Getting the Most Out of Herbaria: In So Many Ways

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Images from Tweet sent by the Georgia Southern University Herbarium

So far in this series of posts on the uses of herbarium specimens in research (1,2,3), I’ve stuck to those that are most commonly discussed:  taxonomic and floristic work, environmental change studies, and phylogenetics.  But there are many other uses, with the variety increasing because digitization makes specimen information more easily available to a broader audience.  There have been studies on the presence of plant pathogens in specimens, including fungal infections (Kido and Hood, 2019).  Anther smut was found detected on specimens through visual inspection under a microscope (Antonovics et al., 2003).  Recently, sensitive DNA sequencing techniques have made it possible to detect bacterial infections by differentiating between pathogen and host DNA.  There is even Defense Department interest in such research.  The Center for the Study of Weapons of Mass Destruction in Washington DC issued a report where they outline why natural history collections can be sources of information in the work of protecting against biological warfare.

Different groups of researchers look at herbarium specimens very differently.  Those investigating fungi might focus on the roots, such as in a study about the successful extraction of arbuscular mycorrhizal fungal DNA from vascular plant roots.  Other botanists have developed techniques for systematically evaluating the amount of herbivore damage to leaves by using a grid system (Meineke & Davies, 2019).  While it’s common to find dead insects on a specimen, snails hiding out are more of a surprise.  Researchers examining lichens and bryophytes from the Galapagos Islands found that 10% of 400 specimens had at least one of eight different micro-mollusk species adhering to them.  There was even a new species discovered.  It is not unusual for new plant species to be found among herbarium specimens (Bebber, 2010), but snails are another thing.

Specimens can also be useful before trips to collect more specimens; Kew Botanic Gardens has a handbook with specimen images as a guide for collectors.  Searching databases for where a particularly narrowly endemic species was found in the past increases a botanist’s chances of finding it again.  One approach is searching for associated species in locality information.  Botanists are being encouraged to list such data to make specimens more valuable in ecological studies.  Another way to enhance specimens is to link them to other types of data such as iNaturalist observations from the same locale.  Heberling and Isaac (2019) describe how they are doing this at the Carnegie Museum of Natural History’s herbarium in Pittsburgh.  The iNaturalist data can include photos taken on the site by citizen scientists.  These visual records may document traits such as flower color and form that are difficult to preserve in dried specimens.   There may also be information about the surrounding habitat.  Having these items linked to specimens is a step toward the development of what is termed the Extended Specimen Network, with the specimen is at the center of linked resources providing information on the genetics, ecology, and morphology of the species (see earlier post).

Besides scientific uses, herbaria can also have what could be termed sociological uses.  There are several ways in which digitization of natural history collections could lead to more diversity among researchers.  Online access means that those interested in taxonomy who are living in developing nations can more easily access not only specimen data but related research through such portals as GBIF.  This also makes it easier for them to find research partners in developed nations.  A very different approach to expanding diversity has been employed by several institutions in the United States:  enlisting those in juvenile detention centers and those recently released from such facilities in digitizing specimens.  These projects not only provide employment, but also broaden the participants’ experience of science and of working with databases.  It is a nice example of thinking more creatively about expanding the population of those interested in nature and opening up herbaria in novel ways.  The iDigBio project held a webinar on this topic to make the natural history collection community aware of this approach, document the progress that has already been made, and encourage other ways to think outside the box in drawing people to natural history.

I haven’t mentioned using herbarium collections in outreach programs because I covered this in a recent post.  However, I have recently come across a few examples that seem too good to ignore.  The first is a “Hookathon: Hacking the Herbarium” at the Royal Botanic Gardens, Kew.  This was an all-day citizen science event to digitize items in Kew’s massive collection of material related to Joseph Dalton Hooker, who led the garden for many years during the second half of the 19th century.  This was also a means to advertise the collection’s existence and its variety, including specimens, manuscripts, letters, and drawings.  At the University of Manchester in Britain, the herbarium opened its doors to students during the exam period for “well-being” events so they could unwind by drawing specimens and incidentally find out what a herbarium is about.   I would like to end with a political, yes a political, example of outreach.  A Tweet from the Georgia Southern University Herbarium reminded residents about voting and put in a plug for the state symbol, the peach, with a beautiful fertile specimen.  This is outreach at its most creative.

References

Antonovics, J., Hood, M. E., Thrall, P. H., Abrams, J. Y., & Duthie, G. M. (2003). Herbarium studies on the distribution of anther-smut fungus (Microbotryum violaceum) and Silene species (Caryophyllaceae) in the Eastern United States. American Journal of Botany, 90(10), 1522–1531.

Bebber, D. P., Carine, M. A., Wood, J. R. I., Wortley, A. H., Harris, D. J., Prance, G. T., Davidse, G., Page, J., Pennington, T. D., Robson, N. K. B., & Scotland, R. W. (2010). Herbaria are a major frontier for species discovery. Proceedings of the National Academy of Sciences, 107(51), 22169–22171.

