dechronization

2011-06-06T11:51:00.005-04:00

Applications for our r-workshop are still being accepted - please apply by June 15!

We are pleased to announce an intensive short course on using R to perform comparative methods to be held in Santa Barbara on July 31-Aug 5, 2011. This course is funded by the National Science Foundation, and a number of stipends to cover or defray travel, room, and board are available to qualified students and post-docs. Topics covered will include an introduction to the R programming language, tree manipulation, independent contrasts and phylogenetic generalized least squares, ancestral state reconstruction, models of character evolution, diversification analyses, and community phylogenetic analysis. Course instructors will include Luke Harmon, Mike Alfaro, Todd Oakley, and Dan Rabosky.

If you are interested please submit your CV along with a short (maximum 1 page) description of your research interests, background, and reasons for taking the course. Admission is competitive, and the best applications come from students with data sets to analyze. International applicants are welcome. Applications should be submitted online at http://bit.ly/liqVQ7 by 15 June 2011.

Thanks-

Luke Harmon and Mike Alfaro

lukeh@uidaho.edu

Nabokov in the pulpit: the story of dead man's gulch

2011-01-30T14:25:00.009-05:00

There is a great NY Times article about Vladimir Nabokov by Carl Zimmer. This article, which links literature, taxonomy, and biogeography, is definitely worth a read. Nabokov is best known as the author of Lolita, a story made even more famous by Stanley Kubrik’s film. As Zimmer points out, Nabakov was also the curator of lepidoptera at the Museum of Comparative Zoology at Harvard, a position now held by Dr. Naomi Pierce. Pierce just published a paper vindicating an old hypothesis of Nabokov (Vila et al. Proc Roy Soc B online early). There have also been a lot of interesting blog comments related to Zimmer’s original article (for example here at Bioephemera and here at Denim and Tweed).

This story of Nabokov reminded me of a striking experience I had last year on a trip to visit my family in the midwest. On the plane ride home, I read a copy of Sean Carrol’s book Endless Forms Most Beautiful. The book has a section about Nabokov, highlighting his work on butterfly evolution.

I was thinking about this book while I sat in the hard wood pews of our Lutheran church that Sunday. The pastor had just begun his sermon, a discussion of selfishness. The sermon caught my attention when the pastor mentioned Nabokov. He told a version of the following story (cribbed from the internet - see below).

You’ve heard of Dead Man’s Gulch? It was named because of the perseveration of a novelist named Vladimer Nabokov, who visited the poet and publisher James Laughlin at his home in Utah. Nabokov was an ardent lover of butterflies, always wandering landscapes wherever he visited to add to his collection. Laughlin told the story that Nabokov, while visiting his house, went looking for butterflies. When he returned at dusk, he told Laughlin that during a hot pursuit of a butterfly over Bear Gulch, he heard someone groaning down by the stream. “Did you stop and check it out?” asked Laughlin. “No,” Nabokov replied, “I had to get that butterfly.” Sure enough, the next day a prospector’s body was discovered there and it was renamed, in Nabokov’s honor, Dead Man’s Gulch.

-- from Preposterous! The Sinning Christian, by Siegfried S. Johnson

http://bit.ly/gE3Ef5

It turns out that pastors and priests draw some of their sermon ideas from the web - I found sermons very close to the one I heard that Sunday on Johnson’s page, but also here, here and here. When attribution is given, the anecdote is credited to Clifton Fadiman’s “The Little Brown Book of Anecdotes,” published in 1985. I can find no reference to this story anywhere outside of Fadiman’s book and thousands of online sermon links.

I think that Nabokov is a useful symbol in today’s church for two reasons. First, he wrote Lolita. I can only suppose that many churchgoers disapprove of this book, even if they haven’t read it. Second, the story ties this morally questionable author to evolutionary biology, effectively making it a parable of the “dangers” of modern science.

I really doubt that this story is true. But tying evolution to questionable morals is an old goal of those who seek to undermine the foundations of science. I thought that this was a particularly good - and timely - example.

Ed: Spelling corrected, thanks!

Twitter: @lukejharmon

Great blog to visit - including interview with Rosie Redfield

2011-01-25T10:05:00.004-05:00

The blog "The Molecular Ecologist" has a number of great posts - everyone should go check it out. This blog is great because the posts have been more in-depth than typical blog posts. For example, Dilara Ally has posted a nice series of essays about the promises and perils of next generation sequencing (example), Brant Faircloth posted a how-to for finding homologous genetic regions, and Tim Vines has been posting about the journal industry and other things.

Recently Dr. Ally has posted part I of a two-part interview of Rosie Redfield, a scientist at UBC known for her innovative work on bacteria. The interview touches on the recent controversy about "arsenic-based life," where Dr. Redfield's blog played a key role in an international debate - and sparked a remarkable and disturbing response from NASA.

Anyway a blog worth reading.

--Luke

UPDATE: Part II posted here.

Felsenstein's phyloseminar

2011-01-24T13:10:00.005-05:00

Joe Felsenstein just gave a really nice talk at phyloseminar. If you missed it live, the talk was recorded and will be archived.

I liked the talk because it gave us some hints about the future of comparative methods. Often it takes the field of comparative biology 20 years to catch up with Joe, but perhaps this time we can shorten the interval a little bit.

The talk included discussion of inferring the evolution of geometric shape on trees, placing fossils on phylogenies using likelihood, and applying threshold models to comparative data. Everything was placed in an historical context, which was nice. I particularly appreciated funny snippets about an argument between Felsenstein and Bookstein, Felsenstein's take on the famous Wright "guinea-pig-as-blackboard-eraser" story, and a really interesting idea about QTLs. The above image is from the movie G-Force - it's terrible, please promise not to watch it.

Felsenstein concluded with two crucial points. First, we're witnessing what he called a "grand reunion" of quantitative genetics and statistical comparative methods - fields that have remained too separate for too long. I will make a similar point in my talk. Second, you need more tips! New comparative methods are data-hungry and even 100 taxon trees can be barely big enough for some methods.

My phyloseminar is up next on Feb. 24 - please tune in! Also I've started a twitter account @lukejharmon.

Phyloseminar - new series on comparative methods

2011-01-21T13:34:00.002-05:00

I wanted to put in a plug for Phyloseminar, which is an online seminar series. You can hear spectacular talks from the comfort of your office / home / wherever!

Phyloseminar is starting a series on "Macroevolution and phylogenetics," featuring talks from Joe Felsenstein, Brian O'Meara, and me. The first talk is coming right up on Monday Jan 24 (see homepage for the time). Joe Felsenstein will be presenting "What poultry breeders and guinea pigs have to tell us about statistical nonmolecular phylogenetics" (a spectacular title, right?). Don't miss it.

You can also listen to archived phyloseminars on alignment, gene tree - species tree concordance, and infectious disease.

New blogs

2010-12-25T14:08:00.005-05:00

The readers of this blog (or at least those that remain) may have been wondering what the authors have been up to as the most recent post accumulates dust on Dechronization's front page (now over a month old, see below). Well, there are two new blogs that myself and Dechronization creator Rich Glor have been contributing to which may have drawn our attention away somewhat from treethinkers.blogspot!
First, Rich has been writing regularly for "Anole Annals" (http://anoleannals.wordpress.com/), which is a great new web-log created by Jonathan Losos and devoted entirely to the wonderful adaptive radiation of Anolis lizards, made famous in evolutionary circles by Ernest Williams and Losos himself. If you find it hard to believe that Anolis can single-handedly sustain a regular web-log, then let Losos, Glor, and regular "Anole Annals" contributors Luke Mahler, Manuel Leal, and Yoel Stuart try to prove you wrong.
Second, I recently started blogging about my R phylogenetic development activities in a separate blog on phylogenetic comparative biology (creatively entitled: "Phylogenetic tools for comparative biology", and located at http://phytools.blogspot.com). Since I started programming in R only relatively recently, this might interest both novice users and experienced R junkies alike. It is also designed to complement my newly created beta test version distribution page, which features the R source code for a growing list of R phylogenetics functions and methods that I have been working on.
Please check out these new blogs, but remember to come back to Dechronization because we promise that blogging here will resume here very soon!

Morris Goodman (1925-2010)

2010-11-16T11:08:00.006-05:00

Morris Goodman, distinguished evolutionary biologist and professor at Wayne State University, passed away last night. Goodman was a pioneer in molecular systematics, known for his early research on primate phylogenetics and the use of phylogenies and ancestral character reconstruction to infer Darwinian evolution of haemoglobin (e.g., 1). Goodman also had important interactions with the founders of the modern synthesis (Mayr, G. G. Simpson, and Dobzhansky) regarding integration of evolution with molecular biology; he even sparred with G. G. Simpson in the 1960s over a revised classification of primates based on molecular data, prompting Simpson to refer to him later as “an old friendly antagonist” (2).

To most practicing systematists, Goodman was best known as the long-time editor and chief of the journal he founded nearly 20 years ago: Molecular Phylogenetics and Evolution. In a prescient editorial published in the first issue of MPE in 1992, Goodman discussed the rapidly expanding body of molecular phylogenetic data and the need to provide an outlet to "help disseminate the results of these molecular studies." Even though DNA sequence data existed for only a few loci sampled from a small number of taxa in 1992, Goodman recognized that "the genie is out of the bottle." Goodman ended his founding editorial noting "We are at the threshold of a new age of exploration that promises to greatly increase our knowledge of the history and ongoing evolution of the ramifying lines of life. It would be gratifying if Molecular Phylogenetics and Evolution became the journal of this age."

Rest in peace, Morris Goodman, no other journal has published more molecular phylogenetic trees over the past 18 years than MPE.

Tips for Writing a Systematics DDIG Part 6: The Little Things

2010-11-10T16:02:00.002-05:00

One of the best ways to ensure that you don't get a DDIG is to not follow the NSF's guidelines for proposal preparation. There are two sets of guidelines you will need to pay attention to as you prepare your DDIG. The first set of guidelines is DDIG specific and can be accessed via the link under Program Guidelines at the main DDIG page. Carefully read this document (yes, the whole document) and ensure that your proposal adheres to all the rules. I'm told that one commonly overlooked component is the required "Context for Improvement" document, a one page statement that discusses how DDIG funding will permit a student to improve their thesis research and how the student's work relates to research being conducted by their advisor(s). The second set of guidelines you need to be mindful of are included in the NSF's more general Grant Proposal Guide. If you don't follow the formatting guidelines in section B of this guide, your proposal won't even make it to review.

Tips for Writing a Systematics DDIG Part 5: Broader Impacts

2010-11-09T13:33:00.001-05:00

This is the last in my brief series of posts on preparing a DDIG.

Although often viewed with some mixture of confusion and frustration, a well thought-out broader impacts section is critical to any proposal being submitted to NSF. Are you a cynic who views broader impacts as little more than an obstacle standing between you and your research? If yes, get over yourself. The way you and your science interact with the rest of the scientific community and society at large deserves your attention. That said, expectations for the broader impacts of a DDIG are commensurate with the relatively low amount of funds they involve (relative to the much larger amounts your PI is likely to be applying for). Your PI may be starting a high school science program as part of her grant, but you shouldn’t feel compelled to go to such lengths in your DDIG. What then should you include in your broader impacts? Most proposals include some mention of one or more of the following broader impacts, many of which are likely to be coincident with your primary research objectives.

1. Undergraduate research opportunities (i.e., ‘training’ undergraduates by having them slave away on your project). This is a no brainer. Everybody wins when you get undergraduates involved in your research. This will be all the more convincing if you can include some ‘preliminary data’ showing that you already have experience recruiting and mentoring undergraduates.
2. Dissemination of data and results on the interwebs. You’re going to put your data online anyways, so why not take some credit for it?
3. Conservation significance. Conservation is a noble goal, but try to avoid vacuous statements like “The group I’m studying including some species of conservation concern.”
4. Outreach to the broader community. Often in the form of a museum exhibit or public presentations. Be creative here – visit a school, give a “keynote” at a science fair, etc., but make sure reviewers aren’t left feeling like you’re not going to follow through.

Tips for Writing a Systematics DDIG Part 4: How Much Methodological Detail?

