DISCO+QR

DISCO+QR integrates DISCO and Quintet Rooting (QR) to root species trees by addressing gene duplication and loss (GDL) through decomposition of multi-copy gene family trees and incomplete lineage sorting (ILS) through quintet-based rooting.

Key Features:

• DISCO decomposition: DISCO decomposes multi-copy gene family trees into single-copy gene trees to address gene duplication and loss (GDL).
• Quintet Rooting (QR): QR applies quintet-based rooting to single-copy gene trees to root species trees while accounting for incomplete lineage sorting (ILS).
• Joint GDL and ILS handling: The method integrates DISCO outputs with QR rooting to account for both GDL and ILS when inferring the species tree root.
• Dataset robustness: Applicable across datasets with varying numbers of species, numbers of genes, rates of gene duplication, degrees of ILS, and levels of gene tree estimation error.

Scientific Applications:

• Phylogenomics: Rooting and accurate estimation of species trees in phylogenomic studies where gene trees differ from species trees due to GDL and ILS.
• Comparative dataset analysis: Analysis of datasets that vary in species/gene counts, duplication rates, ILS levels, and gene tree estimation error to evaluate rooting under complex evolutionary scenarios.

Methodology:

DISCO decomposes multi-copy gene family trees into single-copy gene trees, and QR then roots the species tree using quintet-based rooting on those single-copy gene trees to account for ILS.