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.

Getting the Most Out of Herbaria: Systematics and Chemistry

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Murder Most Florid by Mark Spencer, London: Quadrille, 2019

As mentioned in the last post, herbaria, both real and virtual, are most frequently visited by taxonomists, who are usually studying particular plant taxa or preparing flora of areas ranging in size from city parks to entire countries.  These are the traditional uses of plant collections and are still crucial.  However, several things have changed.  Now the “visit” is often to digital portals rather than onsite, making it much easier for researchers to look at specimens from far-flung institutions, IF the material has been digitized, and particularly if it is available through aggregators such as iDigBio, GBIF or JSTOR Global Plants with their links to massive numbers of specimens.  Still, coverage is uneven, with some collections more fully digitized than others.  Also changed is the way taxonomic information, once generated, is distributed.  Many flora are now published virtually, with or without an accompanying paper format.  The 2012 International Code of Nomenclature for Algae, Fungi, and Plants made it acceptable to publish descriptions of new species digitally as long as they were responsibly published and properly archived.

Plant taxonomy is also changing because of its increasing links with genetics.  Most treatments of species and genera now include DNA sequencing data.  While this has been going on for decades, the last ten years or so have seen greater use of DNA data derived from samples taken from herbarium specimens, with NGS, next-generation sequencing (NSG) making this possible. NGS techniques utilize small pieces of degraded DNA found in dried plant material easier to sequence and to determine how such sequences fit together to provide meaningful results.  That this work has revolutionized taxonomy is hardly news.  Still, it is interesting to look at how the information has solved various puzzles, such as the origin of European potatoes or the origin of the pathogenic Phytophthora strain responsible for the Irish potato famine of the 1840s.  In a study of the genetics of grapes, researchers used over 200-year-old specimens from the herbarium at the Royal Botanical Garden in Madrid.  These plants were collected by Simón de Rojas Clemente y Rubio, considered one of the founders of the botanical study of grape vines, especially varieties used in wine-making.

DNA is not the only chemical being extracted from specimens to glean useful information about plants and also about their ecological relationships.  For example, researchers in Copenhagen tested specimens of four species of Salvia used for medicinal purposes for levels of terpenoids, known to have medicinal applications.  These plants were collected over the past 150 years.  While the terpenoid levels did decrease with the specimen’s age, the “chemical composition of four Salvia species are predominantly defined by species, and there was a substantially smaller effect of year of sampling.  Given these results, herbarium collections may well represent a considerably underused resource for chemical analyses.”  Also being investigated are secondary metabolites that plants produce to control herbivore damage.  In one study researchers were able to extract pyrrolizidine alkaloids from plants in the Apocynaceae family that includes milkweed.  The specimens were as much as 150 years old, and even in those treated with alcohol or mercuric chloride, alkaloids were detectable.

There has also been work on the presence of heavy metal pollutants in collections as a way of tracking contamination.  A study at Brown University in Providence, Rhode Island analyzed samples from specimens collected around the city from 1846 to 1916, compared with newly collected ones.  Levels of copper and zinc remained relatively consistent, but lead levels were much lower in plants growing in Providence today.  It was impossible to test accurately for another toxic heavy metal, mercury, because mercuric chloride was so often used to prevent insect damage to specimens.  While toxic metals in plants might make them seem less palatable as food sources, there is an emerging field of agromining:  growing plants that are hyper-accumulators of metals like lead and mercury to eventually reduce soil contamination.  Herbarium specimens can be used to discover how long areas have been contaminated and also to identify species that are particularly good at extracting metals.  There are even some who think that growing plants in nickel-rich soil could be a way to extract this metal for sale.

Such studies suggest that the possible uses of specimens are only limited by the ingenuity of researchers in coming up with them.  It is fun to see what they can ferret out.   The British botanist Mark Spencer recently published a book on his work as a forensic botanist.  It has a great title:  Murder Most Florid (2019).  He was at the herbarium at the Natural History Museum, London curating the British and European collections when he was first asked by the police to aid in a murder investigation.  Human remains have been found in a forested area and had apparently been there for several years.  Would he be able to determine the time more precisely by studying plants at the site?  I don’t want to spoil this story or the other great ones in the book, but I will say that Spencer explains why a herbarium is essential for the work he does, now that he has become much more involved in forensics.

Reference

Spencer, M. (2019). Murder Most Florid: Inside the Mind of a Forensic Botanist. London, UK: Quadrille.

Getting the Most Out of Herbaria

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Representation of Digitization 2.0 from “Digitization and the Future of Natural History Collections,” Hedrick, et al., BioScience, February 2020.

