Conserving Biodiversity

One of the outgrowths of the Convention on Biological Diversity (CBD) discussed in the last post was the Global Strategy for Plant Conservation (GSPC) of 2002.  Updated 10 years ago, it has five objectives and within them 16 goals or targets.  While not all the targets have been met, there has been a great deal of work done toward them, and herbaria have been at the forefront of these efforts as have botanic gardens.  In fact, Botanic Gardens Conservation International, a global partnership, has taken a lead.  The first objective, not surprisingly was to understand plant diversity and one of the targets was an online flora of all known plants; this effort is headed by the Royal Botanic Gardens, Kew.  Though not complete, the flora does include information on each listed species’ range, with related literature and a sampling of illustrations and herbarium specimens.

Another target was to determine, “as far as possible,” the conservation status of all known plants.  This goal is much more difficult to achieve, but the International Union for Conservation of Nature’s (IUCN) Red List of Threatened Species established in 1964 is the most comprehensive inventory of species vulnerability worldwide.  Those with economic or cultural value, and those most apparent to humans, are more likely to be included because a great deal of work goes into getting a species listed, and delisted if its status improves.  In the case of plants, evaluation includes research in herbarium collections to determine a plant’s range in the past compared to what it is now, and at times to clarify precisely what species is being listed.  To put teeth into the protection of species on the Red List, the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) was presented at a Washington, DC meeting in 1973.  It controls commerce in endangered species and comes into play in botany especially with illicit trade in timber from rare trees and exotic plants such as orchids and cacti. 

About a third of the world’s plants are threatened with extinction.  Such loss could be comparable to some earlier mass extinctions including the one about 65 million years ago that brought the age of dinosaurs to an end.  But it was not just dinosaurs that disappeared, that’s not the way the living world works.  Species are so interdependent that a single extinction can result in greater loss:  the species’ parasites and predators could also suffer population crashes leading to extinction.  That’s why conservationists focus on protecting habitats and ecosystems, not individual species such as a beautiful orchid or bird.  Species that catch the human eye are linked to many others such as microscopic invertebrates and fungi that are less obvious but equally important.

The goals of the second GSPC objective are more multispecies in scope including conserving 15% of each ecological region or vegetation type and 75% of the most diverse areas, the biodiversity hotspots.  Other goals include growing 75% of threatened plant species in situ, that is, in their natural habitat and also ex situ in botanical gardens or other protected areas, preferably in the plant’s home country.  This last goal highlights the importance of botanic gardens in biodiversity conservation.  They have become safe havens for many species, places where plants can be cultivated and propagated.  In a sense, this is an outgrowth of the mission of nineteenth-century colonial botanic gardens and their mother gardens in Europe, such as Kew in London and the Jardin des Plantes in Paris.  Now there are more gardens in plants’ home countries and under the supervision of the countries’ own people, who, thanks to the CBD, can make binding decisions about how these plants will be distributed and used, including for ecosystem restoration projects.  However, the resources of gardens in developed countries are still necessary; they nurture plants on site, also sending them back to the country of origin, with the goal of having 20% of the plants available for restoration work.

In addition, botanical gardens preserve specimens to document what is grown and some saving small samples of plant material under ultra-cold conditions for future use in DNA sequencing studies.  Ideally, each sample is associated with a herbarium specimen voucher for reference.  Just as herbaria were important to economic botany in the nineteenth century, they are crucial to biodiversity research in the twenty-first.  The number of herbaria in developing nations has increased substantially in this century and the number of specimens housed is rising at an even faster pace, in part with the impetus of the GSPC.  The best resource for tracking herbaria and their growth is the annual report of the online Index Herbariorum, the definitive guide to the location and holdings of the world’s herbaria.

The GSPC’s third objective is for plant diversity to be used in a sustainable and equitable manner.  This depends on support from herbaria and from the international community in the form of the CITES treaty to prevent trade in endangered species.  Because of economic deprivation in many developing countries, there is great pressure to profit from natural resources, including plants and animals.  Uprooting rare plants does more than just reduce the population, it damages the entire habitat and makes it less likely that the plants can grow back.  Herbaria play a role in, for example, providing evidence in court cases arising from the seizure of endangered plants.  Taxonomists may be called on to verify that the species is in fact on the Red List.  The same is true of illegal trade in timber from endangered tree species, with xylarium collections’ wood samples compared to recovered timber.  CITES does have a downside as far as herbaria are concerned in terms of shipping specimens internationally.  There are forms that have to be filled out to certify that the material is only for research purposes and not for profit.  At times the red tape can be excessive, making the work of herbarium managers frustrating.

