Corpus Botany

Michael Dosmann, Curator of Living Collections at the Arnold Arboretum at Harvard University, gave this sage advice to anyone working to manage a collection of botanical data: “Don’t spend your life chasing taxonomy!” The world of botanical taxonomy is endlessly complex and dynamic, changing rapidly from month to month. It is a global effort to build a single hierarchical tree that captures reality, with contributors working from different directions using different and evolving techniques to understand a body of data that is expanding with new discoveries and shrinking from anthropogenic changes to the planet. It is built on a foundation that began with Theophrastus in the 4th Century BCE and was canonized by the 17th and 18th century natural philosophers of Europe, but this traditional foundation is being bent rather violently to accommodate three subsequent centuries of new understanding.

The traditional taxonomic ladder is captured in the mnemonic “King Philip Came Over For Good Sex” (shout-out to XKCD): Kingdom, Phylum, Class, Order, Family, Genus, Species.

But the Integrated Taxonomic Information System (ITIS) presents online users with the following: Kingdom, Subkingdom, Infrakingdom, Division, Subdivision, Infradivision, Superclass, Class, Subclass, Superorder, Order, Suborder, Family, Subfamily, Tribe, Subtribe, Genus… (I cut it off at the Genus level, since the point was made).

This list makes clearly shows an ongoing process of rebuilding-the-ship-as-it-sails, shoehorning sub- and super-categories into the ladder in order to reflect a growing understanding of increasing complexity.

Hence Dosmann’s advice: You can’t wait for this to get sorted out before getting down to work.

For Botanica Caroliniana we want to collect and juxtapose useful data on the history of botanical science. We are not in a hurry and are willing to take the time to work methodically, to separate concerns, to recognize that the underlying data is more important than an immediate, glossy online presentation. But we don’t want to wait forever.

And we need to name plants. These names must be unique, stable, and machine-actionable. Linnaean binomials are pretty good, and traditional. They are supposed to be unique. They are not stable, as further study will inevitably split species, rearrange genera; ITIS and IPNI (the Integrated Plant Names Index) will happily provide countless synonyms for any given Linnaean binomial. They are certainly not machine-actionable.

For our digital library we need machine-actionable identifiers that we can use now. They need to be unique and stable within the digital library, while accommodating subsequent changes to the scientific reality of the objects to which they point. Here we can borrow from the disciplines of information science and corpus linguistics.

Corpus Linguistics. It is extremely difficult to make assertions about “how the English Language works”; people keep saying new things, keep changing how they speak, keep encountering new situations that need new word and new constructions. It is much, much easier to make assertions about “the language of New York Times reporting from 1941 - 1945”: How did the NYT refer to the enemies and allies of the United States? What verbs did they use for military victory and defeat, for casualty figures, to describe economic hardships at home? Answers to those questions are easier to formulate, and can be assessed in the context of the explicitly defined corpus. Many answers that are valid for one corpus would be invalid for another—racial slurs that were acceptable to the NYT in 1942 would never be allowed in print today; the language describing the Soviet Union (I bet) changed dramatically between 1943 and 1947. Corpus linguistics allows us to study real phenomena within defined constraints that make intractable datasets manageable.

Namespaces and Arbitrary Identifiers.  Information scientists deal with large numbers of things. Amazon.com sells billions of products; they need to keep track of those products, to share information about them through the digital medium that the company inhabits. Under these circumstances it is immediately obvious that the acts of identification and description must be separate. This is not complicated: each product has a unique, machine-actionable ID, which points to a body of data that includes description, price, reader reviews, and so forth.

Digital librarians have a greater challenge than online merchants, since their IDs need to survive in the wild, outside the confines of a particular database. The “Rachael Ray 1.5 Quart WhistlingTeakettle” has an Amazon ID of 1343145892. That ID, elsewhere on the Internet, points to a product in a Japanese cosmetics catalogue, a Seller Profile on Ebay.com, and a team-building event for Western Union Employees, to name a few.

