Currently this is a mess, ordered by date, but with no links to PDFs, eventually this will change.

Baco, A. R., Etter, R. J., Ribeiro, P. A., Heyden, S. der, Beerli, P., & Kinlan, B. P. (2016). A synthesis of genetic connectivity in deep-sea fauna and implications for marine reserve design. Molecular Ecology.

Liu, P., Elshall, A. S., Ye, M., Beerli, P., Zeng, X., Lu, D., & Tao, Y. (2016). Evaluating marginal likelihood with thermodynamic integration method and comparison with several other numerical methods. Water Resources Research.

Stapper, A. P., Beerli, P., & Levitan, D. R. (2015a). Article; mBE discoveries section.

Stapper, A. P., Beerli, P., & Levitan, D. R. (2015b). Assortative mating drives linkage disequilibrium between sperm and egg recognition protein loci in the sea urchin strongylocentrotus purpuratus. Molecular Biology and Evolution, msv010.

Çilingir, F. G., Akin Pekşen, Ç., Ambarli, H., Beerli, P., & Bilgin, C. (2015). Exceptional maternal lineage diversity in brown bears (ursus arctos) from turkey. Zoological Journal of the Linnean Society.

Zhang, Y., Lu, Y., Yindee, M., Li, K.-Y., Kuo, H.-Y., Ju, Y.-T., … others. (2015). Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the china/Indochina border region. Molecular Ecology.

Palczewski, M. and Beerli, P. (2014). Population model comparison using multi-locus datasets. In Chen, M.-H., Kuo, L., and Lewis, P. O., editors, Bayesian Phylogenetics: Methods, Algorithms, and Applications, pages 187–200. CRC Press, 2014.

Ye, M., Liu, P., Beerli, P., Lu, D., & Hill, M. (2014). Estimating model probabilities using thermodynamic markov chain monte carlo methods. AGU Fall Meeting Abstracts, 1, 3696.

Jackson, J. A., Steel, D. J., Beerli, P., Congdon, B. C., Olavarría, C., Leslie, M. S., … Baker, C. S. (2014). Global diversity and oceanic divergence of humpback whales (megaptera novaeangliae). Proceedings of the Royal Society of London B: Biological Sciences, 281(1786), 20133222.

Chi, H., & Beerli, P. (2014). Quasi-monte carlo method in population genetics parameter estimation. Mathematics and Computers in Simulation, 103, 33–38.

Palczewski, M., & Beerli, P. (2013). A continuous method for gene flow. Genetics, 194(3), 687–696.

Qiu, F., Kitchen, A., Beerli, P., & Miyamoto, M. M. (2013). A possible explanation for the population size discrepancy in tuna (genus thunnus) estimated from mitochondrial dNA and microsatellite data. Molecular Phylogenetics and Evolution, 66(2), 463–468.

Bouzid, W., Štefka, J., Bahri-Sfar, L., Beerli, P., Loot, G., Lek, S., … others. (2013). Pathways of cryptic invasion in a fish parasite traced using coalescent analysis and epidemiological survey. Biological Invasions, 15(9), 1907–1923.

Hotz, H., Beerli, P., Uzzell, T., Guex, G.-D., Pruvost, N. B., Schreiber, R., & Plötner, J. (2012). Balancing a cline by influx of migrants: A genetic transition in water frogs of eastern greece. Journal of Heredity, ess086.

Ayres, D. L., Darling, A., Zwickl, D. J., Beerli, P., Holder, M. T., Lewis, P. O., … others. (2012). BEAGLE: An application programming interface and high-performance computing library for statistical phylogenetics. Systematic Biology, 61(1), 170–173.

Roshier, D. A., Heinsohn, R., Adcock, G. J., Beerli, P., & Joseph, L. (2012). Biogeographic models of gene flow in two waterfowl of the australo-papuan tropics. Ecology and Evolution, 2(11), 2803–2814.

Bradic, M., Beerli, P., García-de León, F. J., Esquivel-Bobadilla, S., & Borowsky, R. L. (2012). Gene flow and population structure in the mexican blind cavefish complex (astyanax mexicanus). BMC Evolutionary Biology, 12(1), 1.