Heberling, J. M., & Isaac, B. L. (2018). iNaturalist as a tool to expand the research value of museum specimens. Applications in Plant Sciences, 6(11).

Kido, A., & Hood, M. E. (2020). Mining new sources of natural history observations for disease interactions. American Journal of Botany, 107(1), 3–11.

Meineke, E. K., & Davies, T. J. (2019). Museum specimens provide novel insights into changing plant–herbivore interactions. Phil. Trans. R. Soc. B, 374(1763), 1-14.

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.

Humboldt and the Cosmos

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Heart of the Andes (1859) by Frederic Church, in the Metropolitan Museum of Art, New York.

The subject of this series of posts (1,2,3) Alexander von Humboldt is known for the breadth of his interests and for his writings that illustrate how all parts of the world, and our experience of it, are connected.  In terms of botany, he wrote that in a rainforest:  “We observed with astonishment how many things are connected with the existence of a single plant” (Wulf, 2015, p. 74).  There were the epiphytes living on the trees along with hosts of insects and other invertebrates, reptiles, amphibians, etc.  Then there were the climatic, geological, and geographical elements that determined what plants grew where.  In the last post, I discussed Humboldt’s contributions to plant geography.  Here I want to broaden the perspective further and describe his writings linking science to the humanities.  While Humboldt mentioned the aesthetics of landscape and of living organisms in many of his writings, he addressed these themes most explicitly in his five-volume Cosmos (1845-1862) written toward the end of his life.  The first two of these books are the ones still most widely read because they are less scientifically dense than the later works.  The first is an introduction and synopsis, and the second a summary of the history of human beings’ appreciation for the natural world.

Though Humboldt wrote Cosmos late in life, his early experiences shaped the views he expressed there.  While a student, he met George Forster who had sailed around the world with Captain James Cook.  Forster had integrated science and aesthetics in his writing, and considered knowing and feeling as parts of a unitary experience of nature.  This approach and Humboldt’s attraction to it is not surprising considering he and Forster were living during the early years of the Romantic movement and its reaction against the emphasis on reason during the Enlightenment.  A little later in his career, while he was working as a mining inspector, Humboldt met Wolfgang Goethe and they became fast friends.  Their first meeting was in the year when Goethe wrote Metamorphosis of Plants (Arber, 1946.)  They visited each other often and at one point Humboldt made a three-month stay at the poet’s home in Jena.  Goethe had created a botanical garden there and had a herbarium.  This fed Humboldt’s interest in plants, and Goethe’s argument that nature must be experienced through feeling also had a profound effect on him.  After his stay in Jena, Humboldt felt that he had “grown new organs,” that he perceived the world in a new way, that “ what speaks to the soul escapes measurement,” which is a meaningful statement for someone who relied so heavily on scientific instruments in his investigation of nature (Wulf, 2015, p. 310).

One element in Humboldt’s linkage of different fields and experiences of nature was his focus on the visual.  While a student, he had received art instruction from a noted graphic artist, Daniel Chodowiecki.  Most of the publications resulting from his voyage to Latin America with Aimé Bonpland were illustrated, often lavishly so.  The botanical artist Pierre Turpin, who worked at the National Museum of Natural History in Paris, did most of the illustrations beginning with their first publication, Essay on the Geography of Plants, with figures that included the monumental diagram of the relationship between altitude and plant species distributions (see last post).  The seven volumes describing the species Humboldt and Bonpland collected had over 700 illustrations, many of them hand-colored.  Turpin worked mostly from dried specimens, though the explorers had made many sketches that guided him; only one by Humboldt is still extant (Lack, 2009).  They also made landscape sketches that Turpin turned into illustrations as well.

One of the most significant sections in the second volume of Cosmos deals with landscape.  Humboldt argues that the scientific and aesthetic come together so powerfully that they cannot be separated.  This reflection, among others, inspired many 19th century landscape painters, perhaps most notably Frederic Church, who traveled to the Andes to experience Chimborazo and other peaks first-hand and created a number of paintings.  Particularly striking is the massive Heart of the Andes, which caused a stir when it was shown in New York, with viewers lined up to pay 25 cents to view it (see above).  A very different artist was also inspired by Humboldt.  The zoologist Ernst Haeckel had trained in art, so it’s not surprising that reading Cosmos solidified his view of the importance of art in communicating about science.  While Haeckel is best known for his book of illustrations called Art Forms in Nature, two other images come to mind when I think of him.  One is of the interior of his home that he filled with furniture, lamps, and wall decorations based on jellyfish forms.  The other is his iconic tree of life diagram with a very realistic leafless tree, a human at the top.

