I am interested in research on how we can analyze complex population genetic models using genetic/genomic data and also how to compare such models efficiently. I prefer genealogical (coalescent) approaches over allele/site-frequency based approaches believing that separating mutation processes from the genealogical process gives more choices in analysis. My software development is aimed at methods that can handle thousands of loci for models with many parameters.
With my students, we explore inference methods that can incorporate uncertainty caused by sequencing errors and model assumption violations.
I am still interested how water frogs colonized Europe after the last glaciation, I have now the tools but not yet the data. I have a long standing collaboration with Joerg Ploetner, Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität in Berlin.
Beerli, P., and Palczewski, M. Unified framework to evaluate panmixia and migration direction among multiple sampling locations. Genetics 185 (2010), 313–326.
Beerli, P. How to use MIGRATE or why are Markov chain Monte Carlo programs difficult to use? In Population Genetics for Animal Conservation, G. Bertorelle, M. W. Bruford, H. C. Hauffe, A. Rizzoli, and C. Vernesi, Eds., vol. 17 of Conservation Biology. Cambridge University Press, Cambridge UK, 2009, pp. 42–79.
Beerli, P. Comparison of Bayesian and maximum likelihood inference of population genetic parameters. Bioinformatics 22, 3 (2006), 341–345.
Beerli, P. Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Molecular Ecology 13, 4 (2004), 827–836.
Plötner, J., Uzzell, T., Beerli, P., Akın, C ̧., Bilgin, C. C., Haefeli, C., Ohst, T., Köhler, F., Schreiber, R., Guex, G.-D., et al. Genetic divergence and evolution of reproductive isolation in eastern mediterranean water frogs. In Evolution in Action. Springer Berlin Heidelberg, 2010, pp. 373– 403.
Akın, C ̧., Bilgin, C. C. C., Beerli, P., Westaway, R., Ohst, T., Litvinchuk, S. N., Uzzell, T., Bilgin, M., Hotz, H., Guex, G.-D., and Plötner, J. Phylogeographic patterns of genetic diversity in eastern mediterranean water frogs are shaped by past geologic events and cyclic climate changes. Journal of Biogeography 37, 11 (2010), 2111–2124.
Beerli, P., Hotz, H., and Uzzell, T. Geologically dated sea barriers calibrate a protein clock for Aegean water frogs. Evolution 50, 4 (1996), 1676–1687.