In our culture there is a direct connection between usefulness and value, so it’s not surprising that the arguments for preserving natural history collections entail how useful they are in many scientific endeavors.  The late Smithsonian taxonomist, Vicki Funk, is well-known for her 2003 commentary, “100 Uses for an Herbarium (Well at Least 72).”  More recently there have been articles on how collections have been utilized in the past and on how they could be employed in the future.  These studies take into account how specimen digitization is opening new ways of employing specimens in biological inquiry.  This series of posts will deal with some of these avenues, beginning with the general overview presented here.

Last fall, Heberling, Prather, and Tonsor published an article (2019) that reported on a computational text analysis of over 13,000 journal articles published between 1923 to 2017 and dealing with plant collections.  Investigation of the abstracts categorized the research into 22 topics ranging from taxonomic monographs and revisions as the most common, to morphology and anatomy ranking twenty-second.  Taxonomic work rated as most frequent throughout the study period and for most subtopics in this area the output was relatively steady over time.  However, the authors found that more recently, there have been a wider variety of topics employing herbarium specimens.  These include DNA sequencing of specimen samples and investigations of shifts in phenology over time, along with other measures of environmental change.

While there is nothing particularly shocking about the findings, this is still an important study.  First, it is broad in terms of both the time span and the number of articles covered.  Also, the authors used a rigorous methodology to come up with categories and to apply these to the texts.  Finally, this publication gives those in the natural history collection community a good citation in bolstering their case for the increasing importance of their work:  its increasing breadth promises to grow in the future if properly supported.  Another interesting, though narrower, survey in the same vein was conducted by researchers at the herbarium of the Natural History Museum, London (Carine et al., 2018).  They used 12 categories condensed from Funk’s longer list, analyzed articles published between 2013-2016 by means of the Web of Science, and then compared these results with a survey of researchers who visited NHM to use the herbarium.  In both approaches, taxonomic work ranked highest, but coming in second among the herbarium visitors was historical research.  This is in light of the herbarium’s large and rich historic collection including the herbaria of Hans Sloane and Joseph Banks.  The authors note that this number also reflects their recent work to encourage historical research.

While the studies just cited looked at past work, several publications highlight the bright promise of natural history collections in the digital age.  The author of one of these articles, “Collections-based science in the 21st Century,” is Vicki Funk (2018).  She notes that it is not only the great increase in specimen data now available on line that renders specimens so useful, but also the fact that what is called “next generation” DNA sequencing makes it more feasible and easier to sequence partially degraded DNA, the type found in most specimens.  This opens all kinds of possibilities for phylogenies based in part on specimen data as well as work in evolutionary medicine and ecology.  Georeferencing specimens also opens the way for several kinds of studies including niche modeling and climate change forecasts.

Shelley James and her coworkers give a long list of research projects using herbarium data:  “The addition of non‐traditional digitized data fields, user annotation capability, and born‐digital field data collection enables the rapid access of rich, digitally available data sets for research, education, informed decision‐making, and other scholarly and creative activities” (p. 1).  However, this bright future will only come about through investment of resources that go beyond just getting data online.  The information has to be properly coded so it can be easily retrieved in many different ways and integrated with a variety of other systems so that specimen data is tied to DNA sequences, as well as to ecological evidence and the taxonomic literature.  These are examples of what is coming to be called Digitization 2.0, that is, building on the initial digitization of label data and imaging by integrating this input with genetic and ecological data and by augmenting it with more sophisticated forms of visualization.

European researchers are coming to similar conclusions.  Besnard et al. list many of the same uses mentioned above, noting that this data can be helpful in managing genetic crop resources and monitoring crop pathogens.  Lang and her coauthors provide a good review of employing specimen data to study global environmental change with an emphasis on tracking climate change, the spread of invasive species, and on the effects of pollution and habitat change.  And while I don’t want to put a damper on these bold plans, Bingham et al. have written a comprehensive article on the large number of portals and other digital projects at various levels from the local to the international.  Many of these are not closely tied to or integrated with other projects, and some closely duplicate the efforts of others, so there seem to be too many cooks in the kitchen.  This doesn’t make sense in light of the limited financial and human resources available and the vast job to be done.  Despite this, there are some very interesting projects successfully using herbarium data, and I will touch on them in the next several posts.

References

Carine, M. A., Cesar, E. A., Ellis, L., Hunnex, J., Paul, A. M., Prakash, R., Rumsey, F. J., Wajer, J., Wilbraham, J., & Yesilyurt, J. C. (2018). Examining the spectra of herbarium uses and users. Botany Letters, 0(0), 1–9.

Funk, V. A. (2018). Collections-based science in the 21st Century. Journal of Systematics and Evolution, 56(3), 175–193.

Heberling, M., Prather, L. A., & Tonsor, S. (2019). The changing uses of herbarium data in an era of global change. BioScience, 69(10), 812–822.