I have to admit that I too have been inspired by Humboldt.  When I first became interested in the aesthetics of biology, it was exhilarating to find an author who both validated my viewpoint and deepened it.  The fact that he also had exciting adventures on his Latin American voyage and was interested in plants, didn’t hurt either.  Since that time in the 1980s when I first read some of his work, Humboldt has received more attention, including Andrea Wulf’s 2015 biography.  He deserves such scrutiny because he still has a great deal to tell us.  A movement in that direction is the Alexander von Humboldt Portal hosted by the Berlin State Library, a good place to start exploring Humboldt’s papers and information about his life and writings.  And to celebrate the 250th anniversary of his birth, Nature Ecology & Evolution has collated a series of articles related to his work and Science published an essay on his importance today.  In addition, Wulf has teamed with the artist Lillian Melcher to create a graphic non-fiction book, The Adventures of Alexander von Humboldt.

References

Arber, A. R. (1946). Goethe’s botany. Chronica Botanica, 10, 63–126.

Lack, H. W. (2009). Alexander von Humboldt and the Botanical Exploration of the Americas. New York, NY: Prestel.

Wulf, A. (2015). The Invention of Nature: Alexander von Humboldt’s New World. New York, NY: Knopf.

Humboldt: Essay on the Geography of Plants

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Plate from Humboldt and Bonpland’s Essay on the Geography of Plants, from the Biodiversity Heritage Library.

When they returned to Paris after their five year expedition (1799-1804) to Latin America, the first publication Alexander von Humboldt and Aimé Bonpland produced was Essay on the Geography of Plants (1805).  This book was really Humboldt’s conception, but since Bonpland was a botanist and had contributed his expertise throughout their journey, Humboldt thought it was fitting that Bonpland’s name should be on the essay as well (Humboldt & Bonpland, 2009).  The evidence they accumulated on the trip was central to Humboldt’s argument, and he set about writing a first draft right after their ascent of Mt. Chimborazo, one of the highest mountains in the Andes.  However, many of the ideas Humboldt presented to demonstrate how geography determines the plant life growing in a particular place, were conceived much earlier when he met George Forster who had been on Captain James Cook’s second round-the-world expedition.  Forster had broad knowledge of vegetation in very different environments and opened Humboldt’s eyes to how plant life varied with access to water, with altitude, and with distance from the equator.

Humboldt wasn’t very interested in taxonomy, in identifying new species, and among the plant descriptions in the first of their 7 botanical journals that logged the plants they collected, Humboldt wrote nine descriptions and Bonpland 682 (Lack, 2009).  This did not mean that plants weren’t important to Humboldt’s vision of the world, rather he was more interested in how the environment influenced the ability of a particular plant to survive in a particular environment.  He didn’t see plants so much as isolated entities but as part of a larger picture, and there is visual evidence of this in the Essay.  The main portion of the book is an explanation of a large diagram—originally printed 2’x3’—that is a complex blend of image and text (see above).  The center panel depicts two peaks in the Andes, Chimborazo and Cotopaxi, both of which Bonpland and Humboldt had climbed.  To the right of them, is a cross-section of the two labeled with the plants found there.

In 1824, Humboldt published a similar diagram where he moved some of the plants to different elevations.  Pierre Moret and his collaborators (2019) have recently revisited these images and compared the plants in the diagrams with the specimens Humboldt and Bonpland collected.  They found that Humboldt’s primary data above the tree line were collected mostly on Mt. Antisana.  Moret’s went to the collection area and found that over 200 years, the tree line has shifted about 215-266 meters.  This is a fascinating study of how old data can illuminate present environmental issues, while at the same time shedding light on how data was used in the past.  There is a great deal more in this image, including subterranean plants that had intrigued Humboldt since his days as a mine inspector in Germany when he studied and wrote about the plants, lichen, and algae he found in the caves and mines where he worked as a mine inspector (Anthony, 2018).

So far, I’ve only discussed the central panel of the Tableau, but there are seventeen other columns, eight to the right and nine to the left of the mountain diagram.  These include elevation, atmospheric pressure, humidity, etc. at various altitudes.  In other words, one chart summarizes a great deal of the data the team collected on their trip.  What is most important to Humboldt is the relationship between elevation and other phenomena.  His major finding is that elevation relates to temperature in influencing what plants grow where:  plants found at a particular elevation, will be found at a lower elevation but at higher latitude, in other words, further north or south of the equator.  In his introduction to a recent edition of the Essay, Stephen Jackson (2009) argues that Humboldt held to the “primacy of plant geography in his overall vision of the world, whereby vegetation is both the most obvious surface manifestation of climate and the determinant of many other natural and human features” (p. 17).  Humboldt is often designated the father of plant geography because of this essay, but he drew on the work of many others who had gone before him.  He is notable because he used his experiences in South America to synthesize a great deal of information and present it in a striking format, drawing on the growing use of diagrams in geological studies (Rudwick, 1976).

