Genome 10K

In the November/December issue of the Journal of Heredity, the first article is the proposal for "Genome 10K" (G10K), a project that aims to sequence the complete genomes of 10,000 vertebrates, a number roughly equivalent to one representative species for every vertebrate genus. The authors (a large community of scientists headed by David Haussler, Steve O'Brien, and Ollie Ryder) contend that it is indeed a feasible project if the cost of DNA sequencing can be reduced by just one additional order of magnitude, over the reduction by 4 orders of magnitude we have seen in recent times. The diversity of vertebrate body forms, life histories, and biochemistries, to name a few things, are hoped to be dissected through these genomes and benefits to conservation, a better understanding of the roles and histories of non-coding DNA, and insights into adaptive radiations in several key vertebrate groups are all obvious incentives. Although it was a bit strange to read what is essentially a grant proposal in a scientific journal, I still found it to be a nice description of the diversity of the major vertebrate groups - complete with pretty phylogenies for each class/major group. More info can be found on the Genome 10K website.

Enrollment for the 2010 Bodega Bay Phylogenetics Workshop Now Open!

Enrollment for the 11th annual Applied Phylogenetics Workshop was announced earlier today. The intensive week-long workshop will be held at the scenic Bodega Bay Marine Laboratory from March 7–13, 2010. The course assembles a team of instructors to provide lectures and hands-on tutorials on a diverse range of topics in the field of phylogenetic biology, including Bayesian and maximum likelihood estimation of phylogeny, divergence times, character evolution, and diversification rates. Additional details and application forms can be obtained from the course website here, and are due by January 8, 2010. It's sure to be a blast!

From Best to Worst?: (Another) Reevaluation of mtDNA as a Molecular Marker

Once the golden child of molecular phylogenetic and phylogeographic analyses, mtDNA has taken a beating over the past five years. There is a bit of irony to this backlash: many of the features that were once thought to make mtDNA a particularly desirable marker (e.g., lack of recombination, maternal inheritance, low effective population size), are now being cited as contributors to its worst problems, introgression and discordance with species boundaries being two of the most serious. Although discussion of these problems isn't hard to come by (1, 2), Galtier et al.'s recent review in Molecular Ecology is a particularly insightful contribution.

Galtier et al. use a myth-busting review of the recent literature to investigate three widespread claims about mtDNA: strict clonal evolution (lack of recombination), selective neutrality, and constant mutation rate. Galtier et al.'s take on clonal evolution provides one of few encouraging findings: although numerous recent studies recover within-species homoplasy that may be interpreted as evidence for recombination, Galtier et al. suggest that this apparent homoplasy may also result from mutational hot-spots.

The suggestion that mtDNA is selectively neutral is an assumption that is most in need of a good thrashing, and Galtier et al. are happy to oblige. After a brief discussion of the powerful evidence for selection and selective sweeps, Galtier et al. provide a nice discussion of both the possible causes for these phenomena and their far-reaching implications. The last paragraph of this section sums things up rather nicely: "Whatever the underlying causes of the patterns [of selection] observed, these studies demonstrate that the withinspecies level of mtDNA diversity per se is not a good marker of population size and species health, as observed both at the metazoa and mammalian levels. Nonequilibrium processes apparently dominate. The classical interpretation of genetic diversity as the product of mutation rate by population size, as expected at mutation-drift equilibrium, is strongly questionable as far as mtDNA data are concerned."

Finally, Galtier et al. provide evidence - primarily from Nabholz et al.'s (2008) recent reviews (1, 2) - that rates of mtDNA evolution are widely variable, both within and among taxa. They conclude suggesting: "The molecular clock, therefore, is certainly not a tenable assumption as far as mtDNA is concerned. Nonclock- like evolution is common, and the departure from homogeneous rates can be very strong."

Conspicuously absent from Galtier et al.'s review is a discussion of the feature of mtDNA that has most challenged recent phylogenetic and phylogeographic studies: introgression. Perhaps Galtier et al. viewed this as a topic already addressed by other reviews, but the mechanisms underling mtDNA introgression remain poorly understood and this topic too would have benefitted from Galtier et al.'s insight.

At the end of the day, Galtier et al. take a rather dire view of mtDNA as a molecular marker, suggesting that its primary value is in its cheapness. Although I have a bit more charitable view, I certaintly hope that Galtier et al.'s review will succeed in opening more eyes to the diversity of problems confronting interpretation of mtDNA.

GALTIER, N., NABHOLZ, B., GLÉMIN, S., & HURST, G. (2009). Mitochondrial DNA as a marker of molecular diversity: a reappraisal Molecular Ecology, 18 (22), 4541-4550 DOI: 10.1111/j.1365-294X.2009.04380.x

New Applications of Population Genetic Methods to Studies of Language Evolution

A recent study in PLoS biology nicely illustrates how modern studies of language evolution and geographic variation are taking advantage of modern population genetic and phylogenetic methods. Although the use of phylogenetic methods in quantititive comparative linguisitics isn't new, this new study is, to my knowledge, the first to use the Bayesian clustering algorithms that are all the rage in population genetics. This study uses these methods to investigate the extraordinarily diverse languages of Sahul (an ancient continent formed from present day Australia, New Guinea and surrounding islands). Previous attempts to infer the history of these languages have been complicated by two problems that will be familiar to any phylogeneticist. The first problem involves identification of homologies - or, in the jargon of a quantitative comparative linguist "phonological and semantic drift [which] make it impossible to identify lexical cognate characters." Another challenge stems from admixture, which may result from the fact that many Sahul languages have been in "long term and intensive contact," . By applying the program Structure to 160 "abstract structural features" quantified for 121 Sahul languages, Reesink et al. are able to recover 10 "ancestral language populations." Many of the clusters recovered by Structure correspond with previously diagnosed language groupings, and the overall patterns of hierarchical clustering suggest plausible historical scenarios. The authors also suggest that, in spite of ample opportunity for interchange, many languages show "negligible amounts of admixture."