2010-11-08T10:13:00.003-05:00

You may feel compelled to give excruciating details of your proposed methods. Done correctly, this can be an excellent way to convince reviewers that you know what you’re talking about. However, space is tight and you can’t be expected to give a completely comprehensive overview of your proposed methods. The most important thing is to convince your reviewers that you understand what you’re talking about and have carefully selected the most appropriate, most sophisticated, and feasible methods possible given the question at hand. If you’re using standard methods (e.g., parsimony analyses in PAUP, Bayesian analyses in MrBayes) its safe to assume your reviewers have at least heard of these methods and the software used to implement them (they’re all going to be practicing systematists, after all). Even with such widely know methods, however, its still a good idea to mention a few specific details to show that you're familiar with the intricacies of your analyses (i.e., which type of search you'll be using in PAUP or how you'll assess convergence of your Bayesian analyses). If your proposal involves relatively new methods, or specialized methods that might not be familiar to other systematists, you should plan on including more detail. Be sure to justify why these methods are the most appropriate for your study, and how they will be used to specifically address the hypotheses/questions framed previously in your proposal.

Tips for Writing a Systematics DDIG Part 3: What About Preliminary Data?

2010-11-04T17:02:00.000-04:00

You’re not going to get a DDIG without some preliminary data. There are several layers of preliminary data to consider. The first layer - showing enough to convince the reviewers that you’re capable of gathering the data that you’ve proposed to gather - is essential. Don’t try telling reviewers you’re going to sequence 10 nuclear genes if you have no published molecular phylogenetic studies and have yet to sequence a single bp for your project. A second layer involves enough data and analyses for the reviewers to determine whether the work you’ve proposed is likely to be sufficient to answer the question at hand. This is the classic chicken and egg problem with grants - you can’t get a grant if you can’t get the data and you can’t get the data if you don’t have a grant. Remember that this is a dissertation improvement grant, not a dissertation grant: you should do what you can to convince your reviewers that you’re already well on your way toward successful completion of your thesis.

Tips for Writing a Systematics DDIG Part 2: How are these things reviewed?

2010-11-04T16:59:00.001-04:00

DDIGs are reviewed using a panel-based system similar to that used to evaluate larger proposals submitted to NSF. The DDIG panel in systematics consists of 20 or so practicing systematists drawn from a wide range of institutions (museums, research universities, liberal arts colleges) and subdisciplines (paleontology, taxonomy, biogeography). The group is supervised by the Systematics and Biodiversity Inventories cluster program officers. Several weeks prior to meeting at NSF headquarters, each proposal will be assigned to three reviewers, one of whom will be designated the primary reviewer. Each of these three reviewers is expected to read your proposal in detail and to provide written comments and a proposal evaluation (excellent to poor) prior to the time the panel convenes. Once the panel has assembled, proposals are dealt with one at a time. When a proposals name is called, the primary reviewer gives a brief overview and assessment before opening things up for discussion. Discussion is generally limited to the three previously assigned reviewers. Others on the panel are free to comment as well, but they’re generally too busy worrying about their own proposals to do so. The panel then arrives at a consensus on each proposal, which generally involves placing into one of three categories: (1) definitely fund, (2) potentially fundable, and (3) unfundable. Once review of all the proposals is completed, there may be a number of proposals in the potentially fundable column that get a second look, perhaps moving to one of the other two columns if it seems warranted with hind sight. The panel does not make final funding decisions, only recommendations.

The point of sharing this information is this: to get a DDIG you need to write a proposal that will impress a potentially diverse group of three practicing systematists.

Tips for Writing a Systematics DDIG Part 1: Organizing Your Proposal

2010-11-02T15:55:00.004-04:00

This time of year just about every PhD candidate in systematics who doesn’t already have one is working on a proposal for one of the NSF’s lucrative Doctoral Dissertation Improvement Grants. The DDIGs are one of the smartest ideas the good folks at NSF have ever had, and represent a critical source of funding for ambitious and independent young systematists. The sad fact is that there aren’t many other grants available to graduate students that offer the type of $10,000+ windfall that can be essential to making a good thesis a great thesis. Although the program is incredibly popular, some find the application process a bit mysterious. The NSF’s formal guidelines certainly provide you with all the basics, but they’re also somewhat open ended.

How one can best prepare a competitive proposal? Although there aren’t any foolproof answers to this question, I’d like to share a few suggestions I’ve developed for my own graduate students. These suggestions, which undoubtedly reflect my own personal biases, are being made on the basis of having read previously successful (and unsuccessful) proposals and discussions with NSF reviewers who have been involved in evaluating these proposals. I’m going to kick things off in this first post with some basic advice on organizing your proposal, followed by subsequent posts on how proposals are reviewed, how best to incorporate preliminary data, how much methodological detail to include, and how to effectively discuss broader impacts.

A good proposal begins with good organization. There are lots of ways to organize a successful proposal, so how you choose to organize yours is a personal decision that requires lots of careful thought. That said, one general organizational feature that tends to characterize successful proposals is the use of a strong hypothesis testing framework. Think of this as getting back to basics: remember how your freshman biology lab reports started by outlining the specific hypotheses you tested? Doing the same here is going to help your reviewers understand exactly what you are trying to accomplish with your work, while at the same time helping you organize the remainder of your proposal.

Instead of making vague claims like “I will investigate the biogeographic history of midges”, try to make a more specific statement like “I will test the hypothesis that the distribution of midge diversity is a consequence of a vicariant event associated with the uplift of the Andean plateau.” Distilling your work into a few explicit hypotheses can feel a bit constraining when your real goal is to understand why midges are so darned diverse, but being explicit about specific hypotheses does not preclude you from following up on other interesting results that might be somewhat peripheral. You need to provide some context for your hypotheses before introducing them, but try to get to them as soon as possible; your reviewers shouldn’t be able to get past the first page of your proposal without being provided with a concise statement of the questions you intend to address. Try to restrict yourself to a manageable number of hypotheses (things get a bit out of hand when proposals try to juggle a half dozen or more hypotheses, for example). Organize the remainder of your proposal (e.g., methods, discussion, preliminary data) around the hypotheses presented on the first page of your proposal. Make sure that your work can feasibly address each of your hypotheses.

City Life - and the Evolution of Immunity

2010-10-28T17:27:00.006-04:00

Much has been made about the very strong association between rural living and protection against allergies and asthma (for instance, in this recent study here). However, a new study (available "Early View" from Evolution) claims a strong effect of urbanization on the genetic basis of disease resistance - at least in human pre-history. In particular, the authors find evidence suggesting that the duration of urbanization strongly predicts the frequency of a TB resistance conferring genetic allele among modern human populations of known historical affinity. The allele is non-randomly distributed geographically, but the authors attempt to control for this non-independence by also analyzing their data using a partial Mantel test (a non-parametric multiple matrix regression procedure). In this test, they fit a multiple regression model with independent variables consisting of a matrix containing the differences in urbanization and a matrix containing F_ST values computed among each pair of populations. They found that the urbanization effect was still very significant in this model.

One concern raised and discussed by the authors is that the domestication and utilization of cattle (a proposed disease vector for TB) roughly coincides with the progress of urbanization in the region. They argue that we can reject this model because correlation is weaker than in the urbanization model; however, in my mind this argument falls short of persuasiveness because (as they admit) the history of cattle domestication for many of their populations is poorly known. This type of error would obviously also have the effect of depressing our perceived correlation between cattle domestication and genetic TB resistance.

Nonetheless, this is a very interesting study. If the result holds up to future scrutiny, then this will no doubt have many relevant human health implications and the study should be broadly cited.

Somebody Missed the Dover Trial...

2010-10-26T18:46:00.002-04:00

I'm a week behind the times on this, but perhaps some of you missed out on Delaware Senatorial candidate Christine O'Donnell's most recent debate performance. This particular debate was made famous by the Republican/Tea Party candidate's ignorance of the constitution ("Can you remind me of what the [14th and 16th amendments] are?") and the fact that she was unaware of the first amendment's establishment clause ("Where in the constitution is separation of church and state?" [laughter from law school audience], "Let me just clarify, you're telling me the separation of church and state is found in the first amendment?"). However, there are also some real gems about evolution and intelligent design, including the claim that creationism and intelligent design are distinct (at the 1:15 mark). Do you think Judge John E. Jones III is available for interventions?

Testing for Trait-Dependent Molecular Evolution

2010-10-22T13:36:00.006-04:00

Itay Mayrose & Sally Otto have just published (Molecular Biology and Evolution Advance Access) a neat new method to test the hypothesis of a discrete extrinsic cause for shifts in the rate of molecular evolution on a phylogeny.

According to this method, the authors first obtain an ultrametric phylogenetic tree for the species in their study. They then generate a set of stochastic character histories (Nielsen, 2002; Huelsenbeck et al., 2003) for the discrete character of interest. Example discrete characters might be a "life history trait, morphological feature, or habitat association" - in their empirical test they examine halophilic and freshwater Daphnia species.

Now armed with a distribution of possible character histories on their estimated phylogeny, the authors simultaneously maximize the likelihood of their sequence evolution model and a scaling factor r, a parameter that increases or suppresses the rate of molecular evolution along stochastically mapped branches in the tree. Then they average across character maps.

In an extremely clear analysis of their method, the authors show it capable of producing remarkably good estimates of r for trees with even a modest number of tips (e.g., 20-60) when the true underlying phylogeny is known without error (Figure panel A). Under these idealized circumstances, estimation of r is only slightly biased for small numbers of species - as is common for maximum likelihood methods.

The situation is slightly more complicated when an estimated phylogeny (rather than the true underlying tree and branch lengths) is used. Here, they show that estimation of r can be quite severely downwardly biased, particularly for large values of r (Figure panel B). They think that this is actually due to error in the ultrametricization of their phylogenies - since in their study they used the same data for phylogenetic inference as they do for the estimation of r. This problem is not at all ameliorated for ultrametric phylogenies obtained by Bayesian relaxed clock methods. In the end, this issue argues strongly for the simultaneous estimation of the phylogeny, the character history, and the concomitant variation in nucleotide substitution rates - something that the authors also recommend.

Leigh Van Valen (1935-2010)

2010-10-18T23:01:00.008-04:00

Friends confirm the reports elsewhere on the web [a,b] that Leigh Van Valen died this Saturday in Chicago. He was 75.

Van Valen published on a wide variety of topics, but may be best known as the originator of the Ecological Species Concept and the Red Queen's Hypothesis. While it is difficult to summon authoritative information, the latter appeared in what may be the most successful self-published manuscript in the history of our field [1], presently cited 1402 times according to Google Scholar.

One of my personal favorites, for its vision and clarity, was his paper on clade selection [2]. It was virtually ignored until very recently, but it will likely receive a renewed look in view of recent developments [e.g., 3].

[1] Van Valen, L. 1973. A new evolutionary law. Evolutionary Theory 1:1-30.

[2] Van Valen, L. 1975. Group selection, sex, and fossils. Evolution 29:87-94.

[3] FitzJohn, R. G. 2010. Quantitative traits and diversification. Systematic Biology (in press) doi:10.1093/sysbio/syq053.

[4] Photo Source 'e&e': http://picasaweb.google.com/ecolevo.students/DirectoryPicsFaculty

Estimating Diversification Rates

2010-10-13T11:32:00.004-04:00

A new study by Wertheim & Sanderson (Evolution; Online Accepted Articles) investigates the sensitivity of existing methods for estimating diversification rates to various types of phylogenetic error. The topic is somewhat related to the recent, provocatively titled Evolution paper by Dan Rabosky clearly showing that when the assumption of constant birth is violated, death (extinction) rates can no longer be reliably estimated from molecular phylogenies.

Especially given Rabosky's (2010) main result - that is, the high sensitivity of extinction rate estimates to certain model assumptions - the new study by Wertheim & Sanderson is particularly intriguing. Although these methods typically assume that the tree and branch lengths are known without error, Werheim & Sanderson demonstrate in their study that diversification rate estimates are not particularly sensitive to phylogenetic errors either in branch length or topology. In fact, they note in the abstract that even a "crude estimate" of the tree provides substantially more power (e.g., 1.6 x more for the conditions of their study) than, for instance, a comparable non-phylogenetic method, the widely used Slowinski-Guyer test (Slowinski & Guyer 1993; Am. Nat.).

Considered together, these two studies remind us that the robustness of a given statistical method cannot be illustrated by a broad brush. Rabosky's study shows that the estimation of extinction rates from phylogenies of extant species is quite sensitive to the underlying assumption that speciation rates are constant throughout the tree. Conversely, Werheim & Sanderson show that the estimation of speciation rate is not sensitive to the underlying assumption that the phylogenetic tree and branch lengths are known without error - and, furthermore, that even a "crude" tree will do.

Note that the figure above is from neither study - but from my 2005 paper (with Dechronization bloggers Harmon & Glor) about the sensitivity of diversification rate estimates to model parameterization. (We found it to be high.)