Protecting Biodiversity

Map of New Guinea

A prime reason for learning about biodiversity (see last post) is to find ways to conserve it.  One approach was developed at a meeting in Rio de Janeiro in 1993 and led to the Convention on Biological Diversity (CBD) that gives each nation sovereignty over its biological wealth.  It aims to prevent developed nations from continuing to exploit the biota of developing nations, most of which had their progress thwarted by centuries of colonial rule.  The CBD represents a major shift in how the biological resources of a country are seen not only economically, but politically and culturally.  For example, the cinchona tree, native to Andean rainforests, is considered not only as the source of a valuable commodity, quinine, but as a resource growing in a particular place and therefore subject to the regulations of the government of that place.  Cinchona also has a long cultural history; it was Andeans who originally discovered its fever-relieving effects centuries ago and this plant has been documented with herbarium specimens, seeds, and also in poetry and art.  It is an integral part of Andean heritage, though it now grows in plantations around the world (Crawford, 2016).

Cultural connections can be found for thousands of plants worldwide, but economic and political issues often are at the fore when it comes to plant collecting.  Since the ratification of the CBD by most of the world’s nations, these issues have had a significant effect on botany, and on herbaria, just as they have had throughout the history of botany.  The difference now is the aim of equitable distribution of value.  Even non-signatory nations must comply with the procedures set down by those that have signed if they want to be allowed to collect, so this and the other international agreements have had a significant impact on how the biological wealth of nations is viewed and treated.  This is especially true since ratification of another UN-sponsored document, the Nagoya Protocol, a 2011 agreement that grew out of the CBD. It deals with the genetic resources of plants and animals, and how their benefits can be shared and used fairly and equitably.  It aims to prevent exploitation of resources, for example, by drug companies collecting plants that have medicinal uses and then developing drugs based on these plants in the companies’ laboratories without sharing profits with the country where the plant was collected and with the people who revealed its medical efficacy.

The Nagoya Protocol gives the host country the right to set strict limits not only on what can and cannot be collected, but also on how it can and cannot be used after collection.  Restrictions along with those of the CBD are meant to prevent the kind of exploitation by wealthy nations carried out for centuries, so they are attempting to right grievous wrongs.  A botanist who wishes to collect in another country must obtain a permit, or a series of permits, to do so.  These delineate what can and cannot be gathered, often only specific plant groups and in specific quantities.  Travel might also be limited to particular geographic areas.  Where possible, unless the plant is very rare, it is collected in multiples, and specimens are retained in an institution in the host country as well as in the collector’s institution. 

Requirements and procedures vary widely from country to country, and it may take months if not years to obtain necessary documents, which in some case are issued across multiple government agencies at levels going from country-wide to state, municipality, or other jurisdiction.  This sounds daunting, and it can be.  Some botanists and policy makers argue that the paperwork can be so difficult as to effectively prohibit or severely curtail collection and therefore hinder biodiversity research; requirements can have the opposite effect to what was intended.  The protocol does prevent exploitation, but in some cases it prevents research that might lead to practical benefits for the country in question.  In a commentary on a recent assessment of the biodiversity on the island of New Guinea, the authors noted that while half the island is part of Indonesia, a signatory to the protocol, the other half, Papua New Guinea, is not.  This is making the latter a more attractive location for biodiversity research (Novotny & Molem, 2020).

More mundane problems also persist.  Travel in many areas is difficult, as is transport and communications.  Shipments can get lost and may turn up eventually, or may be gone for good.  Australian customs officials destroyed type specimens sent from France over a mix-up about proper identification of the plant material (Davidson, 2017).  Restricting movement of plants into Australia is understandable.  These are definitely legitimate issues in preventing spread of invasive non-native species.  Australia, because of its remoteness, has a large number of endemic species and has suffered extinction of native plants and animals due to invasives.  But the invisibility of herbaria and their work has compounded the customs problem, since most nonscientists have never heard of herbaria and do not understand that specimens are dead, not living, plants. 

References

Crawford, M. J. (2016). The Andean Wonder Drug: Cinchona bark and imperial science in the Spanish Atlantic, 1630-1800. Pittsburgh: University of Pittsburgh Press.

