Saturday, December 25, 2010

New blogs

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" (, 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 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!

Tuesday, November 16, 2010

Morris Goodman (1925-2010)

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.

Wednesday, November 10, 2010

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

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.

Tuesday, November 9, 2010

Tips for Writing a Systematics DDIG Part 5: Broader Impacts

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.

Monday, November 8, 2010

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

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.

Thursday, November 4, 2010

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

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?

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.

Tuesday, November 2, 2010

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

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.

Thursday, October 28, 2010

City Life - and the Evolution of Immunity

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 FST 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.

Tuesday, October 26, 2010

Somebody Missed the Dover Trial...

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?

Friday, October 22, 2010

Testing for Trait-Dependent Molecular Evolution

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.

Monday, October 18, 2010

Leigh Van Valen (1935-2010)

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.

Wednesday, October 13, 2010

Estimating Diversification Rates

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.)

Friday, October 8, 2010

New Issue of Systematic Biology

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:

Friday, October 1, 2010

Evolution Since Darwin

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.

Friday, September 17, 2010

Anolis steals cover of "Evolution"

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.

Tuesday, August 31, 2010

Bed Bugs!

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!

Thursday, July 29, 2010

Workshop on HPC for Phylogenetics

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.

Tuesday, July 6, 2010


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!

Tuesday, June 29, 2010

The Evolution of Sex

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.

Monday, June 28, 2010

Calibrating Phylogenies from the Fossil Record

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"

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!")

Sunday, June 27, 2010

Portland 2010

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.

Friday, June 25, 2010

Blogging Evolution 2010 in Portland Oregon

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.

Monday, May 24, 2010

arXiv your paper!

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

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.

Friday, April 23, 2010

Size-advantage in sex changing fish

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.

Wednesday, April 14, 2010

Announcement: Comparative Methods and Macroevolution In R Summer Short Course

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 ( and Luke Harmon ( with any questions.

Application deadline: May 15th.

Monday, April 12, 2010

Arborescence and the Rate of Evolution in Plants

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.

Saturday, April 10, 2010

Goodbye...for now?

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.

Friday, March 26, 2010

Testing for Nonlinear Selection

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.

Friday, March 12, 2010

On the Improbability of One-tailed Hypothesis Tests

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.

Wednesday, March 10, 2010

Resolving the Vertebrate Tree

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!

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.

Tuesday, March 9, 2010

The Price of Parenthood

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.

Monday, March 8, 2010

Bodega Phylogenetics 2010 is Underway

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.

Tuesday, March 2, 2010

Speak now or (forever?) hold your peace

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.

Saturday, February 27, 2010

Toe Pads & Tails

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.

Wednesday, February 17, 2010

One Year of Stimulating Science

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.

Monday, February 15, 2010

In Memoriam: John Thorbjarnarson

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.

Friday, February 12, 2010

Darwin Day at Case Western Reserve University

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!