Monday, September 22, 2014

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 Michaux.org 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:
 

Tuesday.

        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."

Tuesday, January 21, 2014

Spontaneous trefoil?

On the lower left of HS 242 f. 110, one of Lawson's collections, is a label covering what appears to be a plant specimen. It's quite small, and the bit that appears most clearly looks like a trifoliate something-or-other. A Desmodium, perhaps? Who knows. Weakley includes the common name "trefoil" in eight different plant entries - anything with leaves clumped in threes can merit it.

The intriguing thing is the label, which is evocative. (At least, my attempt at deciphering it is evocative.) It appears to read:

"Jan. 27th 1710. Spontaneous [?] trefoil of Carolina growing on the fork of Neus River and in other places having shed [?] from flower like drops of blood a sweet herbage[??] all spontaneous trefoils are more hairy here than in England."


I may have gotten that completely wrong.

But what if I'm right, and it does refer to "spontaneous trefoil"? Did people believe plants could grow spontaneously? Is trefoil a particular weed, common in England?

I found this account in The Farmer's Magazine, London 1851 (MDCCCLI - I hate Roman numerals!) describing a case of trefoil growing in fields sown with clover. Because the seed produced pure clover in most fields, the farmers concluded that the trefoil must have grown spontaneously. The author refuses to believe this, noting that seeds could lie dormant for years until conditions were right for them to germinate, but it is intriguing, no?

Then there's this, from the Annals of Agriculture, and Other Useful Arts, published London 1804: "Gypsum has also another very singular property, that of encouraging the growth of spontaneous trefoil on spots where seed had never been sown, particularly of the yellow and white trefoil. In Alsace I have seen many instances of this singular circumstance."

And this, on the adulteration of forage plants, another author recognizing that yellow trefoil seeds can last a long time.

What is trefoil? I'm not going to attempt to identify this specimen, but I can speculate more on my musings. This UK lawn weed site identifies Trifolium dubium as the noxious weed Lesser Trefoil - it's a Eurasian native, and is introduced to our area, so maybe not that. Plant Guide.org identifies it as Medicago lupulina, also introduced to our area. Weakley includes the common name "trefoil" in eight different plant entries - anything with leaves clumped in threes can merit it.

Sadly, our photographs do not allow us to see through that unfortunate label to further examine the plant specimen. So the mystery will have to stop here for now.

Friday, January 17, 2014

Taxonomic hierarchies

How do we sort things? Let me count the ways....

Modern scientific taxonomy got started with Carl Linnaeus (1707-1778). He was the man, I must say. After spending his younger years exploring the botanical biodiversity of Sweden and northern Europe, he dedicated his mature years to sitting in Uppsala and organizing the pieces of the world that came to him in the mail. Explorers went out to sea at his behest, and some of them - the ones that survived - sent him specimens of plants, animals, stones, whatever.

Linnaeus decided to organize everything. At the time the world must have seemed suddenly knowable, all things coming clear. Everything must belong to a type, and all types must fit into a hierarchical structure. (Could it be Latin grammar that gave him this idea?)

Linnaean organization especially emphasizes two things: kingdom and genus. Kingdom defines the nature of the beast. Genus names a category and allows specification to produce a binomial - a scientific name.

To start with the binomial: The scientific name of a species consists of two names, genus and species. The genus is its generic name, or category. The species is the name of a specific type of organism within that category.

Take the lion, Panthera leo. The generic category is panthers. What kind of panther? The "lion" kind. You could also have the "tiger" kind of panther, Panthera tigris, or the leopard kind of panther, Panthera pardus, which actually means "Panther panther." (The word "leopard" comes from two Greek words meaning "lion panther," so our common name for leopard means the same thing as the scientific name for lion. Haha!)

All those generic panthers belong to the cat family Felidae. So do generic little cats, in the genus Felis, "cat" in Latin. Linnaeus named our domestic cat Felis catus. Catus is another Latin word for cat. So a domestic cat is the "cat" kind of cat. Another little cat is called Felis silvestris, the kind of little cat that lives in the forest. Simple!

Now kingdoms. Linnaeus created three kingdoms - Plants, Animals, and Minerals - to encompass everything in the world. Anything missing? Minerals fell by the wayside pretty quickly, but they weren't the real problem.

The invention of the microscope suggested that microorganisms didn't fit into either Plants or Animals. In the 1860s biologists added a new kingdom, Monera, for all single-celled organisms. But all single-celled organisms aren't alike. Some are small and primitive with no nucleus, and others are large and well-organized with nuclei and membrane-bound organelles. Scientists started calling them prokaryotes and eukaryotes. In 1938 they added another kingdom, Protista, to hold single-celled eukaryotes. The prokaryotes - bacteria and cyanobacteria - stayed in Monera.

Now, fungi are really not at all similar to plants - no chlorophyll, chitin cell walls - so in the 1960s they got taken out of Plantae and put in their own kingdom Fungi. And animals, plants, and fungi are all eukaryotes, so it was kind of important to put them with single-celled eukaryotes if cell structure was going to be a category. But they were ALREADY kingdoms. We needed another level of taxonomy. So that led to the short-lived empires - Prokaryota and Eukaryota. Kingdom Monera went into Prokaryota. Eukaryota got everyone else - Animalia, Plantae, Protista, and Fungi.

But in the 1970s and 1980s, biologists started focusing on common ancestry instead of physical similarity. Microbiologists announced that prokaryotes were not all bacteria, and that some were in fact very very different - so different they deserved their own kingdom. In the 1990s they got rid of Monera and replaced it with Bacteria and Archaea. The empires were changed into domains called Prokarya and Eukarya.

And that didn't even last very long. Now there are three domains. Eukarya still contains animals, plants, fungi, and protists. But the kingdoms Bacteria and Archaea are now in domains called Bacteria and Archaea. This leaves room for more discoveries.

Do we still need kingdoms? Does the genus-species naming structure still work? Clearly many things don't fit into the Linnaean schema. Plant taxonomy is full of subspecies and subfamilies and things just called clades or tribes. Hominin (human ancestor) taxonomy got stuck with a family called Homidae - all the great apes - and several named genera, but then has had to fit lots of categories in between them for extinct taxa. (Chimpanzees are currently grouped in a tribe called ... Panini. That's funny.)

And don't even get me started on the slime molds and water molds! Poor Phytophthora, dumped by Fungi. My kingdom for a kingdom! At least they still fit in Eukarya.

One obvious problem with imposing an organizing structure on the world is that one then forces the world to conform to the structure, rather than the other way around. (It's not an animal, and it's not a mineral, so it MUST be a plant....) On the other hand, we have to be able to talk about stuff. It will be amusing to watch this process unfold over the next decades. Will Linnaeus disappear entirely?