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TESS: Bayesian inference of lineage diversification rates from (incompletely sampled) molecular phylogenies in R

Sebastian Höhna, Michael R. May, Brian R. Moore
doi: https://doi.org/10.1101/021238
Sebastian Höhna
1Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
2Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
3Department of Statistics, University of California, Berkeley, CA 94720, USA
4Department of Mathematics, Stockholm University, Stockholm, SE-106 91, Sweden
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Michael R. May
1Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
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Brian R. Moore
1Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
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Abstract

Summary Many fundamental questions in evolutionary biology entail estimating rates of lineage diversification (speciation – extinction). We develop a flexible Bayesian framework for specifying an effectively infinite array of diversification models—where rates are constant, vary continuously, or change episodically through time—and implement numerical methods to estimate parameters of these models from molecular phylogenies, even when species sampling is incomplete. Additionally we provide robust methods for comparing the relative and absolute fit of competing branching-process models to a given tree, thereby providing rigorous tests of biological hypotheses regarding patterns and processes of lineage diversification.

Availability and implementation the source code for TESS is freely available at http://cran.r-project.org/web/packages/TESS/.

Contact Sebastian.Hoehna{at}gmail.com

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted June 19, 2015.
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TESS: Bayesian inference of lineage diversification rates from (incompletely sampled) molecular phylogenies in R
Sebastian Höhna, Michael R. May, Brian R. Moore
bioRxiv 021238; doi: https://doi.org/10.1101/021238
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TESS: Bayesian inference of lineage diversification rates from (incompletely sampled) molecular phylogenies in R
Sebastian Höhna, Michael R. May, Brian R. Moore
bioRxiv 021238; doi: https://doi.org/10.1101/021238

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