John P Huelsenbeck

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Inferring the root of a phylogenetic tree
    John P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Syst Biol 51:32-43. 2002
  2. ncbi request reprint Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models
    John Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 011, USA
    Syst Biol 53:904-13. 2004
  3. ncbi request reprint Bayesian estimation of positively selected sites
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 0116, USA
    J Mol Evol 58:661-72. 2004
  4. ncbi request reprint Detecting correlation between characters in a comparative analysis with uncertain phylogeny
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093 0116, USA
    Evolution 57:1237-47. 2003
  5. ncbi request reprint Frequent inconsistency of parsimony under a simple model of cladogenesis
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093 0116, USA
    Syst Biol 52:641-8. 2003
  6. ncbi request reprint Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, USA
    Mol Biol Evol 21:1123-33. 2004
  7. doi request reprint A Bayesian perspective on a non-parsimonious parsimony model
    John P Huelsenbeck
    Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA
    Syst Biol 57:406-19. 2008
  8. doi request reprint Alignment uncertainty and genomic analysis
    Karen M Wong
    Section of Ecology, Behavior and Evolution, University of California, San Diego, La Jolla, CA 92093, USA
    Science 319:473-6. 2008
  9. doi request reprint Statistical assignment of DNA sequences using Bayesian phylogenetics
    Kasper Munch
    Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
    Syst Biol 57:750-7. 2008
  10. pmc Bayesian analysis of amino acid substitution models
    John P Huelsenbeck
    Department of Integrative Biology, University of California, Berkeley, 3060 VLSB 3140, Berkeley, CA 94720 3140, USA
    Philos Trans R Soc Lond B Biol Sci 363:3941-53. 2008

Detail Information

Publications33

  1. ncbi request reprint Inferring the root of a phylogenetic tree
    John P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Syst Biol 51:32-43. 2002
    ..We also examined the performance of the criteria for a tree of four species for which the topology and root position are well supported. Results of the analyses of these data are consistent with the simulation results...
  2. ncbi request reprint Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models
    John Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 011, USA
    Syst Biol 53:904-13. 2004
    ..We suggest that the Bayesian method be implemented with the most complex models of those currently available, as this should reduce the chance that the method will concentrate too much probability on too few trees...
  3. ncbi request reprint Bayesian estimation of positively selected sites
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 0116, USA
    J Mol Evol 58:661-72. 2004
    ..Compared to a previous analysis of this data set, the hierarchical model found most of the same sites to be in the positive selection class, but with a few striking exceptions...
  4. ncbi request reprint Detecting correlation between characters in a comparative analysis with uncertain phylogeny
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093 0116, USA
    Evolution 57:1237-47. 2003
    ..We do this in a Bayesian framework and use Markov chain Monte Carlo to perform the high-dimensional summations and integrations required by the analysis. We illustrate the method using comparative characters sampled from Anolis lizards...
  5. ncbi request reprint Frequent inconsistency of parsimony under a simple model of cladogenesis
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093 0116, USA
    Syst Biol 52:641-8. 2003
    ..When taxon sampling is poor or rates of evolution are high, the probability that parsimony will become inconsistent increases...
  6. ncbi request reprint Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California, San Diego, USA
    Mol Biol Evol 21:1123-33. 2004
    ....
  7. doi request reprint A Bayesian perspective on a non-parsimonious parsimony model
    John P Huelsenbeck
    Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA
    Syst Biol 57:406-19. 2008
    ....
  8. doi request reprint Alignment uncertainty and genomic analysis
    Karen M Wong
    Section of Ecology, Behavior and Evolution, University of California, San Diego, La Jolla, CA 92093, USA
    Science 319:473-6. 2008
    ..Using genomic data from seven yeast species, we show that uncertainty in the alignment can lead to several problems, including different alignment methods resulting in different conclusions...
  9. doi request reprint Statistical assignment of DNA sequences using Bayesian phylogenetics
    Kasper Munch
    Department of Integrative Biology, University of California, Berkeley, California 94720 3140, USA
    Syst Biol 57:750-7. 2008
    ..However, there are several cases of chimeric sequences that are comprised of a combination of both Neanderthal and modern human DNA...
  10. pmc Bayesian analysis of amino acid substitution models
    John P Huelsenbeck
    Department of Integrative Biology, University of California, Berkeley, 3060 VLSB 3140, Berkeley, CA 94720 3140, USA
    Philos Trans R Soc Lond B Biol Sci 363:3941-53. 2008
    ..Finally, we consider constraints on the exchangeability parameters as partitions,similar to how nucleotide substitution models are specified, and place a Dirichlet process prior model on all the possible partitioning schemes...
