ArticleNucleic acids research2017
Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species.Proceedings of the National Academy of Sciences of the United States of America · 2019Pooled it
- Accelerated Evolution of Context-Dependent Gene Expression in Primate Immune Cells.bioRxiv : the preprint server for biology · 2026Article
- Evolutionary Complexity of Primate Immune System Uncovered by the Extensive Phylogenomic Sampling.Genome biology and evolution · 2026Article
- Mycobacterium tuberculosis uses intrinsically disordered, fast evolving proteins to interact with conserved host factors.Genome biology · 2025Article
- Article
- Variable efficiency of nonsense-mediated mRNA decay across human tissues, tumors and individuals.Genome biology · 2025Article
- Detecting Interspecific Positive Selection Using Convolutional Neural Networks.Molecular biology and evolution · 2025Article
- Nuclear interferon-stimulated gene product maintains heterochromatin on the herpes simplex viral genome to limit lytic infection.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Article
- FREEDA: An automated computational pipeline guides experimental testing of protein innovation.The Journal of cell biology · 2023Article
- Evolution is not Uniform Along Coding Sequences.Molecular biology and evolution · 2023Article
- FREEDA: an automated computational pipeline guides experimental testing of protein innovation by detecting positive selection.bioRxiv : the preprint server for biology · 2023Article
- Centromere drive: model systems and experimental progress.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2022Review
- Transcriptome innovations in primates revealed by single-molecule long-read sequencing.Genome research · 2022Article
- A functional map of HIV-host interactions in primary human T cells.Nature communications · 2022Article
- Mechanisms of mitochondrial promoter recognition in humans and other mammalian species.Nucleic acids research · 2022Article
- Jack of all trades: Genome assembly of Wild Jack and comparative genomics ofFrontiers in plant science · 2022Article
- Recurrent erosion of COA1/MITRAC15 exemplifies conditional gene dispensability in oxidative phosphorylation.Scientific reports · 2021Article
- Evolutionary genetics and acclimatization in nephrology.Nature reviews. Nephrology · 2021Review
- Functional Diversification of Chromatin on Rapid Evolutionary Timescales.Annual review of genetics · 2021Review
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Hotspots of rapid genome evolution hold clues about human adaptation. We present a comparative analysis of nine whole-genome sequenced primates to identify high-confidence targets of positive selection. We find strong statistical evidence for positive selection in 331 protein-coding genes (3%), pinpointing 934 adaptively evolving codons (0.014%). Our new procedure is stringent and reveals substantial artefacts (20% of initial predictions) that have inflated previous estimates. The final 331 positively selected genes (PSG) are strongly enriched for innate and adaptive immunity, secreted and cell membrane proteins (e.g. pattern recognition, complement, cytokines, immune receptors, MHC, Siglecs). We also find evidence for positive selection in reproduction and chromosome segregation (e.g. centromere-associated CENPO, CENPT), apolipoproteins, smell/taste receptors and mitochondrial proteins. Focusing on the virus-host interaction, we retrieve most evolutionary conflicts known to influence antiviral activity (e.g. TRIM5, MAVS, SAMHD1, tetherin) and predict 70 novel cases through integration with virus-human interaction data. Protein structure analysis further identifies positive selection in the interaction interfaces between viruses and their cellular receptors (CD4-HIV; CD46-measles, adenoviruses; CD55-picornaviruses). Finally, primate PSG consistently show high sequence variation in human exomes, suggesting ongoing evolution. Our curated dataset of positive selection is a rich source for studying the genetics underlying human (antiviral) phenotypes. Procedures and data are available at https://github.com/robinvanderlee/positive-selection.
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