Vicki Funk: Thinking Big about Collections

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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.

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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.

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.

Libraries and Botany

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Peggy Rockefeller Rose Garden at New York Botanical Garden

I recently went to New York, my old stomping ground, for a meeting of the Council of Botanical and Horticultural Librarians (CBHL).  They were celebrating their 50th anniversary and were meeting jointly with the European Botanical and Horticultural Libraries Group (EBHL), celebrating 25 years.  Despite my lack of library expertise, I went because I’m a CBHL member, induced to join by its great website, listserv, and newsletter.  I learn a lot from librarians, particularly when they are involved in things that interest me, namely plants.  I definitely learned a great deal at this conference, ate some great meals, and saw many beautiful plants.  We met at New York Botanical Garden (NYBG) in the Bronx and also spent a day at Brooklyn Botanic Garden (BBG), both possessors of amazingly beautiful gardens and libraries.  Fortunately, the weather was wonderful.  This meeting was in mid-June so both gardens were at their best, and it was great to be able to stroll around them between sessions (see photo above).

On the way to BBG, participants had the opportunity to see another impressive garden, the High Line.  This is an almost 1.5 mile “linear park” on the West Side of lower Manhattan created out of an elevated railway line that had been unused for years.  During that time plants “invaded” the 30-foot-wide expanse, in many areas turning it into green swards.  Residents had climbed onto it illegally to enjoy the greenery and began an effort to make it a park.  I can remember when this effort began.  It seemed quite unrealistic, but it kept gaining support, particularly after 9/11 when the city was looking for ways to restore itself.  The High Line is now an amazing horticultural attraction, with beautiful plants and interesting architectural features.  After being at NYBG the day before, with its 265 acres, it was very interesting for participants to see what can be done within , literally, much narrower constraints.

Then it was on to Brooklyn where we visited the library, which is located in the original administration building and has a small though beautiful reading room.  BBG gave up its science program and herbarium several years ago, a very disturbing decision; its specimens are now on long-term loan to NYBG.  The herbarium and storage for the library were located in a building across the street from the garden.  The structure needed repair so the herbarium was closed, and the librarians had to either de-acquisition material or move it into the original library’s tight quarters.  The process of organizing these resources is still going on.  A beautiful room has been built for BBG’s amazing rare book and botanical illustration collection (see photo below).  It includes the very large format, 34-volume Banks’ Florilegium of plants from Captain Cook’s first voyage around the world.  The head librarian, Kathy Crosby, also displayed a sampling of botanical illustrations created by members of the Brooklyn Botanic Garden Florilegium Society that includes many of the best botanical artists working today.

1 BBG special collections

Special Collections at Brooklyn Botanic Garden

Needless to say, everyone had another feast for the eyes at NYBG.  At the moment, the garden is celebrating the art that Georgia O’Keeffe created in Hawaii, with a number of her works in its art gallery and a display of the plants that inspired her in the conservatory.  During our tour of the library, the archivist Stephen Sinon displayed some of its treasures including its oldest book, a manuscript of the herbal Circa Instans from the  late 12th century, and one of my favorite’s Johannes Gessner’s Tabulae phytographicae, a guide to flowers using the Linnaean system that has wonderful illustrations.  Equally wonderful was a display of herbarium treasures by its director Barbara Thiers, including specimens collected by John Muir, Charles Darwin, and even Thomas Edison.  Since the herbarium has about 7.8 million specimens, this gave just a hint of the wonders it contains, including the work of such 20-21st century botanists as Pat and Noel Holmgren who recently completed the seventh and final volume of Intermountain Flora: Vascular Plants of the Intermountain West, USA (2017).

