| 2006 | Pl¨otner, J., F. K ¨ohler, T. Uzzell, P. Beerli, and C. Spolsky. Molecular Systematics of Amphibians. In Amphibian biology, Volume 5 (Ed. Heatwole, Harold). Surrey Beatty |
| 2006 | Beerli, P. Book review: Statistical methods in (molecular) evolution. Evolution 60: 421-423. (PDF) |
| 2006 | Comparison of Bayesian and maximum likelihood inference of population genetic parameters. Bioinformatics 22(3): 341-345. (PDF) |
| 2005 | Chi, H. , P. Beerli, D. Evans, and M. Mascagni. On the Scrambled Sobo\'l Sequences. Lecture Notes in Computer Science 3615: 775-782. |
| 2005 | 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 |
| 2004 | Beerli, P. Effect of unsampled populations on the estimation population sizes and migration rates between sampled populations. Molecular Ecology 13: 827–836. |
| 2003 | Brumfield, R., P. Beerli, D. Nickerson, and S. Edwards. Single Nucleotide Polymorphisms in Phylogeography. Trends in Ecology and Evolution 18(5): 249-256. |
| 2003 | 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. Early Origin and Recent Expansion of Plasmodium falciparum. Science 300:318-321. |
| 2002 | Beerli, P., and S. V. Edwards. When did the Neanderthals and modern humans diverge?. Centenary Anniversary Anthropology Institute University of Zurich (1999), Supplement Evolutionary Anthropology. |
| 2002 | Arbogast, B., S. Edwards, J. Wakeley, P. Beerli, and J. Slowinski. Estimating divergence times from molecular data on population genetic and phylogenetic time scales. Annual reviews in Ecology and Systematics 33: 707-740. doi: 10.1146/annurev.ecolsys.33.010802.150500. |
| 2001 | Beerli, P. and J. Felsenstein. 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. |
| 2001 | Hoekstra H., J. Hoekstra, D. Berrigan, S. Vignieri, C. Hill, A. Hoang, P. Gibert, P. Beerli, and J. G. Kingsolver. The Strength and Tempo of Directional Selection in the Wild. Proceedings of the National Academy of Sciences, USA 98(16):9157-9160. |
| 2001 | Hotz, H., T. Uzzell, G.-D. Guex, D. Alpers, R. D. Semlitsch, P. Beerli. Microsatellites: a tool for evolutionary genetic studies of western Palearctic water frogs. In: Third international symposium on genetics, systematics, and ecology of western Palearctic water frogs, Eds. J. Pl¨otner, and D. Schmeller. Mitteilungen aus dem Museum f ¨ur Naturkunde in Berlin, Zoologische Reihe 77: 43-50. |
| 2001 | Guex, G.-D., H. Hotz, T. Uzzell, G.-D. , R. D. Semlitsch, P. Beerli, and R. Pascolini. Developmental disturbances in Rana esculenta tadpoles and metamorphs. In: Third international symposium on genetics, systematics, and ecology of western Palearctic water frogs, Eds. J. Pl¨otner, and D. Schmeller. Mitteilungen aus dem Museum f ¨ur Naturkunde in Berlin, Zoologische Reihe 77. |
| 2001 | Kingsolver, J. G., H. Hoekstra, J. Hoekstra, D. Berrigan, S. Vignieri, C. Hill, A. Hoang, P. Gibert, and P. Beerli. The Strength of Phenotypic Selection in Natural Populations. American Naturalist 157:245-261. |
| 2000 | Beerli, P., N. C. Grassly, M. K. Kuhner, D. Nickle, O. Pybus, M. Rain, A. Rambaut, A. G. Rodrigo, and Y. Wang. Population genetics of HIV: parameter estimation using genealogy-based methods. Computational and Evolutionary Analysis of HIV Molecular Sequences. Pp 217-252. In: Computational and Evolutionary Analysis of HIV Molecular Sequences . Eds. A. G. Rodrigo and G. Learn. Kluwer Academic Publishers, Boston. 312 pp. |