Reesink, G., Singer, R., & Dunn, M. (2009). Explaining the Linguistic Diversity of Sahul Using Population Models PLoS Biology, 7 (11) DOI: 10.1371/journal.pbio.1000241

More From Inside (and Outside) the Fringe

A recent post to this blog was regarding the article in PNAS positing a hybrid origin for the larval stage of lepidopterans (the insect order containing moths and butterflies). More specifically, Williamson (2009) proposed that modern lepidopterans, with their highly complex larval life stage and metamorphosis, acquired it not by the traditional neo-Darwinian means of descent with modification, but instead by hybridogenesis with adult onychophorans – the latter being an ancient, distantly related group thought to be the sister group to Arthropoda (the animal phylum of lepidopterans and all other insects, as well as groups as varied as crabs, millipedes, and barnacles).

Considerable negative attention has been directed towards Williamson’s kooky idea since it was published – and even more to the fact that it was published in one of the more prestigious journals of our field – and still more to the (possibly unscrupulous) manner that the article was handled by the communicating National Academy member, Lynn Margulis. Much of this rapid-fire negative attention came from the blogosphere, most notably from Jerry Coyne who dubbed the article the “worst paper of the year” on his popular “Why Evolution is True” blog.

A more formal scientific response was sure to follow. First, Gonzalo Giribet of Harvard responded with a short letter to PNAS entitled “On velvet worms and caterpillars: Science, fiction, or science fiction?” in which he points out that, in making his claims to the hybrid origin of lepidopteran larvae, Williamson has gratuitously overlooked a large body of phylogenetic evidence showing that onycophorans are the sister group to arthropods, and not closely related to either larval or adult lepidopterans.

More recently, Michael Hart and Richard Grosberg went farther, publishing a very thorough and deliberate rebuttal to Williamson (2009). In a "Mythbusters" style article uncreatively (but fittingly) entitled “Caterpillars did not evolve from onychophorans by hybridogenesis” (emphasis mine) they systematically review virtually all of the predictions of Williamson’s hypothesis. . . and just as systematically reject them! For instance, Williamson predicts that under his hybridogenesis theory holometabolous (metamorphic) insects will have larger genomes than non-metamorphic insects. Hart and Grosberg point out that C-value (whole genome size) information exists for a wide range of insect species in metamorphic and non-metamorphic groups. Analysis of these data has revealed that, in fact, species in holometabolous insect orders have genome sizes that are on average smaller (not larger) than non-metamorphic insects, although the ranges of genome size in both groups overlap broadly. Numerous other predictions from Williamson (2009) are similarly tested and rejected.

Since I originally blogged on this subject over two months ago several additional comments about the article, the “crackpot index” of the author, or the submission and review process at PNAS have appeared online (e.g., here, here, and here). Horrifyingly (but predictably) the “Institute of Creation Research” has even picked up on the controversy, labeling it as evidence for “deep disagreement” among evolutionary biologists (I’m loath to link to the article here, lest that in so doing I increase the page rank of the ICR website). My interpretation is to the contrary. Controversy abounds in our field, as it should in any vital, active area of science. However, rarely have I seen a group of evolutionary biologists as unified as they have been against this contrary theory and furthermore its questionable publication in a respected journal of our field!

Dechronization Showcased on Medpedia

Some of you may have noticed the little badge on the left side of our website for Medpedia. The Medpedia Project is the web-based platform that seeks to be a repository for all things health-related, with its goal of linking physicians, scientists, health-related agencies, consumers and others. This week they have added a new feature called "News and Analysis" that links to content from a few select blogs. Dechronization was chosen to be one of these showcased blogs, under the "Science and Research" category.

Dispatches from the 2009 North American Symposium on Bat Research

I just returned from the 2009 North American Symposium on Bat Research, held in - where else? - Portland, Oregon. I know I usually see myself as more of a herpetologist, but some recent work I've been doing on malaria parasites in bats prompted this westward trek to meet other bat biologists and return to my roots (my undergrad advisor, Roy Horst, was one of the founders of the society and my first grad project was on Trinidadian bats with Jerry Wilkinson). A few highlights from these meetings: Aaron Corcoran, a grad student at Wake Forest gave a nice paper describing some very cool experiments that show that tiger moths use "clicks" that they make to jam up the echolocation of big brown bats and avoid predation. That project was published in Science this summer. Sharlene Santana, a student at UMass Amherst demonstrated the spread of the Anthony "Biteforce" Herrel cult, by giving a talk about plasticity in bite force in frugivorous neotropical bats, an evolutionary trend that she suggests contributed to their notable diversification. I gave a talk in a special session on "Health and Disease" in bats and one of my (other) favorites in that session was by Daniel Streicker from the University of Georgia who gave some really nice estimates of rabies virus transmission between species of bats within a community using coalescent-based model approaches, showing that bats are more likely to infect phylogenetically related species, but at unequal rates. Elizabeth Clare, from Guelph, used DNA barcoding (duh - she's at Guelph!) of guano to generate some very intriguing data about resource partitioning in two (to eight - she had somewhat smaller datasets for another six) species of sympatric bats. And the last talk that I got to see before having to run off to catch a plane was by Robert Baker, of Texas Tech, who summarized three important types of speciation in bats - ecological, hybrid and adaptive radiations and gave examples of each. Baker, answering his own question, "Genetics, what have you done for bats lately?" suggested that the number of species of bats may soon increase by as much as 50% just due to better studies of molecular variation in cryptic and hybrid species. The North American Society of Bat Researchers is certainly all like a big family to each other and it was nice to crash their annual reunion.

Urban Wildlife in North Carolina

Although I don't have any exciting new field stories to recount, I haven't had to venture far from NESCent to have had a few close encounters with nature - including one that was much closer than expected. Pictured in the upper panel of the figure at right is a cool praying mantis that we found perched on the rear tire of my Aveo the other day. However, it was what happened to me this evening as I finished an easy run around dusk that really takes the cake. As I was running up the street towards my house in Old West Durham, I suddenly perceived the shadow of something flapping right above my head. Before I had time to react, I felt what later turned out to be talons and the weight of something quite large on my head! Of course, I did what almost any normal person would do (yell "Ahh, ahh!" and swat wildly). After hanging on to my scalp for a second, I felt it release, and then an enormous barred owl flew off my head and up to the telephone wires, where it hung out long enough for me to go back to my house and grab a camera to snap the (admittedly poor) photo in the lower panel at right. My neighbor reports that this is the 4th time he has heard of this owl attacking, and by interesting coincidence, several other owl attacks have recently been reported for North Carolina (here and here).

