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dechronization



Evolution, phylogenetic trees, comparative methods, and natural history



Updated: 2017-12-17T06:58:44.288-05:00

 



1 Comments

2011-06-06T11:53:04.090-04:00

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

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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

2011-01-30T14:57:15.370-05:00

p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica} p.p2 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; min-height: 14.0px} p.p3 {margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; color: #0000ad} span.s1 {letter-spacing: 0.0px} span.s2 {text-decoration: underline ; letter-spacing: 0.0px} span.s3 {text-decoration: underline ; letter-spacing: 0.0px color: #0000ad} 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

2011-01-31T13:50:51.802-05:00

(image) 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

2011-01-24T13:23:35.929-05:00

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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

2011-01-21T13:41:54.778-05:00

(image) 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

2010-12-25T14:41:47.883-05:00

(image) 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)

2010-11-17T20:23:06.509-05:00

(image) 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

2010-11-10T16:15:36.388-05:00

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

2010-11-09T13:35:31.353-05:00

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?

2010-11-08T10:23:03.906-05:00

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?

2010-11-04T17:03:32.142-04:00

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?

2010-11-04T17:01:31.486-04:00

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

2010-11-02T16:00:54.047-04:00

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

2010-10-28T18:26:30.340-04:00

(image) 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.



Somebody Missed the Dover Trial...

2010-10-26T19:05:00.173-04:00

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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

2010-10-22T15:06:39.783-04:00

(image) 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)

2010-10-19T10:50:25.538-04:00

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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.



Estimating Diversification Rates

2010-10-16T21:45:59.776-04:00

(image) 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

2010-10-08T02:13:59.315-04:00

(image) 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:






Evolution Since Darwin

2010-10-01T13:56:51.946-04:00

(image) 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"

2010-09-17T10:24:17.619-04:00

(image) 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!

2010-08-31T04:07:02.119-04:00

(image) 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

2010-07-29T15:47:45.966-04:00

(image) 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!

2010-07-06T23:24:20.492-04:00

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

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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

2010-06-29T17:34:20.670-04:00

(image) 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.