Probability Questions in Phylogenetics

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Assembling the Tree of Life is a fundamental problem in biology that is providing insights into evolution, adaptation, and speciation. Much information about past evolutionary events can be inferred from the analysis of DNA sequence data collected from existing species. A notable feature of the evolution of molecular sequences is the significant role played by chance. In recent years, probability theory, the mathematical study of randomness, has provided key new insights in analyzing the power of statistical methods to reconstruct evolutionary processes in large-scale phylogenetics. The overall goal of this research project is to further investigate these connections. Through the development, analysis, implementation, and dissemination of algorithms for the alignment of molecular sequences and the reconstruction of evolutionary trees, this research will help advance the state of knowledge in evolutionary biology. The project aims to contribute to the numerous benefits to society of phylogenetic research such as the protection of ecosystems from invasive species, the identification of emerging diseases, and the prediction of disease outbreaks. Integration of research and education is a major component of this project. In addition to providing research training for graduate students, course materials will be developed in conjunction with the activities and made widely available. In evolutionary biology, the speciation history of a group of organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves represent current species and whose branchings indicate past speciation events. Phylogenies are commonly estimated from molecular sequences collected from the species of interest. Despite breathtaking advances in sequencing technologies and the development of increasingly more powerful methods, phylogenetic reconstruction remains a challenging problem, and many evolutionary relationships continue to be the source of controversy. Most traditional phylogenetic reconstruction methods involve two steps: multiple sequence alignment and tree estimation. This two-step approach introduces systematic biases that can adversely affect the final tree estimate and other downstream analyses. The general objective of this project is to provide new mathematical insights on alignment methods and their effects on phylogenetic analyses as well as to develop new tools to analyze methodologies that go beyond the traditional two-step approach to phylogenetic reconstruction. This objective will be achieved by further developing the fruitful interface between probability theory and mathematical phylogenetics.