Wednesday, September 24, 2014

Linnaean Taxonomy and Finding Oconee Bells

Linnaeus was the father of taxonomy, but his taxonomy was not our taxonomy. I had never given this concept much thought until Chris, Patrick and I got into the Michaux collections at the Jardin des Plantes this summer.

We photographed nearly 2900 specimens in this collection. They are carefully organized on their shelves in volumes and folders. The volumes are organized by Linnaean classes, the classification scheme Michaux used for his Flora Boreali Americana. Within those classes there are subdivisions by orders (I think they're orders), which are marked by bits of paper stuck in between folders. The genera are contained in individual manila folders, which can contain numerous specimens.

Linnaeus organized plants by numbers of sexual parts - nine male one female, five male three female - that kind of thing. That means his organizational scheme is NOT AT ALL the same as currently used schema (even allowing for the fact that taxonomy is currently in flux, and people are using all kinds of systems to organize their herbaria - Cronquist is still around, though the latest greatest is the APG III scheme, and it's pretty darn different.) Linnaean taxonomy is VERY different.

How different? Very very different. So different that Pinaceae, Cupressaceae, and Euphorbiaceae are in the same category - Monoecia Monadelphia. Gymnosperms grouped with eudicots is decidedly not what we do today.

This makes finding individual specimens a challenge. Say you want to find the specimen of Shortia galacifolia, the famous Oconee bells - a pretty important specimen in Michaux lore.

Oconee bells at South Carolina Botanical Garden

To find this in a modern herbarium, you'd figure out what family contains Shortia and then flip through the folders until you came upon Shortia. There it would be.

But Michaux didn't call this plant Shortia. He called it ... what? No one knew. We looked up the genus on the Jardin's database, but that was no help. So we were sort of stuck - didn't even know how to look it up.

We only found the darn thing because Chris and I photographed EVERY specimen in the Michaux collection. That is why, in the midst of Volume 9, we discovered a photocopy of the Shortia specimen, in the genus Pyrola.

Of course! Pyrola! Duh!

Never heard of it....

Finding the specimen then required following the photocopied clue into the Jussieu materials, where the thing had been refiled for safekeeping or something. (Jussieu 7545 is what you want if you go there.)

I've cataloged the Michaux images now according to volume, genus, and family. I discovered - after the fact, so now I am considerably more clued in than I was at the start of this project - that the herbarium is in fact very carefully organized according to this book. The first specimen in both is Hippuris, and it goes from there.

Once we get all this data together - there's so much! - it will be fascinating to put Linnaean classifications and modern families side by side to see how much they overlap. They do in many cases, just not all.

And my efforts have already proven useful to me. I wanted to find Linnaeus' description of Clethra in his Species Plantarum so that I could quote him for an article. But how to find Clethra? Well, I just pulled up my handy Michaux database in Bento (the late, lamented - how could you ditch us all, Filemaker?) and there it was - Decandria Monogynia, of course. (Ten men, one woman....)

That's what I'd figured....

Monday, September 22, 2014

Data, Tools, & Views

After a busy summer of development, we have online a new web application dedicated to Botanica Caroliniana’s data. This is a customized implementation of CITE/CTS Services, which we have developed in collaboration with the Homer Multitext.

With this in place, we are looking forward to more rapidly putting into place interesting and useful views of the growing body of data. For example, this page is a view of the specimens of Mark Catesby (and images of them) organized by (modern) Family and Genus. We are working to index the specimens of the other 18th century collectors so they will appear in this list as well.

All images remain downloadable directly from the project’s data archive. Data collections, XML texts, and indices are always freely available from the project’s GitHub site.

The CITE architecture provides many different ways of discovering, accessing, reproducing, and using the images, texts, and other data available on this site. We will follow up, on this blog, with more specific tutorials for accessing this data through the CITE/CTS service over the coming weeks.

Type Specimens

A type specimen is an example of an organism or thing that is the ultimate defining example for its category. Any time a scientist creates a scientific name - which means he or she has identified a species, genus, family, or some other taxonomic group that is distinct from all other related groups - that scientist must also choose a type specimen. The type should contain all the distinguishing characteristics of its taxon so it can serve as a reference and comparison for other scientists.

Except that's not strictly true. Really types have most to do with nomenclature - you can't have a valid scientific name without at least one actual object that holds that name.