Opening Up Herbaria: Higher Education

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Website for BLUE: Biodiversity Literacy in Undergraduate Education

When I majored in biology in the late 1960s, the focus was on cellular biology.  Our year-long intro biology course concentrated on molecules, cells, genetics, and human physiology.  Taxonomy was almost completely skipped over.  This was probably worse than eliminating it completely because a quick tour was head-spinning, and we were left with little more than the idea that the living world is full of exotic creatures with tongue-tying names, definitely an aspect of biology to avoid.  During the fall semester, I fell in love with electron microscope images of cells and that set my educational course.  If I could see a living thing, I wasn’t interested in it.  Out of fifteen biology majors in my cohort, only one went into organismal biology, becoming an oceanographer studying copepods.

While many of my generation continued on to careers in ecology, few ended up in systematics, and the movement away from this discipline remains a trend to this day.  The result is that there are not many botanists and zoologists who have expertise in accurate species identification.  This is particularly ironic because species are still being discovered.  However among plants, a quarter are left undescribed for 50 years or more after they were first found (Bebber et al., 2010).  With the dawn of the 21st century, targeted efforts have been underway to bring back what can broadly be called natural history:  studying biology at the organismal level.  In part this trend is the result of the massive NSF project over the past 10 years to work toward digitizing information on the nation’s natural history collections.

As collections are scrutinized, many discoveries are made, and just the scope of the collections has reawakened interest in them, in what they say about the natural world.  The Society of Herbarium Curators is playing a larger and larger role in this work, as it encourages interest in herbaria among many constituencies, including young people considering careers in systematics and botanical biodiversity.  One of the more disturbing discoveries is the number of species known from old collections that haven’t been found again in the 20th and 21st centuries.  Another is that scientific species names are a foreign language for most of us.  I definitely include myself here.  Until I got on my botany kick, I knew more bacterial than plant genera.  Catching up isn’t easy but it feels good when I can identify a species and name it correctly.  And it’s that good feeling, among other things, that botanists are attempting to pass on to more of today’s students.

In the last post, I wrote about bringing natural history into K-12 classrooms.  Here I want to mention programs to do the same in higher education.  This is a huge topic because it has several different strata.  Among undergraduates, there are some who will major in biology and go on to work in ecology, systematics, and related fields.  But the vast majority will not.  These are the students I taught and that I still worry about.  If they are interested in anything biological, besides issues of health, it is organisms they can see.  Yet much of biology education is devoted to cells and molecules.  The first semester I taught I was shocked to find that my nonmajors did not find protein synthesis fascinating, and they still don’t.  I tried to find ways to make it tantalizing, and finally turned to dealing with another problem:  plant blindness.  I found this an easier sell.  Students were much more likely to find trees on campus to observe than to stumble on a ribosome.  There are now many natural history activities geared to such students including a project developed at the Université catholique de Louvain that could be adapted in many ways.  In addition, Brad Balukjian has written persuasively on why he has just begun a natural history and sustainability program at a California community college.

For those majoring in biology, there is definitely an upswing of interest in fields focused on biodiversity.  The NSF-sponsored program, BLUE: Biodiversity Literacy in Undergraduate Education, aims at developing a set of biodiversity competencies for undergraduates.  These would include not only a focus on organismal biology and ecology, but also on digital literacy and bioinformatics, which will be essential for future professionals.  It is exciting to see a field form around these ideas, some of which are centuries old, and some only beginning to gel.   Natural history collections are essential to these efforts because they hold a great deal of the history of the natural world.  They are also where the living world of today will be recorded.  As I have mentioned a number of times, I volunteer at the A.C. Moore Herbarium at the University of South Carolina, Columbia.  It is alive with undergraduate students who as student workers and interns have learned a great deal about botany by digitizing label information and imaging specimens.  Among the specimens are those collected in the mid-19th century by the planter and botanist Henry Ravenel.  These are on permanent loan from Converse College, and provide a picture of the flora of South Carolina of the past.  There are also graduate students in environmental studies who are contributing specimen vouchers from their work in the field.  Herrick Brown, the A.C. Moore Curator, whose doctoral work dealt with seed dispersal and climate modeling (Brown & Wethey, 2019), has plans to foster participation by more students in the herbarium’s activities.  It is an exciting place to be!

References

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

Brown, H. H. K., & Wethey, D. S. (2019). Observations on anthesis, fruit development, and seed dispersal in Gordonia lasianthus (theaceae). Journal of the Botanical Research Institute of Texas, 13(1), 185–196.

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.