New Issue of Systematic Biology

2010-10-08T01:55:00.002-04:00

The October issue of Systematic Biology is online, and there are a few really interesting articles to check out. First of all, the cover image (image stolen from Syst. Biol. website) comes from a paper by Parfrey et al. that seeks to resolve the Eukaryotic portion of the tree of life. One issue with many phylogenetic analyses at this scale is the shape of the data matrix - many characters, sometimes whole genomes, but very few taxa, typically representing "key lineages" in the tree. Parfrey et al. use sequences from a moderate number of genes (16) across many lineages (>400). They have some success in resolving the tree - in particular, they are able to place a few old enigmatic taxa in the tree - but some branches are still unresolved.

Another paper worth checking out is a short note by Folmer Bokma that represents one of the first applications of Approximate Bayesian Computation in comparative methods. If you haven't heard of ABC yet - you will. There is another remarkable aspect of the Bokma paper - let me just quote the funding section:

The author awards SEK 10,000 to the first who provides an analytical form of φ.

According to google currency converter that's about USD $1500, which would just about pay for that R. A. Fisher tattoo you've been wanting.

On another note, please watch this:

Dar-WIN

Evolution Since Darwin

2010-10-01T13:46:00.002-04:00

I spent last night and this morning reading a number of chapters from the book Evolution Since Darwin: The First 150 Years (2010, ed. by Bell, Futuyma, Eanes, and Levinton; link). The book is the results of a symposium that was held at SUNY-Stony Brook in 2009.

I'm really impressed with this volume. Sometimes edited volumes can be a little dry - who wants to say something really new and important in a book chapter, anyway? But this book is much better than most volumes.

The book starts with an amazingly compact yet comprehensive history of the last 150 years in Evolution (Futuyma). There's a really interesting discussion of what the world would be like if Darwin had died young (Bowler), and a nice discussion of solved and unsolved problems in evolutionary genetics (Zhang). I love the whole section on Diversity and the Tree of Life, with contributions from Losos, Hillis, and Wagner, among others. And that's really just scratching the surface.

The authors have all made a deliberate attempt to tie their chapters to Darwin, following the theme of the book and associated symposium. I don't think this works that well in some of the chapters - it feels more like a distraction at times. But I do see the point of celebrating Darwin! Anyway this doesn't detract from the value of the book, which I highly recommend.

Anolis steals cover of "Evolution"

2010-09-17T09:41:00.005-04:00

At the risk of tooting my own horn, I just wanted to share the fact that this month's issue of "Evolution" features a great photo of Anolis fowleri taken by Luke Mahler, and accompanying an article by Mahler, myself, fellow Dechronization blogger Rich Glor, and Jonathan Losos. Anolis fowleri is among the rarest anoles of Hispaniola, and this beautiful picture was obtained in August, 2008 during an expedition documented in a prior Dechronization post (authored by Rich). In our article we develop and apply new phylogenetic methods to document a progressive deceleration of the pace of evolution for some characters among the Greater Antillean anoles as ecological opportunities have become saturated in this famous adaptive radiation. "ScienceDaily" picked up a press release based on our article which can also be read here.
This month's "Evolution" is a good one (even aside from the great choice of cover art), with a number of blog-worthy articles. Look for more Dechronization posts soon.

Bed Bugs!

2010-08-31T03:07:00.003-04:00

I know we've been quiet here for a while, and some of you may be expecting a juicy return, but I have a peripherally related topic, instead: bed bugs.

Several articles in the popular press [1,2,3] have made a big deal about them, backed by the internet amplification [4], so I presume this is a topic of broad interest. If you travel much, or if you live in a major city in the United States, you've probably had bed bug bites, or known someone who has. Here I simply wish to share my two simple tips for not bringing them home. (If you have them in your house, look elsewhere for help, and good luck!)

I've read somewhere early on, maybe 2005, that heat (around 120F) can relatively easily kill them at all life cycle stages. The main problem is exposing your stuff. I have a related pair solutions that seem to have worked, preventing their spread after I've been savaged by them. (My field assistant in Chile suffered from bed-bug-induced PTSD, no joke.) First, in several instances, I placed all of my belongings in black trash bags, and simply left them out in the sun on hot pavement or roof top. Second, I highly recommend using your car as an oven. The last time I was doing field work, I baked all of my stuff in the rental car, parked in full sunlight, and then, after I landed at O'Hare, I left all the luggage inside my car here, which is easily over 120F on most April-October days. I get a towel and shove what I'm wearing into a dryer. So far so good--no bed bugs at home. I don't mean to revel in this fact; it's clear that it is also a matter of luck. (The last time came back, it turned out I also had scabies. Ew.)

The source of the present infestation is unclear, but it seems like a rather straightforward phylogeographic question, taken on by at least a pair of labs [6]. Also, this bed bug sensor seems fairly accessible to biologists, in case you think you may have them, but aren't sure (requires a bottle, dry ice, and a plastic pit fall trap to hold the bottle). I haven't tried tanglefoot yet, but it could be a band-aid solution on the legs of a clean bed.

Hope you never need any of this advice!

Workshop on HPC for Phylogenetics

2010-07-29T15:30:00.003-04:00

The "PAUP running - Do not touch!!!" sign should look familiar to anyone who's done phylogenetic analyses over the past two decades. Fortunately, the days of these signs - and the inevitable lab drama that results - are quickly becoming a thing of the past. As access to high-performance computing (HPC) expands, most modern phylogenetic analyses are being conducted remotely on shared community- or campus-wide resources. Even as access to these resources expands, however, expertise in utilizing them to their full potential remains limited. For this reason, I'm excited to spread the news about The National Institute for Mathematical and Biological Synthesis's (NIMBioS) new workshop titled “Fast, Free Phylogenies: HPC for Phylogenetics Tutorial.” This workshop, which takes place this October in Knoxville, TN, will bring together some of the most knowledgeable experts on HPC for phylogenetics with the goal of teaching others how best to use resources like TeraGrid, CIPRES, iPlant, university clusters, and other free HPC resources. More details are available at the tutorials webpage. Tuition is covered by NIMBioS, but enrollment is limited.

Antz!

2010-07-06T23:12:00.003-04:00

Warning: large video. May take a few seconds to load.

This has been the scene on my front lawn for the past few evenings. Basically, every day in the late afternoon a large swath of ants - not going anywhere in particular or consuming any resource that I can detect - seems to form in the same general region of my front yard in Durham, North Carolina. When I get up to run in the morning and the yard is shaded, they are still there; but as soon as the hot summer sun hits the front lawn they have disappeared. In the evening, when the lawn is again shaded, sure enough - they reappear. Any comments on this peculiar phenomenon are welcome!

The Evolution of Sex

2010-06-29T17:10:00.004-04:00

The 'Evolution' meeting is quickly coming to a close here in Portland. I'm presently blogging from the second last session of the meeting while Marc Johnson gives a fascinating talk on the functional evolutionary loss of sex, via the loss of recombination and segregation, in the evening primrose genus. Among evening primroses (Oenothera) 16% of species have functionally lost the ability to sexually reproduce - but this loss is associated with reciprocal translocations among chromosomes rather than with polyploidy, as it is in most asexual plants. This allows him to study the evolutionary loss of sex independently of the evolution of increased ploidy number. Evidently, asexual species pay a high cost of asexuality in terms of their susceptibility to generalist herbivore insects - although they also exhibit a decreased vulnerability to specialists herbivores (though the underlying mechanism seems a little unclear). In addition, he has found the intriguing, and somewhat counterintuitive, result (but one that had been predicted by some prior theory due to J. Felsenstein) that speciation rates are higher in functionally asexual lineages than in sexual lineages. Extinction also seems slightly elevated in asexual lineages, although this effect was non-significant.

Calibrating Phylogenies from the Fossil Record

2010-06-28T17:34:00.003-04:00

Still at "Evolution 2010," we just saw a great talk by Charles Marshall, formerly at Harvard but now at UC Berkeley, about calibrating molecular phylogenies using the fossil records. This is a much more complicated problem that it would seem at first glance because: 1) the maximum likelihood estimate of a node age based on a fossil series from the descendant lineage is biased (towards the present); 2) an assumption that fossilization is temporally random allows for a simple correction to the maximum likelihood estimate - but this assumption is (invariably) violated in empirical data; 3) fossils are not only temporally, but also geographically, non-random; and, finally, 4) the rock record is globally incomplete in some geological eras. Charles's talk included some fantastic graphical simulations of sedimentation and "de-sedimentation" (the removal of previously deposited sediments) as ocean sea levels rise and fall over geological timescales. Evidently, though, in spite of these significant complications, there is still hope that the use of fossil calibrations can improve molecular phylogenetic estimates of species divergence dates. As usual Charles was an intensively engaging speaker and gave a great seminar!

"Dude Looks Like a Lady"

2010-06-28T03:02:00.005-04:00

The third day of the 'Evolution' conference is officially completed and it was a good one! Among the highlights for me today was a great talk by Graham Slater (a postdoc with Mike Alfaro) about approximate Bayesian computational methods for estimating diversification and phenotypic evolutionary rates from unresolved phylogenetic trees. I think this general approach will probably have considerable utility in this and other problems for years to come.

I also saw a fantastic talk by Jeanne Robertson about courtship and aggressive behavior in dark and white sand dwelling lizards. White sand dwelling lizards have evidently evolved light colored dorsal coloration, obviously for crypsis. However, perhaps even more interestingly, in staged encounters white sand males nearly as often tried to court dark sand males as they tried to fight them. The confusion was one way, however, and Jeanne provided some excellent video of a dark sand male attacking a confused, and simultaneously courting, white sands individual. This unusual tendency is apparently due to a pleiotropic effect that dark dorsal coloration appears to have on ventral patch size - an effect that makes their ventral patches of dark sand males not much larger than the analogous patch on white sand females. So, as Jeanne so elegantly put it in the title of her talk: in white sand lizards, "Dude looks like a lady!" (For the record, Steven Tyler of Aerosmith is pictured above because that "Dude" really does "look like a lady!")

Portland 2010

2010-06-27T02:24:00.004-04:00

The first two days of the meeting have been a blast, capped so far by a thought provoking ASN presidential address by Jonathan Losos and a picnic this evening at the Oregon Zoo. However, in terms of pure irony the most amusing experience thus far was the discovery by Carlos Botero and I (shortly after our arrival) that the Oregon Convention Center is simultaneously hosting the 'Evolution' joint meeting (as you no doubt already know) along with the 'Oregon Christian Home Education Conference.' Note, particularly for non-American readers, that one of the primary reasons children are homeschooled in the United States is so their parents can avoid teaching them about evolution (e.g., refs here and here). Luckily I had the foresight to snap a picture (above), as their conference ended this evening.

Blogging Evolution 2010 in Portland Oregon

2010-06-25T15:09:00.004-04:00

It's that time again - the annual joint meeting of the Society for the Study of Evolution (SSE), the American Society of Naturalists (ASN), and the Society of Systematic Biologists (SSB), commonly referred to as the "Evolution meeting" will be held from today through June 29th in Portland, OR. Dechronization bloggers Glor, Igic, Harmon, and myself are all attending, so we should be able to put up a few posts during the conference. Not to miss tomorrow: Joe Felsenstein's 9am talk on "A comparative method for discrete and continuous characters using the threshold model and MCMC." I look forward to witnessing the famous "Felsenstein effect" described by Rich at Moscow's meeting last year. Please post other must-see talks in the comments.

arXiv your paper!

2010-05-24T20:12:00.017-04:00

In its 20-year history, arXiv has gone from a small physics pre-print repository to a giant archive widely used in many disciplines, and so trusted that it sometimes almost acts as a de facto journal [*]. Its growing body of literature on statistical phylogenetics is sure to boom anytime now.

The way I see it, placement of pre-prints on arXiv is a terrific idea. It (a) provides a good way to 'air out' a manuscript, and obtain feedback in case something is wrong, (b) you can cite your permanent arXiv article ID from the time of submission, (c) a version of the manuscript, unadulterated by (what may have been in your opinion) the unfair mauling it got in review, while still being able to correct errors. All the while, it does not interfere with peer-reviewed journal publication, and your manuscript is out instantly.

Most publishers' policies allow the archiving of pre-review manuscripts (including Nature, Science, PLoS, PNAS, PRSoc, Evolution, SystBiol, AmNat, etc.). Some allow post-review manuscripts to posted, as well. Individual journal policies can be checked at SHERPA/ROMEO, which also contains policies for personal/lab website posting and compliance data for funding agency requirements. My next paper is going here.

