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Beerli, P. 1985. Amphibieninventar des Kantons Thurgau. Mitt. thurg. naturf. Ges. 46: 7-51
*Beerli, P., H. Billing, and B. Schaetti. Taxonomischer Status von Vipera latasti monticola Saint
Girons, 1953. 1986 Salamandra 22(2/3): 101 - 104.
*Hotz, H., P. Beerli, and C. Spolsky. Mitochondrial DNA reveals formation of nonhybrid frogs by
natural matings between hemiclonal hybrids. 1992 Molecular Biology and Evolution 9(4): 610-
620.
Beerli, P. Amphibien des Hudelmoos. 1993. Mitt. thurg. naturf. Ges. 51: 257-260.
Kaden, D. , P. Beerli. Reptilien des Hudelmoos. 1993. Mitt. thurg. naturf. Ges. 51: 261-263.
Kaden, D., P. Beerli. Heuschrecken des Hudelmoos. 1993.Mitt. thurg. naturf. Ges. 51: 207-213.
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.
Beerli, 1995. P. Amphibien in der Umgebung des Nussbaumer Sees. Pp. 319-323 in: A. Schlae?i, ed.
Die Nussbaumer Seen. Eine Naturmonographie. Ittinger Schriftenreihe 5. Stiftung Kartause Ittingen,
Warth (Switzerland).
*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.
*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.
*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.
Beerli, P. 1997. Letter to the Editor: Statistical analyses of population genetic data. Trends in
Ecology and Evolution 12: 488.
Beerli, P. and J. Felsenstein. 1999. Maximum likelihood estimation of migration rates and effective
population numbers in two populations. Genetics 152: 763-773.
*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.
*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.
*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.
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).
*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.
*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.
Guex, G.-D., H. Hotz, T. Uzzell, G.-D. , R. D. Semlitsch, P. Beerli, and R. Pascolini. 2001.
Developmental disturbances in Rana esculenta tadpoles and metamorphs. In: Third international
symposium on genetics, systematics, and ecology of western Palearctic water frogs, Eds. J. Ploetner,
and D. Schmeller. Mitteilungen aus dem Museum fuer Naturkunde in Berlin, Zoologische Reihe
77.
*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.
Hotz, H., T. Uzzell, G.-D. Guex, D. Alpers, R. D. Semlitsch, P. Beerli. 2001. 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. Ploetner, and D. Schmeller. Mitteilungen aus dem Museum fuer Naturkunde in Berlin, Zoologische Reihe 77: 43-50.
*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.
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
*Brum?eld, R., P. Beerli, D. Nickerson, and S. Edwards. 2003. Single Nucleotide Polymorphisms in
Phylogeography. Trends in Ecology and Evolution 18(5): 249-256.
*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.
*Beerli, P. 2004. Effect of unsampled populations on the estimation of population sizes and migration
rates between sampled populations. Molecular Ecology 13: 827 - 836.
*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
*Chi, H. ,P. Beerli, D. Evans, and M. Mascagni 2005. On the Scrambled Sobo´l Sequences. Lecture
Notes in Computer Science 3615: 775-782.
*Beerli, P. 2006. Comparison of Bayesian and maximum likelihood inference of population genetic
parameters. Bioinformatics 22(3): 341-345.
Beerli, P. 2006. Book review: Statistical methods in (molecular) evolution. Evolution 60: 421-423.
*Beerli, P. 2007. Estimation of the population scaled mutation rate from microsatellite data. Genetics 177:1967-1968.
*Hotz, H., G.-D. Guex, P. Beerli, R. D. Semlitsch, and N. Pruvost (2008). Hemiclone diversity in
the hybridogenetic frog Rana esculenta outside the area of clone formation: the view from protein
electrophoresis. Journal of Zoological Systematics and Evolutionary Research 46: 56–62.
Ploetner J., T. Uzzell , P. Beerli, C. Spolsky , T. Ohst, S. N. Litvinchuk, G.-D. Guex, H.-U. Reyer, H.
Hotz (2008). Widespread unidirectional transfer of mitochondrial DNA: a case in western Palearctic
water frogs. Journal of Evolutionary Biology, 21: 668–681.
* Douhan G. W., M. E. Smith, K. L. Huyrn, A. Westbrook, P. Beerli, and A. J. Fisher (2008) Multigene
analysis suggests ecological speciation in the fungal pathogen Claviceps purpurea. Molecular
Ecology 17: 2276–2286.
* Gonzalez, E. G., P. Beerli, and R. Zardoya. (2008) Genetic structuring and migration patterns of
Atlantic bigeye tuna (Thunnus obesus ). BMC Evolutionary Biology 8:252-266.
Book chapters
*Beerli, P. Estimation of migration rates and population sizes in geographically structured populations.
1998. In Advances in molecular ecology (Ed. G. Carvalho). NATO Science Series A: Life Sciences,
IOS Press, Amsterdam. Pp 39-53.
*Schnabel, A., P. Beerli, A. Estoup, D. Hillis. 1998. 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.
Beerli, P., N. C. Grassly, M. K. Kuhner, D. Nickle, O. Pybus, M. Rain, A. Rambaut, A. G. Rodrigo,
and Y. Wang. 2000. 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.
Arbogast, B., S. Edwards, J. Wakeley, P. Beerli, and J. Slowinski. 2002. 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.
*Ploetner, J., F. K ¨
ohler, T. Uzzell, P. Beerli, and C. Spolsky 2007. Molecular Systematics of
Amphibians. In Amphibian biology, Volume 7 (Ed. Heatwole, H.). Surrey Beatty & Sons.
*Beerli, P. 2009. How to use MIGRATE or why are Markov chain Monte Carlo programs dif?cult to
use? Conservation Genetics. Eds. Bertorelle et al.