DOI: 10.1101/461699Nov 4, 2018Paper

Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts

BioRxiv : the Preprint Server for Biology
John GatesyMark S Springer


Genomic datasets sometimes support unconventional or conflicting phylogenetic relationships when different tree-building methods are applied. Coherent interpretations of such results are enabled by partitioning support for controversial relationships among the constituent genes of a phylogenomic dataset. For the supermatrix (= concatenation) approach, several simple methods that measure the distribution of support and conflict among loci were introduced over 15 years ago. More recently, partitioned coalescence support (PCS) was developed for phylogenetic coalescence methods that account for incomplete lineage sorting and use the summed fits of gene trees to estimate the species tree. Here, we automate computation of PCS to permit application of this index to genome-scale matrices that include hundreds of loci. Reanalyses of four phylogenomic datasets for amniotes, land plants, skinks, and angiosperms demonstrate how PCS scores can be used to: 1) compare conflicting results favored by alternative coalescence methods, 2) identify outlier gene trees that have a disproportionate influence on the resolution of contentious relationships, 3) assess the effects of missing data in species-trees analysis, and 4) clarify biases in commonl...Continue Reading

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