Plötner, J., Baier, F., Akin, C., Mazepa, G., Schreiber, R., Beerli, P., … Uzzell, T. (2012). Genetic data reveal that water frogs of cyprus (genus pelophylax) are an endemic species of messinian origin. Zoosystematics and Evolution, 88(2), 261–283.

Chi, H., & Beerli, P. (2011). Poster: Quasi-monte carlo method in population genetics parameter estimation. In Computational advances in bio and medical sciences (iCCABS), 2011 iEEE 1st international conference on (pp. 237–237). IEEE.

Plötner, J., Uzzell, T., Beerli, P., Akin, Ç., Bilgin, C. C., Haefeli, C., … others. (2010). Genetic divergence and evolution of reproductive isolation in eastern mediterranean water frogs. In Evolution in action (pp. 373–403). Springer Berlin Heidelberg.

Boykin, L. M., Shatters, R. G., Hall, D. G., Dean, D., & Beerli, P. (2010). Genetic variation of anastrepha suspensa (diptera: Tephritidae) in florida and the caribbean using microsatellite dNA markers. Journal of Economic Entomology, 103(6), 2214–2222.

Bedford, T., Cobey, S., Beerli, P., & Pascual, M. (2010). Global migration dynamics underlie evolution and persistence of human influenza a (h3N2). PLoS Pathog, 6(5), e1000918.

Beaumont, M. A., Nielsen, R., Robert, C., Hey, J., Gaggiotti, O., Knowles, L., … others. (2010). In defence of model-based inference in phylogeography. Molecular Ecology, 19(3), 436–446.

Corander, J., Panchal, M., Gaggiotti, O., Hey, J., Estoup, A., Knowles, L., … others. (2010). In defence of model-based inference in phylogeography. Paris Dauphine University.

Akin, Ç., Can Bilgin, C., Beerli, P., Westaway, R., Ohst, T., Litvinchuk, S. N., … others. (2010). Phylogeographic patterns of genetic diversity in eastern mediterranean water frogs were determined by geological processes and climate change in the late cenozoic. Journal of Biogeography, 37(11), 2111–2124.

Beerli, P., & Palczewski, M. (2010). Unified framework to evaluate panmixia and migration direction among multiple sampling locations. Genetics, 185(1), 313–326.

Plötner, J., Köhler, F., Uzzell, T., Beerli, P., Schreiber, R., Guex, G.-D., & Hotz, H. (2009). Evolution of serum albumin intron-1 is shaped by a 5′ truncated non-long terminal repeat retrotransposon in western palearctic water frogs (neobatrachia). Molecular Phylogenetics and Evolution, 53(3), 784–791.

Beerli, P. (2009). How to use MIGRATE or why are Markov chain Monte Carlo programs difficult to use. Population Genetics for Animal Conservation, 17, 42–79.

Gonzalez, E. G., Beerli, P., & Zardoya, R. (2008). Genetic structuring and migration patterns of atlantic bigeye tuna, thunnus obesus (lowe, 1839). BMC Evolutionary Biology, 8(1), 1.

Hotz, H., Guex, G.-D., Beerli, P., Semlitsch, R., & Pruvost, N. (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(1), 56–62.

Beerli, P. (2008). Migrate version 3.0: A maximum likelihood and bayesian estimator of gene flow using the coalescent. Distributed over the Internet at Http://popgen. Scs. Edu/migrate. Html.

Douhan, G., Smith, M., Huyrn, K., Westbrook, A., Beerli, P., & Fisher, A. (2008). Multigene analysis suggests ecological speciation in the fungal pathogen claviceps purpurea. Molecular Ecology, 17(9), 2276–2286.

Plötner, J., Uzzell, T., Beerli, P., Spolsky, C., Ohst, T., Litvinchuk, S. N., … Hotz, H. (2008). Widespread unidirectional transfer of mitochondrial dNA: A case in western palaearctic water frogs. Journal of Evolutionary Biology, 21(3), 668–681.

Beerli, P. (2007). Letter to the editor: Estimation of the population scaled mutation rate from microsatellite data. Genetics.

