ArticleiScience2021
Systematic errors in orthology inference and their effects on evolutionary analyses.
Article in iScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes.Genome biology and evolution · 2023Pooled it
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- Evolution of the Metazoan Protein Domain Repertoire Revealed by a Birth-Death-Gain Model.Journal of molecular evolution · 2025Article
- Ultraconserved Elements and Machine Learning Classifiers Enable Robust Phylogenetics and Taxonomy in Model and Non-Model Nematodes.Molecular ecology resources · 2025Article
- ATAC-seq in Emerging Model Organisms: Challenges and Strategies.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025Review
- Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Article
- Inferences on the evolution of the ascorbic acid synthesis pathway in insects using Phylogenetic Tree Collapser (PTC), a tool for the automated collapsing of phylogenetic trees using taxonomic information.Journal of integrative bioinformatics · 2024Article
- Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions.Genome biology and evolution · 2024Article
- Macroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages.Nature communications · 2024Article
- Ocean to Tree: Leveraging Single-Molecule RNA-Seq to Repair Genome Gene Models and Improve Phylogenomic Analysis of Gene and Species Evolution.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree.Nature biotechnology · 2024Article
- DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies.Systematic biology · 2023Article
- Cross-phyla protein annotation by structural prediction and alignment.Genome biology · 2023Article
- Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae.Genome biology and evolution · 2023Article
- Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny.Molecular biology and evolution · 2023Article
- Comparative genomic analysis of 5MFrontiers in plant science · 2023Article
- Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny.PloS one · 2023Article
- Read2Tree: scalable and accurate phylogenetic trees from raw reads.bioRxiv : the preprint server for biology · 2022Article
- Genome Assembly of the Polyclad Flatworm Prostheceraeus crozieri.Genome biology and evolution · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The availability of complete sets of genes from many organisms makes it possible to identify genes unique to (or lost from) certain clades. This information is used to reconstruct phylogenetic trees; identify genes involved in the evolution of clade specific novelties; and for phylostratigraphy-identifying ages of genes in a given species. These investigations rely on accurately predicted orthologs. Here we use simulation to produce sets of orthologs that experience no gains or losses. We show that errors in identifying orthologs increase with higher rates of evolution. We use the predicted sets of orthologs, with errors, to reconstruct phylogenetic trees; to count gains and losses; and for phylostratigraphy. Our simulated data, containing information only from errors in orthology prediction, closely recapitulate findings from empirical data. We suggest published downstream analyses must be informed to a large extent by errors in orthology prediction that mimic expected patterns of gene evolution.
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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.