ArticleMolecular biology and evolution2020
GenomegaMap: Within-Species Genome-Wide dN/dS Estimation from over 10,000 Genomes.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 53 citations in OpenAlex.
- Dormancy regulon reduction was pivotal to the evolution of Mycobacterium tuberculosis.Nature communications · 2026Article
- Whole-genome characteristics of isolates from recurrentMicrobiology spectrum · 2026Article
- Evaluating selection at intermediate scales within genes provides robust identification of genes under positive selection in M. tuberculosis clinical isolates.Tuberculosis (Edinburgh, Scotland) · 2025Article
- Genetic population structure of Haemophilus influenzae at local and global scales.Nature microbiology · 2025Article
- Mycobacterium tuberculosis uses intrinsically disordered, fast evolving proteins to interact with conserved host factors.Genome biology · 2025Article
- Dynamics of dN/dS within recombining bacterial populations.bioRxiv : the preprint server for biology · 2025Article
- Leveraging FracMinHash Containment for GenomicbioRxiv : the preprint server for biology · 2025Article
- Genome-wide evolutionary selection pressures acting onNAR molecular medicine · 2025Article
- Evaluating selection at intermediate scales within genes provides robust identification of genes under positive selection inbioRxiv : the preprint server for biology · 2025Article
- Dinucleotide codon substitutions as a signature of diversifying selection inFrontiers in molecular biosciences · 2025Article
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- Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis.Nature communications · 2024Article
- Patterns of Change in Nucleotide Diversity Over Gene Length.Genome biology and evolution · 2024Article
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- Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis.Research square · 2023Article
- Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis.bioRxiv : the preprint server for biology · 2023Article
- The Global Success of Mycobacterium tuberculosis Modern Beijing Family Is Driven by a Few Recently Emerged Strains.Microbiology spectrum · 2023Article
- Novel Multilocus Sequence Typing and Global Sequence Clustering Schemes for Characterizing the Population Diversity of Streptococcus mitis.Journal of clinical microbiology · 2023Article
- Variation in synonymous evolutionary rates in the SARS-CoV-2 genome.Frontiers in microbiology · 2023Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
The dN/dS ratio provides evidence of adaptation or functional constraint in protein-coding genes by quantifying the relative excess or deficit of amino acid-replacing versus silent nucleotide variation. Inexpensive sequencing promises a better understanding of parameters, such as dN/dS, but analyzing very large data sets poses a major statistical challenge. Here, I introduce genomegaMap for estimating within-species genome-wide variation in dN/dS, and I apply it to 3,979 genes across 10,209 tuberculosis genomes to characterize the selection pressures shaping this global pathogen. GenomegaMap is a phylogeny-free method that addresses two major problems with existing approaches: 1) It is fast no matter how large the sample size and 2) it is robust to recombination, which causes phylogenetic methods to report artefactual signals of adaptation. GenomegaMap uses population genetics theory to approximate the distribution of allele frequencies under general, parent-dependent mutation models. Coalescent simulations show that substitution parameters are well estimated even when genomegaMap's simplifying assumption of independence among sites is violated. I demonstrate the ability of genomegaMap to detect genuine signatures of selection at antimicrobial resistance-conferring substitutions in Mycobacterium tuberculosis and describe a novel signature of selection in the cold-shock DEAD-box protein A gene deaD/csdA. The genomegaMap approach helps accelerate the exploitation of big data for gaining new insights into evolution within species.
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