542 SYSTEMATIC BIOLOGY VOL. 61 systems. The installers include both MrBayes and the re- quired BEAGLE libraries, but the BEAGLE libraries can also be installed separately using the BEAGLE installer, available at http://beagle-lib.googlecode.com. The pro- gram comes with a manual and example files. Further help is available on the program web site, which also provides instructions for reporting bugs and signing up for the MrBayes e-mail list. Instructions for accessing the MrBayes source code repository can be found at http://sourceforge.net/projects/mrbayes/develop. FUNDING The development of version 3.2 of MrBayes would not have been possible without generous support from the Swedish Research Council [2008-5629 to F.R.]; the National Institutes of Health [GM-069801 to J.P.H. and GM-086887, HG-006139 to M.A.S.]; and the National Sci- ence Foundation [DEB-0445453 to J.P.H., DEB-0949121 and DEB-0936214 to B.L., and DBI-0755048 to D.L.A.]. Incorporation of the BEST algorithms and support for the BEAGLE library was greatly facilitated by a workshop in October 2010 sponsored by the Mathe- matical Biosciences Institute at Ohio State University [NSF-DMS-0931642], hosted by Dennis Pearl and Marty Golubitsky. ACKNOWLEDGMENTS F.R., with the assistance of M.T. and P.v.d.M., did most of the programming for version 3.2, whereas J.P.H., as- sisted by F.R., was responsible for the software archi- tecture and initial code base. D.L.A., A.D., and M.A.S. helped with the BEAGLE integration and the related performance testing. L.L. assisted in the incorporation of the BEST algorithms, whereas B.L. and S.H. contributed to the implementation of particular models. We would like to thank Chris Anderson for additional assistance with the BEST algorithms. We would also like to express our deep gratitude to the many MrBayes users, who have generously contributed to the project by submit- ting bug reports, bug fixes, feature requests, and other comments on the software. David Posada, Leonardo Martins, and Jeremy Brown provided constructive criti- cism that helped improve the manuscript. REFERENCES Altekar G., Dwarkadas S., Huelsenbeck J. 2004. Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic in- ference. Bioinformatics. 20:407–425. Ayres D.L., Darling A., Zwickl D.J., Beerli P., Holder M.T., Lewis P.O., Huelsenbeck J.P., Ronquist F., Swofford D.L., Cummings M.P., Ram- baut A., Suchard M.A. 2012. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst. Biol. 61:170–173. Drummond A.J., Ho S.Y.W., Phillips M.J., Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4:e88. Edwards S.V., Liu L., Pearl D.K. 2007. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. U.S.A. 104:5936–5941. Gelman A., Rubin D. 1992. Inference from iterative simulation using multiple sequences. Stat. Sci. 7:457–472. Gernhard T. 2008. The conditioned reconstructed process. J. Theor. Biol. 253:769–778. Goldman N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182–198. Ho¨ hna S., Drummond A.J. 2012. Guided tree topology proposal for Bayesian phylogenetic inference. Syst. Biol. 61:1–11. Ho¨ hna S., Stadler T., Ronquist F., Britton T. 2011. Inferring speciation and extinction rates under different species sampling schemes. Mol. Biol. Evol. 28:2577–2589. Huelsenbeck J., Larget B., Swofford D. 2000. A compound Poisson pro- cess for relaxing the molecular clock. Genetics. 154:1879–1892. Huelsenbeck J.P., Larget B., Alfaro M.E. 2004. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol. 21:1123–1133. Huelsenbeck J.P., Ronquist F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17:754–755. Lakner C., van der Mark P., Huelsenbeck J., Larget B., Ronquist F. 2008. Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics. Syst. Biol. 57:86–103. Larget B., Simon D. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16: 750–759. Lartillot N., Philippe H. 2006. Computing Bayes factors using thermo- dynamic integration. Syst. Biol. 55:195–207. Lepage T., Bryant D., Philippe H., Lartillot N. 2007. A general compar- ison of relaxed molecular clock models. Mol. Biol. Evol. 24:2669– 2680. Liu L., Pearl D.K. 2007. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using esti- mated gene tree distributions. Syst. Biol. 56:504–514. Mau B., Newton M.A. 1997. Phylogenetic inference for binary data on dendograms using Markov chain Monte Carlo. J. Comput. Graph. Stat. 6:122–131. Mau B., Newton M.A., Larget B. 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics. 55:1–12. Newton M., Raftery A. 1994. Approximate Bayesian inference with the weighted likelihood bootstrap. J. R. Stat. Soc. B Stat. Methodol. 56:3–48. Posada D. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics. 14:817–818. Posada D. 2008. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 25:1253–1256. Rannala B., Yang Z. 2008. Phylogenetic inference using whole genomes. Annu. Rev. Genomics Hum. Genet. 9:217–231. Roberts G., Rosenthal J. 2009. Examples of adaptive MCMC. J. Com- put. Graph. Stat. 18:349–367. Ronquist F., Deans A.R. 2010. Bayesian phylogenetics and its influence on insect systematics. Annu. Rev. Entomol. 55:189–206. Ronquist F., Huelsenbeck J.P. 2003. Mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572–1574. Ronquist F., Klopfstein S., Vilhelmsen L., Schulmeister S., Murray D.L., Rasnitsyn A.P. Forthcoming 2012. A total-evidence approach to dat- ing with fossils, applied to the early radiation of the Hymenoptera. Syst. Biol. Stadler T. 2009. On incomplete sampling under birth-death models and connections to the sampling-based coalescent. J. Theor. Biol. 261:58–66. Suchard M.A., Weiss R.E., Sinsheimer J.S. 2001. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 18:1001–1013. Thorne J.L., Kishino H. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51:689–702. Xie W., Lewis P.O., Fan Y., Kuo L., Chen M.-H. 2011. Improving marginal likelihood estimation for Bayesian phylogenetic model se- lection. Syst. Biol. 60:150–160. Yang Z., Rannala B. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717–724.