Species Trees from Highly Incongruent Gene Trees in Rice

Cranston, K. A., Hurwitz, B. L., Ware, D. H., Stein, L. D., Wing, R. A. (2009) Species Trees from Highly Incongruent Gene Trees in Rice. Systematic Biology, 58 (5). pp. 489-500. ISSN 1063-5157

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URL: http://www.ncbi.nlm.nih.gov/pubmed/20525603
DOI: 10.1093/sysbio/syp054

Abstract

Several methods have recently been developed to infer multilocus phylogenies by incorporating information from topological incongruence of the individual genes. In this study, we investigate 2 such methods, Bayesian concordance analysis and Bayesian estimation of species trees. Our test data are a collection of genes from cultivated rice (genus Oryza) and the most closely related wild species, generated using a high-throughput sequencing protocol and bioinformatics pipeline. Trees inferred from independent genes display levels of topological incongruence that far exceed that seen in previous data sets analyzed with these species tree methods. We identify differences in phylogenetic results between inference methods that incorporate gene tree incongruence. Finally, we discuss the challenges of scaling these analyses for data sets with thousands of gene trees and extensive levels of missing data.

Item Type: Paper
Uncontrolled Keywords: Bayesian MCMC gene tree incongruence multilocus analysis phylogenetic inference rice MULTIPLE SEQUENCE ALIGNMENT PHYLOGENETIC ANALYSIS BAYESIAN-ESTIMATION RECONCILED TREES MISSING DATA EST DATA ORYZA EVOLUTION LINEAGE PHYLOGENOMICS
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function
organism description > plant
organism description > plant > rice
CSHL Authors:
Communities: CSHL labs > Stein lab
CSHL labs > Ware lab
Depositing User: Matt Covey
Date Deposited: 19 Feb 2013 16:55
Last Modified: 19 Feb 2013 16:55
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27457

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