2009 Anolis Symposium, Final Day

Day 2 of talks in the 2009 Anolis Symposium hosted by the Museum of Comparative Zoology is drawing to a close this afternoon with some of the final scheduled talks of the meeting by Jonathan Losos, pictured right (upper panel); and by Dechronization blogger-in-chief Rich Glor (lower panel). This meeting has featured a large number of great talks, but I only have time & space to comment on a few here. In the morning session, we saw a whole series of presentations on invasive anoles (a "mini-symposium," to steal Jason Kolbe's words), including a great talk by Todd Campbell on the natural history and ecological interactions of the 6 introduced anoles found in the Miami area of South Florida; and some cool preliminary results from Kolbe suggesting adaptation in thermal tolerance in northern vs. southern populations of introduced Anolis sagrei in Florida. We also saw several talks on the evolution and genetics of development in Anolis, including a genuinely fascinating study (and I'm not usually fascinated by such studies, so this is no small compliment) by Doug Menke showing the association of a deletion in the Tbx4 hindlimb enhancer and "short-limbedness" among anole species. To my knowledge, this is the first study to potentially identify a explicit genetic variant responsible for the quantitative difference in limb lengths among anoles. This afternoon we heard from Joel McGlothlin, a post-doc with Butch Brodie at the University of Virginia, who presented results showing that genetic constraint in the form of the G-matrix is quite conserved among anole species; and from Luke Mahler, a present Losos graduate student, who is examining the relationship between niche availability and the rate of phenotypic evolution in Caribbean Anolis. If recent history can be used as a guide, there should be only 3653 days (and counting) until the next edition of the Anolis symposium. . . . I'll be there!

Blogging the Anolis Symposium. . . .

The Museum of Comparative Zoology at Harvard University is presently (Oct. 2-4) hosting the 4th edition of the "Anolis Symposium," the definitive international meeeting of Anolis biologists worldwide. This edition, my first, seems particularly poignant as it has been accompanied by a dedication of the MCZ Herpetology Library to esteemed former herpetology curator and grandfather to the study of Anolis lizards, Ernest Williams. As a consequence the meeting has been so far highlighted by a series of informal speeches by a prestigious list of former Williams students at last night's dinner. These include, but are not limited to Paul Hertz, Ray Huey, George Gorman, Bob Holt, Richard Etheridge, and (as an undergraduate student in the 1980s), my former advisor, Jonathan Losos. Talk highlights of the day include prominent theoretical ecologist Bob Holt's "aesthetically impaired" but fascinating talk relating his graduate work under Williams in the 1970s on the introduced species pair of Anolis aenus and A. trinitatis on Trinadad; as well as an immensely entertaining talk by Manuel Leal on homing in Anolis gundlachi (evidently they do it very well, but we don't know how!). At right is a picture featuring Steve Poe's opening slide (in the upper panel), and me blogging about Steve Poe's fascinating talk (in the lower panel).

Next...Ms. Rex...Sue Rex?

In this week's PLoS One, Ewan Wolff and colleagues present evidence that a common parasite of birds, Trichomonas, also infected tyrannosaurid dinosaurs, and may have caused several, including the Field Museum's famous "Sue" to have died of starvation. The authors examined 61 tyrannosaurid specimens and found mandibular lesions in 10 of these that were consistent with similar lesions that are observed in modern-day birds that are infected with these parasites. Today, columbiforms are heavily parasitized by Trichomonas gallinae and these birds are likely the source of infection in raptors when they are consumed as prey (if anyone wants a live demonstration of this, come hang out in my office and watch the red-tails pick off pigeons). Wolff et al. argue that although infection via consumption of Trichomonas-laden prey can certainly not be ruled out, many of the specimens that show the lesions also have evidence of bite wounds on their heads, suggesting that face-to-face transmission may be the bigger culprit. While looking up information on T. gallinae, I also came across an interesting article in the Journal of Parasitology from last year that conducted molecular studies of Trichomonas isolates from doves around the U.S. using the parasites' ITS1, 18S and alpha-tubulin genes. The surprise of that paper was that the isolates from doves generally fell into two distinct clades - one similar to T. gallinae, but others that were genetically similar to the human STD, T. vaginalis! Clearly, more sampling of trichomonads should be done as they may play significant roles in the ecology of avian communities...and, as Wolff et al. suggest, may have even been having large impacts on birds' dino ancestors.

The Adaptive Ratchet to Irreversibility

A new paper [1] published in Nature experimentally explores the mechanisms that may generally underpin Dollo's law. With a flurry of recent papers, which exclusively rely on phylogenetic approaches (often demonstrably flawed) to challenge one of the soundest principles of character evolution [2], this original approach to an age-old problem is a stand-out.

The group, led by Joe Thornton at the University of Oregon, previously dissected the genetic basis of a shift in function of the glucocorticoid receptor (a DNA transcription factor), using statistical phylogenetics, functional assays, and X-ray crystallography [3]. They found that a once-promiscuous binding receptor--activated by aldosterone, deoxycorticosterone, and to the lesser extent, cortisol--in the common ancestor of jawed vertebrates, became highly cortisol-specific in the lineage leading to ray-finned fishes and tetrapods.

The key substitutions took place in the receptor ligand-binding domain, with two changes necessary and sufficient to shift preference, and several other changes that restrict receptor sensitivity further and stabilize its structure [3]. The experimental reversal of these same changes in the derived receptor surprisingly renders it useless. It cannot activate transcription in the presence of any ligand. In other words, the forward changes cannot be reversed through the same direct path, because it is unsuccessful in the derived background.

Bridgham and colleagues have now identified the group of mutations that comprise this background, the order in which the groups of changes would have to proceed for a reversal of function to take place, and reveal the underlying mechanism.

The initial sequence of mutations fixed in ligand preference switching is largely unconstrained. Any number of them could improve cortisol binding. However, once a particular evolutionary path is taken, it is unlikely that selection can replay the highly specific sequence of events to revert to the ancestral state.

The process is akin to an evolutionary ratchet, making the receptor intolerant of ancestral features present immediately preceding the present form.

The paper convincingly shows that the initial stages of the reversal must follow a very particular sequence, as well as take steps that do not yield a measurable advantage in either the derived or ancestral function. The reversal paths would thus have to pass through adaptive troughs, even if the selective environment favored the ancestral form. Paraphrasing Günther Wagner in the accompanying news commentary, the receptor's path effectively burns bridges that it just went over, thus making the reverse path exceedingly implausible.

