Gonzalez, E. G., P. Beerli, and R. Zardoya (2008). Genetic structuring and migration patterns

of Atlantic bigeye tuna (Thunnus obesus). BMC Evolutionary Biology (PDF)

Hotz, H., P. Beerli, T. Uzzell, G.-D. Guex, N. M. Pruvost, R. Schreiber, J. Plötner (in prep.).

Balancing a cline by influx of migrants: genetic transition in water frogs of eastern Greece.

Miyamoto, M. M., P. E. Moler, P. Beerli. (in prep.). A structured-coalescence analysis of nuclear

and mitochondrial DNA diversity within the salamander genus Pseudobranchus.

Douhan G. W., Smith M. E., Huyrn K. L., Westbrook A., Beerli P., and Fisher A. J. (2008) Multigene

analysis suggests ecological speciation in the fungal pathogen Claviceps purpurea. Molecular

Ecology 17: 2276-2286. (PDF)

Plötner J., Uzzell T. , Beerli P., Spolsky C. , Ohst T., Litvinchuk S. N. , Guex G.-D., Reyer H.-U.,

Hotz H. (2008). Widespread unidirectional transfer of mitochondrial DNA: a case in

western Palearctic water frogs. Journal of Evolutionary Biology, 21: 668-681. (PDF)

Hotz, H., Guex, G.-D., Beerli, P., Semlitsch, R. D., and Pruvost, N. (2008). Hemiclone diversity

in the hybridogenetic frog Rana esculentaoutside the area of clone formation: the view from

protein electrophoresis. Journal of Zoological Systematics and Evolutionary Research

46: 5662. (PDF)

Beerli, P. (2007). Estimation of the population scaled mutation rate from microsatellite data.

Genetics 177:1967-1968. (PDF)

Plötner, J.,  F. Köhler, T. Uzzell, P. Beerli. (2007). Molecular Systematics of Amphibians.

In Amphibian biology, Volume 7 (Eds. Heatwole, H., and M. Tyler). Surrey Beatty & Sons.

Chipping Norton, Australia. Pp. 2672-2756. (PDF)

Beerli, P. (2006). Comparison of Bayesian and maximum likelihood inference of population

genetic parameters. Bioinformatics 22(3): 341-345. (PDF)

Mu J, Joy D.A., Duan J., Huang Y., Carlton J., Walker J., Barnwell J., Beerli P., Charleston M.A.,

Pybus O.G., Su X.Z. (2005). Host Switch Leads to Emergence of Plasmodium vivax

Malaria in Humans. Molecular Biology and Evolution 22(8):1686-1693 (PDF)

Beerli, P. (2004). Effect of unsampled populations on the estimation population sizes and

migration rates between sampled populations. Molecular Ecology 13: 827 - 836. (PDF)

Joy, D.A., X. Feng, J. Mu, T. Furuya, K. Chotivanich, A. U. Krettli, M. Ho, A. Wang, N. J. White,

E. Suh, P. Beerli, and X. Su. (2003). Early Origin and Recent Expansion of Plasmodium

falciparum. Science 300:318-321. (PDF)

Brumfield, R., P. Beerli, D. Nickerson, and S. Edwards. (2003). Single Nucleotide Polymorphisms

in Phylogeography. Trends in Ecology and Evolution 18(5): 249-256. (PDF)

Beerli, P., and S. V. Edwards. (2002). When did the Neanderthals and modern humans diverge?.

Centenary Anniversary Anthropology Institute University of Zurich (1999), Evolutionary

Anthropology 11: 60-63 Suppl. 1 (PDF)

Kingsolver, J. G., H. Hoekstra, J. Hoekstra, D. Berrigan, S. Vignieri, C. Hill, A. Hoang, P. Gibert,

and P. Beerli. (2001). The Strength of Phenotypic Selection in Natural Populations.

American Naturalist 157:245-261. (PDF)

Hoekstra H., J. Hoekstra, D. Berrigan, S. Vignieri, C. Hill, A. Hoang, P. Gibert, P. Beerli, and J.

G. Kingsolver. (2001). The Strength and Tempo of Directional Selection in the Wild.

Proceedings of the National Academy of Sciences, USA 98(16):9157-9160. (PDF)

Beerli, P. and J. Felsenstein. (2001). Maximum likelihood estimation of a migration matrix and

effective population sizes in n subpopulations using a coalescent approach. Proceedings of

the National Academy of Sciences USA 98(8):4563-4568. (PDF)

Kuhner, M. K., P. Beerli, Jon Yamato, and Joseph Felsenstein. (2000). Usefulness of single nucleotide

polymorphism data for estimating population parameters. Genetics 156:439-447. (PDF)

Kuhner, M. K., and P. Beerli. (2000). Comments in Discussion of paper by Stephens, M. and

Donnelly, P. Inference in molecular population genetics. Journal of Royal Statistical

Society Series B 62(4):605-635 (Comments in pages 642-643). (PDF)

Edwards, S. V., and P. Beerli. (2000). Perspective: Gene divergence, Population divergence, and

the variance in coalescence time in phylogeographic studies. Evolution 54(6):1839-1854. (PDF)

Hotz, H., R. Semlitsch, G.-D. Guex, and P. Beerli. (1999). Spontaneous heterosis in larval life-

history traits of hemiclonal frog hybrids, Proceedings of the National Academy of

Sciences USA 96: 2171-2176. (PDF)

Felsenstein, J. , M. K. Kuhner, J. Yamato, and P. Beerli. (1999). Likelihoods on coalescents: a

Monte Carlo sampling approach to inferring parameters from population samples of

molecular data. Lecture Notes - Monograph Series, Institute of Mathematical Statistics

33: 163-185. (PDF)

Beerli, P. and J. Felsenstein. (1999). Maximum likelihood estimation of migration rates and

effective population numbers in two populations. Genetics 152: 763-773. (PDF)

Beerli, P. (1997). Letter to the Editor: Statistical analyses of population genetic data. Trends in

Ecology and Evolution 12: 488. (PDF)

Semlitsch, R. D., S. Schmiedehausen, H. Hotz, and P. Beerli. (1996). Genetic compatibility between

sexual and clonal genomes in local populations of the hybridogenetic Rana esculenta

complex. Evolutionary Ecology 10(5): 531-543.

Hotz H., T. Uzzell, P. Beerli, and G.-D. Guex. (1996). Are hybrid clonals species? A case for

enlightened anarchy. Amphibia-Reptilia 17: 315–320.  (PDF)

Beerli, P., H. Hotz, and T. Uzzell. (1996). Geologically dated sea barriers calibrate an average

protein clock in water frogs of the Aegean region. Evolution 50(4): 1676-1687. (PDF)

Beerli, P., H. Hotz, H. Tunner, S. Heppich, and T. Uzzell. (1994). Two new water frog species

from the Aegean islands Crete and Karpathos. (Amphibia, Salientia, Ranidae). Notulae

Naturae, Acad. Nat. Sci. Philadelphia (470): 1-9. (PDF)

Hotz, H., P. Beerli, and C. Spolsky. (1992). Mitochondrial DNA reveals formation of nonhybrid

frogs by natural matings between hemiclonal hybrids. Molecular Biology and Evolution

9(4): 610-620. (PDF)

Beerli, P., H. Billing, and B. Schätti. (1986). Taxonomischer Status von Vipera latasti monticola

Saint Girons, 1953. Salamandra 22(2/3): 101 - 104. (PDF)

Beerli, P. (1985). Amphibieninventar des Kantons Thurgau. Mitt. thurg. naturf. Ges. 46: 7-51 (PDF)