Speaker:

Alexei Drummond, The University of Auckland

Title:

Inferring Species Trees Using Integrative Models of Species Evolution

Location:

Owheo G34 - 10:00am, Wednesday 24 October

Abstract:

Bayesian methods can be used to accurately estimate species tree topologies, ancestral divergence times and other parameters, but only when the models of evolution sufficiently account for the underlying evolutionary processes. Multispecies coalescent (MSC) models have been shown to accurately account for the evolution of genes within species in the absence of strong gene flow between lineages, and fossilized birth-death (FBD) models have been shown to estimate divergence times from fossil data in good agreement with expert opinion. Until now dating analyses using the MSC have been based on a fixed clock or informally derived calibration priors instead of the FBD. On the other hand, dating analyses using an FBD process have concatenated all gene sequences and ignored coalescence processes. To address these mirror-image deficiencies in evolutionary models, we have developed an integrative model of evolution which combines both the FBD and MSC models. By applying concatenation and the MSC (without employing the FBD process) to an exemplar data set consisting of molecular sequence data and morphological characters from the dog and fox subfamily Caninae, we show that concatenation causes predictable biases in estimated branch lengths. We show that these biases can be avoided by using the FBD-MSC model, which coherently models fossilization and gene evolution, and does not require an a priori substitution rate estimate to calibrate the molecular clock. We have implemented the FBD-MSC in a new package developed for the BEAST2 phylogenetic software platform.

Biography:

Alexei Drummond is a Professor of Computational Biology in the Department of Computer Science at The University of Auckland and Director for the Centre for Computational Evolution - a centre involved in developing software tools and mathematical models for understanding evolution and molecular ecology from genes to genomes. He completed his BSc in Biology and Computer Science at The University of Auckland in 1996, followed by a PhD in Bioinformatics at the University of Auckland in 2002. This was followed by three years of post-doctoral research in the Department of Statistics and the Department of Zoology at the University of Oxford. Alexei's research interests are centred around probabilistic models at the intersection of computational biology, phylogenetics, population genetics, epidemiology and evolution. He has led a team of students, postdocs, and colleagues in that has transformed the way biologists use genetic data to study evolution. The team has developed software that has become the leading tool for investigating how viruses evolve, and for addressing leading questions about the origin of species. His software is used daily all over the world and is having a major impact in areas such as human health and disease epidemiology.