John Huelsenbeck

Huelsenbeck Lab


Research Overview

I am interested in the phylogeny problem--how one can infer the genealogy of a group of organisms using genetic data--and the genetics of adaptation. In general, I take a statistical approach to the analysis of genomic data. Currently, I am interested in:

  1. analysis of large phylogenetic trees using Bayesian methodology,
  2. treating models in a phylogenetic analysis as random variables,
  3. detecting the footprint of natural selection in protein coding DNA sequences,
  4. accounting for uncertainty in alignment in phylogenetic analysis, and
  5. inferring population structure.

Selected publications

Nielsen, R., J. L. Mountain, J. P. Huelsenbeck, and M. Slatkin. 1998. Maximum-likelihood estimation of population divergence times and population phylogenies in models without mutation. Evolution 52(3):669-677.

Huelsenbeck, J. P. 1998. Systematic bias in phylogenetics: Is the Strepsiptera problem solved? Systematic Biology 47(3):519-537.

Rannala, B., J. P. Huelsenbeck, Z. Yang, and R. Nielsen. 1998. Taxon sampling and the accuracy of large phylogenies. Systematic Biology 47(4):702-719.

Van Den Bussche, R. A., R. J. Baker, J. P. Huelsenbeck, and D. M. Hillis. 1998. Base compositional bias and phylogenetic analyses: A test of the "flying DNA" hypothesis. Molecular Phylogenetics and Evolution 13(3):408-416.

Huelsenbeck, J. P., and R. Nielsen. 1999. Variation in the pattern of nucleotide substitution across sites. Journal of Molecular Evolution 48(1):86-93.

Huelsenbeck, J. P., and R. Nielsen. 1999. Effect of non-independent substitution on phylogenetic accuracy. Systematic Biology 48(2):317-328.

Huelsenbeck, J. P., B. Larget, and D. L. Swofford. 2000. A compound Poisson process for relaxing the molecular clock. Genetics 154(4):1879-1892.

Huelsenbeck, J. P., B. Rannala, and J. P. Masly. 2000. Accommodating phylogenetic uncertainty in evolutionary studies. Science 288:2349-2350.

Huelsenbeck, J. P., B. Rannala, and B. Larget. 2000. A Bayesian framework for the analysis of cospeciation. Evolution 54(2):353-364.

Huelsenbeck, J. P., and B. Rannala. 2000. Using stratigraphic information in phylogenetics. Pages 165-191 in Phylogenetic Analysis of Morphological Data (J. Wiens, ed.). Smithsonian Institution Press, Washington, D.C.

Huelsenbeck, J. P., and J. P. Bollback. 2000. Application of the likelihood function in phylogenetics. Pages 415-444 in Handbook of Statistical Genetics (D. Balding, M. Bishop, and C. Canning, eds.). John Wiley & Sons, Ltd., London.

Huelsenbeck, J. P. 2000. Molecular phylogenetic analysis. Pages 526-532 in Paleobiology II (D. E. Briggs and P. R. Crowther, eds.). Blackwell Science Ltd., Oxford.

Bollback, J. P., and J. P. Huelsenbeck. 2001. Phylogeny, genome evolution, and host specificity of single-stranded RNA bacteriophage (family Leviviridae). Journal of Molecular Evolution 52:117-128.

Huelsenbeck, J. P., and J. P. Bollback. 2001. Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology 50:351-366.

Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754-755.

Swofford, D. L., P. J. Waddell, J. P. Huelsenbeck, P. G. Foster, P. O. Lewis, and J. S. Rogers. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Systematic Biology 50:525-539.

Huelsenbeck, J. P. 2001. A Bayesian perspective to the Strepstipera problem. Tijdschrift voor Entomologie 144:165-178.

Huelsenbeck, J. P., F. Ronquist, R. Nielsen, and J. P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.

Huelsenbeck, J. P., J. P. Bollback, A. M. Levine. 2002. Inferring the root of a phylogenetic tree. Systematic Biology 51(1):32-43.

Huelsenbeck, J. P, and N. S. Imennov. 2002. Geographic origin of human mitochondrial DNA: Accommodating phylogenetic uncertainty and model comparison. Systematic Biology 51(1):155-165.

Huelsenbeck, J. P. 2002. Testing a covariotide model of DNA substitution. Molecular Biology and Evolution 19(5):698-707.

Nielsen, R., and J. P. Huelsenbeck. 2002. Detecting positively selected amino acid sites using posterior predictive p-values. Pages 576-588 in Pacific Symposium on Biocomputing, Proceedings (R. B. Altman, A. K. Dunker, L. Hunter, K. Lauderdale, and T. E. Klein, eds.). World Scientific, Singapore.

Huelsenbeck, J. P., B. Rannala, and B. Larget. 2002. A statistical perspective for reconstructing the history of host-parasite associations. Pages 93-119 in Tangled Trees: Phylogenies, Cospeciation, and Coevolution. (R. D. M. Page, ed.). Chicago University Press, Chicago.

Huelsenbeck, J. P., B. Larget, R. E. Miller, and F. Ronquist. 2002. Potential applications and pitfalls of Bayesian inference of phylogeny. Systematic Biology 51(5):673-688.

