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      DNA sequencing reveals unexpected Recent diversity and an ancient dichotomy in the American marsupial genusMarmosops(Didelphidae: Thylamyini) : Systematics ofMarmosopsOpossums

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          AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics.

          A key element to a successful Markov chain Monte Carlo (MCMC) inference is the programming and run performance of the Markov chain. However, the explicit use of quality assessments of the MCMC simulations-convergence diagnostics-in phylogenetics is still uncommon. Here, we present a simple tool that uses the output from MCMC simulations and visualizes a number of properties of primary interest in a Bayesian phylogenetic analysis, such as convergence rates of posterior split probabilities and branch lengths. Graphical exploration of the output from phylogenetic MCMC simulations gives intuitive and often crucial information on the success and reliability of the analysis. The tool presented here complements convergence diagnostics already available in other software packages primarily designed for other applications of MCMC. Importantly, the common practice of using trace-plots of a single parameter or summary statistic, such as the likelihood score of sampled trees, can be misleading for assessing the success of a phylogenetic MCMC simulation. The program is available as source under the GNU General Public License and as a web application at http://ceb.scs.fsu.edu/awty.
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            Threatened biotas: "Hot spots" in tropical forests

             Norman Myers (1988)
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              Inferring Phylogenies from mtDNA Variation: Mitochondrial-Gene Trees Versus Nuclear-Gene Trees

               William Moore (1995)
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                Author and article information

                Journal
                Zoological Journal of the Linnean Society
                Zool J Linn Soc
                Wiley
                00244082
                April 2016
                April 2016
                March 11 2016
                : 176
                : 4
                : 914-940
                Affiliations
                [1 ]Department of Ecology, Evolution and Behavior; University of Minnesota; 100 Ecology Building, 1987 Upper Buford Circle Saint Paul MN 55108 USA
                [2 ]J.F. Bell Museum of Natural History; University of Minnesota; 100 Ecology Building, 1987 Upper Buford Circle Saint Paul MN 55108 USA
                [3 ]Division of Vertebrate Zoology; American Museum of Natural History; Central Park West at 79th Street New York NY 10024 USA
                Article
                10.1111/zoj.12343
                © 2016

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