DISCO+QR: rooting species trees in the presence of GDL and ILS

Abstract

Genes evolve under processes such as gene duplication and loss (GDL), so that gene family trees are multi-copy, as well as incomplete lineage sorting (ILS); both processes produce gene trees that differ from the species tree. The estimation of species trees from sets of gene family trees is challenging, and the estimation of rooted species trees presents additional analytical challenges. Two of the methods developed for this problem are STRIDE (Emms and Kelly, MBE 2017), which roots species trees by considering GDL events, and Quintet Rooting (Tabatabaee et al., ISMB 2022 and Bioinformatics 2022), which roots species trees by considering ILS. We present DISCO+QR, a new approach to rooting species trees that first uses DISCO to address GDL and then uses QR to perform rooting in the presence of ILS. DISCO+QR operates by taking the input gene family trees and decomposing them into single-copy trees using DISCO (Willson et al., Systematic Biology 2022) and then roots the given species tree using the information in the single-copy gene trees using Quintet Rooting (QR). We show that the relative accuracy of STRIDE and DISCO+QR depend on properties of the dataset (number of species, genes, rate of gene duplication, degree of ILS, and gene tree estimation error), and that each provides advantages over the other under some conditions. Availability: DISCO and QR are available in github.

Statistically Consistent Rooting of Species Trees Under the Multispecies Coalescent Model

“…It remains to be investigated whether other rooting methods can also be proven statistically consistent under models of gene evolution inside species trees, such as the MSC or models of GDL. For example, STRIDE [4] and DISCO+QR [33] are methods that have been developed for rooting species trees from gene family trees, where genes evolve under gene duplication and loss (GDL); however, it is not known whether these methods are statistically consistent under any GDL model.…”