[1] Bridgham, J. T., Ortlund, E. A. & J. W. Thornton. 2006. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461, 515-519.

[2] Gould, S. J. 1970. Dollo on Dollo's law: irreversibility and the status of evolutionary laws. J. Hist. Biol. 3:189–212.

[3] Bridgham, J. T., Carroll, S. M. & J. W. Thornton. 2006. Evolution of hormone-receptor complexity by molecular exploitation. Science 312: 97–101; Ortlund, E. A., Bridgham, J. T., Redinbo, M. R. & J. W. Thornton. 2007. Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317:1544–1548.

A New Holiday

Apparently, today is the First Annual Postdoc Appreciation day. Events have been planned around the country (and Canada and Australia). If you don't see one in your area, perhaps take your postdoc(s) out for a beer at least.

Echidnas, duckbills, and evolutionary rates

I just returned from a two-month trip to Australia, where – for all you twitchers out there – I had a ‘clean sweep’ of Australia’s living monotremes: the platypus and the short-beaked echidna. These are truly bizarre mammals: in addition to obvious modifications of their trophic morphology (duck-bills and “beaks”), they lay eggs and possess a cloaca (on that last subject, we can all be thankful that it was the therian lineage that gave rise to modern humans). Given the phylogenetic and phenotypic distinctiveness of these strange beasts, it is hard to avoid viewing monotremes as “living fossils”, characterized by a long history of low but stable diversity and minimal morphological change. But in this week’s early edition of PNAS, Phillips et al. make the curious claim that terrestrial echidnas are recently derived from aquatic or semi-aquatic ancestors.

The evidence in Phillips et al. hinges on a reinterpretation of the fossil record in conjunction with molecular clock analyses of the echidna-platypus split. Knowing nothing about the cranio-mandibular morphology of monotremes, I am in no position to evaluate much of this work. Still, I found this to be a plausible conclusion and one that seems to make sense: under the new date for the platypus-echidna split (~32 Ma), rates of molecular evolution on both the stem monotreme and subsequent branches are well within the distribution of rates seen in other vertebrates. If, however, the split occurred at least 112.5 Ma, as was proposed previously by Rowe et al. , rates on the monotreme stem would be among the highest reported for vertebrates, and rates after the split would be among the slowest! If Phillips et al. are correct, this is a fascinating bit of natural and evolutionary history. Despite the grumbling of a small but vociferous group of aquatic ape enthusiasts , there are very few well-supported cases of secondarily derived terrestriality from aquatic/semi-aquatic ancestors. So finding that a proto-platypus ecomorph gave rise to Australia’s famous ant-loving “porcupine” is an interesting one indeed.

I think this work challenges some of our assumptions about old, species-poor lineages. Often, such groups are described as “living fossils.” Groups like coelacanths, lungfishes, tuataras, bowfins, and more have persisted for hundreds of millions of years with what appear to be very slow rates of diversification and morphological evolution. Paleontologists have even used the word “inert” to describe the nature of evolution in groups like these. But here we have what appears to be a major adaptive transition between fundamentally different morphologies in one of these living fossil lineages. Why has this group undergone such a radical ecological shift? And conversely, why do so many other groups seem to be inert?

Snake with a Foot?

The Telegraph ran a piece two days ago about the discovery of a snake with a foot in China, including a photo of the animal. Although the photo is too poorly done to permit a real scientific evaluation, a few red flags suggest a possible alternative explanation - that the foot belongs to a prey item. First, the snake's body is obviously bulged in the vicinity of the foot indicating the snake likely just ingested a large prey item. Second, the foot is facing backwards - the direction we'd expect given the snakes tend to consume their prey head first. Third, the foot is really an entire limb complete with digits: although elegant developmental studies have shown that snakes are capable of producing rudimentary limbs, they don't produce the sort of fully formed feature we see in this photo. The Telegraph article suggests that the snake is being studied by the Life Sciences Department at China's West Normal University in Nanchang. My guess is that this study came to an abrupt end when they cut the snake open and found a partially digested lizard in its belly.

Given the quality of the evidence, this story has gotten far more attention than it deserves (1, 2, 3).

UPDATE: I'm not the first to propose that this limb is from a prey item. Comments at Pharyngula suggested the same explanation earlier today.

More on Patents

This is a partial transcript from J.E.M. Supply v. Pioneer Hi-Bred International (U.S. Supreme Court, 1996)

Justice Souter: [A previous case,] Chakrabarty probably should have come out the other way because you had a specific statute, the PPA [Plant Protection Act], which covered this asexually reproducing plant, a bacterium, and yet the Court did not say that the coverage of [patent law section] 101 was thereby defeated.
Attorney: I don't believe that the Chakrabarty Court viewed the bacterium as a plant.
Justice Souter: Well, what else could it view it as? I mean, [...] I wasn't sure myself, and I went to the dictionary, and the dictionary says it's a plant.
Attorney: --I... the Chakrabarty Court spoke of it as a microorganism.
Justice Souter: Which is a generic term. [...] I take it then on... on your position, if we assume that the bacterium is a plant and it asexually reproduces, the decision in Chakrabarty should have been that it's covered by the PPA and there's no 101 patent.

***

One of our previous post topics (inspired by Elizabeth Pennisi's Science news article), on Microsoft's attempt to patent some commonly used phylogenetic methods, spurred some unlikely side reading. Sidelined by an injury, I picked up Robert B. Laughlin's excellent book on excesses of patenting, The Crime of Reason, and perused some entertaining law texts.

Pennisi cites an obviously frustrated Bill Piel whose comment: "Microsoft might as well patent the multiplication tables," is funnier still because they tried something very similar. Microsoft previously tried to patent verb conjugation! (Patent App# 20060195313, Voetberg et al. 08/31/2006; cannot be accessed online.)

It seems to be very important in biology-related lawsuits whether or not some process, method, etc., can receive protection under patent law section 101. While the U.S. Supreme Court decisions state that, "An algorithm, or mathematical formula, is like a law of nature, which cannot be subject to a patent." But section 101 of the patent law reads, "Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefore, subject to the conditions and requirements of this title." Additionally, section 100 defines process as, "process, art, or method, and includes a new use of a known process, machine, manufacture, composition of matter, or material."

