Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts
Abstract
Partitioned coalescence support (PCS) is automated for genome-scale datasets. PCS summarizes the support and conflict among gene trees in coalescence analyses. PCS detects biases in phylogenomic support provided by outlier gene trees. PCS quantifies the effects of missing taxa in gene trees. PCS reveals the instability of clades with high bootstrap or Bayesian support.
- Publication:
-
Molecular Phylogenetics and Evolution
- Pub Date:
- October 2019
- DOI:
- Bibcode:
- 2019MolPE.13906539G
- Keywords:
-
- ASTRAL;
- MP-EST;
- Coalescence;
- Gene tree;
- Incomplete lineage sorting;
- Species tree;
- ASTRAL;
- accurate species tree algorithm;
- ASTRID;
- accurate species trees from internode distances;
- CS;
- coalescence support;
- ILS;
- incomplete lineage sorting;
- ML;
- maximum likelihood;
- MP-EST;
- maximum pseudo-likelihood for estimating species trees;
- MY;
- million years;
- NJ-ST;
- neighbor joining species tree;
- PCS;
- partitioned coalescence support;
- PP;
- posterior probability;
- STAR;
- species tree estimation using average ranks of coalescences;
- UCE;
- ultraconserved element