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Biased sampling

Nicola De Maio
University of Oxford

New routes to phylogeography: a Bayesian structured coalescent approximation

Nicola De Maio
Nicola De Maio

Phylogeographic methods aim to infer migration trends and the history of sampled lineages from genetic data. Applications of phylogeography are broad, and in the context of pathogens include the reconstruction of transmission histories and the origin and emergence of outbreaks. Phylogeographic inference based on bottom-up population genetics models is computationally expensive, and as a result faster alternatives based on the evolution of discrete traits have become popular. In this seminar I will discuss the advantages and disadvantages of different phylogeographic methods, in particular, I will address the issue of the sensitivity of discrete trait methods to the sampling strategy. I will also present a new method called BASTA (BAyesian STructured coalescent Approximation), implemented in BEAST2, that combines the accuracy of methods based on the structured coalescent with the computational efficiency required to handle more than just few populations. I will illustrate the potentially severe implications of model choice for phylogeographic analyses by investigating the zoonotic transmission of Ebola virus and the between-species transmission of the Avian Influenza Virus.