ArticleMolecular biology and evolution2016
Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution.
Article in Molecular biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- DetectNAR genomics and bioinformatics · 2026Article
- 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
- De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods.Genome biology and evolution · 2025Review
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- De Novo Genes.Annual review of genetics · 2024Review
- Article
- A Synergistic, Cultivator Model of De Novo Gene Origination.Genome biology and evolution · 2024Article
- Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions.Genome biology and evolution · 2024Article
- Emergence of an Orphan Nitrogenase Protein Following Atmospheric Oxygenation.Molecular biology and evolution · 2024Article
- Four classic "de novo" genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences.Molecular genetics and genomics : MGG · 2024Article
- The origin and structural evolution of de novo genes in Drosophila.Nature communications · 2024Article
- Somatic genome architecture and molecular evolution are decoupled in "young" linage-specific gene families in ciliates.PloS one · 2024Article
- Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inGenome research · 2023Article
- Protein evidence of unannotated ORFs ineLife · 2022Article
- Strong evidence for the adaptive walk model of gene evolution in Drosophila and Arabidopsis.PLoS biology · 2022Article
- Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes.Current biology : CB · 2022Article
- Random peptides rich in small and disorder-promoting amino acids are less likely to be harmful.Genome biology and evolution · 2022Article
- Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome.Molecular biology and evolution · 2022Article
- The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes.Molecular biology and evolution · 2022Article
Corrections and comments
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2 authors.
Funding
Abstract
The source of genetic novelty is an area of wide interest and intense investigation. Although gene duplication is conventionally thought to dominate the production of new genes, this view was recently challenged by a proposal of widespread de novo gene origination in eukaryotic evolution. Specifically, distributions of various gene properties such as coding sequence length, expression level, codon usage, and probability of being subject to purifying selection among groups of genes with different estimated ages were reported to support a model in which new protein-coding proto-genes arise from noncoding DNA and gradually integrate into cellular networks. Here we show that the genomic patterns asserted to support widespread de novo gene origination are largely attributable to biases in gene age estimation by phylostratigraphy, because such patterns are also observed in phylostratigraphic analysis of simulated genes bearing identical ages. Furthermore, there is no evidence of purifying selection on very young de novo genes previously claimed to show such signals. Together, these findings are consistent with the prevailing view that de novo gene birth is a relatively minor contributor to new genes in genome evolution. They also illustrate the danger of using phylostratigraphy in the study of new gene origination without considering its inherent bias.
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