Since this was a library conference, there were presentations on the latest at a number of institutions.  Amy Kasameyer, archivist at the University of California, Berkeley Herbarium discussed the development of The Silva Center for Phycological Documentation.  Named for Paul Claude Silva (1922-1014), an expert on algae, it includes a library and archives that has been created within the herbarium.  This center is a wonderful adjunct to the herbarium’s extensive phycological collection, the second largest in the country.  Along with this example of physical collection development, there were also a number of presentations on virtual collections.  One was by Deirdre Ryan and Jason Przybylski of JSTOR, which provides access to journals in many fields as well to Artstor for art images and JSTOR Global Plants for botanical journals and over 2 million type specimens, scanned as part of the Andrew W. Mellon Foundation’s Global Plants Initiative.

JSTOR now plans to build on this foundation with a collection called JSTOR Plants & Society that would present botanical, horticultural, and ethnobotanical materials making them useful not only to scientists but to students and to the broader public as well.  In developing this project, JSTOR worked with the Dumbarton Oaks Research Library and Collection to host a workshop on Botany and the Humanities to explore what is most needed for future collaborations.  There’s a fascinating video where the participants discuss the exciting ideas that came out of their meetings.  It’s a great window into some wonderful plans for the future particularly about integrating various digital platforms.  I hope at least a few of them come to fruition as soon as possible!

Reference

Holmgren, N. H., & Holmgren, P. K. (2017). Intermountain Flora: Vascular Plants of the Intermountain West, U.S.A (Vol. 7). New York, NY: New York Botanical Garden.

Botany, History, and Art in BHL

4 Fuch Digitalis

Image of Digitalis from Leonhart Fuchs’s De historia stirpium, available in the  Biodiversity Heritage Library

In the last post, I discussed the Biodiversity Heritage Library’s (BHL) appeal to gardeners, a group not singled out by the library as significant users in one of its marketing images [see below], however, groups so cited include scientists, historians, and artists. I see myself as at least somewhat involved with the first two groups, and though I don’t have sufficient hubris or talent to call myself an artist, I do dabble and to a greater extent appreciate art. Botanical art is where all my interests come together, and there is no place like BHL to nurture them. I use the visual bookmarking tool Pearltrees to organize my finds, and I’m happy to share them with you. I found many of these through the Twitter account @histsciart created by Michelle Marshall that points to interesting images in the BHL collection.

My favorites include early printed herbals that the plant morphologist Agnes Arber wrote about so well more than a 100 years ago. When I first read her book in the 1980s I had to content myself with the images she had selected, now I can go to the sources and feast my eyes on entire volumes. Admittedly, it’s not the same as seeing the original text of the Otto Brunfels or Leonhart Fuchs herbals, as I have been able to do at Mertz Library at New York Botanical Garden (NYBG). However, a library isn’t always accessible, and it’s a tremendous luxury to decide at 10 pm that a Fuchs fix is in order and be able to succumb to the temptation (see figure above). Such books are more important historically than scientifically because they are pre-Linnaean, and botanical science, at least for higher plants, was completely reset with the publication of Species Plantarum in 1753. In fact, another Linnaean classic, Systema Naturae, comes in first as the most viewed book on BHL, with Species Plantarum in sixth place. As far as botany is concerned, BHL is particularly rich in taxonomic sources and it’s wonderful to be able to trace the history of the use of a particular binomial. There are links to BHL sources from both the Encyclopedia of Life (EOL) and Global Plants on JSTOR, which makes them even easier to access. That’s one of the major benefits of BHL: it has been designed to be in a variety of ways, and in fact, EOL and BHL are related projects that were created from the start to interact seamlessly. As I mentioned in an earlier post, BHL pages include taxonomic tags, making all the difference for its use in systematics.