The interpretation of these laws and statutes is ultimately up to the Patent Office and the courts. Both have erred in the past, and judging by the above-cited patently pedestrian exchange in the U.S. Supreme Court over the case involving my two favorite topics, phylogenetics and plant sex, I am not optimistic.

Butterfly Sex and Wild Science: The Curious Tale of Caterpillars and Velvet Worms

Lots of people have peculiar ideas. For example, belief in the Loch Ness monster, alien abduction, and the chupacabra, are widespread. However, most rational scientists don’t expect that their as yet unsupported wild notion will find its way into the pages of a highly prestigious international scientific journal. In fact, many of us are conscious or unconscious adherents to the concept (popularized by Carl Sagan, but perhaps traceable to something called ‘Hume’s maxim’) that “Extraordinary claims require extraordinary evidence.” Or if not extraordinary evidence, at least some evidence. . . . right?

Not so in the pages of the latest issue of the Proceedings of the National Academy of Sciences (PNAS) in which Donald Williamson has recently published his notion that the larval stage of lepidopterans (known to most of us as the caterpillar), arose as a consequence of hybridization between insects and the Burgess Shale living fossil onychophorans (aka. velvet worms, see previous blog post). Although this hypothesis would be very interesting if found to be true, the author provides us with absolutely no evidence to support his claim (aside from observing the superficial similarity between adult velvet worms and larval moths and butterflies, which he illustrates in some very poorly reproduced line drawings that really need to be seen to be believed).

Discussed extensively by Jerry Coyne in his blog post entitled “Worst paper of the year?”, this article has already received more press attention (most of it, unfortunately, negative) than many of us will receive in our lifetimes. Of particular note was a lengthy article on the paper published in “Scientific American” which unflatteringly likens PNAS to the “National Enquirer,” although the analogy might be better suited to the “Weekly World News,” a more frequent purveyor of stories on strange hybrids (such as this gem on a purported goldfish–piranha cross). Much of both Coyne’s blog entry and Scientific American article focus on the very undemocratic review process in place at PNAS that is unique among high-tiered scientific journals in the U. S. At PNAS, candidate articles can be submitted to the journal directly and subject to normal scientific peer review (a process known as “direct submission”), or they can be “communicated” by a National Academy member. In the case of communicated submissions, the communicating member selects referees to review the submitted manuscript. For Williamson’s paper the communicating NAS member was Lynn Margulis, most famous for her revolutionary but now widely accepted theory for the endosymbiotic origin of mitochondria in eukaryotes. (As a point of irony with regard to the Sagan quote, above, Margulis is also a former wife of Carl Sagan.) Margulis admits in the “Scientific American” article that it took six or seven reviews to find the “‘2 or 3’ necessary to make a case for its publication” and is described as having a “fondness for weird theories.”

Scorn has been ladled on a review process that is designed this way (notably, here), but does it also have some merit if it allows the seasoned and respected scientists that mostly compose the National Academy a means of facilitating the publication of potentially revolutionary ideas that might otherwise never land in such a prestigious journal? The Williamson article seems to provide evidence that this merit comes at a cost, but then there’s no such thing as a free lunch is there?

A Velvet Worm!

What better way to celebrate the 100 year anniversary of the Burgess Shale's discovery than by finding one the coolest surviving relatives of the Cambrian explosion? I found the onychophoran pictured to the right while searching under rocks for dwarf geckos in the Sierra de Bahoruco in the Dominican Republic. The Burgess Shale's onychophoran representative (a.k.a. Hallucigenia) may not be as bizarre as Conway Morris or Gould once thought, but this group has no shortage of weird and wonderful habits. One of these can be seen in the form of the sticky strands projecting from this animal's mouth, which are used to subdue prey and repel predators (or the prodding finger of a photographer's assitant). Onycophorans are also known from Dominican amber (1, 2).

Eight Years, Eight Stings, and One Tiny Gecko

You're going to have a hard time finding someone who loves geckos more than Daniel Scantlebury. Dan's been keeping and breeding geckos since he was a teenager and now, at age 24, he continues to maintain a colony of hundreds of species sampled from across the gecko phylogeny. Eight years ago, one of Dan's aunts forwarded him a news article announcing the discovery of one of the world's smallest amniotes - a tiny gecko named Sphaerodactylus ariasae endemic to the southern tip of Hispaniola's Barahona Peninsula and the nearby satellite island of Beata (Hedges and Thomas 2001). Fast forward to today: Dan is PhD student in my lab working on the (much overlooked) adaptive radiation of West Indian Sphaerodactylus with a chance to finally realize his eight year old dream of finding what may be the world's smallest amniote.

For the past week, we've been in the town of Pedernales along the Dominican/Haitian border helping Dan gather ecological data and specimens for his thesis. Over that time we've found all of this region's endemic gecko species, with the exception of S. ariasae. We've been trying to get it for three days now. The first day, our efforts were thwarted by a roadblock along the road to Las Cuevas (a small community near the Bahia de las Aguilas that is the jumping off point for any trip into the range of S. ariasae). The roadblock was organized by locals protesting a Colombian cement companies lease on a waterfront property that they would like to see developed for ecotourism (photo 1 [sorry pics are so small, I need to figure out how to do this as slideshow...]).

The second day, we tried to avoid a costly and time-consuming marine expedition to known S. ariasae localities by making one of the forays that I've come to know as a "Google Earth Goose-chase" or "Google Earth Gambit" starting at the Bahia de las Aguilas. These jaunts involve heading toward promising localities that Dan has identified with the aid of the high resolution satellite images available in Google Earth. In Jaragua National Park and surrounding regions on the Barahona Peninsula, these gambits tend to involve a bit of hardship. Everything on the southern tip of the Barahona Peninsula is hard, sharp, and hot (see photo 2). The terrain is primarily jagged limestone outcroppings, the plants are comprised almost exclusively of spiny acacias and cacti, and the shade is difficult to come by (it's no surprise that this remains one of the most pristine natural areas in all of the Caribbean!). This region is also home to more than its fair share of wasps and bees. Our group has endured more than 20 stings so far, no one more than Dan, who sits atop the leader board with 8 stings (his hand remains swollen today after a three sting outing to a beach locality near Pedernales three days ago). Unfortunately, our attempt to bushwack to new Google Earth-identified localities resulted in hours of hiking, lots of scratches, considerable degradation of my leather boots, and only two geckos (both S. plummeri [see photo 3], a species we'd already sampled for more easily accessible localities). We also saw S. thompsoni, a rock-dwelling species endemic to this region (see photo 4)

