Publications « Rannala Research Group

Publications

Journal Papers

2005-2009

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: 429-437 Erratum.

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. 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.

Rannala Research Group Genome Center and Department of Evolution and Ecology, UC Davis