Davidson, H. (2017, May 8). Australian biosecurity officials destroy plant samples from 19th-century France. Manchester Guardian.

Novotny, V., & Molem, K. (2020). An inventory of plants for the land of the unexpected. Nature, 584(7822), 531–533. https://doi.org/10.1038/d41586-020-02225-4

Cataloguing Biodiversity

This series of posts deals with threats to biodiversity from a botanical perspective.  There is no lack of evidence for climate change and it’s easy to become overwhelmed and pessimistic.  But the only way forward is to learn more about what is happening and why, and then to take action based on that knowledge.  One example of the botanical community’s efforts is a report published by the Royal Botanic Gardens, Kew, with contributions from a global roster of researchers.  State of the World’s Plants and Fungi 2020 is a useful blend of optimism and caution, presenting how biodiversity is catalogued, what is being learned about it, and how it can be preserved and also used into the future.  This latest report is supplemented with articles in a special issue of Plants, People, Planet as well as with a virtual symposium.  Earlier, Kew had published separate reports on plants and on fungi, but it made sense to combine them since this is how they are found in the world. 

It’s no surprise that Kew would have a leadership role in biodiversity research with its impressive staff and the world’s largest herbarium.  It also has a long history of studying plant diversity in developing nations, though granted, for a good portion of this history Kew’s efforts were on behalf of the world’s largest colonial power.  Garden administrators directed far-flung collectors, who relied on the expertise and labor of countless indigenous assistants and enslaved persons in finding plants that often proved economically important to the British (Brockway, 1979).  The past and future are intertwined at Kew in complex ways in its living and preserved plant collections.  Kew sponsored a symposium on the recent work of digitizing its collection of Miscellaneous Reports that colonial botanic gardens sent to Kew.  It is an important step in decolonizing its collection and was a fascinating look into how plants and plant products moved throughout the British Empire.

The present Kew report notes that 1942 new vascular plant species were described in 2019.  Many new finds were recently collected, but herbaria harbor plants awaiting identification and in some cases discovery as new species.  There is no solid estimate of the earth’s total plant diversity, of how many different plants exist.  The best record of known plants runs to around 350,000, with 325,000 of them flowering plants.  The situation with fungi is cloudier.  Almost 150,000 fungal species have been named and described; 1,886 were added in 2019.  With much research now being done on fungi, greater diversity is becoming apparent, and estimates of the number of fungal species now range from over two to nearly four million.  To me this is one of the most fascinating aspects of the report:  how the power of the fungal world is finally coming to be appreciated.  Two books that have done much for fungal publicity are Peter Wohlleben’s The Hidden Life of Trees (2016) on how fungi support plant life and Merlin Sheldrake’s Entangled Life (2020) on how fungi influence so much of the living world. 

The Kew report notes that the great biodiversity in tropical areas means some countries, though explored for centuries, are still yielding many discoveries.  Brazil, Madagascar, India, and South Africa have been collection areas from the sixteenth century on.  There have been a number of projects where these sites have been revisited, with older collections used in planning surveys.  The new work may recollect the same specimens, which can be used in genetic comparisons with the older plants.  Not finding some species points to changes in the habitat due to climate change or other factors, and not surprisingly there may be new species found as well.

Island ecosystems are particularly rich in endemic species found nowhere else:  83% of Madagascar’s 11,138 native plant species are limited to this island, making learning about and protecting its flora especially important.  A recent study in New Guinea reports that it has the world’s richest island flora with 13,634 species, 68% endemic (Cámara-Leret et al., 2020).  This is the first comprehensive plant list for the island, and the study could be a model for future work in other areas, though it may still be quite incomplete.  There are 3,962 tree species on the list, which seems impressive, but the number found in an inventory of the Amazon region was over 10,000.  In South America, researchers surveyed all the plants in almost 2000 study plots, a time-consuming and labor-intensive cataloguing job particularly under difficult conditions.  In New Guinea, only 300 plots were surveyed, which may explain the lower tree species count.  This suggests that discovering biodiversity is both hard work and not near its end, while these species-rich areas are under increasing threat from development (Novotny & Molem, 2020).