  11. pmc RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
    Sebastian Höhna
    Department of Integrative Biology Department of Statistics, University of California, Berkeley, CA 94720, USA Department of Evolution and Ecology, University of California, Davis, CA 95616, USA Department of Mathematics, Stockholm University, Stockholm, SE 106 91 Stockholm, Sweden
    Syst Biol 65:726-36. 2016
    ..RevBayes is freely available at http://www.RevBayes.com [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.]. ..
  12. pmc Biologically inspired phylogenetic models strongly outperform the no common mechanism model
    John P Huelsenbeck
    Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA
    Syst Biol 60:225-32. 2011
    ..With the realistic NCM in the background, then, most parsimonious trees have greatest power to explain available observations. -Farris (2008)...
  13. pmc Inference of population structure under a Dirichlet process model
    John P Huelsenbeck
    Department of Integrative Biology, University of California, Berkeley, California 94720, USA
    Genetics 175:1787-802. 2007
    ..We develop the notion of the mean population partition, which is the partition of individuals to populations that minimizes the squared partition distance to the partitions sampled by the MCMC algorithm...
  14. pmc Quantifying the impact of dependent evolution among sites in phylogenetic inference
    Chris A Nasrallah
    Department of Integrative Biology, University of California, Berkeley, 3060 Valley Life Sciences Building 3140, Berkeley, CA 94720 3140, USA
    Syst Biol 60:60-73. 2011
    ..We introduce the concept of effective sequence length and its utility for considering information content in phylogenetics...
  15. ncbi request reprint Stochastic mapping of morphological characters
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biology, University of California San Diego, La Jolla, California 92093 0116, USA
    Syst Biol 52:131-58. 2003
    ..Biol. 51:729-739) to the mapping of morphological characters under continuous-time Markov models and demonstrate here the utility of the method for mapping characters on trees and for identifying character correlation...
  16. doi request reprint 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
    Matthew C Brandley
    Museum of Vertebrate Zoology, University of California, Berkeley, California 94270, USA
    Evolution 62:2042-64. 2008
    ..Finally, although loss of digits is common, we find statistically significant support for at least six examples of the re-evolution of lost digits in the forelimb and hind limb...
  17. pmc Bayesian analysis of biogeography when the number of areas is large
    Michael J Landis
    Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA Department of Evolution and Ecology, University of California, Davis, Storer Hall, One Shields Avenue, Davis, CA 95616, USA and Biology Department, King Abdulaziz University, Jeddah, Saudi Arabia
    Syst Biol 62:789-804. 2013
    ..Our approach is implemented in the program, BayArea...
  18. ncbi request reprint Potential applications and pitfalls of Bayesian inference of phylogeny
    John P Huelsenbeck
    Section of Ecology, Behavior and Evolution, Division of Biology, University of California San Diego, La Jolla, CA 92093 0116, USA
    Syst Biol 51:673-88. 2002
    ..The results of a Bayesian analysis should be examined with respect to the sensitivity of the results to the priors used and the reliability of the Markov chain Monte Carlo approximation of the probabilities of trees...
  19. ncbi request reprint A nonparametric method for accommodating and testing across-site rate variation
    John P Huelsenbeck
    Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
    Syst Biol 56:975-87. 2007
    ....
  20. pmc Probabilistic graphical model representation in phylogenetics
    Sebastian Höhna
    Department of Mathematics, Stockholm University, Stockholm, SE 106 91 Stockholm, Sweden Department of Evolution and Ecology, University of California, Davis, Storer Hall, One Shields Avenue, Davis, CA 95616, USA Department of Integrative Biology, University of California, Berkeley, CA 94720, USA Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA Bioinformatics and Evolutionary Genomics, Universite de Lyon, Villeurbanne, France Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE 10405 Stockholm, Sweden and Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia Department of Mathematics, Stockholm University, Stockholm, SE 106 91 Stockholm, Sweden Department of Evolution and Ecology, University of California, Davis, Storer Hall, One Shields Avenue, Davis, CA 95616, USA Department of Integrative Biology, University of California, Berkeley, CA 94720, USA Department of Ecology and Evolutionary Biology, University of Kansas, USA
    Syst Biol 63:753-71. 2014
    ..Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution...
  21. pmc A Dirichlet process model for detecting positive selection in protein-coding DNA sequences
    John P Huelsenbeck
    Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 0116, USA
    Proc Natl Acad Sci U S A 103:6263-8. 2006
    ..We implemented the model in a fully Bayesian approach, with all parameters of the model considered as random variables...
