Paul van der Mark
Florida State University
Bayesian probabilityMarkov chain Monte Carlok-nearest neighbors algorithmBayes factorComputer science
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Publications 6
#1Fredrik Ronquist (Swedish Museum of Natural History)H-Index: 47
#2Maxim Teslenko (Swedish Museum of Natural History)H-Index: 2
Last. John P. Huelsenbeck (University of California, Berkeley)H-Index: 62
view all 10 authors...
Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization ...
10.1k CitationsSource
#1Fredrik RonquistH-Index: 47
#2Maxim TeslenkoH-Index: 2
Last. John P. HuelsenbeckH-Index: 62
view all 9 authors...
2 Citations
#1Fredrik RonquistH-Index: 47
#2Paul van der MarkH-Index: 5
Last. John P. HuelsenbeckH-Index: 62
view all 3 authors...
What is the probability that Sweden will win next year’s world championships in ice hockey? If you’re a hockey fan, you probably already have a good idea, but even if you couldn’t care less about the game, a quick perusal of the world championship medalists the last 15 years (Table 7.1) would allow you to make an educated guess. Clearly, Sweden is one of only a small number of teams that compete successfully for the medals. Let’s assume that all seven medalists the last 15 years have the same ch...
77 CitationsSource
#1Isabel Sanmartín (CSIC: Spanish National Research Council)H-Index: 28
#2Paul van der Mark (FSU: Florida State University)H-Index: 5
Last. Fredrik Ronquist (FSU: Florida State University)H-Index: 47
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Aim Oceanic islands represent a special challenge to historical biogeographers because dispersal is typically the dominant process while most existing methods are based on vicariance. Here, we describe a new Bayesian approach to island biogeography that estimates island carrying capacities and dispersal rates based on simple Markov models of biogeographical processes. This is done in the context of simultaneous analysis of phylogenetic and distributional data across groups, accommodating phyloge...
172 CitationsSource
#1Clemens Lakner (FSU: Florida State University)H-Index: 6
#2Paul van der Mark (FSU: Florida State University)H-Index: 5
Last. Fredrik Ronquist (FSU: Florida State University)H-Index: 47
view all 5 authors...
The main limiting factor in Bayesian MCMC analysis of phylogeny is typically the efficiency with which topology proposals sample tree space. Here we evaluate the performance of seven different proposal mechanisms, including most of those used in current Bayesian phylogenetics software. We sampled 12 empirical nucleotide data sets—ranging in size from 27 to 71 taxa and from 378 to 2,520 sites—under difficult conditions: short runs, no Metropolis-coupling, and an oversimplified substitution model ...
98 CitationsSource
#1Fredrik Ronquist (FSU: Florida State University)H-Index: 47
#2Bret Larget (UW: University of Wisconsin-Madison)H-Index: 24
Last. Paul van der Mark (FSU: Florida State University)H-Index: 5
view all 6 authors...
Mossel and Vigoda (Reports, 30 September 2005, p. 2207) show that nearest neighbor interchange transitions, commonly used in phylogenetic Markov chain Monte Carlo (MCMC) algorithms, perform poorly on mixtures of dissimilar trees. 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.
26 CitationsSource