Evolutionary Analyses of Serially Sampled Populations

Allen G. Rodrigo1, Alexei Drummond1, Roald Forsberg2, and David Nickle3

1: Computational and Evolutionary Biology Laboratory, University of Auckland, New Zealand 2: Department of Ecology and Genetics, University of Aarhus, Denmark 3: Department of Microbiology, University of Washington, Seattle

The analysis of serially sampled populations presents a relatively new challenge for evolutionary geneticists. In this presentation, we introduce the concept of the "measurably evolving population", and describe a likelihood ratio test for the accumulation of substitutions from one sampling time to the next. We also described a new method — serial sample UPGMA (sUPGMA) – that allows the phylogeny of serially sampled sequences to be reconstructed under the assumption of a molecular clock. Finally, we discuss the estimation of population and mutation parameters under different models appropriate for measurably evolving populations.

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