  22. pmc Structurama: bayesian inference of population structure
    John P Huelsenbeck
    Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
    Evol Bioinform Online 7:55-9. 2011
    ..The program implements a number of ways to summarize the sampled partitions, including calculation of the 'mean' partition-a partition of the individuals to populations that minimizes the squared distance to the sampled partitions...
  23. ncbi request reprint Geographic origin of human mitochondrial DNA: accommodating phylogenetic uncertainty and model comparison
    John P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Syst Biol 51:155-65. 2002
    ..The geographic origin of modern human mtDNA is inferred to be in Africa, although support for this hypothesis was ambiguous for data from an early paper...
  24. ncbi request reprint Testing a covariotide model of DNA substitution
    John P Huelsenbeck
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Mol Biol Evol 19:698-707. 2002
    ..I show that in nine of the genes examined a covariotide model provides a better explanation of the data than a model that does not allow constraints to change over time...
  25. ncbi request reprint MrBayes 3: Bayesian phylogenetic inference under mixed models
    Fredrik Ronquist
    Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University, Norbyv 18D, SE 752 36 Uppsala, Sweden
    Bioinformatics 19:1572-4. 2003
    ..g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters...
  26. ncbi request reprint Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
    Gautam Altekar
    Department of Computer Science, University of Rochester, USA
    Bioinformatics 20:407-15. 2004
    ..Metropolis coupled MCMC [(MC)(3)], a variant of MCMC, allows multiple peaks in the landscape of trees to be more readily explored, but at the cost of increased execution time...
  27. ncbi request reprint Bayesian phylogenetic analysis of combined data
    Johan A A Nylander
    Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18 D, SE 752 36 Uppsala, Sweden
    Syst Biol 53:47-67. 2004
    ..Thus, Bayes factors appear to be useful for selecting among complex models, but it is still unclear whether their use strikes a reasonable balance between model complexity and error in parameter estimates...
  28. ncbi request reprint Bayesian inference of the metazoan phylogeny; a combined molecular and morphological approach
    Henrik Glenner
    Department of Evolutionary Biology, Biological Institute, University of Copenhagen, Universitetsparken 15, DK 2100 Copenhagen, Denmark
    Curr Biol 14:1644-9. 2004
    ..Parsimony, on the contrary, shows conflicting results, with morphology being congruent to the Bayesian results and the molecular data set producing peculiarities that are largely reflected in the combined analysis...
  29. ncbi request reprint Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty
    Michael E Alfaro
    School of Biological Sciences, P O Box 644236, Pullman, Washington 99164 4236, USA
    Syst Biol 55:89-96. 2006
    ..AIC; Akaike weights; Bayesian phylogenetics; model averaging; model selection; model uncertainty; posterior probability; reversible jump.]...
  30. doi request reprint Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics
    Clemens Lakner
    Department of Biological Science, Section Ecology and Evolution, Florida State University, Tallahassee, Florida 32306 4120, USA
    Syst Biol 57:86-103. 2008
    ..Our results have important implications for developers of Bayesian MCMC implementations and for the large group of users of Bayesian phylogenetics software...
  31. ncbi request reprint Comment on "Phylogenetic MCMC algorithms are misleading on mixtures of trees"
    Fredrik Ronquist
    School of Computational Science, Florida State University, Tallahassee, FL 32306 4120, USA
    Science 312:367; author reply 367. 2006
    ..However, the conditions leading to their results are artificial. Standard MCMC convergence diagnostics would detect the problem in real data, and correction of the model misspecification would solve it...
  32. pmc Modeling the site-specific variation of selection patterns along lineages
    Stephane Guindon
    Bioinformatics Institute, Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Private Bag 92019, Auckland, New Zealand
    Proc Natl Acad Sci U S A 101:12957-62. 2004
    ..We also provide strong evidence that the strength and the frequency of occurrence of selection might not be estimated accurately when the site-specific variation of selection regimes is ignored...
  33. ncbi request reprint Clonal interference is alleviated by high mutation rates in large populations
    Jonathan P Bollback
    Institute of Biology, University of Copenhagen, Copenhagen, Denmark
    Mol Biol Evol 24:1397-406. 2007
    ..Here, we analyze data from experimentally evolved asexual populations of a bacteriophage and find that, in these nonrecombining populations with very large Nmu, recurrent mutation does appear to ameliorate this cost of asexuality...