There are many factors involved in estimating biodiversity.  It is not just the density of sampling, but where the sampling is done.  Studies of the geographic locations on herbarium specimens has uncovered many collection biases because botanists, being human, tend to collect relatively close to home and even during exploration, find some areas easier to access than others.  For former colonies, the regions around botanic gardens were often well studied, or were along supply routes, or near seaports or other urban areas.  Species-rich regions of South Africa were explored from the 17th century (see image above), but there were no collections in some areas until the end of the 19th century when they were opened to agriculture (Cowell, 2020).  Few collections were made in highly diverse portions of Cameroon until they were surveyed over a decade beginning in 2004; 2240 plant species were found with about a tenth under threat of extinction (Demissew, 2015).

References

Brockway, L. B. (1979). Science and Colonial Expansion: The Role of the British Royal Botanic Gardens. Interdisciplinary Anthropology, 6(3), 449–465.

Cámara-Leret, R., Frodin, D. G., Adema, F., Anderson, C., Appelhans, M. S., Argent, G., Arias Guerrero, S., Ashton, P., Baker, W. J., Barfod, A. S., Barrington, D., Borosova, R., Bramley, G. L. C., Briggs, M., Buerki, S., Cahen, D., Callmander, M. W., Cheek, M., Chen, C.-W., … van Welzen, P. C. (2020). New Guinea has the world’s richest island flora. Nature, 584(7822), 579–583. https://doi.org/10.1038/s41586-020-2549-5

Cowell, C. R., Anderson, P. M. L., & Annecke, W. A. (2020). Historic herbarium specimens as biocultural assets: An examination of herbarium specimens and their in situ plant communities of the Agulhas National Park, South Africa. People and Nature, 2(2), 483–494. https://doi.org/10.1002/pan3.10087

Demissew, S., Beentje, H., Cheek, M., & Friis, I. (2015). Sub-Saharan botanical collections: Taxonomic research and impediments. In I. Friis & H. Balslev (Eds.), Tropical Plant Collections: Legacies from the Past? Essential Tools for the Future? (pp. 97–114). Stockholm: Scientia Danica.

Novotny, V., & Molem, K. (2020). An inventory of plants for the land of the unexpected. Nature, 584(7822), 531–533. https://doi.org/10.1038/d41586-020-02225-4

Sheldrake, M. (2020). Entangled Life. London: Bodley Head.

Wohlleben, P. (2016). The Hidden Life of Trees. London: Harper Collins.

Biocultural Ethnobotany

Cotton grown locally in Aiken, South Carolina

Ethnobotanical research has moved beyond just searching for medicinal plants or even food plants.  There is now a more holistic approach to indigenous plant knowledge, one tied not only to finding valuable plants but to saving biological and cultural diversity as well (Cámara-Leret & Bascompte, 2019).  This makes recording the vernacular names for plants important in field notes and even on herbarium sheets as a way to preserve knowledge.  From early in the history of plant exploration, such information has been unevenly respected, though as discussed in previous posts (1,2), some botanists were careful to record not only local names but uses for plants.  Ethnobotanists are now combing herbarium sheets and collecting journals kept in European and North American herbaria for leads in seeking out present-day knowledge held by local populations (Nabhan, 2016). 

This points to the fact that there is a significant gap between the botanical infrastructure of developed and developing nations.  Closing what in many cases is a chasm must involve more than just sending teams of experts to assist in plant collecting, and sponsoring students to attend graduate schools where large plant collections like those at Kew or NYBG are easily accessible.  The infrastructure needs to be developed where the plants are, and this is slowly happening, particularly in countries like Brazil and South Africa, where universities are educating botanists who will fill new academic positions and help to overcome the taxonomic impediment of a lack of professionals.  Assistants in the field are also being trained, with parataxonomists receiving instruction in collecting and in plant identification.  At last those who do the work of collecting are being treated as worthy of education and acknowledgment (Basset et al., 2004).  Visiting botanists can still provide valuable assistance, but they are often as likely to be learning from the permanent staff in local institutions as offering expertise.

Anthropologists and ethnobotanists working together have discovered a close link between extinction of species and extinction of local languages (Gorenflo et al., 2012).  Research shows that neighboring peoples who have different language traditions are unlikely to share plant knowledge, so with the death of a language comes an acute loss of learning.  Close observation going on for centuries has resulted in information on plant blooming and fruiting times, plant/animal interactions, and of course, a host of uses for plant material.  Indigenous expertise is invaluable and in many cases fading fast since younger generations are often less interested in traditions that might well lead the way forward in environmental conservation (Nabhan & St. Antoine, 1993).  Ethnobotanists today are helping to document this information with, among other things, herbarium vouchers, to anchor that knowledge to specific data about plants (Stepp & Thomas, 2010).