At several points in the essay Humboldt noted the environmental damage done by agriculture as forests were replaced by fields that quickly lost their fertility, leaving a degraded and useless landscape that affected local weather patterns.  These observations were taken up and enlarged upon by others in the 19th century who were influenced by his writings.  Henry David Thoreau saw the unity of nature much as Humboldt did, George Perkins Marsh wrote of the toll taken by forest destruction in the United States as did John Muir, and in Humboldt’s native land, Ernst Haeckel coined the term ecology to describe the interrelations among species and the nonliving environment.  They all had read Humboldt and were passionate about his impact on them.  The Essay was one such influence; in the next post I’ll discuss another.

References

Anthony, P. (2018). Mining as the working world of Alexander von Humboldt’s plant geography and vertical cartography. Isis, 109(1), 28–55.

Humboldt, A. von, & Bonpland, A. (2009). Essay on the Geography of Plants (S. T. Jackson, Ed.; S. Romanowski, Trans.). Chicago, IL: University of Chicago Press.

Jackson, S. (2009). Introduction: Humboldt, ecology, and the cosmos. In S. Jackson (Ed.), & S. Romanowski (Trans.), Essay on the Geography of Plants (pp. 1–46). Chicago, IL: University of Chicago Press.

Lack, H. W. (2009). Alexander von Humboldt and the Botanical Exploration of the Americas. New York, NY: Prestel.

Moret, P., Muriel, P., Jaramillo, R., & Dangles, O. (2019). Humboldt’s Tableau Physique revisited. Proceedings of the National Academy of Sciences, 201904585. https://doi.org/10.1073/pnas.1904585116

Rudwick, M. (1976). The emergence of a visual language for geological science. History of Science, 14, 149–195.

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.

Libraries and Botany: New York, New York

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Specimen of Diopyros virginiana collected from the site of the Elgin Botanic Garden in 1829, New York Botanical Garden Steere Herbarium

Since the joint CBHL/EBHL meeting (see earlier post) was held in New York, it’s not surprising that there were several presentations related to the metropolis.  It seems fitting to end this series of posts with a review of them.  After a welcome from Susan Fraser, director of NYBG’s Mertz Library, the first major speaker of the conference was Eric Sanderson of the Wildlife Conservation Society, headquartered across the street from the New York Botanical Garden, at the Bronx Zoo.  For many years Sanderson has had a leading role in research on what New York was like before Henry Hudson sailed into the mouth of the Hudson River in 1609.  The indigenous people called the large island he found Mannahatta, and that became the name for Sanderson’s endeavor and the title of the book he published in 2009.  Using mapping technology coupled with old maps, historical accounts of the area, specimens collected there in the past, and what is known about the ecology and geology of the island, Sanderson’s team identified 54 different ecosystem types on Mannahatta.  This is a large number for that sized piece of land, and the result of its extensive wetlands along with its varied geological features.  There were also an estimated 600 species of plants.

More recently Sanderson has led an effort to produce the same kind of modeling for New York City’s other four boroughs.  Called Welikia, it too has a website that is still under construction, but includes all the information from the Mannahatta Project.  These are not just interesting exercises in environmental history, they aim at helping the citizens of New York understand the biodiversity that once existed there and how to preserve and nurture as much of it as possible.  It is unlikely that bears will again roam Manhattan, but red-tailed hawks are flourishing (Winn, 1998), and I’ve seen a coyote ambling inside NYBG’s fence as I was stuck in traffic trying to get there.

On the second day of the conference, the botanical illustrator Bobbi Angell presented on the formidable botanical art collection housed at NYBG.  Angell has spent her life creating pen-and-ink drawings to illustrate the scientific work of the garden’s botanists, including many for the seven volume Intermountain Flora: Vascular Plants of the Intermountain West, USA.  The last volume was just recently published (2017) and includes not only some of Angell’s illustrations but biographies of her and other illustrators and botanists who worked on this project that was first envisioned by Bassett Maguire in the 1930s.  There will be more on the editors, Patricia Holmgren and Noel Holmgren, in a future post.

Angell didn’t dwell on her accomplishments, but instead discussed some of the other contributors to the 30,000 pieces in the NYBG art collection.  These include the great French botanical painter Pierre-Joseph Redouté with 10 paintings on linen, but Angell concentrated on 20th and 21st-century artists, including Alexandria Taylor and Frances Horne who did illustrations respectively for Elizabeth Britton and Nathaniel Lord Britton.  Both were distinguished botanists and Britton was NYBG’s founding director.  Angell spoke reverently of artists whom she knew including Anne Ophelia Todd Dowden, who left her finished works to the Hunt Institute for Botanical Documentation in Pittsburgh, and her working drawings to NYBG, an interesting division.  Then there was Rupert Barneby a self-taught botanist and artist who did research at the garden and became an expert on legumes.   He created his own illustrations until he injured his hand.  Angell ended with a plea for more of the botanical art in library collections to be made available online and a mention of the American Society of Botanical Artists, which has a wonderful journal for members as well as a website on which they can present their work.

