ArticleMolecular biology and evolution2020
ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 106 papers.
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106 citing papers in PubMed, 287 citations in OpenAlex.
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- Centromeric satellite expansion drives genome evolution in the snowy owl.Genome biology · 2026Article
- Post-polyploid chromosomal diploidization in plants is affected by clade divergence and constrained by shared genomic features.Nature communications · 2026Article
- Transposable Element-Mediated Structural Variation Drives Flower Colour Diversification in Camellia.Plant biotechnology journal · 2026Article
- Discovering and protecting cryptic biodiversity: A case study of a previously undescribed, vulnerable bird species in Japan.PNAS nexus · 2026Article
- A Practical Guide for Harnessing Phylogenomics in Biocontrol: Accounting for Topological Uncertainty and Phylogenetic Distance in the Centrifugal Phylogenetic Method and Beyond.Evolutionary applications · 2026Article
- Comparison of whole-genome assemblies of European river lamprey (Lampetra fluviatilis) and brook lamprey (Lampetra planeri).The Journal of heredity · 2026Article
- Improved phylogenetic resolution within the Neotropical rainforest genusFrontiers in plant science · 2026Article
- UnFATE: A Comprehensive Probe Set and Bioinformatics Pipeline for Phylogeny Reconstruction and Multilocus Barcoding of Filamentous Ascomycetes (Ascomycota, Pezizomycotina).Systematic biology · 2025Article
- Augmenting microbial phylogenomic signal with tailored marker gene sets.Nature communications · 2025Article
- Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding.Nature communications · 2025Article
- Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.Genome biology and evolution · 2025Article
- Chromosome-level Genome Assembly of the Tibetan Medicinal Plant Duyiwei (Phlomoides rotata).Scientific data · 2025Article
- A chromosome-level Mitragyna parvifolia genome unveils spirooxindole alkaloid diversification and mitraphylline biosynthesis.The Plant cell · 2025Article
- An updated phylogeny of Boraginales based on the Angiosperms353 probe set: a roadmap for understanding morphological evolution.Annals of botany · 2025Article
46 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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