ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy

Author:

Zhang Chao1,Scornavacca Celine2,Molloy Erin K3,Mirarab Siavash4ORCID

Affiliation:

1. Bioinformatics and Systems Biology, University of California San Diego, San Diego, CA

2. ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France

3. Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL

4. Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA

Abstract

Abstract 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 programing. 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.

Funder

National Science Foundation

Ira and Debra Cohen Graduate Fellowship in Computer Science

Publisher

Oxford University Press (OUP)

Subject

Genetics,Molecular Biology,Ecology, Evolution, Behavior and Systematics

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