Gene Tree Discordance Causes Apparent Substitution Rate Variation

Gene Tree Discordance Causes Apparent Substitution Rate Variation.

Substitution rates are known to be variable among genes, chromosomes, species, and lineages due to multifarious biological processes. Here, we consider another source of substitution rate variation due to a technical bias associated with gene tree discordance. Discordance has been found to be rampant in genome-wide data sets, often due to incomplete lineage sorting (ILS). This apparent substitu...

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

DiscoVista: Interpretable visualizations of gene tree discordance.

Phylogenomics has ushered in an age of discordance. Analyses often reveal abundant discordances among phylogenies of different parts of genomes, as well as incongruences between species trees obtained using different methods or data partitions. Researchers are often left trying to make sense of such incongruences. Interpretive ways of measuring and visualizing discordance are needed, both among...

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...

Gene tree discordance, phylogenetic inference and the multispecies coalescent.

The field of phylogenetics is entering a new era in which trees of historical relationships between species are increasingly inferred from multilocus and genomic data. A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome. Recent advances in genealogical model...