ArticleGenetics2014
Inference of the properties of the recombination process from whole bacterial genomes.
Article in Genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 52 citations in OpenAlex.
- Article
- Adaptative and ancient co-evolution of integrons withMicrobial genomics · 2025Article
- Article
- Article
- Geographic population structure and distinct intra-population dynamics of globally abundant freshwater bacteria.The ISME journal · 2024Article
- Core genes can have higher recombination rates than accessory genes within global microbial populations.eLife · 2022Article
- Linkage disequilibrium between rare mutations.Genetics · 2022Article
- Horizontal gene transfer and adaptive evolution in bacteria.Nature reviews. Microbiology · 2022Review
- Fast and accurate metagenotyping of the human gut microbiome with GT-Pro.Nature biotechnology · 2022Article
- Population genomics and antimicrobial resistance in Corynebacterium diphtheriae.Genome medicine · 2020Article
- Horizontal transmission and recombination maintain forever young bacterial symbiont genomes.PLoS genetics · 2020Article
- Rates of Molecular Evolution in a MarineViruses · 2019Article
- The Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages.Genome biology and evolution · 2019Article
- A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation.PLoS computational biology · 2019Article
- Inferring bacterial recombination rates from large-scale sequencing datasets.Nature methods · 2019Article
- Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades.Molecular biology and evolution · 2018Article
- Coalescent framework for prokaryotes undergoing interspecific homologous recombination.Heredity · 2018Article
- Weak Epistasis May Drive Adaptation in Recombining Bacteria.Genetics · 2018Article
- Article
- Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination.Molecular biology and evolution · 2017Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Patterns of linkage disequilibrium, homoplasy, and incompatibility are difficult to interpret because they depend on several factors, including the recombination process and the population structure. Here we introduce a novel model-based framework to infer recombination properties from such summary statistics in bacterial genomes. The underlying model is sequentially Markovian so that data can be simulated very efficiently, and we use approximate Bayesian computation techniques to infer parameters. As this does not require us to calculate the likelihood function, the model can be easily extended to investigate less probed aspects of recombination. In particular, we extend our model to account for the bias in the recombination process whereby closely related bacteria recombine more often with one another. We show that this model provides a good fit to a data set of Bacillus cereus genomes and estimate several recombination properties, including the rate of bias in recombination. All the methods described in this article are implemented in a software package that is freely available for download at http://code.google.com/p/clonalorigin/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.