Beerli, P. (2006). Comparison of bayesian and maximum-likelihood inference of population genetic parameters. Bioinformatics, 22(3), 341–345.

Beerli, P., & Futuyma, D. (2006). STATISTICAL mETHODS iN (mOLECULAR) eVOLUTION 1. Evolution, 60(2), 421–423.

Mu, J., Joy, D. A., Duan, J., Huang, Y., Carlton, J., Walker, J., … others. (2005). Host switch leads to emergence of plasmodium vivax malaria in humans. Molecular Biology and Evolution, 22(8), 1686–1693.

Kuhner, M. K., Yamato, J., Beerli, P., Smith, L., Rynes, E., & others. (2005). LAMARC. University of Washington, Seattle.

Chi, H., Beerli, P., Evans, D. W., & Mascagni, M. (2005). On the scrambled soboĺ sequence. In Computational science–ICCS 2005 (pp. 775–782). Springer Berlin Heidelberg.

Beerli, P. (2004a). Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Molecular Ecology, 13(4), 827–836.

Beerli, P. (2004b). Migrate documentation. School of Computational Science and Department of Biological Science. Florida State University, Tallahassee, FL.

Joy, D. A., Feng, X., Mu, J., Furuya, T., Chotivanich, K., Krettli, A. U., … others. (2003). Early origin and recent expansion of plasmodium falciparum. Science, 300(5617), 318–321.

Brumfield, R. T., Beerli, P., Nickerson, D. A., & Edwards, S. V. (2003). The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology & Evolution, 18(5), 249–256.

Arbogast, B. S., Edwards, S. V., Wakeley, J., Beerli, P., & Slowinski, J. B. (2002). Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annual Review of Ecology and Systematics, 707–740.

Beerli, P. (2002). MIGRATE: Documentation and program, part of lAMARC. Department of Genome Sciences, University of Washington, Seattle.

Beerli, P., Grassly, N., Kuhner, M., Nickle, £. D., Pybus, O., Rain, M., … Wang, Y. (2002). Population genetics of hIV: Parameter estimation using genealogy-based methods. Computational and Evolutionary Analysis of HIV Molecular Sequences, 217–252.

Beerli, P., & Edwards, S. V. (2002). When did neanderthals and modern humans diverge? Evolutionary Anthropology: Issues, News, and Reviews, 11(S1), 60–63.

Guex, G.-D., Hotz, H., Uzzell, T., Semlitsch, R. D., Beerli, P., & Pascolini, R. (2001). Developmental disturbances in rana esculenta tadpoles and metamorphs. Zoosystematics and Evolution, 77(1), 79–86.

Beerli, P., & Felsenstein, J. (2001). Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences, 98(8), 4563–4568.

Hotz, H., Uzzell, T., Guex, G.-D., Alpers, D., Semlitsch, R. D., & Beerli, P. (2001). Microsatellites: A tool for evolutionary genetic studies of western palearctic water frogs. Zoosystematics and Evolution, 77(1), 43–50.

Hoekstra, H. E., Hoekstra, J. M., Berrigan, D., Vignieri, S. N., Hoang, A., Hill, C. E., … Kingsolver, J. G. (2001). Strength and tempo of directional selection in the wild. Proceedings of the National Academy of Sciences, 98(16), 9157–9160.

Kingsolver, J. G., Hoekstra, H. E., Hoekstra, J. M., Berrigan, D., Vignieri, S. N., Hill, C., … Beerli, P. (2001). The strength of phenotypic selection in natural populations. The American Naturalist, 157(3), 245–261.

Wilson, L., Stephens, D., Harding, R., Griffiths, B., Joyce, P., Edwards, A., … others. (2000). Inference in molecular population genetics-discussion. BLACKWELL PUBL LTD 108 COWLEY RD, OXFORD OX4 1JF, OXON, ENGLAND.

Edwards, S., & Beerli, P. (2000). Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution, 54(6), 1839–1854.

Kuhner, M. K., Beerli, P., Yamato, J., & Felsenstein, J. (2000). Usefulness of single nucleotide polymorphism data for estimating population parameters. Genetics, 156(1), 439–447.