| 2000 | Edwards, S. V., and P. Beerli. Perspective: Gene divergence, Population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54(6):1839-1854. |
| 2000 | Kuhner, M. K., and P. Beerli. 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). |
| 2000 | Kuhner, M. K., P. Beerli, Jon Yamato, and Joseph Felsenstein. Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics 156:439-447. |
| 1999 | Beerli, P. and J. Felsenstein. Maximum likelihood estimation of migration rates and effective population numbers in two populations. Genetics 152: 763-773. |
| 1999 | Felsenstein, J. , M. K. Kuhner, J. Yamato, and P. Beerli. 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. |
| 1999 | Hotz, H., R. Semlitsch, G.-D. Guex, and P. Beerli. Spontaneous heterosis in larval life-history traits of hemiclonal frog hybrids, Proceedings of the National Academy of Sciences USA 96: 2171-2176. 3 |
| 1998 | Beerli, P. Estimation of migration rates and population sizes in geographically structured populations. In Advances in molecular ecology (Ed. G. Carvalho). NATO Science Series A: Life Sciences, IOS Press, Amsterdam. Pp 39-53. |
| 1998 | Schnabel, A., P. Beerli, A. Estoup, D. Hillis. A guide to software packages for data analysis on molecular ecology. In Advances in molecular ecology (Ed. G. Carvalho). NATO Science Series A: Life Sciences, IOS Press, Amsterdam. Pp 291-303. |
| 1997 | Beerli, P. Letter to the Editor: Statistical analyses of population genetic data. Trends in Ecology and Evolution 12: 488. |
| 1996 | Beerli, P., H. Hotz, and T. Uzzell. Geologically dated sea barriers calibrate an average protein clock in water frogs of the Aegean region. Evolution 50(4): 1676-1687. |
| 1996 | Hotz H., T. Uzzell, P. Beerli, and G.-D. Guex. Are hybrid clonals species? A case for enlightened anarchy. Amphibia-Reptilia 17: 315-320. |
| 1996 | Semlitsch, R. D., S. Schmiedehausen, H. Hotz, and P. Beerli. Genetic compatibility between sexual and clonal genomes in local populations of the hybridogenetic Rana esculenta complex. Evolutionary Ecology 10(5): 531-543. |
| 1995 | Beerli, P. Amphibien in der Umgebung des Nussbaumer Sees. Pp. 319-323 in: A. Schl¨afli, ed. Die Nussbaumer Seen. Eine Naturmonographie. Ittinger Schriftenreihe 5. Stiftung Kartause Ittingen, Warth (Switzerland). |
| 1994 | Beerli, P., H. Hotz, H. Tunner, S. Heppich, and T. Uzzell. Two new water frog species from the Aegean islands Crete and Karpathos. (Amphibia, Salientia, Ranidae). Notulae Naturae, Acad. Nat. Sci. Philadelphia (470): 1-9. |
| 1993 | Beerli, P. Amphibien des Hudelmoos. Mitt. thurg. naturf. Ges. 51: 257-260. |
| 1993 | Kaden, D. , P. Beerli. Reptilien des Hudelmoos. Mitt. thurg. naturf. Ges. 51: 261-263. |
| 1993 | Kaden, D., P. Beerli. Heuschrecken des Hudelmoos. Mitt. thurg. naturf. Ges. 51: 207-213. |
| 1992 | Hotz, H., P. Beerli, and C. Spolsky. Mitochondrial DNA reveals formation of nonhybrid frogs by natural matings between hemiclonal hybrids. Molecular Biology and Evolution 9(4): 610-620. |
| 1986 | Beerli, P., H. Billing, and B. Sch¨atti. Taxonomischer Status von Vipera latasti monticola Saint Girons, 1953. Salamandra 22(2/3): 101 - 104. |
| 1985 | Beerli, P. Amphibieninventar des Kantons Thurgau. Mitt. thurg. naturf. Ges. 46: 7-51 |