The final presentation of the meeting was a public lecture by Victoria Johnson to celebrate the publication of her book, American Eden: David Hosack, Botany, and Medicine in the Garden of the Early Republic (2018).  She began the book and her talk very effectively by telling the story of how David Hosack, a physician, treated a New York boy dying of fever in 1797.  Hosack had tried everything he could without success, and so decided to lower the boy into warm bathwater with cinchona bark mixed in.  Several of these treatments led to the patient’s recovery and to a tearful thank you from his father.  Johnson then paused, and revealed that the father was Alexander Hamilton.  After this surprise, she went on describe some of what she writes about in her book:  how Hosack trained as a physician in the United States and Britain where he developed an interest in botany, even studying with James Edward Smith the founder of the Linnean Society; how he set up a medical practice in New York, obviously attracting an elite clientele; how he developed a plan to create a botanical garden in the city as a way to nurture, study, and teach about medicinally useful plants.  He used his own money to buy 20 acres of land in what is now midtown Manhattan, but was then over three miles north of the city.  He called it the Elgin Botanic Garden after the Scottish town where his family originated.  He built a wall around the property as well as greenhouses and then bought an impressive selection of plants.

Hosack had a long and successful life as a physician, but his story is definitely bittersweet.  He was the attending physician when his friend Alexander Hamilton was shot in the duel with Aaron Burr (it turns out they both were interested in gardening).  The garden, begun in 1801, was destroyed in the 1820s after it had been bought by New York State and then handed over to Columbia College (now Columbia University) for management.  It was neglected and eventually leased by Columbia as real estate prices in that part of Manhattan started to soar. Eventually, it became the site of Rockefeller Center.  However, to end on a happier note, there are a few Elgin Garden specimens in the NYBG herbarium including Diosyros virginiana (see above).

Note: I would like thank all those involved in the wonderful CBHL/EBHL meeting, particularly Susan Fraser, Kathy Crosby, Esther Jackson, and Samantha D’Acunto.  I am also grateful to the participants from whom I learned so much, to Pat Jonas who nudged me to attend, and to Amy Kasameyer who introduced me to CBHL.

References

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.

Johnson, V. (2018). American Eden: David Hosack, Botany, and Medicine in the Garden of the Early Republic. New York, NY: Norton.

Sanderson, E. W. (2009). Mannahatta: A Natural History of New York City. New York: Abrams.

Winn, M. (1998). Red-Tails in Love: A Wildlife Drama in Central Park. New York: Pantheon.

Books Old and New, Part 3: Irish Natural History

3 Ireland

McGill-Queen’s University Press, Montreal, Canada (1997)

This series of blog posts (1, 2) is called “Books Old and New” because I’m covering some that I read years ago and others that are recent publications.  A book that was published 20 years ago, but is new to me is Nature in Ireland (Foster, 1997), a collection of essays that runs the gamut from geological history to present-day issues in forest conservation.  There is botany here, but I didn’t read this book primarily for that, but rather because I am attempting to finally get to know my parent’s native land from the biological perspective.  I’ve been steeped in its culture and history from birth, and since my mother did win a school prize in botany, I learned something of its plant life.  However, this mostly amounted to her complaining about plants that grew well in Ireland, such as primroses, but had to be coaxed in hotter and drier New York.

My mother learned in school that the Irish terrain resembled a soup bowl in that most of the mountains were along the coast with flat plains in the center.  Nothing is that simple, of course, but the first essay, “The Testimony of the Rocks” by John Feehan explains why this is so.  Feehan does a good job of illustrating how the Irish landscape came to be, and why the land in many areas is so rugged and filled with limestone.  His work is a good reminder that in order to understand plants, it’s necessary to understand the substrate on which they grow.  The most intriguing thing I learned here is that oldest known land plant, Cooksonia, can be found in Silurian fossils (428 Ma) from Devil’s Bit Mountain, a name I remember because my grandmother came from near there, and my mother explained that the gap in the mountain was said to be caused by the devil taking a bite out of it.

Several chapters deal with the history of Irish nature study, noting that the first written accounts date from a St. Augustin (not the St. Augustine) in the 8th century, a work studied by the biologist/polymath D’Arcy Thompson.  The next such treatment was by a visitor named Giraldus in the 12th century; some of the information there may have come from natives.  The first report of Irish plants to go into print appears to be that of Richard Heaton, a British cleric posted to Ireland in 1630.  By this time the country was well under Britain’s thumb, so much of the work that follows was done by Anglo-Irish or British botanists.  Arthur Rowdon was a prominent landowner with one of the first greenhouses in Ireland.  He is important to botany because he was a friend of the botanical collector Hans Sloane through whom the British botanist William Sherard came to live at Rowdon’s estate, perhaps as a tutor for his sons.  Sherard studied Irish plants and eventually became professor of botany at Oxford.  He was a friend of another Irishman, Thomas Molyneux, who acquired a herbarium created by the 17th-century pharmacist Antoni Gaymans.  This collection was annotated by Sherard and is still extant (Heniger & Sosef, 1989).  These are the kinds interesting side paths that run through the book.