My research progress is so slow that I have watched BHL change before my eyes. At various points, I’ve wanted to access the papers of George Engelmann, the botanist who helped to found the Missouri Botanical Garden, and there they appeared in BHL thanks to a digitization project at the garden, an original BHL member and still one of its key contributors. More recently, this has happened with John Torrey’s papers at NYBG, another BHL founder. These manuscripts are being digitized and transcribed through a grant from the National Endowment for the Humanities. Already, letters from William Darlington, one of my “people,” are online. I often use the word “luxury” to describe such instant access, what other word really applies? The combination of manuscript and published information is wonderful, as is the ease of downloading sources as PDFs. Also, since everything in BHL is open access, I don’t have to worry about whether or not I can use a quote or an image, as long as I properly cite it. Of course, not everything is in BHL, especially more recent literature, but think about it: as I mentioned in the first post in this series, we have come a LONG way from the days when searching for sources meant pulling Biological Abstracts tomes from the shelves.

Many BHL blog posts are about how researchers use BHL—and how they are helping to improve it. Dean Janiak is an ecosystem ecologist who relies on BHL historical literature in identifying the species he encounters in his work at the Smithsonian Marine Station in Florida. Rod Page, an entomologist at the University of Glasgow, has created tools to both draw information from BHL and also enhance the accessibility of what’s in the library. He has developed BioStor to ease searching through journals at the article level, something that BHL did not originally address. Page has also argued for the use of DOIs (digital object identifiers) not only in BHL but in repositories of all kinds as a way to ensure access to individual items. It’s BHL’s willingness to take such constructive criticism that will make it even more valuable and useable in the future.

I am particularly drawn to BHL because I am interested in the intersection of different fields, and BHL, despite its name, is about a lot more than biodiversity. A case in point is the work of the philosopher Ryan Feigenbaum who created an online exhibit called Poetic Botany as a 2016 Andrew W. Mellon Fellow at the NYBG Humanities Center. It explores the work of 18th century poets and botanists, among them Erasmus Darwin, the author of several book-length poems about botany. There are links to many BHL treasures, including Darwin’s writings, many of which are held by the Mertz Library at NYBG. This is a visual and intellectual joy to explore and a perfect example of how BHL can be mined in fascinating ways. Go to it!

BHL Users and Its Blog

3 BHL users

The image above gives a decent synopsis of users of the Biodiversity Heritage Library (BHL), the portal I’ve discussed in the last two posts (1,2). I would add a couple: students as well as educators use it, though I guess that’s implied. Also there are gardeners for whom BHL is a goldmine, particularly for those interested in heirloom varieties. Last year BHL had a special week-long focus on gardening that showed off its collection beautifully. In what I’ve discussed so far about BHL and about its outreach efforts on social media, the one aspect I’ve neglected is its blog. That was purposeful; I wanted to save what I consider the best for later in my exposition, and specifically now when I am getting to the content. BHL has had a blog since its inception, but the posts have gotten more frequent and richer as time passed. Many entries deal with what’s new with the project, or what tools are available, or what staff have been up to. Much of the content of the two earlier posts I first learned about on the blog, but my favorite posts are those that take up some theme and explore the relevant content or discuss how specific users employ the library.

In the case of gardening, BHL staged “Garden Stories” in March 2015 as a “week-long social media event for garden lovers.” It was advertised through gardening groups and botanical gardens, and included a Twitterchat where people could ask gardening questions of staff at several BHL member institutions; there was even a Garden Stories T-shirt available for sale. However, at the heart of the event was the BHL blog. It must have been difficult for Grace Constantino, the BHL Outreach and Communication Manager, and the other contributors to select what to include. This is indicated by the length of the introduction she wrote on Monday, March 23. It cited references to everything from Emanuel Sweerts’ 1614 Florilegium and Bernard M’Mahon’s 1804 seed catalogue, the first in America in booklet form, to several catalogues from the first half of the 20th century. The latter were just a few of the more than 14,000 seed and nursery catalogs in BHL including the rich collections of New York Botanical Garden, Cornell University, and the Smithsonian. With this intro as a teaser, the second post of the day was about joining in the effort to transcribe the text of catalogues, a citizen science project that allows the BHL audience to contribute to its work.