Try searching arXiv directly, go to their Populations and Evolution collection within Quantitative Biology, or click around to see and arbitrarily chosen sample author. The submission process is reasonable, and one can even submit PDFs generated from MSWord docs (as well as TeX files, and a couple of other formats).

* Perhaps most famously, it is the only place that hosts Grigori Perelman's three-part proof of the Poincaré conjecture [1,2,3; references listed for those who, unlike me, may be both interested and able to understand algebraic topology], which sits on arXiv without a formal peer-review process. He was eventually awarded the Fields Medal that he famously refused.

Life in the Fast Lane for Dogs

2010-05-24T14:45:00.008-04:00

In a recently published article from this month's American Naturalist, Vincent Careau and colleagues (2010) propose a new "pace-of-life" hypothesis for the evolution of behavior / life-history relationships among breeds of dogs. This hypothesis relies on various among-breed correlations, including a strong negative relationship between "trainability" (measured as a combination of success in obedience training and ease of house-breaking) and mass-adjusted mortality (obtained, astonishingly, from a dataset of over 222,000 doggy life insurance policies - originally reported on by Bonnett et al. 1997). These data are shown (with a little post-production illustrative embellishment) above.

The authors speculate that the strong relationship between pace-of-life and longevity has resulted from antagonistic pleiotropy between artificially selected traits and life history; rather than from correlated artificial selection. This certainly makes sense in some cases. For example, it seems unlikely that dog breeders directly selected for high mortality in their lines. The ultimate source of several other among-breed correlations found by the authors is less clear, however. For instance, it is somewhat more plausible that humans may have intentionally or unintentionally selected for the observed among-breed negative correlation between body mass and activity level. In this case, the authors advance the possibility that highly active large dogs may have been selected against, because high activity would become increasingly undesirable (and destructive) in large dogs.

Whatever else we might learn from this article, it should dispel any doubt that the classic Billy Joel mantra of "only the good die young" evidently does not apply to our canine friends.

Size-advantage in sex changing fish

2010-04-23T19:48:00.007-04:00

Did you know that many teleost fish species are sequentially hermaphroditic - starting life in one sex before switching to the other later on? When individuals start life as a male, but then become female this is called protandry; whereas females who later change to males are called protogynous.

One hypothesis for the evolution of protogyny is that in many species size provides a significant advantage to the mating success of males, but has little impact on mating outcome in females. As such, any mechanism allowing individuals to start life in female form (when they are typically small), but then "mature" into males once they have achieved large size, should be favored by natural selection. This evolutionary scenario is not nearly as implausible as it sounds because teleost fish (unlike most other vertebrates whose gonadal tissues differentiate early in development) develop their sex organs from a single, protogynous tissue type. This hypothesis for the evolution of protogyny has been dubbed the "size-advantage hypothesis."

A recent study by Erem Kazancιoǧlu and Suzanne Alonzo [2010; Evolution Accepted] uses phylogenetic comparative methods to examine the evolution of size-advantage and sequential hermaphroditism in labrid fishes: also known as the wrasses. What they find is that, indeed, the evolution of dioecy (separate sexes) from sequential hermaphroditism is relatively unlikely when the size-advantage of large males is high. However, their evidence for the evolution of protogyny from dioecious species with male size-advantage was somewhat ambiguous.

Although I enjoyed this paper quite a bit, and it seemed perfect fodder for some clever fun in photoshop (actually by E. Lu, see above), I also felt that that the study had some methodologically weak areas. For instance, the authors failed to take advantage of a new phylogenetic logistic regression procedure by Ives & Garland [2010], which seems ideally suited to their data. (In their defense, the method is brand new.) Consequently, however, the authors found themselves of the unfortunate position of using an arbitrary scoring system to estimate size-related reproductive skew: adding 1 point for the presence of "pronounced sexual dichromatism," for example, and subtracting 1 point for "alternative reproductive tactics" (which might decrease the advantage of large male size) . With a phylogenetic multivariable logistic regression, the authors could have tested for an association between the log-odds of protogyny and each of their proxies for size-based reproductive skew (which also included sexual size dimorphism, resource defense, and mate defense), while simultaneously controlling for the phylogenetic non-independence of the species in their sample.

In spite of its limitations, I found this study to be a tremendously interesting read. Due in no small part to its unusual and "sexy" subject matter, I'm sure it is destined to attract the authors considerable attention - among evolutionary biologists and lay people alike.

Announcement: Comparative Methods and Macroevolution In R Summer Short Course

2010-04-14T13:15:00.003-04:00

Want to learn R? We have a short course this summer. Grad students + postdocs please apply! We have a good number of full stipends to cover all costs for the workshop in beautiful Santa Barbara, CA.

Announcement: Comparative Methods and Macroevolution In R Summer Short Course

We are pleased to announce an intensive short course on using R to perform comparative methods to be held in Santa Barbara on June 17-21. This course is funded by the National Science Foundation, and a number of stipends to cover or defray travel, room, and board are available to qualified students and post-docs. Topics covered will include an introduction to the R programming language, tree manipulation, independent contrasts and phylogenetic generalized least squares, ancestral state reconstruction, models of character evolution, diversification analyses, and community phylogenetic analysis. If you are interested please send your CV along with a short (maximum 1 page) description of your research interests, background, and reasons for taking the course. We especially encourage applications from graduate students with data sets to analyze. Please contact the co-organizers, Michael Alfaro (michaelalfaro@ucla.edu) and Luke Harmon (lukeh@uidaho.edu) with any questions.

Application deadline: May 15th.

Arborescence and the Rate of Evolution in Plants

2010-04-12T14:11:00.005-04:00

A recent article by Korall et al. (2010; Evolution Online Accepted) reveals a convincing deceleration in the rate of evolution for DNA sequence associated with the origin of arborescence (tree-like growth form and life history) in ferns. This is similar to the pattern found in seed plants, where an association between the rate of sequence evolution and growth form is already known (e.g., Smith & Donoghue 2008; Soria-Hernanz et al. 2008).

In both plants and animals, simple population genetics theory predicts that for a neutrally evolving locus the rate of substitution should be equal to the per generation neutral mutation rate, μ. Since germline cells are sequestered from somatic cells in animals, and germline cells undergo a fixed number of replications that is independent of generation time, theory thus predicts that, in animals, the rate of nucleotide substitution per unit time at a neutrally evolving locus will be μ/t, for generations of length t. However, for plants the prediction is less simple. This is because in plants, germline cells are not sequestered, but are instead derived from somatic tissue. As such, germ cells in older plants should in theory have more opportunity for somatic (and thus gametic) mutation.

This means that the concomitant increase in generation time that characterizes arborescent plants is insufficient in theory to explain the decreased nucleotide substitution rates estimated empirically. The authors suggest a number of possible alternative underlying causes for this pattern. For instance, they note that both arborescent seed trees and tree ferns might share a lower rate of somatic cell replications (as suggested by Soria-Hernanz et al. 2008). This represents a fully testable hypothesis which might (in part or in whole) account for the pattern found by the authors. Alternatively, Korall et al. (2010) propose that the duration of sporophyte/gametophyte life history stages in arborescent and herbaceous plants should also be considered. This is a difficult hypothesis to test comparatively, since all arborescent species have a relatively long sporophyte phase. It might be possible to study mutation accumulation in sporophyte and gametophyte life history stages in a rapidly reproducing species under laboratory conditions.

In spite of the numerous open questions that it leaves, this article extends the relationship between arborescence and slow rates of molecular evolution beyond the seed plants, and thus into a broader group of diverse organisms. This finding will surely stimulate considerable future research.

Goodbye...for now?

2010-04-10T20:15:00.006-04:00

On Monday, I will begin a rotating program officer position at the National Science Foundation in the Systematic Biology and Biotic Inventories Cluster. Thus, this is going to be my last post on Dechronization until my rotation is over. It has been a really great experience being part of this blog and I've met some great people because of it. Keep up the good work Dechron'ers. I'll be reading!

P.S. The photo is of a shovel-snouted lizard (Meroles anchietae), that I got to see on a recent trip to Namibia.

Testing for Nonlinear Selection

2010-03-26T17:04:00.013-04:00

Nonlinear natural selection, particularly stabilizing selection, is often presumed to be widespread in nature. However, it is seldom found in practice. For instance, the now famous Kingsolver et al. (2001) review found that only 16% of estimated nonlinear selection coefficients on single traits (estimates of stabilizing or disruptive selection) were significant; and furthermore that correlational selection was estimated in fewer than 10% of studies. Nonlinear selection is very important in the study of evolution, however, because of its relevance to many very interesting questions, such as the evolution of genetic correlations between characters and the evolution of evolvability (e.g., Arnold et al. 2008).

An increasingly popular approach in recent years has been to first estimate the γ-matrix, which contains the coefficients of stabilizing and disruptive selection on its diagonal and the coefficients of correlational selection in off-diagonal positions, and then to diagonalize γ by solving MγM'=Λ for matrices containing the orthonormal eigenvectors (M) and eigenvalues (Λ) of γ. The widely perceived advantage of this approach is one of increased power: diagonalization identifies (in its first and/or last ranked eigenvectors) the dimensions of strongest nonlinear selection; and, furthermore, it allows for more modest multiple test correction, since the number of coefficients to be tested scales linearly with the number of traits in our analysis (rather than as the square). True to form, some studies (e.g., Blows et al. 2003) have found significant nonlinear selection on the canonical axes where none was found on the original traits.

However, a recent paper by Richard Reynolds and colleagues (2010) has revealed that some of this increased power may be illusory. In particular, the standard double-regression approach for hypothesis testing of the canonical nonlinear coefficients has type I error that goes to 1.0 (i.e., very bad type I error) under pretty realistic conditions. The lower panel of the figure above, copied from Reynolds et al. (2010), shows the type I error for hypothesis tests on the canonical axes for a nonlinear selection analysis of 10 traits. In this study no selection was simulated! The authors also prove analytically that the expected eigenvalues of the estimated γ-matrix for data without nonlinear selection only go to zero as the number of samples used to estimate γ goes to infinite (obviously sample sizes in empirical studies are usually finite. . . unless, of course, you take a really, really long field season).

The implications of this result are quite significant. In particular, it means that some recently published examples of significant nonlinear selection on canonical trait axes could be type I errors. However, the authors also provide a solution. They find that type I errors contract to their nominal levels when a permutation-based hypothesis testing approach is used. (In a self-serving addendum, I'd also like to note that I independently devised and applied the exact simulation test recommended by the authors in a recently published paper - detailed here in a supplement - even though I must admit I was not at all aware of this problem at the time!)

I think this paper also reflects the fact that methods are never static, and that when new ones are devised they must be tested thoroughly - and furthermore that these tests should be conducted with both empirical and simulated data. The rise of canonical rotation in the analysis of nonlinear selection had previously not been accompanied by this level of scrutiny. Reynolds et al. (2010) provides not only a definitive critique, but also a suitable way forward.

On the Improbability of One-tailed Hypothesis Tests

2010-03-12T16:00:00.013-05:00

One-tailed hypothesis tests have fairly wide popularity in ecology and evolution. For instance, an article by Lombardi & Hurlbert (2009) reported that 13% and 24% of "articles with data susceptible to one-tailed tests" used such tests in two recent journal years. Another similar review by Ruxton & Neuhäuser (2010) found that 5% of all articles published in 2008 in the journal Ecology used at least one one-tailed test, although they didn't examine "susceptibility" (i.e., many articles not using a one-tailed test might not have had data appropriate to such a test).

One-tailed hypothesis tests are popular in large part because they provide increased power to reject the null hypothesis if it is false. The lower panel of the figure, right, shows the expected mean absolute value of t for a real (but small) mean difference between populations A and B, for various equal sample sizes of A and B. What it reveals is that the sample required to reject a two-tailed (rather than a one-tailed) null on average is about 50% larger, which could be expensive and time consuming if data are difficult to obtain.

However, there have been repeated articles questioning the general appropriateness of one-tailed tests. For instance, Lombardi & Hurlbert (2009) conclude that "all uses of one-tailed tests in the journals surveyed seemed invalid." Ruxton & Neuhäuser (2010) were a little more generous, but they concluded that in 17 papers using a one-tailed test, only one had appropriate justification to do so.

The problem arises from an apparently widespread belief among ecologists and evolutionary biologists that any a priori hypothesis regarding the direction of the outcome in our statistical test is sufficient grounds to justify a one-tailed null hypothesis. This is not true, but Lombardi & Hurlbert (2009) conclude that the reason for this misperception is fairly well founded, documenting bad or confusing advice regarding the application of one-tailed hypothesis tests in 40 of 52 popular statistical texts (Lombardi & Hurlbert 2009, Supplement).