Another one involves Caleb Threlkeld, who wrote the first Irish flora in 1727.  There is evidence that he must have seen a copy of Heaton’s work, and some of his text is derivative, using material from John Ray’s treatment of Irish plants.  However, Threlkeld made a real contribution of his own by noting when and where he saw the plants he described.  Also, present-day Irish botanists have studied old specimens at the Trinity College, Dublin herbarium and make a case that these were collected by Threlkeld, thus substantiating his observations (Doogue & Parnell, 1992).  The Trinity herbarium was also home base for the algologist William Henry Harvey, who added substantially to its collection with specimens from South Africa and Australia, including his reference herbarium from his visit to the latter.

When I met the Trinity herbarium’s present keeper, John Parnell, he emphasized that Harvey did many of his own illustrations, even to the point of making the engravings, because he wanted to insure the accuracy of what went into print.  Harvey’s work is magnificent, but it is not among the few botanical illustrations reproduced in the book, which is generally short on images.  There is, however, a chapter on “The Art of Nature Illustration” by Martyn Anglesea that cites several noted Irish artists, and highlights two who worked at another Dublin herbarium, that of the National Botanic Gardens of Ireland.  I have seen some of the work of Lydia Shackelton and Alice Jacob at the garden and it is amazing, especially the watercolors they did of orchids for Frederick Moore—a herbarium curator and expert on the family.

Before leaving this book, I have to mention Robert Lloyd Praeger who wrote The Way I Went, what some consider the best book for the general reader on the natural history and topography of Ireland.  He is most noted for his leadership of the Clare Island Survey (1909-1915), which involved over 100 amateurs and professionals and resulted in a landmark publication that set the bar high for future such European studies (Jones & Steer, 2009).  The Royal Irish Academy added to its value by funding a new survey of the island to mark the hundredth anniversary of the first.

References

Doogue, D., & Parnell, J. (1992). Fragments of an eighteenth century herbarium, possibly that of Caleb Threlkeld, in Trinity College, Dublin (TCD). Glasra, 1(2), 99–109.

Foster, J. W. (Ed.). (1997). Nature in Ireland. Montreal, Canada: McGill-Queen’s University Press.

Heniger, J., & Sosef, M. S. M. (1989). Antoni Gaymans (ca 1630–1680) and his herbaria. Archives of Natural History, 16(2), 147–168.

Jones, R., & Steer, M. (2009). Darwin, Praeger and the Clare Island Surveys. Dublin: Royal Irish Academy.

Praeger, R. Ll. (1937). The Way That I Went. Dublin, Ireland: Hodges, Figgis.

Threlkeld, C. (1727). Synopsis stirpium Hibernicarum alphabeticæ dispositarum. Dublin, Ireland: Powell.

The Algal World: Diatoms

haeckel-diatom

Diatom plate from Haeckel’s Art Forms in Nature

I was first attracted to diatoms by their exquisite beauty. When I studied aesthetics many years ago, beauty was often defined in terms of categories such as symmetry and form, and diatoms are definitely exemplars of both. They are one-celled algae, each encased in a glassy silica shell that varies with species. These structures can be elongated, triangular, circular, square, or more elaborately shaped. There is no better introduction to them than the diatom plate [shown above] from Ernst Haeckel’s Art Forms in Nature (1904). There are also great microscope photographs of diatoms on the web, at sites such as Micropolitan University. If you want more than just images, the Natural History Museum, London has Diatoms Online and the Academy of Natural Sciences (ANS) in Philadelphia (now part of Drexel University) has a Diatom Herbarium, both a real and a virtual space.

I visited the diatom collection at ANS two years ago and was drawn into a very different kind of herbarium world. Yes, there are metal cabinets, but they are filled with boxes of microscope slides, not sheets of white paper in folders. This collection was begun in the mid-19th century by members of the ANS who were interested in microscopy. At the time, this was, like seaweed, a hobby for many people who had the money to have leisure time and to buy a microscope. Some were physicians who had some familiarity with microscopes through their profession; others included bankers and industrialists who simply became fascinated with what couldn’t be seen with the naked eye. Like seaweed collecting, this was an area of interest in Britain, and also on the Continent, and had begun in the 17th century (Stafford, 1996). By the mid-19th century, microscope optics had improved and the instruments were easier to use. Many of the ANS microscopists were interested in fossilized diatoms found in diatomaceous earth, which could be found in areas around Philadelphia. This fine, sandy material is used in polishing among other things and represents the remains of organisms that lived in great numbers millions of years ago. Since diatoms are responsible for 20-25% of the earth’s carbon fixation, it’s difficult to overestimate their abundance, both now and in the past.

