ArticleGenetics2010
Coalescent simulation of intracodon recombination.
Article in Genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 70 citations in OpenAlex.
- Heterogeneous Evolution Among SARS-CoV-2 Genes and Variants of Concern.Journal of medical virology · 2025Article
- Immunoglobulin heavy constant gamma gene evolution is modulated by both the divergent and birth-and-death evolutionary models.Primates; journal of primatology · 2022Article
- Evolutionary genomic relationships and coupling in MK-STYX and STYX pseudophosphatases.Scientific reports · 2022Article
- ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation.Bioinformatics (Oxford, England) · 2021Article
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- Two 20-Residue-Long Peptides Derived fromInternational journal of molecular sciences · 2021Article
- Variant antigen diversity in Trypanosoma vivax is not driven by recombination.Nature communications · 2020Article
- Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients.Genes · 2018Review
- Positive selection at sites of chemosensory genes is associated with the recent divergence and local ecological adaptation in cactophilic Drosophila.BMC evolutionary biology · 2018Article
- Microbial sequence typing in the genomic era.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2018Review
- On the Evolution and Function ofFrontiers in genetics · 2018Article
- Tracing the origin and evolution of supergene mimicry in butterflies.Nature communications · 2017Article
- Detection of Regional Variation in Selection Intensity within Protein-Coding Genes Using DNA Sequence Polymorphism and Divergence.Molecular biology and evolution · 2017Article
- The Bacterial Sequential Markov Coalescent.Genetics · 2017Article
- Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes.PLoS computational biology · 2016Article
- Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intrahost HIV Infection.Genetics · 2016Article
- SimBac: simulation of whole bacterial genomes with homologous recombination.Microbial genomics · 2016Article
- Recent Positive Selection in Genes of the Mammalian Epidermal Differentiation Complex Locus.Frontiers in genetics · 2016Article
- Synonymous and nonsynonymous distances help untangle convergent evolution and recombination.Statistical applications in genetics and molecular biology · 2015Article
- CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation.Molecular biology and evolution · 2015Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The coalescent with recombination is a very useful tool in molecular population genetics. Under this framework, genealogies often represent the evolution of the substitution unit, and because of this, the few coalescent algorithms implemented for the simulation of coding sequences force recombination to occur only between codons. However, it is clear that recombination is expected to occur most often within codons. Here we have developed an algorithm that can evolve coding sequences under an ancestral recombination graph that represents the genealogies at each nucleotide site, thereby allowing for intracodon recombination. The algorithm is a modification of Hudson's coalescent in which, in addition to keeping track of events occurring in the ancestral material that reaches the sample, we need to keep track of events occurring in ancestral material that does not reach the sample but that is produced by intracodon recombination. We are able to show that at typical substitution rates the number of nonsynonymous changes induced by intracodon recombination is small and that intracodon recombination does not generally result in inflated estimates of the overall nonsynonymous/synonymous substitution ratio (omega). On the other hand, recombination can bias the estimation of omega at particular codons, resulting in apparent rate variation among sites and in the spurious identification of positively selected sites. Importantly, in this case, allowing for variable synonymous rates across sites greatly reduces the false-positive rate and recovers statistical power. Finally, coalescent simulations with intracodon recombination could be used to better represent the evolution of nuclear coding genes or fast-evolving pathogens such as HIV-1.We have implemented this algorithm in a computer program called NetRecodon, freely available at http://darwin.uvigo.es.
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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.