In fact, a one-tailed hypothesis test is only appropriate if a large effect in the opposite direction of our a priori prediction is exactly as interesting and will result in the same action as a small, non-significant result in the predicted direction. Both articles point out some very restrictive circumstances in which this might be true. (For instance, in the example of an FDA test on a new headache drug - no positive effect and a large negative effect on the pain of test subjects will result in the same action: no approval for the drug.) However, in ecology and evolution it is quite hard to imagine circumstances in which a large, significant result in the opposite direction of that predicted by theory could easily be ignored.

Of course, there are many statistical tests (lots of them common among evolutionary biologists) to which the concept of "tailedness" doesn't really apply. For instance, we are not usually interested in whether our data fit our a priori model better than expected in a goodness-of-fit test (although perhaps we should be).

For statistical tests in which the concept of tailedness does apply, one-tailed tests generally ill-advised. Thus, their use should require substantial justification. Ruxton & Neuhäuser (2010) give two very simple grounds on which they feel a one-tailed need be justified. First, an author using a one-tailed test should clearly explain why the result in a particular direction is expected, and why it is fundamentally more interesting than a result in the opposite direction. Second, importantly the author should also explain why a large result in the unexpected direction should be treated no differently from a non-significant result in the expected direction (Ruxton & Neuhäuser [2010]). These conditions may be rare (or, in fact, nonexistent: Lombardi & Hurlbert [2009]) in our field.

Resolving the Vertebrate Tree

2010-03-10T15:27:00.005-05:00

In a recent paper from BMC Biology, Bob Thomson and Brad Shaffer at the University of Californa - Davis quantify progress toward resovling the vertebrate tree of life. Using a phyloinformatic pipeline and GenBank data from a large sample of vertebrate diversity (100 clades, encompassing about 12,000 species), the authors ask the simple question: "How many nodes in the vertebrate tree do we have some information about?" The brief answer is about a quarter, though this information is highly skewed. Avian and mammalian clades are on average better resolved than the other major vertebrate lineages, and marine clades are on average very poorly resolved. In addition to estimating current 'resolution', Thomson and Shaffer analyze the accumulation of this resolution through time. The superexponential growth curve of sequences in GenBank is now well-known. However, there is little understanding of how this accumulation of data correlates with accumulation of phylogenetic information. These analyses indicate that information is accumulating polynomially and, if current rates continue, we might understand a large majority of the vertebrate tree within a few decades.

Bob has made their data available via a google motion chart, which allows for easy exploration of the studies' results (embedded below):

Slingjaw Wrasse!

2010-03-10T12:56:00.003-05:00

Peter Wainwright is lecturing this morning at the Bodega Bay Applied Phylogenetics workshop on morphological diversification. He just showed his lab's famous video of a slingjaw wrasse (Epibulus insidiator). Best feeding video ever. Peter's lecture will be up on the Bodega Wiki in an hour or so. Samantha Price is going to follow Peter with an awesome new tutorial on investigating character evolution with the program Brownie.

The Price of Parenthood

2010-03-09T11:49:00.009-05:00

Any parent will tell you that reproduction is costly. There are rising health care expenses, child care costs for working parents, expensive sports or extracurricular activities, and, eventually, college enrollment and tuition. From an evolutionary perspective, the only relevant costs of reproduction are those that depress survivorship and as a consequence decrease the future opportunity for subsequent reproductive output (and, in fact, such costs have been found in humans).

A recent study in the pages of 'Evolution' has demonstrated a very high toll of reproduction, indeed. By stymieing reproduction in female Brown Anoles (Anolis sagrei, pictured right) through surgical removal of the ovaries, Bob Cox and Ryan Calsbeek at Dartmouth University have found that female interannual survival increases nearly threefold (relative to females manipulated only with a control "sham" surgery; solid bars, right). In addition to the survival advantage of non-reproduction, ovariectomized females also exhibited higher growth than control females.

Although the result is consistent with abundant life-history theory predicting a trade-off between reproduction and survival, the proximate mechanism of increased growth and survival of non-reproductive adult female anoles remains unclear. In performance trials, females whose egg burden has been surgically relieved improved dramatically in both stamina and sprint speed, suggesting that ovariectomized females might be better equipped to avoid predatory attack. However, in results presented in this year's Society for Integrative and Compative Biology meeting (and discussed in a previous blog post), Bob found that experimental manipulation of predation regime had little effect on the survival probability of sham and ovariectomized females. Perhaps ovariectomized lizards are simply better able to allocate sparse resources to fat reserves, and thus exhibit improved survival during food scarcity. Furthermore, Cox and Calsbeek acknowledge that ovariectomy removes not only the physical burden of reproductive investment, but also the source of steroid hormones - which could also affect growth and survival in lizards.

No doubt these important questions regarding proximate causes for the relationship between reproduction and survival in female anoles will be the subject of future studies.

Bodega Phylogenetics 2010 is Underway

2010-03-08T19:02:00.005-05:00

The annual Bodega Bay workshop in applied phylogenetics kicked off last weekend. Participants have already heard Mike Sanderson's take on the State of the (Phylogenetics) Union, learned about Bayesian phylogenetic inference from John Huelsenbeck and Jeremy Brown, and run tutorials on the use of programs BEST, RAxML, R, and BEAST. Don't worry if you couldn't be here in person - lecture material and tutorials are being posted at the Bodega Phylogenetics Wiki! The next few days will feature lectures on comparative methods, morphological evolution, phylogenomics, diversification rates, and community phylogenetics (see the complete schedule). Photo captions: John Huelsenbeck introducing students to programming, Peter Wainwright organizes group projects, students learn about maximum likelihood with 10-sided die.

Speak now or (forever?) hold your peace

2010-03-02T12:11:00.005-05:00

Got an idea for a new program at NSF? Think you know of a way that data and other information can be better shared? Have you concocted a plan for better linking the public, the government and scientists? For the next 17 days, you're invited to post these opinions and any other feedback at OpenNSF. Even if you don't think you have any original ideas, there's a mechanism to vote on whether you like or dislike others' suggestions and leave comments.

Toe Pads & Tails

2010-02-27T14:54:00.004-05:00

The adhesive toepads of lizards are one of life's most spectacular inventions. Humans are even using this innovation as the inspiration for new adhesive nanostructures. Did you know that some geckos have similar adhesive structure on the tips of their prehensile tails, as well as on their toes? I caught one such gecko in northern Australia a number of years ago during an expedition to Arnhem Land with Jane Melville and Museum Victoria. The species we found - Pseudothecadactylus lindneri - is closely related to geckos on New Caledonia and could be found wandering Arnhem Land's impressive rock outcrops at night. The photo above is of a juvenile P. lindneri and close-ups of the toepads (top) and tailtip (bottom) of an adult animal. It seems likely that the tailpad results from similar genetic and developmental mechanisms to the toepads found in the same animal, but this has yet to be investigated in any detail. Remarkably similar toepads are known to have evolved independently in geckos, anoles, and skinks.

One Year of Stimulating Science

2010-02-17T21:17:00.012-05:00

Last year was a good year for science. Thanks to a $3 billion dollar windfall from the American Recovery and Reinvestment Act, the NSF enjoyed a 50% increase in its expected level of funding for 2009. Scientific American just published an nice piece on the ARRA's impact on science over the past year (this article is the source for most of the facts mentioned below) . Anyone who's applied for funding from the NSF over the year and half doesn't need an article in Scientific American to tell them that the NSF devoted the bulk of its boost to grants. At the evolution meetings in Moscow Idaho last summer it wasn't hard to find others like me who had just been awarded ARRA funds. Those of us receiving these funds were told that our prosposals were deemed worthy of funding by the NSF's review process, but wouldn't have received funds in an ordinary year due to budgetary constraints.

For years, the NSF has received many more worthy proposals than it was able to fund, resulting in a logjam of high quality proposals and stifling progress in many important disciplines. Indeed, nearly 80% of the NSF's ARRA funds went to clearing the NSF's backlog, being used to fund highly rated, but unfunded, awards that were submitted the previous year. Although those who didn't submit proposals eligible for ARRA support might feel like they've been left out, the clearing of NSF's backlog is sure to result in higher funding for proposals submitted more recently.

Short-sighted politicians are likely to find fault with the fact that the NSF ranks second to last among federal agencies in spending their stimulus funds (only $136 million of the NSF's ARRA award has been spent). The reason for this are clear - most grants from NSF are multi-year awards and are going to sit in the bank accounts of awardee's institutions as they are allocated over the years to come. This does not mean, of course, that these awards are not having an immediate impact. The bulk of the money associated with my award is going directly to salaries of PhD students and undergraduate employees. My collaborator is using his share of the funds to hire two post-doctoral scholars. Our award, therefore, will directly fund three-four full time positions and a number of additional part-time positions for the next two and half years. Perhaps more importantly than providing jobs today, our award is also contributing tremendously to training the next generation of scientists. While it may not have the same immediate impact as other worthy investments like hiring jobless construction workers to build bridges and roads, the ARRA's gift to the NSF is likely to be a gift that keeps on giving both to the academic community and the country at large for many years to come.

In Memoriam: John Thorbjarnarson

2010-02-15T09:53:00.004-05:00

We are sad to report that John Thorbjarnarson passed away yesterday morning. John was a Conservation Officer for the Wildlife Conservation Society, based in Gainesville, Florida. He was a PhD student of Wayne King and then spent the next nineteen years leading in situ conservation efforts of reptiles for WCS. He was a noted expert on the conservation biology of crocodiles worldwide --- having led efforts in the recovery of both Orinoco crocodiles in Venezuela and Chinese alligators in Anhui, China. He is also well know for his long term efforts focused on capacity building and conservation of crocodiles in Cuba and Black caiman in Brazil. John was in India to give a course at the Wildlife Institute when he succumbed to a severe case of falciparum malaria. He will be sadly missed by his colleagues and friends who will always remember his dedication to learning more about crocs and other herps and doing everything he could to protect them.

The photo came from this website, which has a nice interview with John about his work.

You may also see John in action in the Amazon in this National Geographic clip.

Darwin Day at Case Western Reserve University

2010-02-12T15:28:00.006-05:00

Happy 201st birthday Charles Darwin!

I'm spending Darwin day at Case Western Reserve University as one of several folks speaking on the topic of phylogenetics and evolution. The event's two headliners just wrapped up their talks. University of Michigan paleontologist Philip Gingerich gave an enlightening talk about evolutionary rates. Discussing a result that dates back to his famous debate with Stephen Jay Gould over punctuated equilibrium in early 1980s, Dr. Gingerich showed why the dramatic inverse correlation between rates of evolution and the interval of time over which they are measured is a simple mathematical artifact. For those interested in more on this work, Dr. Gingerich published a nice review in the Annual Review of Ecology, Evolution and Systematics. Gingerich also provided an interesting anecdote about Gould. Early in his talk today, Gingerich asked the audience how many figures were in the Origin. As any phylogeneticist knows, the answer is one: Darwin's classic illustration of the branching tree of life. Apparently when Gingerich asked this same question when Gould was in the audience Gould quickly, and incorrectly, blurted out "two!"

The other headliner today was the godfather of phylogeography, John Avise. This is the first time I've seen him speak, so it was nice that he provided a 22 point retrospective on the lessons learned from phylogeography. It's amazing to think that his first papers on this topic were published over 30 years ago now!

Thanks to Case Western's Institute for the Science of Origins for sponsoring today's event!

The End of Adaptive Radiation?

2010-02-07T00:27:00.014-05:00

In a provocative new Bioessays article, Olson and Arroyo-Santos attempt to kill the term "adaptive radation." Olson and Arroyo-Santos are certainly correct when they suggest that interest in adaptive radiation is paradoxical: although it is almost universally regarded as an important (if not the most important) mode of biological diversification, evolutionary biologists have argued for decades about how to diagnose and define it. Olson and Arroyo-Santos suggest that this century-old debate stems fundamentally from the fact that "adaptive radiation cannot be winnowed to any core meaning, because there is no phenomenon in nature to which the term corresponds, simply arbitrary divisions of continua."