Eventually, the microscopists’ diatom collections morphed into the ANS Diatom Herbarium, which now houses the second largest such assemblage in the world. Along with slides, there are small glass bottles filled with diatomaceous earth collected in various locations. These are particularly difficult to catalog because each sample contains many species. In some cases, small portions of these sands have been separated out with individual species mounted on slides, but as Maria Popanova, the curator of the collection, notes the bottle that was the source of a particular mount wasn’t always recorded on the slide. There are ways of backtracking using dates and collection sites, but it’s time-consuming work and slows down digitization of the collection. However, 63,000 specimens are now available online. Also at ANS are rare 19th-century exsiccatae that contain many type specimens. These are store in book-like boxes with specimens either mounted on slides or in tiny envelopes. A counterpoint to these historically important items are posters on the walls of scanning electron microscope images of diatoms revealing an even more elaborate detail than that provided by a light microscope. The images are more expensive to produce so not every diatom receives this attention, but these images highlight the complexity of these minute structures.

I could easily dwell on the aesthetic aspects of these creatures, but I want to also stress their scientific significance. There are good reasons why the herbaria such as the ANS and NHS, among many others, maintain diatom collections. The cells can tell us a great deal about aquatic life of the past, the present, and the future. Diatoms serve as useful markers of aquatic ecosystem health. Their shells remain after death, providing stable evidence of water quality. A water sample’s use in monitoring usually deteriorates with time as organisms die, but this is a lesser problem with diatoms. Also, they are ubiquitous, found all over the world in both fresh and salt water. The species present at a site depend upon the presence or absence of pollution, among other factors.

Part of the research done at ANS involves water monitoring studies and having a rich diatom collection, including many type specimens, as reference adds weight to the findings. This work has a long history at the ANS, and the person most responsible for building its stature was Ruth Patrick (1907-2013). She had a doctorate based on diatom research from the University of Virginia and wanted to volunteer at the ANS in the 1930s. She was kept out for several years because they didn’t accept women. She finally became a volunteer in 1935, serving first as a virtual servant to the Microscopy Section, setting out specimens for their meetings among other duties. She eventually became the first woman member of the ANS. In the late 1940s, after she became a paid employee, Patrick founded the ANS Limnology Department. Through her work, the ANS developed a focus on freshwater diatoms; before that it had collected mostly fossils and saltwater species. She directed studies on rivers and streams, especially in terms of using diatoms to gauge water quality, and her influence lives on in the ANS’s Patrick Center for Environmental Research.

References

Haeckel, E. (1904). Art Forms in Nature (Vol. 1974 ed.). New York: Dover.

Stafford, B. M. (1996). Artful Science: Enlightenment Entertainment and the Eclipse of Visual Education. Cambridge, MA: The MIT Press.

Uses of Herbaria: Biogeography and Climate Change

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iDigBio is an NSF-funded program to digitize US natural history collections

Alexander von Humboldt (1759-1769) is often considered the father of biogeography because of his crucial work on this subject in South America, and his writings and diagrams showing the link between terrain and vegetation (Humboldt & Bonpland, 2009). However, even during the Renaissance it was becoming obvious that terrain and climate greatly influence plant life. Many of the plants of northern Europe turned out to be different from the Mediterranean plants described by ancient authors including Theophrastus and Dioscorides. Place mattered and as botanists went on field trips and collected specimens, they become more aware of local differences in plant habitats. Now plant distribution is a major focus for botanists and ecologists, and herbaria are important in documenting what grows where. Species distribution maps are a staple of floras.

Today, with the combination of GPS coordinate mapping and digitization of specimen data, it’s possible to generate distribution maps relatively easily from online herbarium data. However, there is a question as to how accurate these maps are. As with any output, the answer depends upon the input: the accuracy of the localities. There is software such as GEOLocate and the MaNIS Calculator that will generate the probability of a plant being within a particular radius. Doing georeferencing well is time-consuming, and there are millions of sheets requiring attention. Even if all the data were optimal, there is the question of what percentage of the sheets are available online? If the species distribution maps are based on online data, and that only represents, say, a quarter of the specimens, then how accurate is it? In addition, there is collection bias. In other words, rarely are regions sampled uniformly. Studies show that areas accessible via roads, rivers or railroads are more likely to be thoroughly canvased than are more remote locales, so all the error can’t be blamed on computers (Vetter, 2016). Some of the best studies are those that combine herbarium data with direct observation in an area (Martin et al., 2014; Mohandass & Campbell, 2015).

At the present there can’t be any discussion of biogeography without bringing up climate change. At the moment, interest in this topic is driving not only research on herbarium collections but also their digitization. Herbaria are among the few places where there are records that range over more than 100 years, in some cases 200-400 years, and they become more valuable by the day. Records can be studied in a variety of ways to glean information on climate and habitat characteristics in the past. The area that has been developed most substantially is phenology, the study of natural events that can be pinpointed in time. For plants this is often budding, flowering, or seed setting. Though this has not always been true in the past, it is now standard herbarium practice to collect specimens that are in flower or have seeds or fruit. Since collection data are always recorded for specimens, researchers can track flowering or fruiting over the years to detect differences that might be related to climate change. Again, if digitized and imaged specimens are used, the study is limited by the richness of the sample, but it does make for more efficient investigation. There have been several studies validating the methods used in this research (Davis et al., 2015; Spellman et al., 2016). To date, changes in flowering times have been noted in orchids (Molnar et al., 2012), eucalypts (Rawal et al., 2014), and perennial herbs (Matthews & Mazer, 2015) among others; changes were also recorded in leaf-out times for trees (Everill et al., 2014; Zohner & Renner, 2014). With projects like NSF’s iDigBio, which has resulted in a portal with access to over 75 million natural history specimens, the problems of small sample sizes are dwindling, but still significant.