On the Road, Learning about Herbaria: The ESN

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

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

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

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

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

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

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

References

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

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

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

BLUE Port: Biodiversity Literacy in Undergraduate Education

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

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

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

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

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

On the Road, Learning about Herbaria: Digitization

iDigBio Portal

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

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

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

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

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

Book Tour: The Art of Naming

4 gaga

Specimen of Gaga marginata (Kunth) Fay W.Li & Windham (formerly Cheilanthes marginata) from the United State National Herbarium

This is the last post in a series (1,2,3) on books I read on a recent trip.  I found The Art of Naming by Michael Ohl (2018) on an earlier trip and brought it along on this one.  Ohl is a German entomologist at the Natural History Museum of Berlin, and he tackles many aspects of the question: how do species get named?  This is a work about nomenclature and taxonomy that sometimes borders on the technical, but always in a way that’s accessible to the general reader.  Of course, there is the issue of whether or not the general reader really wants to know this much about nomenclature, but Ohl provides enough good stories along the way to keep his audience engaged.  This work was translated from the German by Elisabeth Lauffer, and I think she is also partly responsible for its readability, though there is always a slight hint of the difficulty of smooth translation.

While understandably Ohl takes most of his examples from the insect world, or at least from zoology, I found this a fascinating book because he is so good at describing the ins and outs of taxonomy, a field in which I am definitely not an expert.  Yes, the rules of nomenclature are different in zoology and botany, but most of the problems are similar.  For example, at one point he deals with the issue of those who have named a great many taxa, thousands of them.  Here he refers to an article by Daniel Bebber and coauthors (2010) in which they describe “big hitters,” those who collected many new species.  In their study Bebber’s group found that just 2% of plant collectors were responsible for over half the type specimens in a sample of 100,000 types.

Ohl found “big hitters” in entomology as well, but they were not collectors, rather those who described and named new species.  There are such individuals in botany as well, and in both cases, their reputations are not all stellar.  A Ohl notes, taxonomy seems to cause a certain mania in some practitioners, a passion for naming as many new species as possible.  A number of these individuals are considered “splitters,” focusing on small differences and tending to write brief descriptions.  In naming so many species, it’s not surprising that they might name the same species twice or even three times, and a taxonomist’s rate of synonymy is considered a measure of reliability, the lower the better.  Ohl relates several stories of taxonomists gone wild, but tempers his criticism by mentioning all the good work these individuals did as well.  This sense of balance is what makes the book so interesting; he is not afraid to look at both sides of nomenclatural debates.

One topic Ohl covers in detail is what makes a name acceptable or not.  The rules here vary somewhat from those in botany, but many are similar:  not naming a species after oneself, following rules of Latin or Greek grammar, and not applying a name that has already been used.  He relishes the subject of naming as a way to draw attention to a species, or to the one for whom it’s named.  I know there is a fern genus named after Lady Gaga, but now I know that there’s a spider named for David Bowie.  Ohl also tackles the topic of naming as fund-raising, which apparently has been going on for some time.  The German organization BIOPAT was founded in 1999; it makes undescribed species available to donors.  Rates start at 2,600 euros per species and depend on what the market will bear, in other words how attractive in some way the species is.  By 2013, the organization had raised 620,000 euros.  But there are other approaches, including an auction in 2005 to name a new titi monkey species in Bolivia’s Madidi National Park.  The British biologist describing it, Robert Wallace, decided to set up the auction to raise money for the Park.  Ultimately, the name was “sold” for $650,000 to the Golden Palace online casino, and now the monkey is Callicebus aureipalatti.  There are auctions on eBay to name plants, but the stakes are definitely not that high.  In this survey, Ohl again balances questions about naming-for-money against the sadly underfunded world of conservation biology.

Besides telling such fascinating stories, Ohl also deals with fundamental issues:  “getting at the essence of a species is one of the most difficult, controversial, and yet most important questions in biology” (p. 84).  He explores the issue in terms of deciding on a type specimen or specimens and what this designation signifies:  “Type species are not representatives of biological species from representations of names of biological species” (p. 108).  He points out how types have become essential in taxonomy and discusses the ins and outs of designating a lectotype (in zoology, a type designated after the species has already been named) for humans.  It was in fact a botanist, William Stearn, who chose Carl Linnaeus’s remains as representative for all Homo sapiens.  While Ohl doesn’t deal much with the digitization of natural history collections and using bioinformatics to bring order to nomenclature, that may be because these projects are farther along in botany than in zoology.  In any case, this was definitely a good read on a rather “interesting” trip north.

References

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

Ohl, M. (2018). The Art of Naming. Cambridge, MA: MIT Press.

Stearn, W. T. (1959). The background of Linnaeus’s contributions to the nomenclature and methods of systematic biology. Systematic Zoology, 8(1), 4–22.