The answer for a digital library is to use Namespaces. There are no doubt billions of digital objects in the online universe with an ID of 19. But there is only one with an ID that is urn:cite:botcar:sloane.19. That is, “a URN using the CITE protocol, in the BOTCAR namespace, in the Sloane collection, number 19.”

Corpus Botany. For Botanica Caroliniana, we give each object of our interest a URN identifier: herbaria, folios in herbaria, specimens on folios, digital images of folios, and the notional species which these represent.

These species URNs are the glue that holds this digital library together. So the species Acer negundo L. has a URN: urn:cite:botcar:species.Acernegundo. The last element of the URN is somewhat human-readable, but it is worth emphasizing that this is an ID, an arbitrary identifier, and nothing more. As a data-object, urn:cite:botcar:species.Acernegundo identifies a notional species that we can label, for human readers, Acer negundo L., that we can supply with bibliography, or that we can link to an ITIS record (TSN serial no. 28749).

The important thing, though, is that we can build our digital library simply by creating a graph of URNs, with each URN maintaining a strict separation of concerns. A specimen (urn:cite:botcar:sloane.422) appears on a folio (urn:cite:fufolio:CatesbyHS212.12) and is an example of a species (urn:cite:botcar:species.Acernegundo), which belongs to a genus (urn:cite:botcar:genera.Acer), which in turn belongs to a family (urn:cite:botcar:family.Sapindaceae); the folio (urn:cite:fufolio:CatesbyHS212.12) is illustrated by a digital image (urn:cite:fufolioimg:Caroliniana.Catesby_HS212_012_0493), and the specimen itself is illustrated by a region of interest on that image (urn:cite:fufolioimg:Caroliniana.Catesby_HS212_012_0493:0.423,0.2,0.549,0.715).

In the above sentences, every noun is represented by a URN, and each verb can be as well. This is the subject of a subsequent posting on this blog.

For now, it is enough to say that we do not have to capture the entire taxonomic world in order to build a useful digital library of historical scientific data. We can give URNs to the objects of our concern, and only to those objects. Because our linking mechanisms are arbitrary identifiers, the structure of our digital library can accommodate advances in scientific understanding easily. If genus Acer is split in two, and Acer negundo suddenly belongs to a new genus, we need make only one change to the hundreds of thousands of points in our graph.* We change one entry from:

urn:cite:botcar:species.Acernegundo isMemberOf urn:cite:botcar:genera.Acer

to 

urn:cite:botcar:species.Acernegundo isMemberOf urn:cite:botcar:genera.SomeNewGenus

If Acer is renamed by some authority, but remains a member of Sapindaceae and the parent of Acer negundo, then we are under no obligation to change our URN, which can remain “the genus is referred to in Botanica Caroliniana as urn:cite:botcar:genera.Acer”. We can and should update any data fields pointed to by that URN to reflect the new scientific reality.

So this is what we are calling “corpus botany”: comprehensive coverage of data in a constrained, publicly defined corpus, with separation of concerns, tied together with namespaced, arbitrary identifiers.

The evolving collections of URN identifiers are store in public Google Fusion Tables:

Hortus Siccus Facsimile Model (Google Fusion Table)

Catesby Specimen Collection URNs (Google Fusion Table)

Botanical Species URNs (Google Fusion Table)

Botanical Genus URNs (Google Fusion Table)

Botanical Family URNs (Google Fusion Table)

The organization of these URNs into Collections, how we can use them in online publications, and the important topic of how to link them together, will be the subject of subsequent posts.

* Genus Aster is problematic. Alan S. Weakley, in the Flora of the Southern and Mid-Atlantic States, says, “It is now abundantly clear that the traditional, broad circumscription of Aster, as a genus of some 250 species of North America and Eurasia, is untenable.”

Endangered Species in my backyard

The New York Times had two good articles on endangered species in May. First there was on zoos, which must choose which species to save while letting others in their collections go extinct - a concept relevant to botanical gardens as well, which can only grow so many plants. Then there was an op-ed on endangered ecosystems, which mentioned the IUCN Red List, which at the moment contains nearly 20,000 endangered species. This caught my eye because I've been reading IUCN reports of endangered plants for my work updating a guide to endangered species. I only look at IUCN listings of plants that are also listed under the U.S. Endangered Species Act, so it's not that many, but what have noticed is that the Red List information is not always current. Many listings date from 1998, which was a long time ago in a world whose human population now adds a billion people every decade. This is NOT to criticize the IUCN, but to suggest that things may be much worse than we know.