Yesterday, with only one day left in Pedernales, Dan decided to stop messing around by heading straight for the type locality of S. ariasae. Because the only way to reach this locality is by boat, we arranged to depart at 6AM to avoid choppy seas along the 2+ hour trip from Las Cuevas to Cabo Beata and Isla Beata. Unfortunately, we didn't get far before our motor failed just off the coast (photo 5). After an hour at sea spent attempting to repair a bum carborator, we limped back to the docks. Given it was our last day in the region, our hopes of finding S. ariasae were in jeopardy. With a bit of quick thinking and luck though, we were able to find a local fisherman who agreed to take us to Isla Beata. We downgraded our motor from a 75 to a 40, but were assured that we could still get to the S. ariasae localities in less than 3 hours.

Once we'd transfered to the new boat, we took a route that hugged the coast in an effort to avoid the worst of the whitecaps. Nevertheless, we still endured a bone-jarring ride that I'm sure we'll be feeling for days. We stopped briefly at a mainland locality for S. ariasae (Cabo Beata, a.k.a. Piticabo), but had a hard time finding habitat that seemed appropriate. We quickly decided our time would be best spent on Isla Beata itself and made our way across the shallow channel to the Dominican navy outpost on the island's north side (photo 6). Knowing our time was short (we didn't get to the island until 2PM and knew that we would need to begin our return to the mainland by 4:30PM to avoid boating in the dark), we headed immediately to the type locality. Once there, Dan and Miguel (a Dominican naturalist and photographer who is the fourth member of our group) quickly descended into the limestone sinkhole described by Hedges and Thomas (photo 7), while Julienne and I began sifting through the leaflitter along the rim. After just a few minutes I heard Dan shout "I got one!" At virtually the same moment, I saw another directly in front of me, but, in the words of Albert Schwartz, I "failed to secure the specimen." The last photo is an adult male S. ariasae on my thumbnail.

In another two hours of searching I heard four more shouts of joy from Dan and Julienne as they observed one S. ariasae after another (inevitably, of course, these proclaimations were scattered around at least one shout of pain and suffering as Miguel was stung mid-back by the cliff nesting bee). Another cost of our quest for S. ariasae would be evident later when we broke out in nasty rashes on our arms and ankles from having spent time on our hands and knees searching in the litter beneath poisonwood trees).

At then end of the day, we made a triumphant return to Pedernales. Although I can't claim that finding S. ariasae was the culmination of an eight year dream, it was a joy to share even a small part of the satisfaction the day had brought to the lab's gecko enthusiast.

Role Reversal

Frequently on Dechronization, we are writing about scientific publications, hoping to point out new and interesting papers to the readers and inviting discussion. A new paper entitled, "Blogging Evolution", just published in Evolution: Education and Outreach (a relatively new journal founded by fellow AMNH'er Niles Eldredge and his son Gregory), though is a journal article about evolutionary blogs, including this one. Adam Goldstein, (the philosophy professor at Iona College, not the DJ who just died) gives a very thorough and very detailed summary of what blogs are and how they work (it was at some points like reading a users manual for blogging - and I mean that in a complimentary way). He divides up blogs into professional (by science writers, like Olivia Judson's), amateur (like ours -- not that we're not professional scientists, we just have day jobs), organization and project-based blogs, apostolic (his example is Pharyngula), imaginative (Carl Zimmer's The Loom, is one example), and networks of blogs. So, in the hope that this doesn't become too horribly circular, here's a posting about an article about our blog...

A Day of Highs and Lows in Haiti

Field biology is full of highs and lows. A day spent looking for two anoles endemic to the western portion of Haiti's Massif de la Hotte resulted in highs and lows that were both metaphorical and literal.

We began the day with a visit to the type locality of the first endemic - the cliff dwelling Anolis rupinae. Like numerous Haitian anole species, A. rupinae is known from only a small area, in this case the cliffs along a small river valley adjacent to the remote mountain town of Castillon. After driving all day long on really bad roads to reach this locality, we were braced for the possibility that the only known locality had been wiped out by habitat destruction. Fortunately, this turned out not to be the case: although we did find the habitat in this region was severly degraded, some forest in the river valley was intact (mostly due to the fact that it exists on sheer cliff faces). After a short hike from of Castillon, we succeeded in finding a few A. rupinae skittering along an impressive rock face (one of the high points of our trip). The males - with their blue and red dewlaps - were particularly impressive to behold (top photo). We took ecological data on the animals we found, and even filmed a pair mating!

After checking A. rupinae off our list, our next goal was to find what we knew would be our most challenging Haitian endemic - Anolis darlingtoni. This highly unusual twig anole is legendary among anole biologists. Discovered as a single individual by the famed coleopterist and biogeographer P. J. Darlington in 1934, it went unseen for 50 years until Richard Thomas and Blair Hedges found a handful of additional specimens in 1984. By the time we arrived, another 25 years interval had passed without a reported sighting of A. darlingtoni. Thomas and Hedges noted that the locality they visited in 1984 was in the latter stages of deforestation,and we were certain it would be in no better condition when we arrived. Nevertheless, our local guide - Willie - ensured us that he knew the location of an intact forest patch that would be appropriate for a twig dwelling anole. Better still, the patch was only a few kilometers from the small shack we were staying in.

We arranged to walk to the forest patch the afternoon after finding A. rupinae. The plan was to hike to the locality with daylight, find the appropriate habitat before sunset, and to lay out a transect ahead of time for our night searching. The real search for A. darlingtoni would begin once the sun had set, as twig anoles are virtually impossible to find during the day (they're much easier to nab while sleeping on twigs at night). We set off with Willie at around 3PM, after being repeatedly ensured that this would give us plenty of time to reach the forest patch with a couple hours of daylight to get the lay of the land. We were dubious from the start, and we hiked HARD. After hiking up and down a slippery mountain trail for over an hour without seeing a single patch of accessible forest, we unexpectedly arrived at the home of Willie's family! With images of THE FOREST transfixed in our minds’ eyes, we were reluctant to stop, but we allowed a dose of genuinely warm hospitality to temporarily melt our callous resolve (second photo from top). At this family homestead, we were treated to some locally grown and roasted coffee, spiced with local herbs (delicious!), and we swapped snake stories (a timeless exchange).

