Leveraging weighted quartet distributions for enhanced species tree inference from genome-wide data

Abstract Species tree estimation from genes sampled from throughout the whole genome is challeng-ing in the presence of gene tree discordance, often caused by incomplete lineage sorting (ILS), where alleles can coexist in populations for periods that may span several speciation events. Quartet-based summary methods for estimating species trees from a collection of gene trees are becoming popular due to their high accuracy and theoretical guarantees of robustness to arbitrarily high amounts of ILS. ASTRAL, the most widely used quartet-based method, aims to infer species trees by maximizing the number of quartets in the gene trees that are consistent with the species tree. An alternative approach (as in wQFM) is to infer quartets for all subsets of four species and…