Fredrik Ronquist

Summary

Affiliation: Uppsala University
Country: Sweden

Publications

  1. ncbi request reprint Evolution of the gall wasp-host plant association
    F Ronquist
    Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University, Sweden
    Evolution 55:2503-22. 2001
  2. 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
  3. 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
  4. ncbi request reprint Southern hemisphere biogeography inferred by event-based models: plant versus animal patterns
    Isabel Sanmartín
    Department of Systematic Zoology, Evolutionary Biology Centre, Norbyvagen 18D, SE 752 36 Uppsala, Sweden
    Syst Biol 53:216-43. 2004
  5. 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
  6. 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
  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. 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
  9. 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
  10. ncbi request reprint Heterotachy processes in rhodophyte-derived secondhand plastid genes: Implications for addressing the origin and evolution of dinoflagellate plastids
    Kamran Shalchian-Tabrizi
    Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway
    Mol Biol Evol 23:1504-15. 2006

Detail Information

Publications11

  1. ncbi request reprint Evolution of the gall wasp-host plant association
    F Ronquist
    Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University, Sweden
    Evolution 55:2503-22. 2001
    ..Many shifts have been onto plant species already exploited by other gall wasps, suggesting that interspecific parasitism among cynipids facilitates colonization of novel host plants...
  2. 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...
  3. 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...
  4. ncbi request reprint Southern hemisphere biogeography inferred by event-based models: plant versus animal patterns
    Isabel Sanmartín
    Department of Systematic Zoology, Evolutionary Biology Centre, Norbyvagen 18D, SE 752 36 Uppsala, Sweden
    Syst Biol 53:216-43. 2004
    ..Our results also confirm the hybrid origin of the South American biota: there has been surprisingly little biotic exchange between the northern tropical and the southern temperate regions of South America, especially for animals...
  5. 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...
  6. 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...
  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. 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...
  9. 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...
  10. ncbi request reprint Heterotachy processes in rhodophyte-derived secondhand plastid genes: Implications for addressing the origin and evolution of dinoflagellate plastids
    Kamran Shalchian-Tabrizi
    Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway
    Mol Biol Evol 23:1504-15. 2006
    ..In addition, the refined topologies suggest the red algal order, Porphyridales, as the endosymbiont ancestor of the secondary plastids in cryptophytes, haptophytes, and heterokonts...
  11. ncbi request reprint A maximum-likelihood analysis of eight phylogenetic markers in gallwasps (Hymenoptera: Cynipidae): implications for insect phylogenetic studies
    Antonis Rokas
    Institute of Cell, Animal, and Population Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
    Mol Phylogenet Evol 22:206-19. 2002
    ..In contrast, the 18S rDNA marker is likely to be useful for the resolution of above-family-level relationships...