After coffee and a quick greeting, we rapidly resumed our hike, tearing up and down slope and ravine, gaining and losing altitude in chunks greater than 150m numerous times along the way. After another hour we could see forest on the horizon, but it remained miles away (third photo from top). Willie reassured us that we'd make it but our doubts were growing as the sun set.We eventually reached the forest patch, but well after dark and after hours of brutal hiking. We can’t say a lot about where this forest lies, how extensive it is (we did come to several edges, but it’s hard to be conclusive from our night search), or what the surrounding area is like, as we never saw it in daylight. But we can say that the forest was magical after spending the entire day trekking through completely deforested land. Almost everything was growing directly on cavernous, toothy limestone, which is forbidding to work on, and probably largely responsible for the persistence of the remainging patch. The trees were larger than almost anything we had seen in Haiti, and they were luxuriously covered in moss and epiphytes. The patch was incredibly rich in land snails and Eleutherodactylus frogs, which formed a diverse and nearly deafening chorus. And yes, there were anoles! We found common species along the edges, and the beautiful Anolis monticola nearby. One real treat was a brilliant green Anolis ricordi – Haiti’s representative Crown-Giant anole - that we found sleeping on a large branch. Sadly, despite spending as much time as our lights would allow searching the patch, we did not find Anolis darlingtoni.

It was incredibly difficult to turn our backs on the forest without finding this enigma to face the daunting trail back to the vehicle, this time in the middle of the night. Just as we began our hike home, however, we recieved a bittersweet surprise. Luke noticed on the GPS that seemed very close to our truck and that we were taking a different route back. Willie then casually explained that our truck was just over the ridge, only a few kilometers away. What?!? We knew from the GPS that the truck was not, as the crow flies, far away, but we had been told on the way out that a direct path was impossible because of the mountainous terrain. As you can see on the map of our entire journey, this was not the case (bottom photo). We had hiked up and down the mountains for more than 7km to reach a locality that was only 2km from our truck! Yes, it certainly would have required a rather steep ascent, but one that was certainly doable.After plotting the location of Willie's home, the reason for the extended voyage became clear: Willie had brought us to his house for a bit of extracurricular show and tell! Although we were happy to skip the brunt of the return journey, we would have gladly searched longer if we had known the truck was in close range. Due to other circumstances, this ended up being our last shot at the forest patch on this expedition.

We were delighted to have found a seemingly decent patch of forest so close to Castillon, but somewhat less than happy that Willie's antics provided us with only a few nighttime hours to search this habitat. An exhaustive search for Anolis darlingtoni will have to wait for the next expedition (which, of course, is already being planned)!

[post coauthored by D. Luke Mahler]

Women in Science

As the sole woman member of this blog team, I think the duty of posting about this new publication falls upon me. The L'Oreal Foundation, along with Science, has just published a booklet called "Young Women in Science", which very attractively features a photo of a woman happily displaying an Anolis carolinensis on her face. Featured are 17 women in various scientific careers including herpetologist Devi Stuart-Fox, whose dissertation work was on dwarf chameleons.

Make Killer Figures with R

The blog Learning R is featuring a series of posts about making awesome figures with the R libraries lattice and ggplot2. The examples don't directly involve phylogenetic trees or comparative methods, but the lessons are easily applied to data in our field. Check it out!

[Thanks to Jeet Sukumaran and Rafe Brown at KU for bringing this blog to our attention!]

Amazing Anoles of the Tiburon Peninsula

I just arrived in the Dominican Republic after 2+ weeks of highly successful anole hunting in Haiti. Luke Mahler and I managed to snag all the Haitian endemics, with the notable exception of Anolis darlingtoni, an enigmatic twig anole that has only been collected twice previously. I hope to dwell on this failure a bit more in a subsequent post, but I'll focus on the positives here.

The photos to the right feature some highlights from our time on the Tiburon Peninsula. I'll work through them from top to bottom. (1) One major highlight for me was seeing A. distichus vinosus, a subspecies of a widespread and highly polymorphic trunk anole species that has a particularly spectacular red and white dewlap. My student Julienne Ng is actively studying speciation in A. distichus and the samples we collected on the Tiburon will be important contributions to her work. (2) The über long-snouted A. dolichocephalus was another of the Tiburon beauties. The males are virtually dewlap-less, but have some striking head coloration that may act to compensate for this deficiency. (3) Anolis coelestinus is a bright green trunk-crown anole found across southern Hispaniola. In this photo you can see a male displaying on an agave with a female out of focus in the background. Males from the western Tiburon have gray dewlaps that differ rather dramatically from the yellow dewlaps that predominant to the east. (4) The fourth photo is of A. monticola, a really attractive species with scapular spots that was recently featured on the cover of Losos's new book on anoles (photo by Luke Mahler). (5) The final photo is of a female A. koopmani, a grass anole that we found hanging out in an abandoned fort (photo by Luke Mahler). It was pretty cool to be searching for herps among abandoned 18th century canons!

Tomorrow I join my students on a search for dwarf geckos (Sphaerodactylus) near the remote Dominican fishing village of Pedernales - wish us luck!

Boas and bats in western Puerto Rico

Puerto Rico has a number of threatened, endangered, or extinct reptiles and amphibians. Among the most famous is the Golden Coquí (Eleutherodactylus jasperi; an ovoviviparous eleutherodactyline frog last seen in 1981) and the critically endangered Puerto Rican Crested Toad (Bufo lemur; a victim of fierce competition and predation from the ubiquitous invasive cane toad, Bufo marinus).

Also on the IUCN red list is the near threatened Puerto Rican Boa (Epicrates inornatus). Prior to my latest trip to Puerto Rico (with Luke Mahler in May), the only state in which I’d ever seen a Puerto Rican Boa was dead at the side of the road (as during this 2006 field trip with Butch Brodie).

However, in the karst region of northwest Puerto Rico it is still possible to see boas, sometimes several at a time, waiting patiently around cave mouths for the nightly emergence of tens of thousands of bats (and, hopefully, a warm meal).