It may also to be to express a wish that reports on endangered and rare species include dates when describing abundance and distribution - it makes no sense to use the present tense when reporting data that was gathered in the past and that almost certainly does not describe a current state of affairs. A claim that "There are currently 15 populations with a total of 150 plants" is senseless if it is based on censuses done in 1982, 1991, and 1993, with different sites visited at different times.

Our own endangered species list contains some alarming reports. Eragrostis fosbergii, Fosberg's love grass, has not been seen since 1996. There are no specific conservation measures currently underway for this species - how could there be? For the moment it is still considered "in danger of extinction throughout its range." I'll say. But is it extinct? How can we know?

In this job I got to update the reports on two endangered plants that I know personally, the bunched arrowhead, Sagittaria fasciculata,

and the mountain sweet pitcher-plant, Sarracenia rubra ssp. jonesii. 

 
The depressing thing is that my updates were nothing of the kind. The USFWS has not published 5-year reviews on these species. The most current information on these two plants comes from Recovery Plans that date from the 1990s. The Center for Plant Conservation's reports are not much more recent. Likewise the Nature Conservancy's. I've noticed this about other Carolina plants, such as Geum radiatum from Roan Mountain. California and Hawaii have good up-to-date information on their endangered plants. Our neck of the woods? Not so much.

Anyway, these are nice little plants. Much collected, perhaps trampled by hogs. Not many left. I'm not saying where they are, but it's not hard to figure out if you're interested in grabbing the last ones.

Painting and Specimen, side by side

Mark Catesby's Natural History of Carolina, Florida and the Bahama Islands, published between 1729 and 1747, is justifiably famous for being the first work in English to describe the natural history of a region of North America. Catesby illustrated this volume himself with engravings of the plants he had seen and collected during his travels in the Carolinas, etc., between 1721 and 1726. Catesby apologized for his deficits as a painter, a trade for which he was untrained, but on the whole did a decent job. The publication of the Natural History was a big deal among western European naturalists; Catesby got elected to the Royal Society in 1733 on the strength of his work, and Linnaeus himself cited a number of Catesby's plates while describing North American species in his Species Plantarum.

But here's the thing - Catesby only painted a small portion of the plants he saw, and only a very small portion of the plants he collected. Of the 432 (or so) vascular plant specimens in the two volumes in the Sloane, 64 of them have corresponding engravings in the Natural History, and many of those are duplicates. That leaves 368 specimens with no paintings. That correspondence is not entirely accurate, either; it's based on notes made on the folio pages by previous scholars who examined the Sloane collections with an interest mainly in their relationship to the Natural History. There are some specimens that do not appear to be exactly what Catesby has painted.

Digitizing these collections makes two new things possible. First, we can now examine the full body of Catesby's scientific work, his actual collected data (a collection that will be fuller once we combine the Sloane materials with the Sherard specimens from Oxford). Second, we can easily examine Natural History engravings and herbarium specimens side by side.

You can see these images side by side here, Alignment of Mark Catesby's Hortus Siccus with his Natural History. We've transcribed the printed descriptions from the Natural History along with any handwritten notes on the specimen pages. There are a few specimens that previous researches linked with different pages in the Natural History from the ones that we identified; in those cases, we've posted both Natural History pages so you can see for yourself what's going on.

Cultivation and Conservation

Many plant species would not exist at all today if gardeners had not preserved them. The native American tree Franklinia alatamaha survives thanks to John and William Bartram, who collected seeds from the tree in Georgia in 1765 and began propagating it shortly before it disappeared completely from the wild around 1800. The spectacular Dove Tree, Davidia involucrata, exists in European and North America gardens through sheer luck; in 1900 plant collector E.H. Wilson went to China seeking the fabled tree only to discover that the one known specimen had been cut down for lumber. He searched far and wide in the woods to find a few more trees growing wild and thus managed to collect enough seed to introduce the tree to the nursery trade.