Throughout the world, herbarium collections are being formed by indigenous peoples to document the flora important to them—a way to preserve plants and the knowledge attached to them.  Two tribes in California are working with the University of California, Berkeley’s Jepsen Herbarium in making such collections, and the Newe people in Idaho have created a herbarium to document what grows on their lands.  These are manifestations of a desire to maintain their identity in a particularly important way, since plants provide so many of the resources that supported these groups and shaped their cultures.  These peoples were shaped by their ecosystems as much if not more than they shaped them, and specimens help to tell this story.

Learning about such projects and about how language, history, and ecology are woven together can also help those not part of such cultures to appreciate that they too are shaped by the plants they have relationships with.  Awareness of plant connections might generate some thought about how buying carrots in a plastic bag provides an impoverished experience of this vegetable.  If this is the only way someone sees carrots, they have no idea how beautiful their leaves and flowers are, or how good a fresh carrot tastes.  The fact that in the same country where carrots come in plastic bags, there are indigenous peoples preserving their biological heritage in herbaria, suggests how biocultural issues can vary greatly within a geographical area.  Looking at the culture of plant use across the board could make everyone more aware of how important plants are to our lives and spur finding better ways to appreciate our links to them.

In the United States, houseplant sales have increased significantly during the Covid pandemic.  So has cat and dog ownership, but let’s stick with the plants here.  In the 1980s, E.O. Wilson published Biophilia in which he argued that attraction to other species is an innate human trait.  For most of our species’ history, humans have lived intimately with nature.  It would be peculiar if we didn’t have adaptations as a result.  Also as a result of Covid there are more and more studies substantiating Wilson’s view:  time spent in natural settings improves mental health and increases a sense of wellbeing.  I can envision ethnobotanical studies, vouchered of course, that investigate how plants are used for what we term decorative purposes.  As someone who wrote an article on the biology of interior decorating (Flannery, 2005), I think this is a great idea.  What plants are sprouting in peoples’ homes?  Are they being grown from seed or purchased fully grown, in which case the ecology of big box stores and garden centers needs to be investigated.  And how long term are these plant-human cohabitations:  until the plant stops blooming, or loses all its leaves, or are they together for the long term?  Just as anthropology has broadened its focus and now investigates groups beyond the indigenous populations traditionally studied—for example, scientists—the same move would be helpful in ethnobotany (Lynch & Woolgar, 1990).  Since everyone uses plants, it would support the future of botany, and of society, to delve into the relationships of all people to plants, if for no other reason than to alleviate the problem of plant blindness.

References

Basset, Y., Novotny, V., Miller, S. E., Weiblen, G. D., Missa, O., & Stewart, A. J. A. (2004). Conservation and biological monitoring of tropical forests: The role of parataxonomists. Journal of Applied Ecology, 41(1), 163–174. https://doi.org/10.1111/j.1365-2664.2004.00878.x

Cámara-Leret, R., & Bascompte, J. (2019). Indigenous Knowledge Networks. The Ethnobotanical Assembly. https://www.tea-assembly.com/issues/2019/9/29/indigenous-knowledge-networks

Flannery, M. C. (2005). Jellyfish on the Ceiling and Deer in the Den: The Biology of Interior Decoration. Leonardo, 38(3), 239–244.

Gorenflo, L. J., Romaine, S., Mittermeier, R. A., & Walker-Painemilla, K. (2012). Co-occurrence of linguistic and biological diversity in biodiversity hotspots and high biodiversity wilderness areas. Proceedings of the National Academy of Sciences, 109(21), 8032–8037. https://doi.org/10.1073/pnas.1117511109

Lynch, M., & Woolgar, S. (1990). Representations of Scientific Practice. Cambridge, MA: MIT Press.

Nabhan, G., & St. Antoine, S. (1993). The loss of floral and faunal story: The extinction of experience. In S. Kellert & E. O. Wilson (Eds.), The Biophilia Hypothesis (pp. 229–250). Washington, DC: Island Press.

Stepp, J. R., & Thomas, M. B. (2010). Managing ethnopharmacological data: Herbaria, relational databases, literature. Medical and Health Sciences, 13, 116–123.

Wilson, E. O. (1984). Biophilia. Cambridge, MA: Harvard University Press.

