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Systematic Zoology Advance Access published online on November 11, 2009
Systematic Zoology, doi:10.1093/sysbio/syp075
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© The Author(s) 2009. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles

Robert C. Thomson* and H. Bradley Shaffer

Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA

* Correspondence to be sent to: Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA 95616, USA; E-mail: rcthomson{at}ucdavis.edu.


  Abstract

As phylogenetic data sets grow in size and number, objective methods to summarize this information are becoming increasingly important. Supermatrices can combine existing data directly and in principle provide effective syntheses of phylogenetic information that may reveal new relationships. However, several serious difficulties exist in the construction of large supermatrices that must be overcome before these approaches will enjoy broad utility. We present analyses that examine the performance of sparse supermatrices constructed from large sequence databases for the reconstruction of species-level phylogenies. We develop a largely automated informatics pipeline that allows for the construction of sparse supermatrices from GenBank data. In doing so, we develop strategies for alleviating some of the outstanding impediments to accurate phylogenetic inference using these approaches. These include taxonomic standardization, automated alignment, and the identification of rogue taxa. We use turtles as an exemplar clade and present a well-supported species-level phylogeny for two-thirds of all turtle species based on a ~50 kb supermatrix consisting of 93% missing data. Finally, we discuss some of the remaining pitfalls and concerns associated with supermatrix analyses, provide comparisons to supertree approaches, and suggest areas for future research.

Keywords: Alignment; GenBank; phyloinformatics; rogue taxa; supermatrix; taxonomy; Testudines; turtle phylogeny

Received January 7, 2009; Revised April 18, 2009; Accepted September 28, 2009

Associate Editor: Thomas Buckley


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