ArticleMolecular biology and evolution2017
No Evidence for Phylostratigraphic Bias Impacting Inferences on Patterns of Gene Emergence and Evolution.
Article in Molecular biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 89 citations in OpenAlex.
- Emergence and evolution of protein-coding de novo genes.Nature reviews. Genetics · 2026Review
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- Developmental phylotranscriptomics in grapevine suggests an ancestral role of somatic embryogenesis.Communications biology · 2025Article
- Functional innovation through new genes as a general evolutionary process.Nature genetics · 2025Review
- Gene age and genome organization inFrontiers in microbiology · 2025Article
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease.bioRxiv : the preprint server for biology · 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
- Human-specific features and developmental dynamics of the brain N-glycome.Science advances · 2023Article
- Towards understanding paleoclimate impacts on primate de novo genes.G3 (Bethesda, Md.) · 2023Article
- Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence inGenome research · 2023Article
- Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra.Genome biology · 2023Article
- Pleomorphic Variants ofInternational journal of molecular sciences · 2023Article
- Molecular and cellular evolution of the primate dorsolateral prefrontal cortex.Science (New York, N.Y.) · 2022Article
- In search of a Drosophila core cellular network with single-cell transcriptome data.G3 (Bethesda, Md.) · 2022Article
- Strong evidence for the adaptive walk model of gene evolution in Drosophila and Arabidopsis.PLoS biology · 2022Article
- Heterologous expression of naturally evolved putative de novo proteins with chaperones.Protein science : a publication of the Protein Society · 2022Article
- Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation.Molecular ecology resources · 2022Article
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Authors and funding
7 authors at 5 institutions in 4 countries.
Funding
Abstract
Phylostratigraphy is a computational framework for dating the emergence of DNA and protein sequences in a phylogeny. It has been extensively applied to make inferences on patterns of genome evolution, including patterns of disease gene evolution, ontogeny and de novo gene origination. Phylostratigraphy typically relies on BLAST searches along a species tree, but new simulation studies have raised concerns about the ability of BLAST to detect remote homologues and its impact on phylostratigraphic inferences. Here, we re-assessed these simulations. We found that, even with a possible overall BLAST false negative rate between 11-15%, the large majority of sequences assigned to a recent evolutionary origin by phylostratigraphy is unaffected by technical concerns about BLAST. Where the results of the simulations did cast doubt on previously reported findings, we repeated the original analyses but now excluded all questionable sequences. The originally described patterns remained essentially unchanged. These new analyses strongly support phylostratigraphic inferences, including: genes that emerged after the origin of eukaryotes are more likely to be expressed in the ectoderm than in the endoderm or mesoderm in Drosophila, and the de novo emergence of protein-coding genes from non-genic sequences occurs through proto-gene intermediates in yeast. We conclude that BLAST is an appropriate and sufficiently sensitive tool in phylostratigraphic analysis that does not appear to introduce significant biases into evolutionary pattern inferences.
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