Tuesday’s post focused on genetic modification of agricultural and garden plants, and on Wednesday, there were two posts on “Leading Ladies in the World of Seeds,” beginning with the inaugural 1900 catalogue of Miss Ella V. Baines “The Woman Florist” of Springfield, Ohio, whose establishment was still going strong in 1930. Such plants-women obviously saw their gender as a plus with the covers of their catalogues referring to “Miss” or “Mrs.” and sometimes including a photo of the owner, as well as the de rigueur image of some offerings. Part two focused on a woman whose gardening interests were more scientific. Ethel Zoe Bailey was the daughter of the horticulturalist and botanist Liberty Hyde Bailey, whom I discussed in an earlier post. There I mentioned her cataloging of where and when particular plant varieties appeared for sale, but this was just one of many tasks she performed for her father, one she continued well after his death. She also traveled widely with him and helped in plant collecting, doing most of the processing and cataloguing at his home herbarium. This was later donated to Cornell University where he spent his career. The BHL post has links to items in what is now called the Ethel Z. Bailey Horticultural Catalogue Collection that she tended for 70 years. It was interesting to learn about Ethel Bailey and about how one of the collections in BHL came to be, just one of many fascinating stories of collection development sequestered within its holdings. The next topic for “Gardening Stories” week was the use of art to sell plants, a massive topic in itself and one that was again well illustrated with BHL resources. This was a two-parter on Thursday, with the first on botanical illustrators and the second on the introduction of photography into horticultural marketing.

While it’s clear that stories on gardening could go on for much longer than a week, the series ended on Friday, March 27 with two posts, the first a discussion of the Shakers as a religious group that marketed seeds and also medicinal herbs, an aspect of the sect I hadn’t known about. I also didn’t know much about the topic of the last post of the week on how a number of BHL partners are continuing the work of digitizing horticultural collections and devising ways to increase accessibility for a variety of users. One of the behind-the-scenes difficulties is that one library may input a company’s catalogues as separate records, as books would be. Another sees the catalogue as a series, such as a journal would be. Before both can be uploaded into BHL a joint spreadsheet must be created and the differences reconciled. This is the kind of work I have no desire to do, but it’s interesting to know about because it makes users appreciate how non-trivial the building of a digital library is.

In the last post in this series, I’ll discuss some of the ways people like me take advantage of BHL. But before I end, I want to mention another useful tool BHL provides: it has organized relevant materials into collections by subject, including seed and nursery catalogues. There are now 56 of these, ranging from Charles Darwin and Antarctic exploration, to the history of cats and whales. The collection list is another great entrée into BHL.

BHL and Social Media

I have a Facebook account that I ignore. I go into it about once every six months with the intention of using it, but I can never figure out its attractions, so I abandon it yet again. However, I use Twitter a lot, not to communicate so much as to keep up on the doings at institutions that interest me such as botanical gardens, herbaria, and natural history museums. Along the way, I’ve found several people and institutions posting notable items and I follow them too. For example, Donna Young (@HerbariumDonna) of the World Museum of Liverpool tweets and re-Tweets great material, as does the herbarium at St. Andrews University, Scotland (@STA_herbarium). Needless to say, in light of my last post, I also follow the Biodiversity Library, BHL (@BioDivLibrary). This is how I can keep up with its blog and all its latest endeavors. Because it’s trying to engage with as large an audience as possible, BHL communicates through a variety of social media outlets, since, like me, people have different tastes in their favorites apps. In 2016 it added Instagram and Tumblr to its internet presence along with its more longstanding Twitter and Facebook accounts. In total, it had a 76% increase in followers between 2015 and 2016, suggesting that these efforts have been successful. Perhaps its most fruitful outreach has been through Flickr where it has posted over 100,000 images from its resources, but I’ll get back to that later. I also want to note that there was a 54% increase in the number of visits to BHL from other social media sites—almost 100,000 in all, indicating users are coming to BHL from a variety of platforms. The most notable is Pinterest; posts from its accounts provided for more than half this traffic. Obviously many Pinterest users posted images sourced from BHL directly or from its Flickr account. These numbers suggest the general expansion of the social media universe and particularly of BHL’s participation in it. They also indicate its sophisticated approach to outreach.

