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.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Zhang C,Scornavacca C,Molloy EK,Mirarab Sdoi
10.1093/molbev/msaa139subject
Has Abstractpub_date
2020-11-01 00:00:00pages
3292-3307issue
11eissn
0737-4038issn
1537-1719pii
5850411journal_volume
37pub_type
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