Botanical gardens have bred plants extinct in the wild to reintroduce them to their native ranges. For example, Sophora toromiro, a small tree from Easter Island, went extinct in its natural habitat but was preserved for reintroduction by the Bonn University Botanical Garden. (Maunder et al. 2000) The Royal Botanic Garden, Kew, has collaborated with the Seychelles Botanic Garden to cultivate Rothmannia annae, a plant native to the Seychelles that is nearly extinct in its home environment.

Kokia cookei, a tree endemic to Molokai, Hawaii, went extinct in the wild in 1918 but has been cultivated in botanical gardens since then; as of 2008, it was growing at Waimea Audubon, Lyon Arboretum, Volcano Rare Plant Facility, and the National Tropical Botanical Garden. The last known wild Cyanea pinnatifida, endemic to Oahu, died in 2001, leaving its cultivated progeny in the Lyon Arboretum and the National Tropical Botanical Garden. Lysimachia minoricensis, a plant of the Balearic Islands, went extinct in the first half of the 20th century, but botanists at the Botanical Garden of Barcelona cultivated plants from collected seed in 1926. The species is now found only in cultivation and seedbanks. Both of these plants have been the subject of experimental outplantings, in which propagated plants are reintroduced to the wild, though neither has produced self-sustaining wild colonies.

Some plants thought to be extinct have been rediscovered in the wild. The Hawaiian plant Cyanea truncata was thought to be extinct after the last known individual died in the 1980s. Subsequent surveys discovered a few more wild plants, three of which survived as of 2006, and which provided genetic material that botanists have used to propagate more plants and outplant them into a protected habitat. As of 2007 the state of Hawaii’s Genetic Safety New Program and the Lyon Arboretum were maintaining seeds and tissue samples that could be used to propagate more plants in the future.

When it was listed as an endangered species in 1996, Hibiscadelphus giffardianus was extinct in the wild. Only one tree has ever been known in the wild, from Kipuka Puaulu in Hawaii Volcanoes National Park. This tree died in 1930, but Giffard, its namesake, collected seed before the tree died. These seeds have been propagated, and have produced genetically unique offspring (cause they’re from seeds, which are the product of sexual reproduction.) Cuttings from these cultivated trees were planted back into the now fenced original habitat at Kipuka Puaulu. As of 2008, over 400 plants survived, many of them fruiting or flowering.

I know I keep going on about Hawaiian plants, which may seem to have little to do with Carolina botany. But they certainly have a problem with native species going extinct. Hawaii really is an astonishing hotbed of endangered species, most of which appear to have been destroyed by invasive introduced species – plants, pigs, goats, slugs. Ants – Argentine ants are a terrible problem, eating seeds and pollinators.

So without apology, I'll mention a couple more Hawaiian plants. Hibiscadelphus hualalaiensis was historically known from three populations, located in the Puu Waawaa region of Hualalai, on the island of Hawaii. The last known wild tree was in Puu Waawaa Plant Sanctuary, owned and managed by the Department of Land and Natural Resources, State of Hawaii. This tree died in 1992. BUT - as of 2008, there were about 100 reintroduced plants living. 50 were planted at Puuwaawaa Sanctuary cabin after 1997; they were fruiting and flowering and the oldest of those had produced seedlings by 2007. There were also ten trees below the highway at Puu Waawaa, seven at Kaloko-Honokohau National Historical Park planted in 2006, and unknown numbers of plants at Kaupulehu Forest Reserve and Makala-Ooma forest. These plants were all producing seed every year, and seeds were geminating well. The species is widely available in cultivation. So is it extinct?