Naming types is governed by strict rules. The International Commission on Zoological Nomenclature sets rules for naming animal types. An animal type can be an animal, a part of an animal, the work of an animal (fossilized footprints, wasps' nests if built before 1931), a colony, or a microscope slide. A photograph CANNOT serve as a type. Bacteria have their own nomenclatural code, which used to include rules for fungi. Fungi are now part of the exciting International Code of Nomenclature for algae, fungi, and plants. Obviously, so are plants.

I can only imagine how much fun it must be to attend the meetings that arrive at these codes.

The International Code gives use rules for typification. These rules are ... complex.

The different types of types are especially complicated. The most basic include:

1. Holotype, which is the main type designated by the author of the name.
2. Isotype, which is a duplicate of a type. Say, the author collects two specimens on the same day at the same place and designates the best one as the holotype - the other one can be an isotype.
3. Lectotype, a specimen - or illustration - created at the time that the name was created if the author didn't name a holotype at that time.
4. Neotype, a type chosen after the fact if there is no holotype or other original material.
5. Epitype, a type chosen to clarify an ambiguous holotype or lectotype.

There are others.

To designate plant types, botanists publish descriptions in the journal Taxon, which specializes in this field. Before Taxon was founded in 1951, botanists published these descriptions ... well, I don't really know. This is an area of plant taxonomy that I have always found opaque. How is it that botanists can keep track of these things, the designations of names and specimens and changes? Where do these types live? Anywhere? If so, how does anyone get to see them?

The Index Kewensis has kept up with nomenclature since 1885. This work continues with the International Plant Names Index (IPNI), which is trying to eliminate the need to consult umpteen primary sources. The Linnaean Plant Name Typification Project has been finding and digitizing the type specimens Linnaeus used for his names. Even so, botanical nomenclature and typification seems to assume a vast amount of pre-existing knowledge, and an inordinate attention to botanists, some of whom are so well-known they go by obscure abbreviations. If you don't already know the prevailing practices in this field, it's fairly hard to figure them out on your own. And it's very easy to get stuff wrong.

It's almost like practicing law.

Wednesday, September 3, 2014

Plants on the Art Loeb Trail - and barefoot shoes!

We hiked the Art Loeb Trail over Labor Day weekend - Chris, me, and our two kids. We did it in two days, mainly because no one felt like camping out two nights.

We spent Friday night in Brevard so that we could catch the 6 a.m. shuttle run by Pura Vida Adventures. That way we could do the trip with just one car, which we left in Brevard at the Davidson River Campground. The shuttle dropped us off at Camp Daniel Boone so we could hike the trail north to south. This is the easier direction because the majority of the altitude gain happens all at once at the beginning, on the hike up to Cold Mountain. As we proceeded down the route, I felt increasingly sorry for the poor souls hiking in the other direction.

This walk took us through an incredible variety of plant communities. I will confess that though I initially regretted that I hadn't brought any collection gear with me, I soon lost the energy to think about plant identification beyond an idle appreciation of what grew on the sides of the trail. But it did make me think of my friends André, Mark, John, and Joseph - up in the wilderness, it's possible to see some of what they saw.

On our first high ridge, between Deep Gap and Shining Rock, we walked through fields of Ageratina altissima, common white snakeroot, and endless nettles, Laportea canadensis. The nettles sting. We saw chestnut oak, Quercus montana, and American chestnut, Castanea dentata. In places the ground was thick with shiny green Galax ureceolata.

The area between Shinking Rock and Black Balsam Knob is awash in blueberries, Vaccinium corymbosum. One year Chris and I gorged on them like black bears; this year we just nibbled as we walked, though we saw plenty of collectors armed with plastic containers. We also saw lots of black bear scat - on the trail! - laden with blueberry bits.

Just south of the Blue Ridge Parkway we entered a quiet, soft-grounded forest of spruce and fir. Patrick finds these areas sadly devoid of diversity, but we've always found the ambiance pleasant, somewhat Middle-Earth-like. We camped in a grove of what I seem to recall as sycamores and tulip poplars, but I might have been insane after 15 miles of hiking, and it was both dark and pouring down rain, so all I can recollect is the wind that blew up amongst the broad leaves - broad leaves and a high thick canopy that actually stopped much of the rain from reaching us. At first.

The next morning we climbed Pilot Mountain, home to more Castanea and endless rhododendrons and mountain laurels.

As we descended toward Brevard we saw more of those, plus numerous Magnolia fraseri. It was like dinosaur land. We were set upon by a nest of yellow jackets tiptoeing through a rhododendron thicket near Butter Gap. The climate grew warmer and more jungly as we approached Brevard.