The problem with this argument is that it focuses exclusively on the one feature of adaptive radiation that is controversial - namely, whether extraordinary diversification is intrinsic to adaptive radiation. While I agree with Olson and Arroyo-Santos's suggestion that efforts to define adaptive radiation on the basis of the extraordinary levels of diversity are hopelessly ambiguous and arbitrary, I disagree with the fundamental premise that extraordinary diversification, in any form, is intrinsic to adaptive radiation. If we focus on the shared features of modern definitions of adaptive radiation, we find that it can be universally defined as a response to natural selection and ecological opportunity involving divergence of species and associated adaptive features. In this sense, adaptive radiation is analogous to the ‘principle of divergence’ that Darwin introduced in the Origin by suggesting that “the more diversified the descendants from any one species become in structure, constitution, and habits, by so much will they be better enabled to seize on many and widely diversified places in the polity of nature, and so be enabled to increase in numbers.” Perhaps we should replace 'adaptive radiation' with 'principle of divergence,' but abandoning efforts to label the profoundly important evolutionary phenomenon that underlies these terms seems like a bad idea to me.

Phriday Phun with Photoshop

2010-02-05T16:47:00.009-05:00

It seems like everyone blogging about the bat alcohol tolerance story in PLoS One has come up with their own Photoshopped image of a bat getting drunk. This is your chance to vote for your favorite! For a larger version of this image, go here.

Which is the best photoshopped image of a bat getting drunk?

Designated Fliers

2010-02-04T14:49:00.005-05:00

In a "is it Friday yet?" kind of way, I thought I would share this little post. A recent paper in PLoS One by Orbach et al. presents results showing that frugivorous and nectarivorous bats do not appear to be affected by consuming alcohol. The authors fed bats either a sugar solution or sugar+alcohol (strawberry daquiri?) solution. They then gave the bats an aerial obstacle course to test their speed and agility. They also recorded the bats' echolocation calls. Although there were differences between the species that they tested, there were no observed effects of treatment - the "drunk" bats did just as well as the "sober" bats. This was true, even though the estimated BAC's of the bats were sometimes very high - more than 0.3%. Thus, these bats seem perfectly capable of utilizing rotting fruits as food sources with no chiropteran "slurred speech" and little or no danger to themselves or others. Large, virtually hairless primates such as ourselves, do not appear so well adapted and should exercise caution.

I give thanks to Sam Crane who patiently walked me through PhotoShop again so I could make this picture.

Going Rogue

2010-02-03T23:30:00.001-05:00

If we've learned anything from US politics over the past year and half its that adding 'rogues' to an an otherwise orderly system can result in rapid descent to the lowest common denominator. In the latest issue of Systematic Biology, Thomson and Shaffer show that the same is true in phylogenetics. With the goal of reconstructing a robust phylogenetic hypothesis for turtles using existing sequence data, Thomson and Shaffer use a new pipeline and the data available via the PhyLoTA browser to assemble a dataset that is noteworthy for both its size and incompleteness: 223 taxa, 53,406 bp, 7.59% complete. Although Thomson and Shaffer explore the influence of a variety of factors on phylogenetic inference, they conclude that rogue taxa "probably represent the most insidious problem for supermatrix phylogenetics." For those unfamiliar with rogue taxa, the term is used to describe taxa whose phylogenetic position can vary dramatically without having a strong effect on a tree's overall score. Thomson and Shaffer identify rogues using the taxonomic instability index (I) calculated by Mesquite from a sample of trees generated using standard bootstrapping methods. To explore the influence of rogues on phyogenetic resolution, Thomson and Shaffer remove those taxa exhibiting the most roguish behavior and redo their analyses. The top panel of their Fig. 4 provides a compelling visual representation of the results of this exercise, with the completely unresolved tree on the left being generated before pruning rogues and the nearly fully-resolved tree on the right resulting from analysis of the same dataset subsequent to de-roguing. Although one might challenge the wisdom of deleting problematic taxa until a resolved tree is produced, this practice may be justified in some instances. How we deal with rogue taxa is sure to be a topic of debate in the years to come, but, for the time being Thomson and Shaffer's analyses suggest that simply deleting the taxa with the worst I values may be a reasonable solution.

Rotten Fish and the Chordate Tree of Life

2010-02-02T21:10:00.007-05:00

The origin of vertebrates is part of a larger story involving the evolution of a more inclusive group of kin, the chordates that along with vertebrates include urochordates (tunicates) and cephalochordates (lancelets). Recent decades have been an exciting time for our understanding of chordate evolution, with the discovery and evolutionary analysis of important chordate fossils that date to the Cambrian (542 to 488 million years ago). On the basis of distinct morphological features preserved in the fossils, scientists have been able to integrate these extinct lineages into phylogenetic hypotheses of chordates, extinct early vertebrate lineages, and extant vertebrates.

In a very clever study published last week in Nature, Sanson et al. allowed specimens of lancelets and larval lampreys (ammocoetes) to decay in artificial seawater in the laboratory. The anatomical features that are the most important for distinguishing clades in the phylogeny were the most prone to decay, while the least informative (pleisiomorphic) characters were more resistant to decay. The results are striking and have important implications for the evolutionary interpretation of early chordate and vertebrate fossils. The bias in anatomical decay will result in placement of derived lineages further down the stem of the phylogeny, a phenomena the authors refer to 'stem-ward slippage.' As a result, placement of chordate and vertebrate fossil taxa on the stem of their respective phylogenies may be an artifact of character preservation. As such, the phylogenetic position of fossil taxa lacking derived features, but possessing character states of stem chordates or vertebrates, may be suspect. A video showing time lapse photography of a rotting lamprey is available on Nature's youtube channel. Picture of the cleared and stained ammocoete from www.biology.uco.edu/PersonalPages/CButler/.

Trees in Pop Culture: The Darwin Electro-Opera

2010-02-01T13:39:00.010-05:00

Did you ever think you'd see a phylogenetic tree displayed in laser light as the backdrop to an opera? Well, neither did I, but that's exactly what happens during an opera based on Darwin's life and works written by the Swedish synth-pop innovators and Pitchfork darlings known as The Knife. The image above is a screen capture from the 2:37 mark of a 7 minute preview video in which one of Darwin's hand-drawn trees is clearly visible. The soundtrack releases via theknife.net tomorrow, but you can preview it now at NPR. Reviews and commentaries on this work are all over the place. NPR's All Songs Considered blog links to a twenty minute roundtable discussion with The Knife and their collaborators (Mt. Sims and Planningtorock) that is almost as bizarre as the video. If one thing is clear, it's that they've taken the task of learning about Darwin and his theory rather seriously. The resulting music is fascinating and full of meaning, but its also a bit abstract for the minds of most scientists.

Step Back from the Species Description, Ma'am...I'm a Taxonomist

2010-01-25T16:15:00.006-05:00

Here at AMNH, I am surrounded by drawers and drawers, bottles and bottles, and cabinets and cabinets of specimens. A fair number of these are type specimens and my colleagues have spent their careers carefully describing and depositing these and other specimens into collections. They publish these species descriptions in journals according to the rules of the International Code of Zoological Nomenclature. Bacterial taxonomists are an even stricter lot - they insist that all papers that name a new species are published in a single journal, the International Journal for Systematic and Evolutionary Bacteriology. (I have bucked that rule.) In my work on malaria parasites, I have often been met with harsh reviews when I have tried to publish anything that has a sequence, but not a matching bloodsmear. Working on parasites with multiple life stages can be particularly challenging for species descriptions - ideally one would have specimens, images, measurements, etc from each step of the life cycle..but those can be hard to obtain for many - or even most - parasites. In a recent paper, Chris Austin and I argued that incorporating DNA sequences into species descriptions can help bridge that gap.

The use of these sequences, however, should not come at the expense of traditional morphological analyses. Two recent papers "describe" new species of malaria parasites without really describing them. One was published in a the high impact journal PLoS Pathogens, and names a new species of Plasmodium in chimpanzees. Even though the authors say they examined slides of the new species under a microscope, there are no images, measurements, or discussions of morphological features that might allow a reader to visually differentiate the new species. To the contrary, they remark that the samples look a lot like P. falciparum. There is no type specimen. A subsequent paper with other samples from chimpanzees definitely hints that it may not be a new species, but may instead be another species known to infect chimps: P. reichenowi. Similarly, another paper recently reported a new species of Plasmodium in capybara. This discovery was particularly surprising given that no New World mammal malaria parasites are known, save for some in primates that are genetically indistinguishable from a human parasite. In this paper, again, there is no traditional description, there is no type specimen, there is a single image of the parasite's smallest and most challenging to identify stage, and the genetic results are of a paralogous gene represented by an unrooted cladogram.

I know that there has been a lot of discussion about electronic journals and ePubs ahead of print either work with or violate the "code", but I have to ask, has traditional taxonomy gone extinct? Is this happening in other fields, too?

Online Phylogenetics Seminar!

2010-01-23T13:42:00.003-05:00

Erick Matsen and colleagues have organized an online phylogenetics seminar that should be of interest to many Dechronization readers. The stated goals of the seminar series are to provide a forum for the discussion of phylogenetics methodology, disseminate information about ‘best practice’ phylogenetics, and to reduce our carbon footprint by reducing air travel. This seems like a really cool idea and I’m impressed by the present and past lineup of speakers they’ve assembled. I haven’t tuned in yet, but both Marc Suchard and Ward Wheeler gave seminars in the fall – you can view both of their seminars here.

I’m looking forward to the next set of seminars, which will include species tree estimation using BEAST. Coming up this Monday, January 25 (1300 PST) is Joseph Heled, who will be talking about “Gene-tree species-tree discordance.” And Noah Rosenberg and Jens Lagergren are on deck to give seminars during February and March. One cool idea that these folks are floating is to allow seminar “attendees” to vote on upcoming seminar topics, and you can email Erick to suggest both potential speakers and topics. Check out the Phyloseminar website for instructions on connecting - seems pretty straightforward and I’ll try and give it a shot today.

Masters Programs in Systematics

2010-01-22T09:29:00.002-05:00

Every year I find myself advising a few students interested in masters programs in systematics. Most of these students express an interest in earning a doctoral degree, but lack the research experience required to know whether a PhD program is right for them or to be competitive for the best doctoral programs. My problem as an adviser is that I just don't know about many masters programs that are appropriate for such students. Because I'm sure there are plenty of programs out there, I'm asking for your help in finding them. By having this discussion on the blog, I'm hopefully that other students and advisers will be able to benefit from the information we're able to share.

In addition to inviting comments to this post, I'd like to invite anyone involved in a masters program in systematics to submit a brief blurb about their program as a guest post on Dechronization. Just send a concise one paragraph statement to me via e-mail (rglor -at- ur.rochester.edu), being sure to include information on how your students are funded and whether your program is course- or research-based.

Phylogenetic Model Selection, Sans PAUP*

2010-01-17T14:01:00.003-05:00

Given that an increasing share of statistical software in ecology and evolution is essentially free – e.g., open source and/or non-proprietary – I used to be bothered by the lack of suitable alternatives to PAUP* (which requires a licensing fee) for certain phylogenetic applications. Foremost among these is perhaps the ability to perform statistically rigorous phylogenetic model selection. There are now a number of free alternatives for phylogenetic model selection, that do not require PAUP* (which is required by the widely used Modeltest and MrModeltest programs ). I've probably been living in a bubble, because I just learned of several of these yesterday, but I thought I'd flag a few for Dechronization readers who might find this info useful.

One that I have used extensively is ModelGenerator , from the nice folks at the NUI Maynooth Bioinformatics Group. This is quite useful, not least because it has a web interface that lets you upload batches of fasta-formatted alignments. Because the computation is distributed across many “idle” desktop computers at NUI Maynooth, the processing time is low – I’ve uploaded batches of alignments only to get a results file emailed back to me within ~20 minutes or so. You can also run the program locally on your own machine or email the author for source. Additional options that I have yet to explore include jModeltest , FindModel (another web-based tool), and MrAIC . I'm sure this list is incomplete and welcome comments on programs I've missed as well as strengths and weaknesses of those I've listed.