Some stories are just depressing. Hibiscadelphus woodii was discovered in 1991 and first described as a species in 1995. When it was listed as an endangered species in 1996 it was known only from a single population of four individuals occurring at an elevation of 3,250-3,280 ft (991-1,000 m) at the site of its discovery in Kalalau Valley within the Na Pali Coast State Park on the island of Kauai. A falling boulder killed one plant and damaged two, so that by 2001 there were only two individuals left. By 2006 only one plant remained in the wild. There were no plants at all in cultivation.

All of this raises a question, of course: can a botanical garden, or even a network of botanical gardens, seedbanks, etc, really conserve anything? It a species has ten plants left in the wild (or did in 2002, but may have none today for all we know), can growing its progeny in a greenhouse or a living collection really make a difference? These reintroductions - will they amount to anything? And the business of scientific control of plant collection - some of these older plants exist because random gardeners collected them for the horticulture trade. It was dumb luck that they also happened to preserve endangered species.

What is certain is that without the work of the USFWS, the IUCN, and many random gardeners we would not know anything about the state of plant extinctions, and we probably wouldn't have the genetic material we have now. That's worth something.

Threatened, Endangered, Extinct in the Wild

I've been updating a guide to endangered species - I'm doing all the plants, 576 of them. The previous edition was published in 2001. When I accepted the job, I knew it could leave me depressed. The odds of conditions having improved in the past ten years were low. I've completed about 80 entries, mostly based on information published by the U.S. Fish and Wildlife Service, supplemented by the IUCN, and here are my initial reactions:

1. Conditions have not improved. Out of 80 species covered in the previous edition, maybe one or two have increased their numbers. Most have declined.

2. There is no current information on many endangered species. For a good percentage of the entries, I can't find any reports or data from the past decade. This is particularly common with Puerto Rican plants. For example, the U.S. Fish and Wildlife Service has not published anything new on Crescentia portoricensis since 1991. Is it alive? Is it extinct? Who knows?

3. Some plants listed as endangered might actually be extinct. Example: the US Fish and Wildlife Service ranks Ochrosia kilaueaensis as endangered. The IUCN gives it a Red List status of Critically Endangered, but that ranking dates from 1998. No one has reported seeing one since the 1940s.

4. Some plants have inconsistent listings. Take the Hawaiian plant Cyanea pinnatifida. The U.S. Fish and Wildlife Service published a 5-year review in 2007 that maintained its endangered status. The IUCN Red List ranks it Extinct in the Wild. The last wild population consisted of single plant that died in 2001. The thing still exists in the Lyon Arboretum and some clones of the last survivor that have been planted in the Honoliuli Preserve. So I guess it's not exactly extinct. But you could hardly call it thriving.

5. Some plants have such small populations as to be extinct for all practical purposes. The entire population of the Island barberry, Berberis pinnata spp. insularis, consisted of four plants in 2007. Four plants growing in separate locations, which makes natural cross pollination harder.

What else? The U.S. Fish and Wildlife Service has some enthusiastic workers, at least on behalf of particular species. It seems that some species are well loved and some largely ignored, or perhaps so inaccessible as to be impossible to study carefully. Kudos to the Federal Register for making all its publications available in PDF format. What I like most to see are 5-year Reviews published on individual species. These are usually quite thorough assessments of the current state of a species. I like to see them published since 2007 - there are even a few from 2010 and 2011, but 2007 and 2008 is the best I can usually hope for. What I don't like to see are calls for information for 5-year reviews on species - those are not at all helpful, and often a sign that no one has updated the information in two decades. I hate to have to rely on a 1991 endangered species ranking report for my "update".

The IUCN has a pretty nice website, with some good search capability. NatureServe is an excellent source for information on some plant species and published its own set of rankings. Those three are the best sources, especially the USFWS.

There are a few other sites that are of somewhat limited utility for my purposes because they tend to repeat USFWS reports but that have assembled some good data on plant biodiversity. The Center for Plant Conservation has some information. The USDA Plants Database is a good place to look for taxonomic synonyms - important since taxonomy is not the USFWS's strongest suit. Likewise the Integrated Taxonomic Information System, for which I have high hopes for the future - wouldn't it be great to have all taxonomy organized, and have all plants linked to an ITIS number that would allow garden and herbarium curators to update taxonomy at the touch of a button? There also the USDA's Agricultural Research Service's Germplasm Resources Information Network, which hasn't been terribly useful yet for this project but I expect it could be. Good old Wikipedia often has links to the most up-to-date information on particular species. The Hawaiian Ecosystems at Risk Project is keeping tabs on Hawaiian endangered species, of which there are many, many, many. So many.

