ArticleMolecular biology and evolution2015
Phylostratigraphic bias creates spurious patterns of genome evolution.
Article in Molecular biology and evolution, 2015. 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 77 papers.
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Who cites it
77 citing papers in PubMed.
- A comprehensive and accessible database of jawed-vertebrate ohnologs.Science advances · 2026Article
- Emergence and evolution of protein-coding de novo genes.Nature reviews. Genetics · 2026Review
- Disordered but Different: Functional and Evolutionary Divergence of Transcription Factor Intrinsically Disordered Regions.bioRxiv : the preprint server for biology · 2026Article
- Structure and Disorder Predictions of Microproteins: Usage, Applications, and Pitfalls.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Machine learning can distinguish orphans that have resulted from sequence divergence beyond recognition.Bioinformatics advances · 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
- Propensity for proto-gene emergence in bacteria.Genome biology · 2025Article
- Functional and evolutionary characteristics of human genes encoding cell surface receptors involved in the regulation of appetite.Journal of integrative bioinformatics · 2025Article
- Article
- Functional innovation through new genes as a general evolutionary process.Nature genetics · 2025Review
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Gene age and genome organization inFrontiers in microbiology · 2025Article
- Diverse Origins of Near-Identical Antifreeze Proteins in Unrelated Fish Lineages Provide Insights Into Evolutionary Mechanisms of New Gene Birth and Protein Sequence Convergence.Molecular biology and evolution · 2024Article
- Ancestral Sequence Reconstruction as a Tool to Detect and Study De Novo Gene Emergence.Genome biology and evolution · 2024Article
- De Novo Emerged Gene Search in Eukaryotes with DENSE.Genome biology and evolution · 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
- The origin and structural evolution of de novo genes in Drosophila.Nature communications · 2024Article
- Towards understanding paleoclimate impacts on primate de novo genes.G3 (Bethesda, Md.) · 2023Article
17 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
Abstract
Phylostratigraphy is a method for dating the evolutionary emergence of a gene or gene family by identifying its homologs across the tree of life, typically by using BLAST searches. Applying this method to all genes in a species, or genomic phylostratigraphy, allows investigation of genome-wide patterns in new gene origination at different evolutionary times and thus has been extensively used. However, gene age estimation depends on the challenging task of detecting distant homologs via sequence similarity, which is expected to have differential accuracies for different genes. Here, we evaluate the accuracy of phylostratigraphy by realistic computer simulation with parameters estimated from genomic data, and investigate the impact of its error on findings of genome evolution. We show that 1) phylostratigraphy substantially underestimates gene age for a considerable fraction of genes, 2) the error is especially serious when the protein evolves rapidly, is short, and/or its most conserved block of sites is small, and 3) these errors create spurious nonuniform distributions of various gene properties among age groups, many of which cannot be predicted a priori. Given the high likelihood that conclusions about gene age are faulty, we advocate the use of realistic simulation to determine if observations from phylostratigraphy are explainable, at least qualitatively, by a null model of biased measurement, and in all cases, critical evaluation of results.
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