ArticleSystematic biology2022
DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition.
Article in Systematic biology, 2022. 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 24 papers, 1 of them a synthesis that pooled it.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Bibliometric analysis of kinship analysis from 1960 to 2023: global trends and development.Frontiers in genetics · 2024Pooled it
- A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.Genome biology · 2026Article
- A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.bioRxiv : the preprint server for biology · 2026Article
- New insights into mitochondrial segregation from the Doubly Uniparental Inheritance system in bivalves.BMC biology · 2025Article
- Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.Genome biology and evolution · 2025Article
- Comparative Genomics of Sex-Determination-Related Genes Reveals Shared Evolutionary Patterns Between Bivalves and Mammals, but Not Fruit Flies.Molecular ecology · 2025Article
- Avian Lifespan Network Reveals Shared Mechanisms and New Key Players in Animal Longevity.Aging cell · 2025Article
- The Early Evolution of Tudor Genes in Holozoa and How Their Distribution Was Influenced by Life History Traits in Metazoa.Genome biology and evolution · 2025Article
- Insect Phylogenomics: From Experiment Planning to Post-phylogenetic Analyses.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Phylotranscriptomics reveals the phylogeny of Asparagales and the evolution of allium flavor biosynthesis.Nature communications · 2024Article
- Article
- wQFM-DISCO: DISCO-enabled wQFM improves phylogenomic analyses despite the presence of paralogs.Bioinformatics advances · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- Weighted ASTRID: fast and accurate species trees from weighted internode distances.Algorithms for molecular biology : AMB · 2023Article
- Phylogenomic branch length estimation using quartets.Bioinformatics (Oxford, England) · 2023Article
- Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data.Bioinformatics (Oxford, England) · 2023Article
- DISCO+QR: rooting species trees in the presence of GDL and ILS.Bioinformatics advances · 2023Article
- Recent progress on methods for estimating and updating large phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees.PLoS biology · 2022Article
- Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages.Genome biology and evolution · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Species tree inference from gene family trees is a significant problem in computational biology. However, gene tree heterogeneity, which can be caused by several factors including gene duplication and loss, makes the estimation of species trees very challenging. While there have been several species tree estimation methods introduced in recent years to specifically address gene tree heterogeneity due to gene duplication and loss (such as DupTree, FastMulRFS, ASTRAL-Pro, and SpeciesRax), many incur high cost in terms of both running time and memory. We introduce a new approach, DISCO, that decomposes the multi-copy gene family trees into many single copy trees, which allows for methods previously designed for species tree inference in a single copy gene tree context to be used. We prove that using DISCO with ASTRAL (i.e., ASTRAL-DISCO) is statistically consistent under the GDL model, provided that ASTRAL-Pro correctly roots and tags each gene family tree. We evaluate DISCO paired with different methods for estimating species trees from single copy genes (e.g., ASTRAL, ASTRID, and IQ-TREE) under a wide range of model conditions, and establish that high accuracy can be obtained even when ASTRAL-Pro is not able to correctly roots and tags the gene family trees. We also compare results using MI, an alternative decomposition strategy from Yang Y. and Smith S.A. (2014), and find that DISCO provides better accuracy, most likely as a result of covering more of the gene family tree leafset in the output decomposition. [Concatenation analysis; gene duplication and loss; species tree inference; summary method.].
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.