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Systematic Biology 2008 57(5):772-784; doi:10.1080/10635150802434394
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© 2008 Society of Systematic Biologists

Wagner and Dollo: A Stochastic Duet by Composing Two Parsimonious Solos

Alexander V. Alekseyenko1, Christopher J. Lee2 and Marc A. Suchard1,3,4

1 Department of Biomathematics, David Geffen School of Medicine at UCLA Los Angeles, California 90095, USA; E-mail: alexander.alekseyenko{at}ucla.edu (A.V.A.)
2 Department of Chemistry and Biochemistry, Institute for Genomics and Proteomics, Molecular Biology Institute, UCLA Los Angeles, California, 90095, USA
3 Department of Human Genetics, David Geffen School of Medicine at UCLA Los Angeles, California, 90095, USA; E-mail: msuchard{at}ucla.edu (M.A.S.)
4 Department of Biostatistics, UCLA School of Public Health Los Angeles, California 90095, USA

Edited by Laura Kubatko


  Abstract

New contributions toward generalizing evolutionary models expand greatly our ability to analyze complex evolutionary characters and advance phylogeny reconstruction. In this article, we extend the binary stochastic Dollo model to allow for multi-state characters. In doing so, we align previously incompatible Wagner and Dollo parsimony principles under a common probabilistic framework by embedding arbitrary continuous-time Markov chains into the binary stochastic Dollo model. This approach enables us to analyze character traits that exhibit both Dollo and Wagner characteristics throughout their evolutionary histories. Utilizing Bayesian inference, we apply our novel model to analyze intron conservation patterns and the evolution of alternatively spliced exons. The generalized framework we develop demonstrates potential in distinguishing between phylogenetic hypotheses and providing robust estimates of evolutionary rates. Moreover, for the two applications analyzed here, our framework is the first to provide an adequate stochastic process for the data. We discuss possible extensions to the framework from both theoretical and applied perspectives.

Keywords: Alternative splicing evolution; Bayesian phylogenetic inference; immigration-mutation-death process; intron conservation; stochastic Dollo

Received February 6, 2008; Revised April 8, 2008; Accepted August 25, 2008
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