Monthly Archives: March 2009

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Pushing CotA back one day

Because I know there are one or two people scrambling to come up with something for CotA, I’m going to publish it on Thursday rather than Wednesday. Send in your submissions! And thanks to those of you who’ve submitted already. The list is a little shorter than for the previous CotAs, but there are some damn fine posts here.

Some happier jaguar news

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A jaguar whiles away its life at the Arizona-Sonora Desert Museum. FWS Photo.

From the Arizona Daily Star:

A federal judge overruled an agency’s decision today that had stopped preparation of a recovery plan and designation of prime protected habitat for the endangered jaguar in the Southwest.
District Judge John Roll’s ruling essentially said that the U.S. Fish and Wildlife Service had failed to prove its case that the jaguar is primarily a foreign species and that there is no important habitat for it in Arizona and New Mexico. Roll ordered the service to return on January 8 of next year with a new decision on critical habitat and a recovery plan.
The ruling is a big victory for the Center for Biological Diversity, which had filed suit challenging service decisions on both issues, and the Defenders of Wildlife, that had sued against the recovery plan decision only.

The Center for Biological Diversity has more.

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Jaguar Death Was Unnecessary

Some upsetting news from our friends at the Center for Biological Diversity. Cut and pasted from an email alert sent out by CBD’s Kieran Suckling:

Two weeks ago the last known American jaguar died. Not in the wild. Not by mistake. He was euthanized on a stainless-steel table in Phoenix.

When the state-sanctioned vet said it was better for Macho B to die this way than in the wilderness, where he had lived for 15 years, I was taken aback. When the vet said Macho B could have lived another two months, I wondered: Why the rush to euthanize him? When the vet said Macho B’s death was “necessary” due to long-term kidney failure, I called for an independent investigation.

The story just didn’t add up.

The first of the independent investigations is complete, but state and federal wildlife agencies won’t release it. The Arizona Daily Star, however, talked to the investigators and confirmed my worst fears.

Tissue samples show no sign of kidney failure. Indeed, University of Arizona pathologist Sharon Dial stated that, “For a supposed 15-year-old cat, he had damned good-looking kidneys.”

The euthanization was rushed and unnecessary. Macho B was likely suffering from severe dehydration, probably brought on by his snaring, anesthetizing, and collaring. Rather than being killed, said Dial, Macho B should have been given intravenous fluids for 24 to 48 hours. There was just not enough information to support euthanizing him so quickly.

Macho B was injured, possibly fatally, during capture. Though the wildlife agencies publicly denied Macho B’s death was caused by “capture myopathy” (i.e. stress and injury), internal memos stated: “Department personnel suspected capture myopathy/renal failure.” Only after the Star’s investigation was it revealed that Macho B’s paw was severely swollen, and deep scratch marks were found seven feet up the tree where he was snared.

The necropsy was botched. Investigations into the cause of death have been hampered by a decision to do a “cosmetic” rather than a full necropsy so that Macho B’s pelt could be stuffed for “educational” presentations. Why and who deemed this more important than a full investigation?

The only good news to report is that the Center for Biological Diversity’s lawsuit to establish a federal recovery plan and protected critical habitat for the jaguar is going well. In a hearing last Monday, the federal judge peppered the government’s lawyer with skeptical questions, showing his discomfort with how the agency has continually changed its rationale for not protecting America’s jaguars.

Establishment of a federal recovery plan would likely have prevented the death of Macho B, and it certainly would have prevented what one pathologist called a “lack of total transparency” in how the post-capture handling has been conducted

More on the story is available here. CBD’s Jaguar Legal Defense Fund is asking for your donations.

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Stargazing

Under this vault of stars I am content.
Stuck fast to this small rock I am at ease.
Minuscule, ego fading by degrees
and what remains of little consequence.
Only the wind and stars, and nighttime shades
of loves abandoned, fire going cold
as in the embers images unfold.
Crushed there, beneath the fallen palisades
of what my life had been, of all my owned
identity, the burdensome façade
torn down abrupt, as by a jealous god;
beneath my stony wrack, all limber-boned
and new, pellucid, clear, I watch the stars
my vision all the clearer for the scars.

Dragon Trees and Spanish Needles

One of the steadiest jokes in the plant world — for rather nerdly definitions of the word “joke” — is the degree to which a person must constantly relearn the proper Latin names of plants. Just as soon as you get used to calling something a Zauschneria, it becomes an Epilobium. When I first started paying attention to such things, older works of reference still referred to Mahonia species as Berberis; now there are some advocating that Mahonia be stripped of its rank and re-subsumed into Berberis.

The general impression seems to be that the scientists change the names because they have nothing better to do, that they spend hours in academic symposia arguing whether a cholla is an Opuntia or a Cylindropuntia or an Austrocylindropuntia, for no more reason than that their academic reputations are staked on the outcome: a counting coup on the giant shaggy beast of taxonomy. Or maybe it’s the influence of the multinational nursery plant label printing cartel, who respond to sluggish third-quarter earnings by pushing for a whole slew of renamings so that sales will rise as nurseries relabel their stock.