Still other ways to document climate change with specimens include counting the stomata on leaves. This is obviously more time-consuming, but the number of studies in this area suggest that it’s considered a fertile area of investigation. Stomata are the pores in a leaf through which plants absorb CO2, the fuel for photosynthesis. Since global warming is precipitated by the increase in atmospheric CO2 due to fossil fuel combustion, it’s not surprising that in several species, there has been a decrease in stomatal density. Plants just don’t need as many pores to absorb the same amount of CO2. In addition, leaves can give evidence of other types of environmental change. An alteration in leaf area over the past three centuries has been noted for some species (Peñuelas & Matamala, 1990). Also, there was a marked decrease in leaf sulfur levels in the years after the clean air act was passed and an increase in nitrogen with increased use of fertilizers (Peñuelas & Filella, 2001). Someone has even studied the distance over time between leaf teeth in the mulberry Hedycarya angustifolia over the past 160 years to see if an increase in temperature had affected this trait. However, despite the painstaking analysis, researchers couldn’t find any significant change (Scarr & Cocking, 2014). This work shows how many ways climate change can affect plants, and how clever botanists and ecologists employ varied plant characteristics in collecting data on this phenomenon. Having different types of data strengthens the case for the significant impact of climate on plant growth and also on the survival of species. I’ll present more evidence for this in the next post.

References

Davis, C. C., Willis, C. G., Connolly, B., Kelly, C., & Ellison, A. M. (2015). Herbarium records are reliable sources of phenological change driven by climate and provide novel insights into species’ phenological cueing mechanisms. American Journal of Botany, 102(10), 1599–1609.

Everill, P. H., Primack, R. B., Ellwood, E. R., & Melaas, E. K. (2014). Determining past leaf-out times of New England’s deciduous forests from herbarium specimens. American Journal of Botany, 101(8), 1293–1300.

Humboldt, A. von, & Bonpland, A. (2009). Essay on the Geography of Plants. (S. T. Jackson, Ed., S. Romanowski, Trans.). Chicago, IL: University of Chicago Press.

Martin, M. D., Zimmer, E. A., Olsen, M. T., Foote, A. D., Gilbert, M. T. P., & Brush, G. S. (2014). Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance. Molecular Ecology, 23(7), 1701-1716.

Matthews, E. R., & Mazer, S. J. (2015). Historical changes in flowering phenology are governed by temperature × precipitation interactions in a widespread perennial herb in western North America. The New Phytologist, 210(1), 157-167.

Mohandass, D., & Campbell, M. J. (2015). Assessment of Roscoea population size in the Central Himalayas based on historical herbarium records and direct observation for the period 1913-2011. Journal of Biological Records, 0022015, 10–16.

Molnár, A., Tökölyi, J., Végvári, Z., Sramkó, G., Sulyok, J., Barta, Z., & Bronstein, J. (2012). Pollination mode predicts phenological response to climate change in terrestrial orchids: A case study from central Europe. Journal of Ecology, 100(5), 1141–1152.

Peñuelas, J., & Filella, I. (2001). Herbaria century record of increasing eutrophication in Spanish terrestrial ecosystems. Global Change Biology, 7(4), 427–433.

Peñuelas, J., & Matamala, R. (1990). Changes in N and S leaf content, stomatal density and specific leaf area of 14 plant species during the last three centuries of CO2 increase. Journal of Experimental Botany, 41(9), 1119–1124.

Rawal, D. S., Kasel, S., Keatley, M. R., & Nitschke, C. R. (2014). Herbarium records identify sensitivity of flowering phenology of eucalypts to climate: Implications for species response to climate change. Austral Ecology, 40(2), 117-125.

Scarr, M. J., & Cocking, J. (2014). Historical responses of distance between leaf teeth in the cool temperate rainforest tree Austral Mulberry “Hedycarya angustifolia” A. Cunn. from Victorian herbarium specimens. Victorian Naturalist, 131(2), 36–39.

Spellman, K. V., & Mulder, C. P. H. (2016). Validating herbarium-based phenology models using citizen-science data. BioScience, 66(10), 897–906.

Vetter, J. (2016). Field Life: Science in the American West during the Railroad Era. Pittsburgh, PA: University of Pittsburgh Press.

Zohner, C. M., & Renner, S. S. (2014). Common garden comparison of the leaf-out phenology of woody species from different native climates, combined with herbarium records, forecasts long-term change. Ecology Letters, 17(8), 1016-1025.