Publications

Journal Papers

2016-

Z. Yang and B. Rannala. 2017. Species Identification by Bayesian Fingerprinting: A Powerful Alternative to DNA Barcoding. Molecular Ecology (In Review). bioRxiv.

Z. Yang and B. Rannala. 2017. Efficient Bayesian species tree inference under the multispecies coalescent. Systematic Biology (In Press).

B. Rannala. 2016. Conceptual issues in Bayesian divergence time estimation. Phil. Trans. R. Soc. B 371, 20150134.

B.R. Moore, S. Höhna, M.R. May, B. Rannala, and J.P. Huelsenbeck. 2016. Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures. Proceedings of the National Academy of Sciences 113: 9569-9574.

H. Alhaddad, C. Zhang, B. Rannala, L. A. Lyons. 2016. A glance at recombination hotspots in the domestic cat. PLoS ONE 11: e0148710.

2011-2015

B. Rannala. 2015. The art and science of species delimitation. Current Zoology 61: 846-853.

Z. Yang and B. Rannala. 2014. Unguided species delimitation using DNA sequence data from multiple loci. Molecular Biology and Evolution 31: 3125–3135..

Y. Wang and B. Rannala. 2014. Bayesian inference of shared recombination hotspots between humans and chimpanzees. Genetics 198: 1621–1628..

C. Zhang, B. Rannala, and Z. Yang. 2014. Bayesian species delimitation can be robust to guide tree inference errors. Systematic Biology 63: 993-1004.

S. H. Lockwood, A. Guan, A. S. Yu; C. Zhang, A. Zykovich, I. Korf, B. Rannala, and D. J. Segal. 2014. The Functional Significance of Common Polymorphisms in Zinc Finger Transcription Factors. G3: Genes| Genomes| Genetics 4: 1647-1655.

A. D. Leaché, R. B. Harris, B. Rannala, and Z. Yang. 2013. The Influence of Gene Flow on Species Tree Estimation: A Simulation Study. Systematic Biology 63: 17-30.

B. Rannala and Z. Yang. 2013. Improved reversible jump algorithms for Bayesian species delimitation. Genetics 195: 245-253.

B. Padhukasahasram and B. Rannala. 2013. Meiotic gene-conversion rate and tract length variation in the human genome. European Journal of Human Genetics (early edition).

C. Zhang, B. Rannala, and Z. Yang. 2012. Robustness of compound Dirichlet priors for Bayesian inference of branch lengths. Systematic Biology 61: 779-784.

Z. Yang and B. Rannala. 2012. Molecular phylogenetics: principles and practice. Nature Reviews Genetics 13: 303-314.

B. Rannala, T. Zhu, Z. Yang. 2012. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Molecular Biology and Evolution 29: 325-335.

B. Padhukasahasram and B. Rannala. 2011. Bayesian population genomic inference of crossing-over and gene-conversion. Genetics (Aug. 11 [Epub]).

A. D. Leaché and B. Rannala. 2011. The accuracy of species tree estimation under simulation: A comparison of methods. Systematic Biology 60: 126-37.

2005-2010

Z. Yang and B. Rannala. 2010. Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences USA 107: 9264-9269.

Y. Wang and B. Rannala. 2009. Population genomic inference of recombination rates and hotspots. Proceedings of the National Academy of Sciences USA 106: 6210-6214.

Y. Wang and B. Rannala. 2008. Bayesian inference of fine-scale recombination rates using population genomic data. Philosophical Transactions of the Royal Society B 363: 3921-3930.

C. D. Fetterman, B. Rannala and M. A. Walter. 2008. Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies. BMC Evolutionary Biology 8: 261 .

B. Rannala and Z. Yang. 2008. Phylogenetic inference using whole genomes. Annual Review of Genomics and Human Genetics 9: 217-231.

K. Bumroongkit, B. Rannala, P. Traisathit, M. Srikummool, Y. Wongchai, and D. Kangwanpong. 2008. TP53 gene mutations of lung cancer patients in upper northern Thailand and environmental risk factors. Cancer Genetics and Cytogenetics 185: 20-27.

L. Mateiu and B. Rannala. 2008. Bayesian inference of errors in ancient DNA caused by postmortem degradation. Molecular Biology and Evolution 25: 1503-1511.

S. Ro and B. Rannala. 2007. Inferring somatic mutation rates using the stop-enhanced green fluorescent protein mouse. Genetics 177: 9-16.

K. Cranston and B. Rannala. 2007. Summarizing a posterior distribution of trees using agreement subtrees. Systematic Biology 56: 578-590.

B. Rannala and Z. Yang. 2007. Inferring speciation times under an episodic molecular clock. Systematic Biology 56: 453-466.

L. Mateiu and B. Rannala. 2006. Inferring complex DNA substitution processes on phylogenies using uniformization and data augmentation. Systematic Biology 55: 259-269.

