Affiliation: University of Wisconsin
- The estimation of tree posterior probabilities using conditional clade probability distributionsBret Larget
Departments of Botany and Statistics, University of Wisconsin, Madison, WI 53706, USA
Syst Biol 62:501-11. 2013..Furthermore, the method can be used to estimate the total probability of the set of sampled trees which provides a measure of the thoroughness of a posterior sample...
- A Bayesian approach to the estimation of ancestral genome arrangementsBret Larget
Department of Botany, University of Wisconsin, Madison, USA
Mol Phylogenet Evol 36:214-23. 2005..We compare and contrast a Bayesian approach with a parsimony approach to infer phylogenies and ancestral arrangements from genome arrangement data by re-analyzing a number of previously published data sets...
- Bayesian estimation of concordance among gene treesCecile Ane
Department of Statistics, University of Wisconsin, USA
Mol Biol Evol 24:412-26. 2007..We demonstrate the method on a set of 106 genes from 8 yeast species...
- A Bayesian model of AFLP marker evolution and phylogenetic inferenceRuiyan Luo
University of Wisconsin, Madison, WI, USA
Stat Appl Genet Mol Biol 6:Article11. 2007..We compare the results of our analysis with a clustering method based on Nei and Li's restriction-site distance and a two-state Bayesian analysis using MrBayes...
- A bayesian analysis of metazoan mitochondrial genome arrangementsBret Larget
Department of Botany, University of Wisconsin at Madison, USA
Mol Biol Evol 22:486-95. 2005..We present summaries of Bayesian posterior distributions of tree topology on the basis of these two data sets...
- An assessment of transgenomics as a tool for identifying genes involved in the evolutionary differentiation of closely related plant speciesRaul Correa
Department of Botany, University of Wisconsin Madison, Madison, WI 53706, USA
New Phytol 193:494-503. 2012..We identify methods to reduce false positives and false negatives in the future. 11_11B can be viewed as a potential speciation gene, illustrating the value of transgenomics for studying the molecular basis of reproductive isolation...
- Exploring Tree-Like and Non-Tree-Like Patterns Using Genome Sequences: An Example Using the Inbreeding Plant Species Arabidopsis thaliana (L.) HeynhNoah W M Stenz
Department of Botany, University of Wisconsin Madison, WI, 53706, USA
Syst Biol 64:809-23. 2015..Our study illustrates how we can use genome sequence data to evaluate whether phylogenetic relationships are strictly tree-like or reticulating. ..
- Specificity in the symbiotic association between fungus-growing ants and protective Pseudonocardia bacteriaMatias J Cafaro
Department of Bacteriology, University of Wisconsin, Madison, 4325 Microbial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA
Proc Biol Sci 278:1814-22. 2011..Our findings support a model that many fungus-growing ants maintain specialized Pseudonocardia symbionts that help with garden defence...
- 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...
- 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...
- 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....
- Hastings ratio of the LOCAL proposal used in Bayesian phylogeneticsMark T Holder
School of Computational Science, Florida State University, Tallahassee, 32306 4120, USA
Syst Biol 54:961-5. 2005
- Bayesian phylogenetic model selection using reversible jump Markov chain Monte CarloJohn 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....
- 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...
- Improving Bayesian PhylogenyBret Larget; Fiscal Year: 2006..abstract_text> ..