These two great photos were taken by Luke at Mata de Plátano Reserve near Arecibo. The picture above is of two boas lying in wait, and the picture below captures the bat emergence in full glory (at least one snake is also visible in this latter photo, although it is more difficult to spot). Click on the image, above, to enlarge.

Microsoft Patents Phylogenetic Comparative Methods. . . Say What?

I read my first (and hopefully last) patent application today, entitled “Clustering Phylogenetic Variation Patterns.” Although the title of the application sounds more like a late 1950s era manuscript on numerical taxonomy than it does a modern (Jan. 29, 2009) patent filing; it is nonetheless invoking considerable concern in the systematics community, as well it should.

According to this interesting article on the filing by Elizabeth Pennisi (published in last week’s Science), David Hillis’ first response to the news that Microsoft had filed a patent pertaining to evolutionary inference from phylogenetic trees was that it must be a joke akin to “The Onion article about Microsoft attempting to patent 1’s and 0’s.”

The patent filing, by Stuart Ozer, claims invention of a variety of techniques already in wide use by systematists and evolutionary biologists – and (so far as I could tell) none of these inventions are original in quality. The whole patent filing can be read (at one’s own risk) in its entirety here, however I have also chosen a few select passages for reproduction, below.

Among the claims of invention in this patent filing, the author purports to originate:

“a method of generating biomolecular clustering patterns”

“mapping at least a portion of the plurality of sequences to an evolutionary tree, the evolutionary tree including a plurality of nodes corresponding to the sequences in a hierarchical arrangement”

“counting evolutionary events in each of the identified plurality of positions at each identified node in the evolutionary tree”

“pruning the evolutionary tree”

“identifying the identified node as a leaf node based on the species count of the corresponding child nodes” for example if “the species count for each of the corresponding child nodes is less than a predetermined number”

“mapping evolutionary events”

“counting evolutionary events further includes: generating an event rate . . . wherein identifying related positions includes identifying related positions based on the event rate”

Without knowing the details of these “new” methods, the claims of invention are hard to evaluate. However, the language of the patent is so broad that it seems possible that if this ridiculous patent is ever approved, we might find that in doing what systematists have done for years, we will be infringing on a patent held by Microsoft Corporation!

Perhaps most nefarious about the filing is the following claim (pointed out by Roberto Keller commenting on the Myrmecos blog):

“Efficient and accurate identification of related groups of monomers of biomolecular sequences is important in achieving biotechnological advances in research and development. However, there is currently no efficient method for determining groupings of monomers in a biomolecular sequence, or among related interacting sequences.”

The author of the patent filing is apparently unaware of the last 50 or so years of research in this area (and should perhaps familiarize himself with a wonderfully interesting chapter on the subject in Felsenstein’s book).

For more on this story, see the following links:

Elizabeth Pennisi's article (link also above)
Systematic Biology
John Hawks weblog
Myrmecos blog
Kevin Zelnio's blog

Haiti: Not a Tourist Destination

Here is a snapshot of the parking lot of our hotel in Motrois, Haiti. Our truck is the silver Mitsubishi sandwiched between the UN security and red cross vehicles. Suffice to say that we haven't come across many tourists during our field work in Haiti. We just arrived back in Port-au-Prince after our trip north. Along the way, we resampled a transect that was part of one of the first molecular genetic studies of cryptic species (see Webster and Burns 1973 Evolution paper on variation in A. brevirostris).

The Haitian Cascade Anole - It Lives!

One of the most remarkable lizards in the world was discovered three decades ago on and around waterfalls in northern Haiti. With it's remarkably long, spider-like limbs and tendency to scramble over slick rocks and underwater when sighted the Haitian Cascade Anole (Anolis eugenegrahami) is unlike other lizards in the world. It's been reported only once since the 1980s (by a Dominican naturalist who visited Haiti around four years ago). The man who made the most recent observations reported that the species' only known habitat was heavily degraded, with extensive human activity and none of the impressive native trees that were reportedly present when the species was first discovered. A week ago, I came to Haiti on a trip led by my colleague Luke Mahler from the Museum of Comparative Zoology with the goal of reporting on the natural history and conservation status of this species, as well as obtaining fresh tissue samples for phylogenetic and population genetic analyses.

After two days of searching, we located a few streams near the type locality that seemed appropriate (albeit only marginally given the lack of large trees and rapidly flowing water). Then, while wandering up a small trickle that was being actively used by dozens of locals for bathing and the washing of clothes we spotted a striking black lizard on a rock face. Success! It was an adult male cascade anole! We quickly found a few more animals in the same vicinity. While capturing the first specimen, a gaggle of more than 30 local Haitians accumulated. By the time I caught it, there was literally a man playing a guitar immediately behind me, making the scene a bit surreal (see photo). Although we were initially overjoyed, the discovery was bittersweet. We couldn't find any more animals in the region, or even any more habitat that seemed remotely suitable. The exposed rock of the other streams in the region was 43C in the sun, hardly suitable for a black lizard whose only known locality was heavily shaded. Fearing we might cause the extinction of this remarkable animal, we released the only animals we caught.

The next day, we decided we needed to seek out more habitat and followed a tip from a local that we could find a series of waterfalls not far from the city of Plaisance if we walked a 6km trail. What we found after an hour and half of hiking was the most remarkable scene I've ever encountered during my career as a field biologist. As soon as we spotted the waterfalls I rose my binoculars to my eyes and began scanning the rock faces. Within seconds I'd spotted a large adult male cascade anole immediately adjacent to whitewater rushing over rocks. Moving further, we found that the rocks in this area were crawling with cascade anoles. We saw more than a dozen in less than an hour. After obtaining ecological data, video and tissue samples, we made our most remarkable observations when we watched the animals behavior underwater (more on that later!). Lizard lovers rejoice - the Haitian cascade anole lives on! Now the work must begin to preserve the scant habitat that remains.

Image legend: (1) an adult male cascade anole displaying! (photo by Mahler), (2) close-up of cascade anole, (3) cascad anole paradise, (4) attempting to noose a specimen from the waterfall locality (photo by Mahler), (5) first locality at which we found the cascade anole (note the people bathing and washing clothes and the pig in the foreground), (6) the scene behind me after catching the first animal.