ArticleGenome biology and evolution2017
Further Simulations and Analyses Demonstrate Open Problems of Phylostratigraphy.
Article in Genome biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Emergence and evolution of protein-coding de novo genes.Nature reviews. Genetics · 2026Review
- Structure and Disorder Predictions of Microproteins: Usage, Applications, and Pitfalls.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Evolution of the Metazoan Protein Domain Repertoire Revealed by a Birth-Death-Gain Model.Journal of molecular evolution · 2025Article
- De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.Genome biology and evolution · 2025Review
- Functional and evolutionary characteristics of human genes encoding cell surface receptors involved in the regulation of appetite.Journal of integrative bioinformatics · 2025Article
- Unbiased anchors for reliable genome-wide synteny detection.Algorithms for molecular biology : AMB · 2025Article
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions.Genome biology and evolution · 2024Article
- Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra.Genome biology · 2023Article
- A Thermodynamic Model for Water Activity and Redox Potential in Evolution and Development.Journal of molecular evolution · 2022Article
- Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome.Molecular biology and evolution · 2022Article
- Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants.Nature plants · 2021Article
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- Many, but not all, lineage-specific genes can be explained by homology detection failure.PLoS biology · 2020Article
- A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila.Journal of molecular evolution · 2020Article
- Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes.eLife · 2020Article
- Article
- Highlight: New Solutions and Open Questions in Computational Evolutionary Biology.Genome biology and evolution · 2019Article
- A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution.Genetics · 2019Article
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2 authors.
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Abstract
Phylostratigraphy, originally designed for gene age estimation by BLAST-based protein homology searches of sequenced genomes, has been widely used for studying patterns and inferring mechanisms of gene origination and evolution. We previously showed by computer simulation that phylostratigraphy underestimates gene age for a nonnegligible fraction of genes and that the underestimation is severer for genes with certain properties such as fast evolution and short protein sequences. Consequently, many previously reported age distributions of gene properties may have been methodological artifacts rather than biological realities. Domazet-Lošo and colleagues recently argued that our simulations were flawed and that phylostratigraphic bias does not impact inferences about gene emergence and evolution. Here we discuss conceptual difficulties of phylostratigraphy, identify numerous problems in Domazet-Lošo et al.'s argument, reconfirm phylostratigraphic error using simulations suggested by Domazet-Lošo and colleagues, and demonstrate that a phylostratigraphic trend claimed to be robust to error disappears when genes likely to be error-resistant are analyzed. We conclude that extreme caution is needed in interpreting phylostratigraphic results because of the inherent biases of the method and that reanalysis using genes exhibiting no error in realistic simulations may help reduce spurious findings.
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