Antz!

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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

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

Calibrating Phylogenies from the Fossil Record

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!")

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.

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.

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.

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.

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 (michaelalfaro@ucla.edu) and Luke Harmon (lukeh@uidaho.edu) with any questions.

Application deadline: May 15th.