"El terremoto" (the earthquake), as experienced in Santo Domingo

2010-01-14T14:40:00.006-05:00

Kudos to Rich for helping to point out the various ways in which individuals can contribute to the recovery effort in Haiti, which most people know by now was devastated by an earthquake two days ago. I don't have much to add to his post, but since I happened to have been in Santo Domingo in the Dominican Republic at the time, I wanted to relate my experience.
A few people know that I was in the D. R. this past week helping Luke Mahler, along with Bryan Falk and Jose Luis Herrera, to collect several large series of anoles for an ongoing collaborative project between Jonathan Losos and Butch Brodie on the evolution of G and P matrices in Anolis lizards of the Caribbean. While Luke and Jose Luis were out dealing with the Dominican permitting authorities, Bryan and I spent all of Tuesday (our penultimate full day on the island) preparing the last of our large specimens series. This was to ensure that the specimens had at least 24 hours of "fixing time" before they'd need to be repackaged for transportation back the MCZ at Harvard. When the earthquake struck, Bryan and I had just been rejoined by Luke and we were all sitting around the kitchen table (aka., makeshift lab bench).
To both Bryan and I alike, the sensation of the earthquake was very strange. Since the notion of an earthquake seems totally preposterous to anyone who hasn't experienced one before (myself included), my first reaction was that to think that I was just a little dizzy (perhaps from hours spent bent over trays of 95% ethanol). The whole world seemed to be swaying back and forth in front of me and I felt lightheaded. But at the moment that Bryan (who had been thinking the same thing) and I made eye contact, it was clear that we were not shaking - the world was. The tremor seemed to last about 10 seconds or so, during which time I got up and walked to the window to try and figure out if the it was the building that was shaking, or the tree next to it (undoubtedly both were). Naturally, our reaction was something to the effect of "holy $%!*, was that an earthquake?" Luke said something like "that was crazy - you guys need to remind me about this later so we can check and see if it made the news." Someone might have also said - "Liam, you should write a Dechronization post about this." We then proceeded to debate what numerical on the Richter scale the earthquake might of been worth, and so forth (although neither Luke nor I had ever experienced one before), as we continued fixing lizards. At the time, we hadn't the slightest inkling of the devastation that had been wreaked in Port-au-Prince by the same tremors that we were discussing so casually over the dissecting tray.
So, I second Rich's suggestion that we all try and find ways (large or small) to help alleviate the pressure on Haiti that has been wrought by this latest disaster. It also seems clear that the devastation of these natural disasters is massively exacerbated by the generally low level of economic development in the region. Imagine 40,000-50,000 deaths from a natural disaster in the United States? It's inconceivable.
Since I have never been to Haiti, the picture above is one snapped by Bryan of a Haitian boy in the mountains near Polo, in the Barahona Province of the the Dominican Republic.

Haiti Getting Kicked While Down (Again)

2010-01-13T13:43:00.008-05:00

My students were on a mountain in the Dominican Republic close to the Haitian border when the 7.0 magnitude quake struck near Port-au-Prince. They described watching the horizon shake in front of them for a solid 10-15 seconds. Although estimates for the loss of life resulting from this brief episode remain unavailable, they are sure to reach into the tens of thousands.

Last summer, I blogged about field work in Haiti (1, 2, 3, 4). At that time, Haiti seemed like a country in shambles; its denuded earth was washing out to sea before our eyes, roads between major cities were barely passable, electricity was absent even in towns as large as 80,000 people, and clean water was sometimes impossible to come by. Nevertheless, a glimmer of hope accompanied the sense that things were better than they'd been in years. Whatever fragile progress Haiti may have made over the past few years, however, has just crumbled to the ground.

This quake, of course, is just another in a long string of injustices and misfortunes for Haiti and its people. Please consider making a small donation to one of the many aid organizations that are mobilizing to help Haiti through its latest (and perhaps greatest) crisis. Possibilities include Doctors without Borders and UNICEF. Donations are especially encouraged from countries like the United States or France, whose governments that have spent the better part of the last 200 years doing little but destabilizing Haiti.

Music Video Tribute to Dolph Schluter

2010-01-12T17:40:00.005-05:00

The seemingly increasing popularity of Darwin Day video parodies (and originals) made it pretty much a sealed deal that someone had to post one on YouTube that would be broadly appeal within evolutionary biology circles. With the Lonely Island's single "I'm on a Boat" turning gold last summer, and UBC's evolution group being filled with creative smarties, I was barely surprised to see an excellent parody of a parody, "I'm in a Pond," appear last month. You can turn on closed captioning (CC) for clarified lyrics, which include, "I'm writing Nature papers/And you're stuck at Am Nat," and "Believe me when I say/I love E-d-a."

(I would like to encourage everyone to send in their Darwin Day videos. You can just post links in comments. We'll highlight the best ones on February 12th.)

[Thanks RichF!]

Parasite of the Day

2010-01-11T11:50:00.004-05:00

Hoping that parasites do not get left out of the whole "International Year of Biodiversity" thing, I have started a new site, "Parasite of the Day". I'm appealing to my parasitology colleagues to contribute - and to anyone with a favorite parasite to nominate it. Today's parasite is Plasmodium minuoviride, a cool lizard malaria that Chris Austin and I described last year. Go to the new parasite-of-the-day site to find out why.

Priors and convergence in BEST

2010-01-11T10:59:00.005-05:00

Over the past year, I’ve heard a bit of grumbling about how difficult it is to achieve convergence using the program BEST ( Bayesian Estimation of Species Trees ). I was recently using BEST to analyze a reasonable-size multilocus dataset (20 taxa, 5 loci), but things were looking grim: convergence was not happening, and the trees looked nothing like concatenated and single locus trees estimated using RAxML. Then I came across this nice paper by Adam Leache , where he demonstrates a strong effect of priors on convergence in BEST. BEST requires setting two priors that are specific to the hierarchical species tree model: a prior on species population sizes (theta; thetapr), and a prior on the relative gene mutation rates (GeneMuPr). Leache showed that by increasing the mean of thetapr, he was able to obtain much faster convergence (inset).

Inspired, I set up a series of runs with my data where I increased the mean of thetapr – up to shape=3 and scale = 0.1 [for a mean of scale / (shape – 1)]. I found that performance improved immediately and dramatically: I was achieving significantly higher log-likelihoods within 200K gens of sampling than I had previously found in tens of millions of generations. After just 30m generations – a single night’s worth of sampling – my analyses pass a battery of convergence tests, including AWTY-based sliding window analyses of the actual species tree sample. While I’ll run this out for a few more days to see what happens, the results are pretty encouraging.

As an aside, I found that the default prior on gene mutation rates (uniform on 0.5 – 1.5) is not adequate if you have substantial among-gene heterogeneity in rates. I had mtDNA mixed with nuclear loci in my analysis, and the mtDNA rates were far too high for the defaults: the estimated mtDNA rates were simply piling up on the upper bound of the prior distribution (1.5). Because the mean rate across all loci is 1, the ratio of the bounds of this distribution represent the theoretical maximum relative rate difference that you will allow to occur within your dataset. If you have K loci, the theoretical maximum value this can take is K (which, if observed, would require that you have K-1 loci with relative rates approaching zero). So, I suggest using a uniform (0, K) prior on this parameter – it is a uniform distribution, so using an overly broad range isn’t likely to have any pathological consequences for your analyses – and this seems much better than the defaults, which allows at most a 3-fold difference in mutation rates among loci (eg, upper = 1.5 divided by lower = 0.5).

Blogging SICB 2010

2010-01-07T13:31:00.002-05:00

The beginning of January is marked annually by the Society of Integrative Biology (SICB) meeting. This year's was in foggy Seattle. I had planned to post a few blog posts during the meeting (as Rich did for last year's 'Evolution' meeting, e.g., here; or as I did more successfully at the Anolis Symposium). Life is full of good intentions, however, and here I am posting about SICB for the first time as I wait for my delayed flight out of Seattle. A confluence of factors contributed to this negligence, not the least of which was the fact that I wasn't scheduled to speak until this morning. The conference hotel was also charging (almost unbelievable) $11/day for internet access, which somewhat limited my ability to pop open the laptop and write a quick blog post. (I actually pay $15/month for nationwide broadband access through my phone, so I was actually not as hampered as others might have been - but tethering the phone and dialing up to the Verizon network is much slower and less convenient that hopping quickly on a wi-fi network would have been.)
Costly internet access aside, this was a great meeting. For people who have not attended SICB in the past, the composition and interests of presenters and posters is much more widely varied than in the major summer meetings. For example, concurrent sessions this morning included a session on "Spiralian Development," another on the "Mechanics of Defensive Structures," a third on "Sexual Selection," and a fourth (my session, actually) on "Predation and Predator Avoidance." With such as eclectic assemblage of sessions, it was pretty easy to identify those to avoid (for example, I did not attend the session on "Neurobiology - Molecular Neurobiology & Neuroanatomy" - no offense to neurobiologists). The meeting by no means lacked for interesting talks. For example, Bob Cox from Dartmouth College gave a fascinating talk on the survival costs of reproduction in Anolis, Katrina McGuigan gave a really interesting talk on the quantitative genetics of intraspecific allometry, and Eduardo Rosa-Molinar gave a fantastically illustrated talk on the neurological basis of reproductive behavior in Gambusia fishes. The latter talk featured both impressive high speed video of mosquitofish copulation, as well as wild three dimensional imagery of associated neural circuitry.
My talk was on the ultimate day of the meeting, which almost felt like it was after the meeting had already ended - since the last day was a half-day of talks and since there had been a concluding reception the previous evening. I talked about using mathematical and computer models to draw inferences about predation regime from the rate and pattern of tail autotomy in several species of Puerto Rican anoles. This project actually arose out of a collaborative venture with a great Harvard undergraduate, Karen Lovely, and perennial "Dechronization" third wheel Luke Mahler. My talk was about as well attended as one could hope for on the last (half) day of the meeting at 8:20am in the morning - but this is a really neat project, so I hope that when our in press article comes out in Evolutionary Ecology Research later this month, a few of the people that read this blog or happened to see my talk will check it out!

Welcome to Our World

2010-01-06T15:51:00.003-05:00

Many of you are probably frantically finishing up grant proposals that are due at the NSF this week. Yet, across the river in Bethesda, some changes in the NIH grant proposal length limit are causing a stir. Beginning with the February 5th deadline, the page limit will drop from 25 to 12...and it appears many grant-writers are a little unhappy. This week's Nature News has a little blurb talking about the new format and the reaction it's getting. The featured quote in that piece says, "In the past I would have easily put in at least ten figures. That's impossible now." I bet that all of you trimming references, adjusting line spacing, and resizing figures for your 15-page NSF proposal are salivating at even the thought of having room for 10 figures. Nevertheless, some folks are fine with the new short format, with the expectation that it will force greater clarity. Needless to say, reviewers are also likely to be relieved by the changes. Having recently served on an NIH study section (which in not done confidentially, as it is at NSF), I can say that being faced with a stack of 100-page proposals, with 25 pages of narrative on the project, was a little exhausting. But not nearly as exhausting as writing one myself. Good luck getting those in, everybody.

That Darn LBA

2010-01-05T20:07:00.006-05:00

Ah...I remember the days. Being a young grad student, trying to wrap my head around systematic biology and finding myself immersed, and sometimes confused, about the debates going on in the literature - and in seminar rooms - over parsimony vs. maximum likelihood. One favored topic of discussion was susceptibility to long-branch attraction (LBA). In my case, I went so far as to organize a graduate seminar that involved reading lots of papers and dragging John Huelsenbeck and Mark Siddall up to Burlington in the dead of winter to try to set us straight. I don't know about the rest of my cohort, but I finished the semester thinking that the only reasonable solution was to do my best to sample enough taxa to disrupt LBA as much as possible. And then, much of the controversy died down for a while. Part of this, I speculate, was due to the development and growth in popularity and theory of using Bayesian inference in phylogenetic analyses. BI was thought to have an advantage over ML in that it could incorporate uncertainty over the "nuisance parameters" in an analysis. A recent paper in PLoS One by Bryan Kolaczkowski and Joe Thornton, however, has raised the ugly head of LBA again. In this paper, Kolaczkowski and Thornton presented convincing data that BI is very susceptible to inconsistency and bias, particularly in cases of LBA (the "Felsenstein zone") - and that these problems are exacerbated when the amount of sequence data increased, with the posterior probability support values for incorrect clades converging to 1.0. Kolaczkowski and Thornton explored these effects with classical four-taxon trees, with real, known-to-be-problematic datasets (the troublesome Encephalitozoon), and other datasets with prescripted heterotachy and other heterogenous parameters in the evolutionary model. Importantly, they contend that "more sophisticated MCMC algorithms and more complex priors" cannot alleviate the bias that BI shows. The blossoming field of phylogenomics and the desire to incorporate larger and larger matrices into our systematic analyses, may thus lead us to produce well-supported but false trees if BI is used, if our datasets contain instances of LBA - and really, whose don't? This was a good read with some very important implications. I'm anxious to hear what others think of it.

Fun with new open access journals...

2010-01-04T15:01:00.005-05:00

Science is an incremental process, and the foundation upon which new results and discoveries are built is composed largely of previous research. It almost goes without saying that the long-term stability and accessibility of such previous research is fundamental to what we do as scientists. This is why accurate, long-term archiving of published, peer-reviewed research is such a big deal. The recent rise of Open Access journals has raised many questions about how we should deal with long-term archiving.

