Brian O'Meara Lab

Methods using phylogenetic information have become powerful tools for addressing the evolution of morphological, behavioral, geographical, genetic, biochemical, and physiological traits. Information on the relevant literature and software is widely scattered and often segregated into different sub-disciplines, leading to empiricists choosing to use suboptimal methods or giving up on certain types of questions and to theoreticians failing to develop models where needed and occasionally duplicating the work of others. I am creating a relational database of relevant questions, methods, and software, and developing a website based on this database (development site at http://treetapper.nescent.org; the final url is http://www.treetapper.org; there is also a progress blog). Users will eventually be able to search for software to address a particular question; developers will be able to search for questions lacking adequate methods and methods not yet implemented in software. This is different from existing tools, like Felsenstein's excellent list of phylogenetic software, in that it can highlight  areas not connected to software (the white boxes in the diagram on the right), allowing holes to be filled. There will also be implementation differences (TreeTapper adds information about links between authors, how popular various programs or methods are, and a faster search, but Felsenstein's site covers a broader range of programs, including those that make, rather than just use, trees).
Problems inspiring this: I want to build methods, and for that it's good to know where the holes are; I also got annoyed at papers using what seemed to be less powerful methods when existing methods, perhaps in a slightly different field, would have served better, suggesting that finding appropriate methods is difficult.
Results: TreeTapper (development in progress)

Delimiting species is a hard problem, especially because speciation is (often) a gradual process but we require species to be discrete. There are a variety of conventional methods for splitting populations into different species (looking for distinctness in sympatry, looking for traits that would prevent interbreeding, etc.) and several new "DNA barcoding"-like techniques, using a tree with branch lengths from a single marker to infer species boundaries. I have made a new approach to complement existing approaches: it uses a set of topologies from independent genes and by looking at the conflict and consistency between the gene trees, infers the species tree and species boundaries simultaneously, not requiring any a priori statements about which samples belong in which species. The first method I created is nonparametric; to my great surprise, it actually seems to work in many cases (it has been accepted, pending major review, for Systematic Biology). On the right are ten gene trees with samples from Drosophila pseudoobscura, D. persimilis, and D. ps. bogotana, with name colors corresponding to species; the program correctly infers the true rooted species topology, assigning all samples correctly, to return the tree on the lower right. I am now investigating making a parametric version.
Problem inspiring this: Brad Shaffer collecting many gene sequences from what may be multiple species and lacking a good method for using them to understand species boundaries.
Results: A new nonparametric method coded in Brownie for jointly estimating the species tree and boundary (in review)

One of the reasons I work in this area of biology is the amazing power using phylogenetic trees gives us for understanding how evolution occurs. People have used phylogenetic methods to infer how adaptive radiations occur, how extinct species attracted mates, how behavior and morphology coevolve, and more. With collaborators, I made a method to test for different rates of evolution on different parts of a tree. I've now extended this to allow testing for correlations between discrete states and continuous rates, discrete character changes and continuous rates, discrete states and continuous character means, and other questions. I've also developed a method to look at branch-specific transition rates to create a test for faster rates of gene loss in specialist rather than generalist herbivores.
Problems inspiring this: Peter Wainwright wanting a measure of disparity correctly taking into account phylogeny; questions I wanted to address for my ants but for which there were no appropriate techniques; Lindy McBride having a question about gene loss in Drosophila; obvious holes needing filling
Results: Various methods implemented in Brownie, publications in Evolution and Genetics [the latter a signed appendix], two more manuscripts nearing submission.

Myrmecocystus (Westmael 1838) ants occur in arid regions of western North America. They are probably best known (even to Darwin) for their habit of having replete workers: specialized workers with greatly swollen gasters that store liquids, such as nectar, for times of scarcity. These ants also do dynamic territory allocation using ritual combat,  have inter- and intraspecific slavery, and, in some species, do burst foraging, where all the foragers for the day will leave in one or a few clumps but then forage singly. Different species, generally divided into different subgenera, will forage at different times: some species only forage during the hot part of the desert day, skittering over painfully hot (at least to me) rocks and picking up dead insects and nectar; some only forage during the cold of the night, and some only forage at sunset or dawn. Foraging time might plausibly be correlated with certain morphological traits, like eye size or leg length; one could also postulate that it might be harder for the ants to invade the diurnal foraging time period than other time periods (some ants with other foraging periods die within ten minutes of exposure during the day). I developed methods to test these ideas. First, though, I needed a phylogeny, so I sequenced one mitochondrial and eight nuclear genes for the majority of the species in the group (some of the missing species have only been collected a  handful of times, sometimes in regions now paved by Los Angeles). To infer the phylogeny, I wanted to use a mixed model but wanted to avoid the potential pitfalls of Bayesian methods (see Yang & Rannala 2005), so I modified MrBayes to turn it into a likelihood search program, MrFisher. I also did over thousand morphological measurements for ecologically-interesting traits and created interactive online keys (dichotomous or multi-entry (1, 2, 3)), species pages, and range maps.
Problem inspiring this: Wanting to understand the evolution of these critters.
Results: Two manuscripts in the pipeline, new methods & software, new genes for ant phylogeny, a new phylogeny and measurements, new online resources.

I also address other interesting problems as they come up. For example, I was part of a group creating trees from Genbank using a sparse supermatrix approach. I've also done phylogenies of bark beetles and Dryophthorid weevils (the latter two projects as part of the Farrell lab as an undergraduate).