Felsenstein, J., Kuhner, M. K., Yamato, J., & Beerli, P. (1999). Likelihoods on coalescents: A monte carlo sampling approach to inferring parameters from population samples of molecular data. Lecture Notes-Monograph Series, 163–185.

Beerli, P., & Felsenstein, J. (1999). Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics, 152(2), 763–773.

Hotz, H., Semlitsch, R. D., Gutmann, E., Guex, G.-D., & Beerli, P. (1999). Spontaneous heterosis in larval life-history traits of hemiclonal frog hybrids. Proceedings of the National Academy of Sciences, 96(5), 2171–2176.

Kingsolver, J., Hoekstra, H., Hoekstra, J., Berrigan, D., Vignieri, S., Hill, C., … Beerli, P. (1999). The strength of phenotypic selection in natural populations: A review. In American zoologist (Vol. 39, pp. 9A–10A). SOC INTEGRATIVE COMPARATIVE BIOLOGY 1313 DOLLEY MADISON BLVD, NO 402, MCLEAN, VA 22101 USA.

Estoup, A. S. P. B. A. (1998). A guide to software packages for data analysis in molecular ecology. Advances in Molecular Ecology, 306, 291.

Beerli, P. (1998). Estimation of migration rates and population sizes in geographically structured populations. NATO ASI SERIES A LIFE SCIENCES, 306, 39–54.

Hotz, H., Uzzell, T., Beerli, P., & Guex, G.-D. (1996). Are hybrid clonals species? A case for enlightened anarchy. Amphibia-Reptilia, 17(4), 315–320.

Semlitsch, R. D., Schmiedehausen, S., Hotz, H., & Beerli, P. (1996). Genetic compatibility between sexual and clonal genomes in local populations of the hybridogeneticRana esculenta complex. Evolutionary Ecology, 10(5), 531–543.

Beerli, P., Hotz, H., & Uzzell, T. (1996). Geologically dated sea barriers calibrate a protein clock for aegean water frogs. Evolution, 1676–1687.

RECOM, D. P. T. (1995). Genetics 357360, ilniversity of washington, seattle, wA 98195, u: IA (beerli@ genetics. washington. edu). Genetics, 140, 1130.

Semlitsch, R., Hotz, H., Guex, G., & Beerli, P. (1994). Balancing interclonal selection and the maintenance of more than one hemiclone in populations of the hybrid frog rana esculenta. Zoologica Poloniae, 3(39).

Hotz, H., Beerli, P., Guex, G., Semlitsch, R., & Uzzell, T. (1994). Clonal diversity and hybrid frequency are not correlated in water frogs. is the frozen niche variation model wrong? Zoologica Poloniae, 39(3-4).

Beerli, P., Hotz, H., Guex, G., & Uzzell, T. (1994). Differential dispersal rates among water frog populations in two eastern mediterranean pleistocene refugia. Zoologica Poloniae, 39(3-4).

Beerli, P. (1994). Genetic isolation and calibration of an average protein clock in western palearctic water frogs of the aegean region (PhD thesis).

Uzzell, T., Hotz, H., Guex, G., & Beerli, P. (1994). S of western s: S in s. Zoologica Poloniae, 3(39).

Gutmann, E., Hotz, H., Semlitsch, R., Guex, G., Beerli, P., Berger, L., & Uzzell, T. (1994). Spontaneous heterosis in larval life-history traits of hemiclonal water frog hybrids. Zoologica Poloniae, 39(3-4).

Beerli, P., Hotz, H., Tunner, H. G., Heppich, S., & Uzzell, T. (1994). Two new water frog species from the aegean islands crete and karpathos (amphibia, salientia, ranidae).[et al.].

Hotz, H., Beerli, P., & Spolsky, C. (1992). Mitochondrial dNA reveals formation of nonhybrid frogs by natural matings between hemiclonal hybrids. Molecular Biology and Evolution, 9(4), 610–620.

Beerli, P., Billing, H., & Schätti, B. (1986). Taxonomischer status von vipera latasti monticola saint girons, 1953 (serpentes: Viperidae). Salamandra, 22(2-3), 101–104.