What else did we see? Trilliums with dried flowers still attached. Goldenrods. Some sort of Lysimachia? Red oaks and white oaks. Pines. Tulip poplars. Red maples. Lots and lots of other things I can't recall. It wasn't the trip for collecting or taking notes.

Biggest breakthrough: Chris and I both hiked the whole thing in Merrell Barefoot shoes. I wore the Pace Glove, no socks, and he wore the Vapor Glove with thick wool socks. It was great! We had no blisters, and the groundfeel was wonderful. We've been doing the minimalist thing for several years now so our feet must be pretty strong, but still, it was a revelation to see what our own feet are capable of. Allowed complete freedom they do a great job of walking - way better than heavy cast-like hiking boots. No more boots for me!

We also ate what I think of as a more genuinely paleo diet than the currently popular silliness, all dried fruits and nuts and a small amount of beef jerky. Plus some tortillas with peanut butter. No stove, no camping food. That is also the way to go - lots of energy, low bulk, and very little trash.

Tuesday, September 2, 2014

André Michaux

This July, Chris, Patrick, and I traveled to Europe with the generous support of the Andrew Mellon Foundation. We tried to make good use of our time. In London we gave talks at the British Library and the Natural History Museum and met with colleagues at RBG Kew. We spent the weekend in Hamburg, getting to know colleagues at the Botanischer Garten there - a wonderful weekend! Then we hopped over to Paris and spent several days at the Jardin des Plantes, examining the entire Michaux herbarium. I have a whole series of things to blog about that, only awaiting the posting of the images, but I will begin today with just a bit about Michaux.

André Michaux was born in Versailles in 1746. Versailles has extensive and fabulous gardens - if you wanted to learn about plants and gardens, 18th-century Versailles might just have been the perfect place to be born. (Elizabeth Gilbert presents a similar character raised near Kew in one of my favorite books, The Signature of All Things.)

He studied with Bernard de Jussieu, a botanist who created his own system of classification that he employed in the design of the Trianon gardens at Versailles and whose name lingers on University of Paris VI and its accompanying Metro stop.

Michaux got himself appointed government botanist, of all things. After an exciting botanical mission to Persia, the French government sent him to the brand spanking new United States in 1785. His mission? It was the same as all of those guys - find plants that might be useful. In France's case, they particularly wanted some good oaks, having cut down all their own forests and being in need of ships in which to fight the British.

Michaux spent ten years in America. He set up a home base near Charleston, where he planted a botanical garden. He explored up and down the east coast and well into Kentucky and Ohio. (Charlie Williams and have posted timelines of Michaux's activities, as well as more biographical information.) He collected thousands of plant specimens, nearly 3000 of which are in the Herbier Michaux in Paris. His son worked with him some of the time.

If you look at the years Michaux spent in the U.S. - 1785 to 1796 - and think about your history, you will realize that this period spanned one of the most unstable epochs in French history. The French Revolution of 1789 caused some real problems for Michaux, who had received his salary from the crown. Once there was no more crown, there was no more salary. So Michaux, like many scholars and academics, had to scramble for money. He applied for the job that eventually went to Lewis and Clark - almost got it, too. He finally went back to France, failed to collect his back salary, and resigned himself to organizing his herbarium and writing his books, the Flora Boreali-Americana and the Histoire des Chênes de l'Amerique. Both were published after Michaux died in Madagascar in 1800.

Patrick and I have been working on a master list of all the Michaux specimens. Many of these include notes on habitat and other tidbits, in Latin and French. They're organized according to Linnaean taxonomy, which bears no relation to the current APG system. The collection contains hundreds of specimens marked as types. So there's a lot to explore!

Sunday, May 11, 2014

Crowdsourcing Taxonomy

Crowdsourcing is an old idea. All of the plants in Botanica Caroliniana are the result of a large effort to crowdsource taxonomy.

James Petiver (1665-1718) was an apothecary in London. Petiver was a member of the Royal Society and a collector - of all sorts of things. Except for a brief period studying entomology in the Netherlands, Petiver worked in London. He kept a shop "at the sign of the white cross in Aldersgate, London."