Z. Yang and B. Rannala. 2006. Bayesian estimation of species divergence times under a molecular clock using fossil calibrations with soft bounds. Molecular Biology and Evolution 23: 212-226.

S. Ro and B. Rannala. 2005. Evidence from the stop-EGFP mouse supports a niche-sharing model of epidermal proliferative units. Experimental Dermatology 14:1-6.

Z. Yang and B. Rannala. 2005. Branch-length prior influences Bayesian posterior probability of phylogeny. Systematic Biology 54: 455-470.

Y. Wang and B. Rannala. 2005. In Silico Analysis of Disease-Association Mapping Strategies Using the Coalescent Process and Incorporating Ascertainment and Selection. American Journal of Human Genetics 76:1066-1073.

K. Cranston and B. Rannala. 2005. News and Commentary (Molecular Clocks): Closing the gap between rocks and clocks. Heredity 94: 461-462.

2000-2004

J.P. Huelsenbeck and B. Rannala. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Systematic Biology 53: 904-913.

Y. Wang and B. Rannala. 2004. A novel solution for the time-dependent probability of gene fixation or loss under natural selection. Genetics 168: 1081-1084.

S. Ro and B. Rannala. 2004. A stop-EGFP transgenic mouse to detect clonal cell lineages generated by mutation. EMBO Reports 5: 914-920.

Y. Wang and B. Rannala. 2004. Simulating a coalescent process with recombination and ascertainment. Lecture Notes in Bioinformatics 2983: 84-95.

M.A. Beaumont and B. Rannala. 2004. The Bayesian revolution in genetics. Nature Reviews Genetics 5: 251-261.

Z. Yang, S. Ro and B. Rannala. 2003. Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics 165: 695-705.

B. Rannala and Z. Yang. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences From multiple loci. Genetics 164: 1645-1656.

J.P. Huelsenbeck and B. Rannala. 2003. Detecting correlation between characters in a comparative analysis with uncertain phylogeny. Evolution 57:1237-1247.

B. Rannala. 2003. Stationary allele frequency distributions. Encyclopedia of the Human Genome. Nature Publishing, London.

G.A. Wilson and B. Rannala 2003. Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163: 1177-1191.

B. Rannala and J.P. Reeve. 2003. Joint Bayesian estimation of mutation location and age using linkage disequilibrium. Pacific Symposium on Biocomputing 8:526-534.

B. Rannala. 2002. Identifiability of parameters in MCMC Bayesian inference of phylogeny. Systematic Biology 51:754-760.

M.C. Fisher, B. Rannala, V. Chaturvedi and J.W. Taylor. 2002. Disease surveillance in recombining pathogens: Multilocus genotypes identify sources of human Coccidioides infections. Proceedings of the National Academy of Sciences USA 99:9067-9071.

J. Reeve and B. Rannala. 2002. DMLE+: Bayesian linkage disequilibrium gene mapping. Bioinformatics 18: 894-895].

B. Rannala. 2001. Finding genes influencing susceptibility to complex diseases in the postgenome era. American Journal of Pharmacogenomics 1: 203-221.

S. Ro and B. Rannala. 2001. Commentary: Methylation patterns and mathematical models reveal dynamics of stem cell turnover in the human colon. Proceedings of the National Academy of Sciences USA 98: 10519-10521.

B. Rannala and G. Bertorelle. 2001. Using linked markers to infer the age of a mutation. Human Mutation 18: 87-100.

B. Rannala and J. P. Reeve. 2001. High-resolution multipoint linkage-disequilibrium mapping in the context of a human genome sequence. American Journal of Human Genetics 69: 159-178.

B. Rannala and M. Slatkin. 2000. Methods for multipoint disease mapping using linkage disequilibrium. Genetic Epidemiology 19: S71-S77.

J.P. Huelsenbeck, B. Rannala and J.P. Masly. 2000. Accommodating phylogenetic uncertainty in evolutionary studies. Science 88: 2349-2350.

B. Rannala, W. Qui, and D. E. Dykhuizen. 2000. Methods for estimating gene frequencies and detecting selection in bacterial populations. Genetics 155: 499-508.

Slatkin, M., and B. Rannala. 2000. Estimating allele age. Annual Review of Genomics and Human Genetics 1:225-249.

Huelsenbeck, J.P., B. Rannala, and B. Larget. 2000. A Bayesian framework for the analysis of cospeciation. Evolution 54: 352-364.

1995-1999

Knowles, L.L., D.J. Futuyma, W.F. Eanes, and B. Rannala. 1999. Insight into speciation from historical demography in the phytophagous beetle genus Ophraella. Evolution 53: 1846-1856.

Rannala, B., J. P. Huelsenbeck, Z. Yang, and R. Nielsen. 1998. Taxon sampling and the accuracy of large phylogenies. Systematic Biology 47: 702-710.