Huelsenbeck, J. P., R. Nielsen, and J. P. Bollback. 2003. Stochastic mapping of morphological characters. Systematic Biology 52(2):131-158.

Huelsenbeck, J. P., and B. Rannala. 2003. Detecting correlation between characters in a comparative analysis with uncertain phylogeny. Evolution 57(6):1237-1247.

Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes version 3.0: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12):1572-1574.

Huelsenbeck, J. P., and K. M. Lander. 2003. Frequent inconsistency of parsimony under a simple model of cladogenesis. Systematic Biology 52(5):641-648.

Altekar, G., S. Dwarkadas, J. P. Huelsenbeck, and F. Ronquist. 2004. Parallel Metropolis Coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20(3):407-415.

Nylander, J. A. A., F. Ronquist, J. P. Huelsenbeck, and J. L. Nieves-Aldrey. 2004. Bayesian phylogenetic analysis of combined data. Systematic Biology 53(1):47-67.

Huelsenbeck, J. P., and K. A. Dyer. 2004. Bayesian estimation of positively selected sites. Journal of Molecular Evolution 58(6):661-672.

Huelsenbeck, J. P., B. Larget, and M. E. Alfaro. 2004. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Molecular Biology and Evolution 21(6):1123-1133.

Guindon, S., A. G. Rodrigo, K. A. Dyer, and J. P. Huelsenbeck. 2004. Modeling the site-specific variation of selection patterns along lineages. Proceedings of the National Academy of Sciences, U.S.A. 101(35):12957-12962.

Glenner, H., A. J. Hansen, M. V. Sørensen, F. Ronquist, J. P. Huelsenbeck, and E. Willerslev. 2004. Bayesian inference of the metazoan phylogeny: A combined molecular and morphological approach. Current Biology 14:1644-1649.

Ronquist, F., J. P. Huelsenbeck, and T. Britton. 2004. Bayesian supertrees. Pages 193-224 in Phylogenetic supertrees: Combining information to reveal the tree of life, Computational Biology, Volume 4 (O. Bininda-Emonds, ed.). Kluwer Academic Publishers, The Netherlands.

Huelsenbeck, J. P., and B. Rannala. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Systematic Biology 53(6):904-913.

Huelsenbeck, J. P., and R. Ronquist. 2005. Bayesian analysis of molecular evolution using MrBayes. Pages 183-232 in Statistical Methods in Molecular Evolution (R. Nielsen, ed.). Springer-Verlag.

Alfaro, M. E., and J. P. Huelsenbeck. 2006. Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty. Systematic Biology 55(1):89-96.

Huelsenbeck, J. P., S. Jain, S. W. D. Frost, and S. L. K. Pond. 2006. A Dirichlet process model for detecting positive selection in protein-coding DNA sequences. Proceedings of the National Academy of Sciences, U.S.A. 103(16):6263-6268.

Ronquist, F., B. Larget, J. P. Huelsenbeck, J. B. Kadane, D. Simon, and P. van der Mark. 2006. Comment on "Phylogenetic MCMC algorithms are misleading on mixtures of trees." Science 312:367.

Huelsenbeck, J. P., and P. Andolfatto. 2007. Inference of population structure under a Dirichlet process model. Genetics 175:1787-1802.

Bollback, J. P., and J. P. Huelsenbeck. 2007. Clonal interference is alleviated by high mutation rates in large populations. Molecular Biology and Evolution 24(6):1397-1406.

Huelsenbeck, J. P., and M. A. Suchard. 2007. A nonparametric method for accommodating and testing across-site rate variation. Systematic Biology 56(6):975-987.

Wong, K. M., M. A. Suchard, and J. P. Huelsenbeck. 2008. Alignment uncertainty and genomic analysis. Science 319:473-476.

Lakner, C., P. van der Mark, J. P. Huelsenbeck, B. Larget, and F. Ronquist. 2008. Efficiency of MCMC proposals in Bayesian phylogenetics. Systematic Biology 57(1):86-103.

Huelsenbeck, J. P., C. Ané, B. Larget, and F. Ronquist. 2008. A Bayesian perspective on a non-parsimonious parsimony model. Systematic Biology 57(3):406-419.

Ronquist, F., J. P. Huelsenbeck, and P. van der Mark. In Press. Bayesian phylogenetic analysis using MrBayes. Pages xx-yy in The Phylogenetics Handbook, Second Edition. (A. M. Vandamme, M. Salemi M, and P. Lemey, eds). Cambridge University Press.

Bollback, J. P., and J. P. Huelsenbeck. In Press. Parallel genetic evolution within and among bacteriophage species of varying degrees of divergence. Genetics.

Brandley, M. C., J. P. Huelsenbeck, and J. J. Wiens. In Press. Rates and patterns in the evolution of snake-like body form in squamate reptiles: Evidence for repeated re-evolution of lost digits and long-term persistence of intermediate body forms. Evolution.

Munch, K, W. Boomsma, J. P. Huelsenbeck, E. Willerslev, and R. Nielsen. In Press. Statistical assignment of environmental DNA sequence. Systematic Biology.

Huelsenbeck, J. P., P. Joyce, C. Lakner, and F. Ronquist. In Press. Bayesian analysis of amino acid substitution models. Proceedings of the Royal Society of London, B.