Online Phylogenetics Seminar!

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

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

Masters Programs in Systematics

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

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

Phylogenetic Model Selection, Sans PAUP*

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

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

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

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

Haiti Getting Kicked While Down (Again)

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

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

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

Music Video Tribute to Dolph Schluter

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

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

[Thanks RichF!]

Parasite of the Day

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

Priors and convergence in BEST

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

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

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

Blogging SICB 2010

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

Welcome to Our World

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