Bertorelle, G., and B. Rannala. 1998. Using rare mutations to estimate population divergence times: a maximum likelihood approach. Proceedings of the National Academy of Sciences 95: 15452-15457.

Rannala, B., and M. Slatkin. 1998. Linkage disequilibrium mapping and Parkinson’s disease. Science 280: 175a.

Rannala, B., and M. Slatkin. 1998. Likelihood analysis of disequilibrium gene mapping and related problems. American Journal of Human Genetics 62: 459-473.

Rannala, B. 1997. On the genealogy of a rare allele. Theoretical Population Biology 52: 216-223.

Slatkin, M., and B. Rannala. 1997. The sampling distribution of disease-associated alleles. Genetics 147: 1855-1861.

Rannala, B., and J. L. Mountain. 1997. Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences USA 94: 9197-9201.

Yang, Z., and B. Rannala 1997. Bayesian Phylogenetic Inference Using DNA Sequences: A Markov Chain Monte Carlo Method. Molecular Biology and Evolution 14: 717-724.

Rannala, B. 1997. Gene genealogy in a population of variable size. Heredity 78: 417-423.

Huelsenbeck, J. P., and B. Rannala. 1997. Maximum likelihood estimation of phylogeny using stratigraphic data. Paleobiology 23: 174-180.

Huelsenbeck, J. P., B. Rannala, and Z. Yang. 1997. Statistical tests of host-parasite cospeciation. Evolution 51: 410-419.

Huelsenbeck, J. P., and B. Rannala. 1997. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276: 227-232.

Slatkin, M., and B. Rannala. 1997. Estimating the age of alleles by use of intraallelic variability. American Journal of Human Genetics 60: 447-458.

Rannala, B., and Z. Yang. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution 43:304-311.

Rannala, B. 1996. The sampling theory of neutral alleles in an island population of fluctuating size. Theoretical Population Biology 50:91-104.

Rannala, B., and J. A. Hartigan. 1996. Estimating gene flow in island populations. Genetical Research 67:147-158.
Brown, C. R., Brown, M. B., and Rannala, B. 1995. Ectoparasites reduce long-term survival of their avian host. Proceedings of the Royal Society of London Series B 262: 313-319.

Rannala, B. 1995. Polymorphic characters and phylogenetic analysis: a statistical perspective. Systematic Biology 44: 421-429.

Brown, C. R. and Rannala, B. 1995. Colony choice in birds: models based on temporally invariant site quality. Behavioral Ecology and Sociobiology 36: 221-228.

Rannala, B. and Hartigan, J. A. 1995. Identity by descent in island-mainland populations. Genetics 139: 429-437Erratum.

1990-1994

Rannala, B. and Brown, C.R. 1994. Relatedness and conflict over optimal group-size. Trends in Ecology and Evolution 9: 117-119.

Rannala, B. 1991. Comparative evolutionary genetics of trematode parasites (Plagiorchiidae) and their anuran hosts. Canadian Journal of Zoology 70: 993-1000.

Rannala, B. 1991. Evidence for host allozymes on electrophoretic gels of trematode parasites Digenea, Plagiorchiiformes). Journal of Parasitology 77: 805-808.

Rannala, B. 1990. Genetic distance and parasite taxonomy. Journal of Parasitology 76: 929-930.

Rannala, B. 1990. Electrophoretic evidence concerning the relationship between Haplometrana and Glypthelmins (Digenea, Plagiorchiiformes). Journal of Parasitology 76: 746-748.

Book Chapters

B. Rannala and Z. Yang. 2013. Molecular clock dating (Chap. II.3). In: The Princeton Guide to Evolution (J. Losos, ed.). Princeton Univ. Press: Princeton.

B. Rannala. 2013. Stationary allele frequency distributions. In: Encyclopedia of Life Sciences. John Wiley and Sons, Ltd: Chichester.

B. Rannala. 2002. Molecular phylogenies and virulence evolution. In: Adaptive Dynamics of Infectious Diseases: In Pursuit of Virulence Management. (eds. U. Dieckmann, J.A.J. Metz, M.W. Sabelis and K. Sigmund). Cambridge University Press, Cambridge.

Huelsenbeck, J.P., B. Rannala and B. Larget. 2002. A statistical perspective for reconstructing the history of host-parasite associations. In: Tangled Trees: Phylogenies, Cospeciation and Coevolution (ed. R.D.M. Page). University of Chicago Press, Chicago.

B. Rannala and Y. Michalakis. 2002. Population genetics and cospeciation. In: Tangled Trees: Phylogenies, Cospeciation and Coevolution (ed. R.D.M. Page). University of Chicago Press, Chicago.

Huelsenbeck, J. P., and B. Rannala. 2000. Using temporal information in phylogenetics. In: Phylogenetic Analysis of Morphological Data (J. Weins, ed.). Smithsonian Press, Washington.