Ethnobotany in Practice

Swamp-Pink, Helonias bullata, threatened in South Carolina, photo from USFWS

At the moment, most ethnobotanic work outlined in the last post is done in developing countries.  Despite the vast geographical expanses and travel challenges, the richer biodiversity nearer the equator remains a magnet for collectors.  However, large-scale expeditions are long gone and collecting in the developing world is now tightly regulated.  This is the result of a post-colonial world with all nations justifiably wishing to have sovereignty over their biological resources.  Several international agreements are helping to make this possible.  The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) was presented at a United-Nations sponsored meeting in Washington, DC meeting in 1973.  It controls commerce in endangered species presented in the IUCN Red List.  It comes into play in botany especially with timber from rare trees and exotic plants such as orchids and cacti.  It is the first of several international agreements on the earth’s biodiversity.  CITES regulations are strict, but depend on enforcement which varies among the signatories and with the economic value of the species.

A meeting in Rio de Janeiro in 1993 led to the Convention on Biological Diversity (CBD) that gives each nation sovereignty over its biological wealth.  It aims to prevent developed nations from continuing to exploit the biota of developing nations, most of which had their advance thwarted by centuries of colonial rule.  The CBD represents a major shift in how the biological resources of a country are seen not only economically, but politically and culturally.  Since the ratification of the CBD by most of the world’s nations, these issues have had a significant impact on botany and on herbaria, as they had throughout the history of botany.  The difference now is the aim of equitable distribution of value.  Even non-signatory nations must comply with the procedures set down by those that have signed, so this and the other international agreements have had a significant impact on how the biological wealth of nations is viewed and treated.  This is particularly the case since the ratification of another UN-sponsored document the Nagoya Protocol, a 2011 agreement that grew out of the CBD.  It deals with the genetic resources of plants and animals, and how their benefits can be shared and used fairly and equitably.  It aims to prevent exploitation of resources, for example, by drug companies collecting plants that have medicinal uses and then developing drugs based on them in their home country’s laboratories without sharing profits with the country where the plant was collected and with the people who revealed its medical efficacy.  

Such agreements give a host country the right to set strict limits not only on what can and cannot be collected, but also on how it can and cannot be used after collection.  These restrictions are meant to prevent the kind of exploitation by wealthy nations that was carried out for centuries.  A botanist who wishes to collect in another country must obtain a permit, or a series of permits, to do so.  These delineate what can be gathered, often only specific plant groups and in specific quantities.  Travel might also be limited to particular geographic areas.  Where possible, unless the plant is very rare, it is collected in multiples, and specimens are retained in an institution in the host country as well as in the collector’s institution. 

Requirements and procedures vary widely from country to country, and it may take months if not years to obtain the necessary documents, which in some cases are issued across multiple government agencies at levels going from nation-wide to state, municipality, or other jurisdiction.  This sounds daunting, and it can be.  Some botanists and policy makers argue that the paperwork can be so difficult as to effectively prohibit or severely curtail collection and therefore hinder biodiversity research.  They contend that the requirements can have the opposite effect to what was intended.  The protocol does prevent exploitation, but in some cases it thwarts research that might lead to practical benefits for the country in question.  In a commentary on a recent assessment of the biodiversity on the island of New Guinea, researchers noted that while half the island is part of Indonesia, a signatory to the protocol, the other half, Papua New Guinea, is not.  This is making the latter more attractive for biodiversity research (Novotny & Molem, 2020).

More mundane problems also persist.  Travel in many areas is difficult, as is transport and communication.  Shipments can get lost and may turn up eventually, or may be gone for good.  This is a real concern since there are strict regulations about transporting living material, or material that was at one time living, across borders.  These are definitely legitimate issues about the possible spread of invasive non-native species.  Australia, because of its remoteness, has a large number of endemic species and has had severe problems with invasives causing extinction of native plants and animals.  The invisibility of herbaria and their work have compounded the customs problem, since most nonscientists haven’t heard of herbaria and do not appreciate that specimens are dead not living plants.  The case of Australian customs officials destroying types specimens sent from the herbarium at the National Museum of Natural History in Paris led to an international incident.

Reference

Novotny, V., & Molem, K. (2020). An inventory of plants for the land of the unexpected. Nature, 584(7822), 531–533. https://doi.org/10.1038/d41586-020-02225-4

Getting the Most Out of Herbaria: In So Many Ways

4 Georgia

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

2 Florid

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

4 BLUE

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.