Somehow Petiver got into the business of collecting natural history specimens, especially insects and plants. Ships were visiting all parts of the world, and Mr. Petiver and his friends evidently had an insatiable appetite for the curiosities they might bring back. So he started printing pamphlets asking for contributions to his collections, with explicit directions for collectors to follow for collecting and storing herbarium specimens. The collectors - Lord, Lawson - would package up their materials and send them to London when they could. Petiver then organized them according to some taxonomic scheme - if you look at the order of Lord's specimens, they are pretty much arranged by current families - and bound them in books.  By the time he died in 1718, Petiver had the largest collection of dried plants in the world.

Hans Sloane (1660 - 1753) jumped on this opportunity, purchasing Petiver's collections and many others, which eventually became the basis of the Natural History Museum, London. Sloane himself spent some time in Jamaica and is famous for his descriptions of Jamaican natural history, but the vast majority of his collection - some 120,000 specimens - came from people he never met and places he never visited. Catesby was one of his contributors. William Sherard (1659 - 1728), another of Catesby's sponsors, was doing much the same thing in Oxford.

The big man himself, Carolus Linnaeus, used this same business model. His travels were mostly restricted to places close by - Lapland, central Sweden, the Netherlands - and he did most of his work from his comfortable facilities in Uppsala. To fill his coffers, he sent his students on voyages of discovery. Daniel Solander and another student traveled around the world with Captain Cook. Others visited Japan, the Americas, Australia, and anyplace else they could reach. The ones who survived gave their specimens to Linnaeus, who worked them into his Systema Naturae.

Why do it this way? Well, for one thing, traveling was dangerous. Lots of Linnaeus' students died on their journeys, cutting short their aspirations for scientific discovery.

But more practically, you can't do two big things at once. Exploring and collecting specimens is one job. Assembling a collection is another. To make a collection, you have to be physically present at your research site, and you are encumbered by lots of stuff - camping gear, the specimens themselves. You can visit only a restricted area, and you might have to visit that area repeatedly to catch your subjects in bloom.

Assembling a collection, on the other hand, requires peace and quiet, a large flat surface and a roof overhead, lots of paper and glue, and reference materials. It's not easily done in the field. More importantly, a good collection requires a large body of specimens. Specimens from multiple collectors can offer perspective that the work of a single collector cannot. If you want to organize the world's plants, you need lots of contributors in lots of different places. You want to see the big picture.

This is how crowdsourcing works today. Project Budburst, the Great Backyard Bird Count, and NASA's Disk Detective program (sorting out stars with disks from nebulae and galaxies) all use non-scientist volunteers to collect and process data. The professional scientists then process what the citizen scientists send them, and the result is much better than they could achieve trying to gather data alone.

Like our historic collectors, today's citizen scientists are motivated by a desire to be part of something bigger - to make a contribution to science and maybe learn a little more science themselves. Lord and Lawson collected for Petiver out of interest in the world around them and the hope that what they saw might be of use - and as a way of making contact with London intellectual life, in short supply in the Carolinas in 1700. And their contributions did turn out to be real, useful both to the botanists creating modern taxonomy and to those of us studying them today.

Wednesday, May 7, 2014

Winchester Wedding

In A New Voyage to Carolina, John Lawson records this scene:


        Next Morning we set out early, breaking the Ice we met withal, in the stony Runs, which were many. We pass'd by several Cottages, and about 8 of the Clock came to a pretty big Town, where we took up our Quarters, in one of their State Houses, the Men being all out, hunting in the Woods, and none but Women at home. Our Fellow Traveller of whom I spoke before at the Congerees, having a great Mind for an Indian Lass, for his Bed-Fellow that Night,

