Below is a brief description of several recent projects to give you a sense of the kinds of research questions we address. The biggest emphasis currently is on Bayesian phylogenetic inference. This field is perhaps not in its infancy anymore, but it certainly has not yet achieved adulthood, and there are many important problems still needing work, especially in areas such as model comparison, mixing, and convergence diagnostics. A list of published and in press papers follows the project descriptions.
Bayesian Star Tree Paradox
If sequence data are simulated using a 4-taxon star tree (such as the one shown on the right) and evaluated with standard software tools for Bayesian phylogenetic inference, one of the 3 possible fully-resolved trees is often supported very strongly. This is paradoxical in that most people expect the three possible resolutions to be equally supported in this case, but such an outcome is only seen when the sequence length is tiny (e.g. 1 site). It appears that uncertainty in this case is manifested in the inability to predict, from dataset to dataset, which of the 3 possible fully-resolved tree topologies will be favored. This behavior is troubling, and possible examples of this behavior have been pointed out by several researchers. Many more potential examples can be found in the literature by looking for high posterior probabilities but low bootstrap support, combined with tiny internal edges.
We argue that the central problem here is the non-identifiability of the tree topology, and propose a solution using reversible-jump MCMC. Our rjMCMC sampler visits not only fully-resolved tree topologies, but can visit topologies containing hard polytomies as well. This effectively places a point mass prior probability on polytomies, providing an alternative in situations in which a fully-resolved topology is not a reasonable option. The analysis can be made as conservative as desired by modifying the prior distribution assumed for topologies, but in our (albeit limited) experience it does not appear easy to destroy support for real edges by using a prior that strongly supports polytomous topologies.
Reference: Lewis, P. O., Holder, M. T., and Holsinger, K. E. 2005. Polytomies and Bayesian phylogenetic inference. Systematic Biology 54(2): 241-253 [link to online resource].
Phylodiversity in Desert Green Algae (the other land plants)
A major thrust in the laboratory of Louise Lewis is diversity and systematics of green algae (Phylum Chlorophyta) living in the soils of North American deserts. These unicellular green algae are capable of tolerating the harsh conditions posed by desert soil environments, and represent an important (yet not well understood) component of desert microbiotic crust communities. The 18S rDNA sequences of a number of green algal isolates have been determined, and these data suggest that several lineages of green algae have diversified within deserts. One might be tempted to think that the green algal cells isolated from desert soils are simply the result of spores dispersed into deserts from distant aquatic sources. This study shows that the 18S sequences of these desert isolates are more divergent from their nearest aquatic relatives than would be predicted if they were merely incidental visitors. We characterize the molecular phylodiversity of desert green algae and demonstrate with a Bayesian analysis of 150 green algal 18S sequences that all freshwater classes of green algae have yielded desert lineages. The numerous transitions from desert to aquatic existence apparent from the phylogeny argue that it is no longer accurate to portray land plants as resulting from a single origin. The highly celebrated origin leading to the embryophytes is but one of many transitions to terrestriality.
Reference: Lewis, L. A., and Lewis, P. O. 2005. Unearthing the molecular phylodiversity of desert soil green algae (Chlorophyta). Systematic Biology 54(6): 936-947 [link to online resource].
Frequently Asked Questions:
Holder, Mark T., Lewis, P. O., Swofford, D. L., and Larget, B. 2005. Hastings ratio of the LOCAL proposal used in Bayesian phylogenetics. Systematic Biology 54(6): 961-965 [link to online resource]
Brauer, M. J.,, Dries, L. A., Zwickl, D. J., , and Hillis, D. M. 2002. Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference. Molecular Biology and Evolution 19: 1717-1726.
Holsinger, K. E.,, and Dey, D. K. 2002. A Bayesian approach to inferring population structure from dominant markers. Molecular Ecology 11: 1157-1164.
Swofford, D. L., Waddell, P. J., Huelsenbeck, J. P., Foster, P. G.,, and Rogers, J. S. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Systematic Biology 50: 525-539.
2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50:913-925.
, and 2001. Effects of nucleotide composition bias on the success of the parsimony critierion in phylogenetic inference. Molecular Biology and Evolution 18: 1024-1033.
, and Swofford, D. L. 2001. Back to the future: Bayesian inference arrives in phylogenetics. Trends in Ecology and Evolution 16: 600-601. (conference report)
1998. Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data. Pages 132-163 in: Soltis, D. E., Soltis, P. S., and Doyle, J. J., Molecular Systematics of Plants II. Kluwer, Boston.
1998. A genetic algorithm for maximum likelihood phylogeny inference using nucleotide sequence data. Molecular Biology and Evolution 15:277-283.
Gaut, B. S., and1995. Success of maximum likelihood phylogeny inference in the four-taxon case. Molecular Biology and Evolution 12:152-162.
, and Crawford, D. J. 1995. Pleistocene refugium endemics exhibit greater allozymic diversity than widespread congeners in the genus Polygonella (Polygonaceae). American Journal of Botany 82:141-149.
Williams, C. G., Hamrick, J. L., and1995. Multiple-population versus hierarchical conifer breeding programs: a comparison of genetic diversity levels. Theoretical and Applied Genetics 90: 584-594.
, and 1995. MEGA: Molecular evolutionary genetics analysis, version 1.02. Systematic Biology 44: 576-577. (software review)
Kaplan, N.L.and Weir, B. S. 1994. Age of cystic fibrosis mutation. Nature Genetics 8: 216.
Snow, A. A., and1993. Reproductive traits and male fertility in plants: empirical approaches. Annual Review of Ecology and Systematics 24: 331-351.
Govindaraju, D.,, and Cullis, C. 1992. Phylogenetic analysis of pines using ribosomal DNA restriction fragment length polymorphisms. Plant Systematics and Evolution 179: 141-153.
, and Snow, A. A. 1992. Deterministic paternity exclusion using RAPD markers. Molecular Ecology 1:155-160.
1991. Allozyme variation in the rate Gulf Coast endemic Polygonella macrophylla Small (Polygonaceae). Plant Species Biology 6: 1-10.