Schedule for: 17w5104 - Mathematical Approaches to Evolutionary Trees and Networks

A buffet dinner is served daily between 5:30pm and 7:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.

Breakfast is served daily between 7 and 9am in the Vistas Dining Room, the top floor of the Sally Borden Building.

Usual statistical inference techniques for the tree of life like maximum likelihood and bayesian inference through Markov chain Monte Carlo (MCMC) have been widely used, but their performance declines as the datasets increase (in number of genes or number of species). I will present two new approaches suitable for big data: one, importance sampling technique for bayesian inference of phylogenetic trees, and two, a pseudolikelihood method for inference of phylogenetic networks. The proposed methods will allow scientists to include more species into the tree of life, and thus complete a broader picture of evolution.

A buffet dinner is served daily between 5:30pm and 7:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.

A buffet dinner is served daily between 5:30pm and 7:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.

A buffet dinner is served daily between 5:30pm and 7:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.

A buffet dinner is served daily between 5:30pm and 7:30pm in the Vistas Dining Room, the top floor of the Sally Borden Building.

Ever since Darwin’s first sketch of a phylogenetic tree, such trees are the model of choice for most evolutionary studies. But unfortunately, trees are unable to explain phenomena like horizontal gene transfer and hybridization. As many organisms are known to be subject to these evolutionary events, phylogenetic trees are more and more replaced by so-called phylogenetic networks. The aim is then to find the best network for a given dataset according to an optimization criterion. One such criterion often used for phylogenetic tree reconstruction is Maximum Parsimony. In my talk, I will present different ways to extend the parsimony concept from trees to networks, and I will explain some interesting properties of parsimony on networks. In particular, I will show that in networks, even the so-called “small parsimony problem” is hard, and I will also show that, in contrast, the “big” parsimony problem has some trivial solutions. The results presented in my talk are joint work with Leo van Iersel, Steven Kelk and Céline Scornavacca (small parsimony problem) as well as with Christopher Bryant, Simone Linz and Charles Semple (big parsimony problem).

Processes such as hybridization, horizontal gene transfer, and recombination result in reticulation which can be modeled by phylogenetic networks. Earlier likelihood-based methods for inferring phylogenetic networks from sequence data have been encumbered by the computational challenges related to likelihood evaluations. Consequently, they have required that the possible network hypotheses be given explicitly or implicitly in terms of a backbone tree to which reticulation edges are added. To achieve speed required for unrestricted network search instead of only adding reticulation edges to an initial tree structure, we employ several fast approximate inference techniques. Preliminary numerical and real data experiments demonstrate that the proposed method, PhyloDAG, is able to learn accurate phylogenetic networks based on limited amounts of data using moderate amounts of computational resources.

5-day workshop participants are welcome to use BIRS facilities (BIRS Coffee Lounge, TCPL and Reading Room) until 3 pm on Friday, although participants are still required to checkout of the guest rooms by 12 noon.