Page 41 spoke to our Guide, who soon got a Couple, reserving one for himself. That which fell to our Companion's Share, was a pretty young Girl. Tho' they could not understand one Word of what each other spoke, yet the Female Indian, being no Novice at her Game, but understanding what she came thither for, acted her Part dexterously enough with her Cully, to make him sensible of what she wanted; which was to pay the Hire, before he rode the Hackney. He shew'd her all the Treasure he was possess'd of, as Beads, Red Cadis, &c. which she lik'd very well, and permitted him to put them into his Pocket again, endearing him with all the Charms, which one of a better Education than Dame Nature had Bestow'd upon her, could have made use of, to render her Consort a surer Captive. After they had us'd this Sort of Courtship a small time, the Match was confirm'd by both Parties, with the Approbation of as many Indian Women, as came to the House, to celebrate our Winchester-Wedding. Every one of the Bride-Maids were as great Whores, as Mrs. Bride, tho' not quite so handsome. Our happy Couple went to Bed together before us all, and with as little Blushing, as if they had been Man and Wife for 7 Years. The rest of the Company being weary with travelling, had more Mind to take their Rest, than add more Weddings to that hopeful one already consummated; so that tho' the other Virgins offer'd their Service to us, we gave them their Answer, and went to sleep. About an Hour before day, I awak'd, and saw somebody walking up and down the Room in a seemingly deep Melancholy. I call'd out to know who it was, and it prov'd to be Mr. Bridegroom, who in less than 12 Hours, was Batchelor, Husband, and Widdower, his dear Spouse having pick'd his Pocket of the Beads, Cadis, and what else should have gratified the Indians for the Victuals we receiv'd of them. However that did not serve her turn,but she had also got his Shooes away, which he had made the Night before, of a drest Buck-Skin. Thus dearly did our Spark already repent his new Bargain, walking bare-foot, in his Penitentials, like some poor Pilgrim to Loretto.        After the Indians had laugh'd their Sides sore at the Figure Mr. Bridegroom made, with much ado, we muster'd up another Pair of Shooes, or Moggisons, and set forward on our intended Voyage, the Company (all the way) lifting up their
Page 42 Prayers for the new married Couple, whose Wedding had made away with that, which should have purchas'd our Food.

Stole his shoes! That's cold!

This story seems to be a popular one. I've found it in this blog and mentioned in this book on humor and the American Indian. The author of the essay in question suggests that portrays himself and his fellow European explorers as the greenhorn butt of jokes, and the Winchester Wedding as a big joke by the Indians on the whole expedition.

So what is a "Winchester Wedding"? Just what it looks like, apparently - a hookup. The term appears in broadside ballads from the time. Lawson wrote more on the subject of Indians and Winchester Weddings in a description of Indian women (scroll down a bit; these pages are undifferentiated, so the links aren't that useful):

"As for the Indian Women, which now happen in my Way; when young, and at Maturity, they are as fine-shap'd Creatures (take them generally) as any in the Universe. They are of a tawny Complexion; their Eyes very brisk and amorous; their Smiles afford the finest Composure a Face can possess, their Hands are of the finest Make, with small long Fingers, and as soft as their Cheeks, and their whole Bodies of a smooth Nature. They are not so uncouth or unlikely, as we suppose them; nor are they Strangers or not Proficients in the soft Passion. They are most of them mercenary, except the married Women, who sometimes bestow their Favours also to some or other, in their Husbands Absence. For which they never ask any Reward.
As for the Report, that they are never found unconstant, like the Europeans, it is wholly false; for were the old World and the new one put into a Pair of Scales (in point of Constancy) it would be a hard Matter to discern which was the heavier. As for the Trading Girls, which are those design'd to get Money by their Natural Parts, these are discernable, by the Cut of their Hair; their Tonsure differing from all others, of that Nation, who are not of their Profession; which Method is intended to prevent Mistakes; for the Savages of America are desirous (if possible) to keep their Wives to themselves, as well as those in other Parts of the World. When any Addresses are made to one of these Girls, she immediately acquaints her Parents therewith, and they tell the King of it, (provided he that courts her be a Stranger) his Majesty commonly being the principal Bawd of the Nation he rules over, and there seldom being any of these Winchester-Weddings agreed on, without his Royal Consent. He likewise advises her what Bargain to make, and if it happens to be an Indian Trader that wants a Bed-fellow, and has got Rum to sell, be sure, the King must have a large Dram for a Fee, to confirm the Match. These Indians, that are of the elder sort, when any such Question is put to them, will debate the Matter amongst themselves with all the Sobriety and Seriousness imaginable, every one of the Girl's Relations arguing the Advantage or Detriment that may ensue such a Night's Encounter; all which is done with as much Steadiness and Reality, as if it was the greatest Concern in the World, and not so much as one Person shall be seen to smile, so long as the Debate holds, making no Difference betwixt an Agreement of this Nature, and a Bargain of any other.
If they comply with the Men's Desire, then a particular Bed is provided for them, either in a Cabin by themselves, or else all the young people turn out, to another Lodging, that they may not spoil Sport; and if the old People are in the same Cabin along with them all Night, they lie as unconcern'd, as if they were so many Logs of Wood. If it be an Indian of their own Town or Neighbourhood, that wants a Mistress, he comes to none but the Girl, who receives what she thinks fit to ask him, and so lies all Night with him, without the Consent of her Parents."