The whole project is testimony to the value of digital information projects that assemble data and make it accessible. Our information on individual taxa is far from complete - but because all this data has been published online, I can see that, and can see what is known and what is not. Twenty years ago? No way could I have done this work with any accuracy. So three cheers for the world brain, which at least gives us a very clear picture of the progress of this catastrophe.

A pretty little orchid

HS 212 f 55, Platanthera integra (Nutt.) A. Gray ex Beck.

This plant is the yellow fringeless orchid. Catesby collected one in Carolina. Look hard at his, because you probably won’t ever see it growing in the wild in this state.

Alan Weakley gives this range in his 2011 flora: “Savannas in the Coastal Plain, bogs in the Mountains and Piedmont. July-September. Essentially endemic to the Southeastern Coastal Plain, ranging from s. NJ south to FL and west to se. TX, with disjunct occurrences in TN (Eastern Highland Rim) and in bogs at low elevations of the Blue Ridge of NC. It is apparently now extirpated in the Mountains and Piedmont of NC.”

This large range notwithstanding, the yellow fringeless orchid is nearly extinct in South Carolina today. NatureServe lists it as critically imperiled in the state. The South Carolina Department of Natural Resources listed it as S2 in 2006, meaning that it was imperiled state-wide because of rarity or factors making it vulnerable.

What threatens our little orchid? Land use conversion, habitat fragmentation, and forest management practices such as fire suppression all cause problems. So does collection – so if you see one, don’t dig it up to plant it at home! (That doesn’t work for orchids anyway – they need specialized soil fungi to survive, so a transplanted orchid will likely die.)

What to do about rattlesnake bites

Early settlers took a keen interest in rattlesnake bites and what to do about them. It must have come as a shock to Europeans to encounter snakes that could deliver such nasty bites, along with those alarming rattles.

One wonders, though, how serious the risk really was. Currently about 4000 to 7000 snakebites are reported every year in the U.S., out of a much bigger population than in the early 18th century. Epidemiology? Well, it’s a little embarrassing, but the overwhelming majority of snakebite victims are young white males, most of whom are bitten on the hands. North Carolina has the highest frequency of snakebites, and Georgia had the third-highest rate of fatalities. “Hey, ya’ll, it’s a snake! I'll git ’im!”


So maybe Catesby and his ilk had reason to worry. Demographically and geographically they were in snakebite central.

One sure cure for snakebite was a poultice made with rattlesnake root, from the genus Prenanthes. Prenanthes altissima, for example, grows widely in the woods in the Upstate. Here’s one growing near Oconee Station.

Catesby collected a related rattlesnake root, Prenanthes autumnalis (HS 212 f 83). It’s just as good for treating rattlesnake bites. Catesby didn't mention the bite-treating properties, though.

He did, however cite Aletris aurea, HS 232 f 105, as a possible cure: “The Root of this plant the Indians esteem good for the Bite of the Rattlesnake.”

Now this is interesting. I can’t find anyone else recommending Aletris aurea as a cure for snakebite. I consulted Dr. William M. Hand’s 1849 work The House Surgeon and Physisian: Designed to Assist Heads of Families, Travellers, and Sea-Faring People, in Discerning, Distinguishing, and Curing Diseases; with Concise Directions for the Preparation and Use of a Numerous Collection of the Best American Remedies: Together with Many of the Most Approved, from the Shop of the Apothecary. All in Plain English. Dr. Hand informed me that Aletris Aurea can be used in the same was as its relative Aletris Alba, known as colic-root, among other colorful names. Made into a tea it can be used as a purgative to treat dropsy, indigestion, and to treat hysteric and flatulent colic. But nothing about snakebite. For that you’ll need to find a Prenanthes.