At the moment BHL’s efforts in this area are being substantially assisted through the work of five one-year interns in the National Digital Stewardship Residency (NDSR) developed by the Library of Congress in conjunction with the Institute of Museum and Library Services (IMLS). The five residents, now at the half-way point in their work, are at five different BHL member institutions. Pamela McClanahan at the Smithsonian Library has posted a user survey and will analyze the results, which are important to planning BHL’s future direction and where it will focus its resources. Ariadne Rehbein at the Missouri Botanical Garden has joined a Codergirl cohort in St. Louis and is also interviewing Flickr and BHL volunteer taggers about their work and how the work flows can be improved. These contributors to bettering BHL participated in a two-year grant from the NEH to develop a system for volunteers to identify and tag images in BHL volumes. This is a great example of a citizen science project where a pool of interested and committed individuals can help to enhance BHL.

At the Natural History Museum of Los Angeles County, Marissa Kings, along with several summer interns, is creating and editing metadata for the museum’s Contributions in Science publications in preparation for uploading these and other in-house publications to BHL. She is also exploring how recently digitized museum entomology specimens and related data can be linked to the relevant literature in BHL. I have very limited experience in this area, but I know enough to realize that none of this is trivial. Having well-defined workflows and metadata can make all the difference when it comes to linking different types of data. Another intern, Alicia Esquivel at the Chicago Botanic Garden, is doing statistical analyses to estimate the size of the total amount of biodiversity literature—a difficult task to say the least. But even a rough estimate would give some idea of what percentage of that literature is now in BHL, in other words, how big its impact could be on the biodiversity research community. At Harvard’s Museum of Comparative Zoology, the fifth NDSR resident, Katie Mika is learning about adding structured bibliographic metadata in Wikidata to improve the quality of references in the Wikimedia universe and to reconcile messy data. By adding BHL IDs to Wikidata, it becomes a more robust knowledge base and improves the discoverability of BHL’s content. As you can see from these brief synopses, the NDSR program is providing BHL with expertise in several key areas and allowing it to both strengthen its foundations and move in new directions.

Before I close this post on BHL and social media, I want to get back to Flickr. BHL’s Flickr site is quite literally a joy to behold. There are now over 100,000 images from BHL content in Flickr and that number continues to rise. The contributions are arranged in albums, with each album representing one publication. For example, the album for Curtis’s Botanical Magazine, Volume 136 from 1910 has 60 images. Searching for this item in BHL will provide all these images as well as the related text, but to just enjoy the beautiful illustrations, BHL at Flickr is the way to go. All these images are copyright free and downloadable. I should note that while I gravitate to the botanical literature, Audubon’s birds are here and Gessner’s animals. Needless to say, many people stumble upon this treasure trove when they are surfing in Flickr and don’t investigate further, don’t go into BHL at all. However, some do, and that is the point of social media outreach, the more the right outlets are used, the larger the payoff.

Flickr has turned out to be an effective tool for BHL. It is also a wonderful place for a biologist to spend time on one of those days when spreadsheets and graphs make no sense and it’s easy to forget what makes biology so wonderful. Another fun way to join in is with Color Our Collections. Users can download black and white illustrations contributed by member institutions and then satisfy their urge to color them in any way they want. This project, which has become popular on the web and is continuing, grew out of a social media exchange between a librarian from the New York Academy of Medicine and a committed citizen scientist/BHL tagger from Australia—a beautiful example of BHL’s global scope (Garner, Goldberg & Pou, 2016).

Reference

Garner, A., Goldberg, J., & Pou, R. (2016). Collaborative social media campaigns and special collections: A case study on #ColorOurCollections. RBM: A Journal of Rare Books, Manuscripts, and Cultural Heritage, 17(2), 100–117. https://doi.org/https://doi.org/10.5860/rbm.17.2.9663