ASTRAL-Pro: Quartet-based species-tree inference despite paralogy

Phylogenetic inference from genome-wide data (phylogenomics) has
revolutionized the study of evolution because it enables accounting for
discordance among evolutionary histories across the genome. To this end,
summary methods have been developed to allow accurate and scalable
inference of species trees from gene trees. However, most of these
methods, including the widely used ASTRAL, can only handle single-copy
gene trees and do not attempt to model gene duplication and gene loss. As
a result, most phylogenomic studies have focused on single-copy genes and
have discarded large parts of the data. Here, we first propose a measure
of quartet similarity between single-copy and multicopy trees that
accounts for orthology and paralogy. We then introduce a method called
ASTRAL-Pro (ASTRAL for PaRalogs and Orthologs) to find the species tree
that optimizes our quartet similarity measure using dynamic programming.
By studying its performance on an extensive collection of simulated data
sets and on real data sets, we show that ASTRAL-Pro is more accurate than
alternative methods.