Thursday, October 30, 2014

Algae, sea urchins, introduced pathogens

Here's a story of small things making big differences.

First, we have the long-spined sea urchin, Diadema antillarum. These little guys look like pincushions stuck full of porcupine spines. They are echinoderms, like starfish, distinguished by radial symmetry and a marine lifestyle. Their ancestors first appeared in the Cambrian period, 541 to 485 million years ago. They have no heads, and just a single hole on their undersides that serves as a mouth. They move around the ocean floor on little tube feet, which can propel them with astonishing speed when they feel threatened. They eat algae, vast amounts of algae.

Now, algae. Algae are not plants, though they are autotrophs that conduct photosynthesis. They are at least eukaryotes, organisms with membrane-bound organelles. The algae aren't really a true taxonomic grouping, because there are many different types and not all of them share a common ancestor. (Like slime molds and water molds, algae are now taxa without a kingdom. They just get a domain, Eukarya.) Green algaes do look like plants, and so we sometimes call them seaweed.

Algae are ubiquitous in the seas around the Bahamas. So are coral. For millenia (eons?), algae populations on coral reefs by animals that ate them. Parrotfish eat some algae off the coral, along with some of the coral, but sea urchins are the real stars. They're little vegetarian (algaetarian?) vacuum cleaners that spend their nights gorging on new algal growth on coral reefs, and their days hiding in cavities within the coral. It keeps the urchins happy and the coral clean and beautiful.

(Parrotfish start off life as females and then turn into males. Scientists call them sequential hermaphrodites.)

Third character: a pathogen. No one knows what kind, bacteria or virus or fungus. In any case, a pathogen is a disease-causing organism.  In 1983 a pathogen entered the Atlantic through the Panama Canal, perhaps in the ballast water of a cargo ship. It was deadly to sea urchins and spread rapidly through the water. Within a year, some 97 percent of the Diadema from South America to the Bahamas had died

The resulting algae growth on the coral was entirely predictable and unstoppable. Today Caribbean reefs look like shaggy green monsters.

Various organizations have been working to correct this situation. Some have been breeding sea urchins and restoring them to habitats. Others have been collecting urchins from the few places they still live and moving them to algae-covered reefs.

Blackbeard's Cruises and the Cat Ppalu have been conducting Diadema restoration trips for around a decade. I went on one of these trips with the Cat Ppalu back in 2005. It was hard work! We went out every night to free dive for urchins, brought them back to the boat, and then delivered them to their new homes that day. Urchins hide in daylight, which makes them nearly impossible to catch without seriously damaging them, so it has to be done by darkness, when they walk around the sandy bottom. The idea is to create a critical mass of adult urchins so that they're close enough to one another to breed successfully - they do that echinoderm thing of everyone spawning at once one very special night each year.

Reportedly these efforts have been paying off, and some reefs with restored urchins are looking cleaner. I'll get to see next week because I'm heading off to do another urchin restoration week on the Cat Ppalu.

Monday, October 27, 2014

Living Fossils Everywhere

The ginkgo is often described as a "living fossil." But what the heck does that mean?

Charles Darwin coined the term in On the Origin of Species in reference to the platypus. Discover Online suggests that living fossils are animals (sic) that have remained relatively unchanged since they first evolved - like the platypus. The coelacanth is famously called a living fossil, though Smithsonian notes that it's more living than fossil.

Darwin suggested that these archaic forms somehow are immune to the ravages of natural selection, surviving when their compatriots go extinct due to inhabiting a protected niche without much competition. Without pressures that affect survival, there is little incentive to evolve much.

I like Darwin, and think he had great ideas. I think the term "living fossil," though, is overused and a little silly, because fossils aren't living and the experience of living long after an evolutionary starting date is hardly rare or unique. Brian Switek has a great blog posting at Wired on this very topic, entitled "Unless they're zombies, fossils don't live."

Organisms that meet the definition of living fossil are absolutely everywhere. Almost every single plant species should qualify. The various plant families originated in the antedeluvian past, some long before dinosaurs. See a moss or fern lately? A magnolia? A crazy sago palm?

The ginkgo gets star billing because it had faded out of human view for millennia, only to be revived by adventurous botanists in the 1700s and then discovered for what it was by a Japanese botanist with a microscope in 1896. Lo and behold, it was found to have exceedingly archaic sperm, characteristic of very primitive plants. Turns out that our current landscape species, Ginkgo biloba, first hit the scene about 56 million years ago. Its genus appeared 170 million years ago, in the Jurassic - dinosaur central. Its order appeared in the Permian, before the horrendous end-Permian extinction - ginkgoes made it through that bottleneck.

So the ginkgo is a special case. But plants everywhere have been around for ages and ages, way more than our paltry 200,000 years. Even the most recently evolved families, such as the Asteraceae and Fabaceae and Poaceae, are millions and millions of years old. You can look at any landscape and view snapshots from the history of life on earth. So what's a living fossil? Either all of them, or none of them.

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 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!