Accurate archiving of peer-reviewed research means that, once a paper has been published, its identifying attributes - page numbers, volume, etc - should not be changed. Otherwise, this creates a duplicity in the literature and makes it difficult to track down potentially important pieces of information. This is why journals are (in my experience, anyway) uncompromising on any further changes once a paper has been officially published.

I was thus surprised to find that a paper I published in 2006 has had, at some point, a change in page numbers. The journal in question is Evolutionary Bioinformatics Online, published by Libertas Academica, which has been the subject of some prior discussion here on Dechronization (see this previous post ). The original version was 2006:257-260, now shifted to 2006:247-250 and any attempts to find the 257-260 version on the Evol Bioinfo website will fail - those original page numbers are now part of a different article.

This is - at most - a mild annoyance. Still, it is pretty difficult to track how people are using the software I described in that note, because ISI does not have a record of the article using original pagination - which is what people (including myself) generally cite. So - citing the 257-260 version effectively falls into a black hole. But this does raise some worrisome questions about the long-term management of information, especially if this is not an isolated incident. Has anyone had similar experiences with LA or other open access publishers (or non-OA publishers, for that matter)?

Dechronization: A Review of 2009

2010-01-01T14:39:00.003-05:00

Happy New Year everyone! Hope that everyone had a nice holiday time. Thought I'd post a little "wrap-up" of some of the highlights of the year on our blog - at least as I see them. Feel free to chime in!
Dechronization turned 1 in 2009 - that was exciting - and we added two new authors: Dan Rabosky and Liam Revell. We started our interview series, kicking off with Joe Felsenstein, Jack Sullivan, and Rob Desalle. More to come - who would you like to see interviewed in 2010? There was a lot of Geneious love (and a few snarky accusations that we might be getting paid off by them - we assure you we're not!), a lively discussion of the swine flu (sorry, H1N1) epidemic - something that got the attention of Medpedia and resulted in our blog being showcased on their site. There were lots of good discussions about Bayesian methods - when they fail and when we fail them (twice). We had some fun with the infamous "Snake with a Foot" photo and a few posts poking at the bizarre PNAS paper touting that "forbidden love" between butterflies and onychophorans had resulted in caterpillar love children. There were posts from the Evolution meetings in Moscow, Idaho in June as well as the Anolis Symposium at Harvard in October and Rich gave us glimpses into some exciting fieldwork in Haiti. Thanks to everyone (our stats counter says 19,970 returning readers for 2009!) for reading our blog. Looking forward to 2010!

Genome 10K

2009-12-19T15:24:00.005-05:00

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!

2009-12-08T15:42:00.008-05:00

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

2009-11-22T20:17:00.014-05:00

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

2009-11-20T18:12:00.009-05:00

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

2009-11-20T10:57:00.016-05:00

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

2009-11-11T13:19:00.005-05:00

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

2009-11-08T11:02:00.005-05:00

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

2009-10-13T19:55:00.005-04:00

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

2009-10-04T15:39:00.002-04:00

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. . . .

2009-10-03T15:23:00.005-04:00

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?

2009-10-01T09:36:00.006-04:00

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

2009-09-24T20:27:00.014-04:00

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

2009-09-24T13:45:00.005-04:00

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

2009-09-24T01:03:00.002-04:00

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?

2009-09-16T16:59:00.005-04:00

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

2009-09-15T21:08:00.013-04:00

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

2009-09-12T13:00:00.009-04:00

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!

2009-09-04T20:49:00.007-04:00

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

2009-08-31T14:54:00.005-04:00

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

2009-08-31T14:42:00.004-04:00

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

2009-08-27T21:54:00.005-04:00

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

2009-08-26T16:34:00.005-04:00

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

2009-08-23T12:51:00.006-04:00

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

2009-08-22T22:36:00.008-04:00

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

2009-08-18T20:19:00.009-04:00

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?

2009-08-17T11:07:00.016-04:00

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

2009-08-10T23:11:00.004-04:00

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!

2009-08-09T08:31:00.008-04:00

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.

Source of a Scourge

2009-08-04T09:29:00.008-04:00

We now know that humans are the hosts of five different species of malaria parasites. The most virulent of these is Plasmodium falciparum, which is thought to be responsible for close to two million deaths a year. Early molecular phylogenetic studies proposed that humans acquired this parasite from chickens, but subsequent studies showed that that result was an artifact of taxon sampling and paralogous genes and that the closest relative of P. falciparum is a chimpanzee parasite, named Plasmodium reichenowi, which was discovered in the 1920's. For decades, though, only a single strain of P. reichenowi existed in the lab or in any form from which DNA could be extracted and sequenced. Recently, eight new isolates of P. reichenowi were obtained from wild and wild-born chimps and the phylogenetic history of these lineages was studied and published online yesterday in PNAS by Steve Rich of U Mass Amherst and colleagues. These new results now show very nicely that P. falciparum represents a recent host shift from chimps into humans, which may have occurred as recently as 10,000 years ago. It has long been known that these two parasites cannot be reciprocally cross-reared, i.e., chimps cannot be infected with P. falciparum and humans cannot be infected with P. reichenowi (the discoverers of this species tried to give it to themselves!). Rich et al. cite another recent study that demonstrated a different preference for erythrocyte receptors in the two parasites. Perhaps our human ancestors acquired these mutations for receptors and enjoyed a period of being malaria-free, only to have a new - and deadlier - parasite evolve that preferred the human receptor form. Unfortunately, blood smears were not made from these new chimpanzee samples, so it's not yet possible to confirm that these samples share the same distinctive morphology of P. falciparum, but Rich has assured me that they're working on this. It would also be interesting to add the second "ape" parasite, Plasmodium schwetzi, from gorillas, a species that no one has samples of for DNA analysis. What I liked the best about this new study, though, is that these results mean that P. falciparum as a species should be sunk. Think the medical community could handle that?

A Haitian Ghost

2009-08-03T11:03:00.003-04:00

In honor of Rich's collecting trip to Haiti, which begins this week, I thought I'd do a little post on a creature that's even more elusive than Anolis dolichocephalus and which graced the pages of last week's Science: the solenodon. Solenodons are very unusual mammals - they are venomous, injecting it with their teeth, like snakes. They are also likely to be critically endangered - but it's hard to say since hardly anyone has ever seen one. In 2007, biologist Samuel Turvey went looking for them on Hispaniola for 11 days and found remains of just 3 dead ones (one of which had apparently been gnawed on by a hungry Haitian). A new survey to be conducted this October will try to get a better handle on the distribution of and threats to the solenodon as well as to do molecular phylogenetic work to help to unravel its taxonomy and population structure.

Plants 1 : Anolis 0

2009-07-21T11:37:00.004-04:00

The June 2009 number of the Carnivorous Plant Newsletter marks a low point for the lizard genus Anolis. Joel McNeal from Athens, Georgia reports the capture of a small green anole (Anolis carolinensis) by the venus flytrap (Dionaea muscipula). The lizard was dead by the time he found it, but he never got a chance to see if it would be digested because the lizard and most of the trap were gone the following day, presumably due to bird predation.

Herptastic Articles in Science

2009-07-16T14:27:00.004-04:00

Science magazine features some interesting herpetological research in its most recent issues. Last week's number had an interesting piece on the evolution and development of the turtle shell (see also the enlightening summaries of this article by Olivier Rieppel and Ed Yong). Although elegant, the results are unlikely to satisfy researchers who favor the account provided in the Little Golden Book. Tomorrow, we get another report on the swimming behavior of lizards in sand (already featured in the NYT). Because the article hasn't yet been posted at Science, it's difficult to tell how it differs from previous work on this subject published by Baumgartner et al. last year in PLoS ONE. In any case, the visuals are more inticing because the current study uses high speed x-ray rather than NMR (the new x-ray video can be viewed along with a press release).

Large Tree Extraction, Viewing, and Printing

2009-07-07T18:00:00.007-04:00

Extracting trees from various idiosyncratically formatted databases is a pain, as is the task of printing very large trees for visual inspection of showing off. Many software packages are competent or good at one or both sets of tasks--I use some combination of APE package for R and FigTree, which work well for most of my needs, but not all. There are two new tools that help partly solve a couple of vaguely related problems.

Archaeopteryx, written by Christian Zmasek, is a Java-based application potentially useful in broad comparative analyses for extraction of trees from various source formats. With open source Java and Ruby libraries, it reads and displays trees in common formats (e.g. newick and nexus) as well as NCBI Taxonomy, TOL, and PhyloXML. For a nice example, take a look at the amphibian tree, then go to 'View as Text' and copy the newick formatted tree. Why? If you were to wish to print this or another large tree, you'd be out a nice chunk of time, and experience moderate hassle. No longer.

Tred, Rick Ree's web-based tree printing tool, can import, manipulate, and print very large trees. The most exciting feature for me is the duplication of sections near the margins for easy pasting of multi-page trees! The amphibian tree can be easily printed over three pages, taped together at convenient overlaps, and posted above your desk.

I can barely contain the urge to outdo the Hillis and Bull Lab tree, pictured above, by using the above tools to print out and unfurl a gigantic tree of life from Sears Tower. (Nevermind the uncertainty or accuracy.) A cheap way into the Guinness Book of World Records?

[Thanks to MudPuppy for pointing out Archaeopteryx!]

Sunday Book Review: Why Evolution is True

2009-07-02T15:42:00.017-04:00

I try to avoid reading about the science of evolution versus the dogma of creationism. Too often, I find the science presented in this type of writing to be repetitive and intolerably over-simplified. Although this is surely a symptom of my own academic elitism, I can't escape the impression that many of the journalists or professional writers discussing evolution aren't keeping up to speed on the latest advances or, in some cases, don't really get the science of evolution at its deepest levels. This is why Jerry Coyne's new book Why Evolution is True is such a welcome contribution (see also the associated blog). While many contemporary scientists have written in defense of evolution, few have the academic credentials of Coyne, whom many evolutionary biologists (myself included) regard as one of the best scientists of his generation.

Although Coyne shares Richard Dawkins's view that evolution and religion are fundamentally incompatible (as well as Dawkins's literary agent John Brockman), his book sticks mostly to scientific facts. In this sense, Coyne's book lives up to expectations by providing an excellent synthesis of the evidence supporting evolution, including reference to many recent discoveries and examples that are rarely discussed elsewhere. His lengthy chapter on human evolution was particularly enlightening because it cuts through much of the BS perpetuated by competing camps of scientists that are directly involved in this research. As Coyne notes, this field suffers from the problems endemic to many disciplines where "students far outnumber the objects of study." One problem is that the names for specific ancestral human fossils and resulting controversy "can't be taken too seriously" because there are "too few specimens, spread out over too large a geographic area, to make these decisions with any confidence." Coyne avoids this needless debate by focusing our attention on "the general trend of the fossils over time, which clearly shows a change from apelike to humanlike features."

On matters that are likely to be of particular interest to readers of this blog, I must offer a somewhat mixed review. On the one hand, Coyne's impassioned defense of biogeography and its importance is inspiring. I could identify only a few places where studies and facts were somewhat out of date (e.g., the suggestion on p. 100 that Madagascar is an old island the formed 160 million years ago when it separated from Africa, when it now seems clear that Madagascar enjoyed at Late Cretaceous connection with present-day South America and Antarctica). On the other hand, I was a bit dissapointed with the lack of coverage of modern phylogenetics and its contribution to the evidence supporting evolution. Shouldn't the the similarities seen in the DNA of related organisms be recognized as one of the most powerful lines of evidence supporting the truth of evolution? Although this subject is mentioned in passing, the scant attention devoted to it may stem from Coyne's view that "molecular methods have not produced much change in the pre-DNA era trees of life" (p. 10). I think most modern phylogeneticists could take exception to this remark by citing any number of insights on the tree of life that were only possible with the use of molecular data. Indeed, some of these insights are brushed under the carpet by the few figures of phylogenetic trees contained in Coyne's book. Figure 1 (see image) and the accompanying discussion on page 6 about the relationship between birds and reptiles, for example, exclude tuataras, turtles and crocodiles, imply that lizards and snakes are distinct groups (they're not because snakes are nested within lizards), and suggest that most modern non-avian reptiles are a monophyletic sister group to dinosaurs and birds (this is only true if crocs and turtles are included with the birds and dinosaurs). The exclusion of turtles is particularly relevant because they are one of the most striking examples of how the visible traits of organisms and their DNA sequences do not give similar information about evolutionary relationships.

Nit-picky criticisms aside, Newsweek was right to include Why Evolution is True among it's 50 top books for our time. If you're going to read one book in preparation for your next encounter with a doubter of evolution, Why Evolution is True should be at the top of your list.