Data from: Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3

Derrick J. Zwickl, Joshua C. Stein, Rod A. Wing, Doreen Ware & Michael J. Sanderson
We describe new methods for characterizing gene tree discordance in phylogenomic datasets, which screen for deviations from neutral expectations, summarize variation in statistical support among gene trees, and allow comparison of the patterns of discordance induced by various analysis choices. Using an exceptionally complete set of genome sequences for the short arm of chromosome 3 in Oryza (rice) species, we applied these methods to identify the causes and consequences of differing patterns of discordance in...
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