DiscoVista: Interpretable visualizations of gene tree discordance.

Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer.

With the increasing interest in recognizing the discordance between gene genealogies, various gene tree/species tree reconciliation methods have been developed. We present here the first attempt to assess and compare two such Bayesian methods, Bayesian estimation of species trees (BEST) and BUCKy (Bayesian untangling of concordance knots), in the presence of several known processes of gene tree...

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

We describe new methods for characterizing gene tree discordance in phylogenomic data sets, 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 (...

Gene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time.

Phenotypic convergence is an exciting outcome of adaptive evolution, occurring when different species find similar solutions to the same problem. Unraveling the molecular basis of convergence provides a way to link genotype to adaptive phenotypes, but can also shed light on the extent to which molecular evolution is repeatable and predictable. Many recent genome-wide studies have uncovered a st...

RATE VARIATION CAUSED BY DISCORDANCE Gene tree discordance causes apparent substitution rate variation

Gene tree discordance generates patterns of diminishing convergence over time

1 Gene tree discordance generates patterns of diminishing convergence over time Fábio K. Mendes, Yoonsoo Hahn , Matthew W. Hahn Department of Biology, Indiana University, Bloomington, IN, 47405, USA 5 Department of Life Science, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 06974, Republic of Korea School of Informatics and Computing, Indiana University, Bloomingt...