Journal
SYSTEMATIC BIOLOGY
Volume 58, Issue 5, Pages 489-500Publisher
OXFORD UNIV PRESS
DOI: 10.1093/sysbio/syp054
Keywords
Bayesian MCMC; gene tree incongruence; multilocus analysis; phylogenetic inference; rice
Categories
Funding
- National Science Foundation (NSF) Division of Biological Sciences [0321678, 0733365, DBI-0321678]
- United States Department of Agriculture - Agricultural Research Service
- Bud Antle Endowed Chair
Ask authors/readers for more resources
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.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available