Improved gene tree error correction in the presence of horizontal gene transfer

• Main Authors: Bansal, Mukul S. (Contributor), Wu, Yi-Chieh (Contributor), Alm, Eric J. (Contributor), Kellis, Manolis (Contributor)
• Other Authors: Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory (Contributor), Massachusetts Institute of Technology. Department of Biological Engineering (Contributor), Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science (Contributor)
• Format: Article
• Language: English
• Published: Oxford University Press, 2015-06-26T12:30:02Z.
• Subjects: Article
• Online Access: Get fulltext

Motivation: The accurate inference of gene trees is a necessary step in many evolutionary studies. Although the problem of accurate gene tree inference has received considerable attention, most existing methods are only applicable to gene families unaffected by horizontal gene transfer. As a result, the accurate inference of gene trees affected by horizontal gene transfer remains a largely unaddressed problem. Results: In this study, we introduce a new and highly effective method for gene tree error correction in the presence of horizontal gene transfer. Our method efficiently models horizontal gene transfers, gene duplications and losses, and uses a statistical hypothesis testing framework [Shimodaira-Hasegawa (SH) test] to balance sequence likelihood with topological information from a known species tree. Using a thorough simulation study, we show that existing phylogenetic methods yield inaccurate gene trees when applied to horizontally transferred gene families and that our method dramatically improves gene tree accuracy. We apply our method to a dataset of 11 cyanobacterial species and demonstrate the large impact of gene tree accuracy on downstream evolutionary analyses. Availability and implementation: An implementation of our method is available at http://compbio.mit.edu/treefix-dtl/
National Science Foundation (U.S.) (CAREER Award 0644282)
National Institutes of Health (U.S.) (RC2 HG005639)
National Science Foundation (U.S.). Assembling the Tree of Life (Program) (0936234)
University of Connecticut