Aaron A. King, Ph.D.

Nelson G. Hairston Collegiate Professor of Ecology, Evolutionary Biology,
Complex Systems, and Mathematics, 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
Theoretical Population Biology 143:  77–91, 2022.
Markov genealogy processes for phylodynamic inference.

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 nonlinear filtering equation which can be used to design efficient Monte Carlo inference algorithms. We demonstrate these calculations with several examples. Existing full-information approaches for phylodynamic inference are special cases of the theory.

The official version of the paper is here.   Please contact Prof. King if you'd like a reprint.

© 2024 Aaron A. King
3038 Biological Sciences Building
1105 North University Avenue
Ann Arbor MI 48109-1085 USA