One renamed genus of special interest here in Southern California bears the common-names Lord’s Candle or Spanish Bayonet, names inconveniently shared with related species in other parts of the country. It’s a prominent denizen of the chaparral, or at least it’s prominent when it sends up ten-foot-tall spikes of creamy white flowers. It’s also prominent when you walk into one. There is just about no way to touch a Hesperoyucca whipplei without feeling pain. You can bring your fingertip up to a leaf’s terminal spine as asymptotically as Zeno’s tortoise approached the finish line, and in all likelihood you’ll still yelp when the fiendishly sharp point makes contact.

a great big Hesperoyucca flower stalk

Calling the plant “Hesperoyucca whipplei” can prompt almost as many yelps among SoCal botanizers. The plant is still widely known as Yucca whipplei, not just in hikers’ conversation but in august references such as the Jepson Manual. Despite the unfamiliarity of the longer name, people have been using it for almost as long as the shorter alternative. It was 1871 when botanist Georg Engelmann divided the genus Yucca into two “sections,” Hesperoyucca and Euyucca, the first comprising nothing but Yucca whipplei. Assigning Hesperoyucca the rank of genus was first suggested in 1892 by Kew Gardens botanist John Gilbert Baker.

In 1902 William Trelease, in the Annual Report of the Missouri Botanical Garden, seconded Baker:

Yucca whipplei is the name proposed by Dr. Torrey, and still commonly employed, for a plant which, when in bloom, forms one of the most striking and beautiful features of the Coast-range vegetation of southern California. From all other Yuccas it differs in the slender style rising abruptly from the top of the ovary and capitately enlarged into a papillate stigma, and in possessing somewhat glutinous pollen, as well as in certain capsular characters, which led Dr. Engelmann to give it the sectional name Hesperoyucca, which both Mr. Baker and the writer have proposed to employ as a generic name.


The Yucca queen Susan McKelvey — a compelling historical figure who renounced an affluent life and marriage to botanize in the desert Southwest — disagreed with Baker and Trelease in her out-of-print, impossible-to-find-a-copy-of magnum opus Yuccas of the Southwestern United States, demoting “Hesperoyucca” to a mere division of genus Yucca.

My own true love the Joshua tree, Yucca brevifolia, was also split out of genus Yucca by Trelease in that self-same 1902 paper:

The Joshua tree of the Mohave desert region, the largest and most imposing of the Yucceae of the United States, which was first called Yucca draconis arborescens by Torrey, subsequently Y. brevifolia by Engelmann, and which is now commonly known as Y. arborescens, differs in its collective flower and fruit character about as much from typical Yuccas as does Hesperoyucca. In separating it from Yucca, I have thought best to apply to it as a generic name the sectional name Clistoyucca under which Dr. Engelmann separates it from the other species of Yucca, since there can be no question as to the applicability of that name to this particular tree, though Dr. Engelmann subsequently found it desirable to add Y. gloriosa to this section, to which the writer afterwards added Y. gigantea. Only the one species is known.

Clistoyucca arborescens is a pretty name, but it was rejected by McKelvey as well, and Clistoyucca, minus Y. gloriosa and Y. gigantea (now Y. elephantipes), was relegated to reduced status within Yucca, as “section Clistocarpa.”

Yucca draconis is an even prettier name, and the shame of its having been previously assigned to the species now known as Yucca aloifolia can scarcely be withstood. (John Torrey, in first describing the Joshua tree, had apparently guessed it to be an arborescent form of the already kinda arborescent Y. aloifolia.) But for a chance arrangement of historical events, Southern Californian rock climbers might revere Dragon Tree National Park as their local mecca. As it is, one can only gaze at historical documents and sigh wistfully, as with this 1880 photograph by Landscape Photography Patriarch Carleton Watkins:

”Yucca

In any event, the arguments over whether a given species, or group of species, best fit one generic pigeonhole or another may seem a bit arbitrary to the lay person. And in the past, the justifications for the rearrangements could tend toward the subjective. Taxonomists chose one characteristic or another — often floral or fruit anatomy, as those tend to vary more among related species, and Old Two-Name himself, Karolus Linnaeus, used floral morphology as the basis of his plant classification system anyway — and sorted species into genera based on sets of those characteristics. Many of the judgments were subjective. If half the plants in your sample have a floral tube three inches long, and the other half have a floral tube a millimeter long, is that difference enough to justify two genera? What if half of each group has spongy fruit, half the remainder of each group have gelatinous fruit, and one or two species in each group never sets fruit but reproduces vegetatively? The arguments could last for centuries. It’s hard enough, sometimes, to determine whether two groups of plants belong to the same species, and species at least have one possible objective standard: members can usually interbreed and produce fertile offspring. Determining a genus adds another layer of abstraction to the mix. 

