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.