Aaron A. King, Ph.D.

Nelson G. Hairston Collegiate Professor of Ecology, Evolutionary Biology,
and Complex Systems, University of Michigan
External Professor, Santa Fe Institute
Fellow of the American Association for the Advancement of Science

Markov genealogy processes

A. A. King, Q. Lin, and E. L. Ionides
arXiv 2105.12730 2021.

We construct a family of genealogy-valued Markov processes that are induced by a continuous-time Markov population process. We derive exact expressions for the likelihood of a given genealogy conditional on the history of the underlying population process. These lead to a version of the nonlinear filtering equation, which can be used to design efficient Monte Carlo inference algorithms. Existing full-information approaches for phylodynamic inference are special cases of the theory.


A preprint of the paper is here.   Please contact Prof. King if you'd like a reprint.

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