A genus is a hypothesis more than anything else. Until a couple decades ago, a genus was a hypothesis that attempted to answer a rather vague set of questions: given available data about physical characteristics, are the species in the potential genus more like one another than not, are they more like each other than they are like species outside the potential genus, and is the potential genus relatively compact? I know: my eyes are glazing over too. It’s a pretty good system nonetheless, once you get away from the abstract and start talking actual traits. Take several dozen examples of each species, measure the multiple traits you have in mind, plot them all on a scatter chart, and the clumps of dots might just support your contention that species X and Y deserve to be split out into their own genus, or that genus A ought to be folded into genus L.

But two technological advancements happened in the early 1990s that changed everything. One was the advent of powerful computers cheap enough that a biology lab at a small state-funded college could afford a dozen of them. The other was the development of DNA replication by way of the polymerase chain reaction. Suddenly, it became rather straightforward to generate huge amounts of a given organism’s DNA, which could then be read — “sequenced” — with any of a number of complex technologies. The sequences of different organisms could then be compared, with the number crunching done by shiny new, massively powerful 486es and Apple Quadras.

Biologists could thus take equivalent stretches of DNA from groups of related organisms, say 500 base pairs or so at a time, compare and contrast the sequences, and figure out which groups shared which accumulated mutations.

This may seem unduly wonkish, a mere shift of the plants’ compared physical characteristics to the molecular level. But the DNA information is more than mere physical makeup: it is a map of the organism’s ancestry.

This changed everything. As evolutionary theory quickly spread through the world of the biological sciences in the late 19th and early 20th centuries, biologists had increasingly sought to make their taxonomic pigeonholes bear some relationship to actual ancestry. With DNA sequencing an everyday reality, they could do so accurately. There was a sort of internecine war for a few years between the old-line, compare the gross morphologies taxonomists (pheneticists) and new-wave DNA-sequencing taxonomists (cladists), which the cladists soon won. A lot of things get called a paradigm shift that don’t really deserve the label. This really was one.

It was a new approach to how we even think of taxonomy. The whole notion of Linnaean taxonomy was subtly undermined. It had long been accepted that the definitions of different taxonomic ranks were fuzzy, somewhat arbitrary, at best close approximations of the diversity of life. It was the closest thing we had to an accurate system, and it served us well. But with the advent of cladistics, an alternative loomed: instead of a categorizing system that described what possible relationships among organisms could well be, we could now start mapping the actual lines of descent of each living thing on Earth. Linnaean taxonomy was the bitmap, cladistics is the vector art — or maybe the better allegory would be fractal generator.

The seemingly constant renamings, then, rather than being a source of irritation and resentment of one-upmanship by show-off botanists, become a cry of joy.  We thought there was such a thing as a Zauschneria, but it turns out we were misled by surface appearances and thought they were distinct from Epilobiums, and they’re not, so we correct our earlier error. We have discovered something new about the relationships among all living things! We got it wrong before, and now maybe we have it right, and it’s not about the names so much as it is about the unique history of each species, each genus.

And the definition of a genus has been affected profoundly. It now has a discrete physical model: a genus is a clade. A clade, the notion from which cladistics derives its name, is essentially a common ancestor and all its descendants. The clade “pine trees,” for instance, contains the most recent common ancestor of all pines, and every one of its descendants that has ever lived.

That “every one of its descendants” thing is important. If you exclude any descendents, the group becomes what the cladists call “paraphyletic,” and thus not a clade. Take reptiles, for instance: the class Reptilia, one of the four canonical groups of vertebrate land animals (birds, mammals and amphibians being the other three) is paraphyletic. The most recent common ancestor of all reptiles has descendants that are generally left out of the set of “reptiles”: the birds, who are the descendants of dinosaurs. Unless you include birds in the category reptiles, “reptiles” isn’t a clade.

This becomes important in defining which genus the SoCal Bayonet belongs to. Yucca, to be a valid genus, should be a clade. That’s not a hard and fast rule, but biologists do try to follow it. If the common ancestor of Yucca whipplei and all other Yuccas has any descendants that aren’t Yuccas, then there’s a problem.

And in fact it turns out, based on data from DNA seqencing, that Yucca whipplei seems to be much more closely related to plants in the genus Hesperaloe than it is to any other Yucca. (Hesperaloe, a genus with about half a dozen species, was tentatively included in Yucca in the 19th century but Engelmann split it out in 1871, and as far as I know no one’s tried to put it back.) So either we have to move all Hesperaloes to genus Yucca, it would seem, or Yucca whipplei needs to come out. And given the Law of Priority, in which the earliest valid name takes precedence over more recent names, Hesperoyucca whipplei the SoCal Spanish Bayonet must become. (It’ll probably take another century for the name to catch on among the public.)

As for Yucca brevifolia, a.k.a. Clistoyucca arborescens, a.k.a. Yucca draconis arborescens? It turns out that once you exclude Hesperoyucca, genus Yucca with Joshua trees included is a perfectly good clade. Joshua trees will not be getting their own genus anytime soon.