digital Resources

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Second edition of Basil Soulsby’s catalog of the works of Linnaeus, Biodiversity Heritage Library

One of the attractive features of the meeting of botanical and horticultural librarians that I attended in New York recently (see the last two posts 1,2) is that it included both Europeans and Americans.  Since Europe is home to so many historical collections of specimens, manuscripts, and botanical art, it was great to learn more about these treasures.  It was even better to discover how many of these resources are now available digitally.  One of the high points of the meeting for me was the presentation by Félix Alonso, head librarian at the Royal Botanic Garden in Madrid.  I already knew that this library has a magnificent collection because many of its treasures are available through the Biodiversity Heritage Library (BHL), and I was glad to hear that the institution is developing a new interface to make it more user-friendly.  Accessibility was Alonso’s major theme, as he outlined plans to move the library from a collection-centered to a service-centered focus, including opening it to children for the first time in its 250-year history.

Yet another group meeting at NYBG along with the European and American librarians, was the Linnaeus Link Project, an international collaboration among libraries with significant holdings dealing with Carl Linnaeus.  It is funded, maintained, and coordinated by the Linnean Society of London, which holds the bulk of Linnaeus’s specimens, manuscripts, and books, bought from his widow by the British botanist James Edward Smith in 1784.  However, a number of institutions also have substantial holdings, and the project aims to make all the Linnaeus material available through a union catalog.  Lynda Brooks and Isabelle Charmantier of the Linnean Society Library presented on Linnaeus Link and that’s how I was introduced to “Soulsby numbers” used to identify each record.  Basil Soulsby produced the second edition of his Catalogue of the Works of Linnaeus in 1933, recording all Linnaean writings and works about Linnaeus published up to 1931; the last entry was number 3874.  Linnaeus Link uses these numbers to identify items in the Union Catalogue and is also assigning post-Soulsby numbers to items not mentioned by Soulsby; there are over 400 of these.  This project gives a glimpse into the world of librarianship and the meticulous processes involved in coordinating materials spread out over several countries.

Isabelle Charmantier also presented on the work being done to digitize the Linnean Society collections, which go well beyond those of Linnaeus and include the herbarium of the society’s founder James Edward Smith, as well as his seed collection that is now being conserved.  The seeds are still enclosed in their original wrappers that include letters, sermons, newspapers—obviously of value in themselves.  There are also the archives of Linnean Society Fellows such as Charles Darwin and Alfred Russel Wallace, and art including the watercolors of Nepalese plants that were done by an Indian artist under the direction of Francis Buchanan Hamilton.  He traveled to Nepal in 1802-1803 and recorded over a thousand species there.  Charmantier noted that at the moment, the Society has data on three platforms with variable metadata and would like to undertake the major task of uniting them, thus making the information available to users through a single search engine.

Another great botanical library is at the Royal Botanic Garden, Kew and the head of the library, Fiona Ainsworth, described its massive holdings: 300,000 books and pamphlets, 200,000 works of art, and 7,000,000 archive sheets.  At the moment, there is no digital catalog for the art collection, and it would be ideal to have it along with the herbarium and economic botany collections cataloged in one system with the library.  That is part of Kew’s plans for the future.  For the present, it is working on a five-year project to digitize and transcribe over 2000 Joseph Dalton Hooker letters, that are available on the Kew Library website.  This is a tremendous resource, especially when seen in relation to the letters of two great American botanists Asa Gray, whose correspondence has been digitized at Harvard University, and John Torrey, whose letters are now being digitized and transcribed at New York Botanical Garden (NYBG).

Stephen Sinon, NYBG’s archivist and curator of Special Collections, described the ongoing Torrey Transcription Project.  The noted 19th-century botanist John Torrey spent his life in New York and taught at both Columbia and Princeton.  He gave his letters and herbarium to Columbia College (now Columbia University), but these were transferred to NYBG when it was founded in 1898.  Most of the Torrey letters are incoming correspondence.  Almost ten thousand pages have been digitized and over 2,500 transcribed by volunteers through a crowdsourcing website.  This massive undertaking is being funded by NEH and the Carnegie Foundation of New York.  The resulting digital images are available not only through the NYBG’s Mertz Library website, but on BHL, Archive.org, and the Digital Public Library of America (DPLA).  Mentioning this project moves me away from my focus on Europe in this post, but it’s a reminder that botany knows no borders and has always been a global enterprise.  Torrey, Gray, and Hooker knew each other, wrote extensively among themselves, and visited each other’s countries.  The Americans and the British were also rivals in describing American plants, with Hooker and his colleague George Bentham avidly courting collectors, particularly in Canada, but they did not spurn US collections as well.  Torrey and Gray were well aware of this; the letters between them have many mentions of needing to name American plants quickly to prevent the British from doing it first.