Affiliation: Uppsala University
- Evolution of the gall wasp-host plant associationF 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...
- MrBayes 3: Bayesian phylogenetic inference under mixed modelsFredrik 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...
- Bayesian phylogenetic analysis of combined dataJohan 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...
- Southern hemisphere biogeography inferred by event-based models: plant versus animal patternsIsabel 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...
- Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogeneticsClemens 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...
- 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...
- A Bayesian perspective on a non-parsimonious parsimony modelJohn P Huelsenbeck
Department of Integrative Biology, University of California, Berkeley, CA 94720 3140, USA
Syst Biol 57:406-19. 2008....
- Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inferenceGautam 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...
- Potential applications and pitfalls of Bayesian inference of phylogenyJohn 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...
- Heterotachy processes in rhodophyte-derived secondhand plastid genes: Implications for addressing the origin and evolution of dinoflagellate plastidsKamran 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...
- A maximum-likelihood analysis of eight phylogenetic markers in gallwasps (Hymenoptera: Cynipidae): implications for insect phylogenetic studiesAntonis 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...