ArticlePLoS biology2020
Many, but not all, lineage-specific genes can be explained by homology detection failure.
Article in PLoS biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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112 citing papers in PubMed.
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- The diverse functions of viral microproteins.bioRxiv : the preprint server for biology · 2026Article
- A comprehensive and accessible database of jawed-vertebrate ohnologs.Science advances · 2026Article
- Remote homology and functional genetics unmask deeply preserved Scm3/HJURP orthologs in metazoans.Science advances · 2026Article
- Emergence and evolution of protein-coding de novo genes.Nature reviews. Genetics · 2026Review
- Remote homology and functional genetics unmask deeply preserved Scm3/HJURP orthologs in metazoans.bioRxiv : the preprint server for biology · 2026Article
- Cosmopolitan Gene Families With Known Functions Are Hotspots for the Evolution of Novel Genes in Stony Corals.Genome biology and evolution · 2026Article
- Deep homology and design of proteasome chaperone proteins in Candidozyma auris.Nature communications · 2026Article
- Bacterial Siderophore Production in Metal-Rich Environments: Underexplored Sources of Siderophores and Insights into Bioremediation.Journal of natural products · 2026Review
- Disordered but Different: Functional and Evolutionary Divergence of Transcription Factor Intrinsically Disordered Regions.bioRxiv : the preprint server for biology · 2026Article
- Brain transcriptome analysis reveals novel long non-coding RNAs in Dryophytes arenicolor (Canyon Treefrog).G3 (Bethesda, Md.) · 2026Article
- Phylostratigraphic Analysis Reveals the Evolutionary Origins and Potential Role of New Genes in the Adaptive Evolution ofInternational journal of molecular sciences · 2026Article
- Novel genes arise from genomic deletions across the bacterial tree of life.bioRxiv : the preprint server for biology · 2026Article
- Machine learning can distinguish orphans that have resulted from sequence divergence beyond recognition.Bioinformatics advances · 2026Article
- Comparative functional and evolutionary analysis of essential germline stem cell genes across the genus Drosophila and two outgroup species.G3 (Bethesda, Md.) · 2025Article
- A Multi-level Perspective on the Evolution of Orthologs and Their Functions.Journal of molecular evolution · 2025Review
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- Orphan and de novo Genes in Fungi and Animals: Identification, Origins and Functions.Genome biology and evolution · 2025Review
52 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
Genes for which homologs can be detected only in a limited group of evolutionarily related species, called "lineage-specific genes," are pervasive: Essentially every lineage has them, and they often comprise a sizable fraction of the group's total genes. Lineage-specific genes are often interpreted as "novel" genes, representing genetic novelty born anew within that lineage. Here, we develop a simple method to test an alternative null hypothesis: that lineage-specific genes do have homologs outside of the lineage that, even while evolving at a constant rate in a novelty-free manner, have merely become undetectable by search algorithms used to infer homology. We show that this null hypothesis is sufficient to explain the lack of detected homologs of a large number of lineage-specific genes in fungi and insects. However, we also find that a minority of lineage-specific genes in both clades are not well explained by this novelty-free model. The method provides a simple way of identifying which lineage-specific genes call for special explanations beyond homology detection failure, highlighting them as interesting candidates for further study.
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