ArticleHeredity2014
Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation.
Article in Heredity, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Empirical substitution models of protein evolution: database, relationships, and modeling considerations.Database : the journal of biological databases and curation · 2025Article
- Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation.Bioinformatics (Oxford, England) · 2024Article
- Review
- Consequences of Genetic Recombination on Protein Folding Stability.Journal of molecular evolution · 2023Article
- Methodologies for Microbial Ancestral Sequence Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2022Review
- ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation.Bioinformatics (Oxford, England) · 2021Article
- Global Patterns of Recombination across Human Viruses.Molecular biology and evolution · 2021Article
- Evolutionary dynamics of the human pseudoautosomal regions.PLoS genetics · 2021Article
- SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal.Bioinformatics (Oxford, England) · 2019Article
- Microbial sequence typing in the genomic era.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2018Review
- Improved Versions of Common Estimators of the Recombination Rate.Journal of computational biology : a journal of computational molecular cell biology · 2016Article
- Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow.Current genomics · 2015Article
- Advances in computer simulation of genome evolution: toward more realistic evolutionary genomics analysis by approximate bayesian computation.Journal of molecular evolution · 2015Article
- CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation.Molecular biology and evolution · 2015Article
- Recombination in viruses: mechanisms, methods of study, and evolutionary consequences.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2015Review
- Trends in substitution models of molecular evolution.Frontiers in genetics · 2015Article
- Spatial and temporal simulation of human evolution. Methods, frameworks and applications.Current genomics · 2014Article
- Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories.Molecular biology and evolution · 2014Article
- The importance and application of the ancestral recombination graph.Frontiers in genetics · 2013Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The estimation of parameters in molecular evolution may be biased when some processes are not considered. For example, the estimation of selection at the molecular level using codon-substitution models can have an upward bias when recombination is ignored. Here we address the joint estimation of recombination, molecular adaptation and substitution rates from coding sequences using approximate Bayesian computation (ABC). We describe the implementation of a regression-based strategy for choosing subsets of summary statistics for coding data, and show that this approach can accurately infer recombination allowing for intracodon recombination breakpoints, molecular adaptation and codon substitution rates. We demonstrate that our ABC approach can outperform other analytical methods under a variety of evolutionary scenarios. We also show that although the choice of the codon-substitution model is important, our inferences are robust to a moderate degree of model misspecification. In addition, we demonstrate that our approach can accurately choose the evolutionary model that best fits the data, providing an alternative for when the use of full-likelihood methods is impracticable. Finally, we applied our ABC method to co-estimate recombination, substitution and molecular adaptation rates from 24 published human immunodeficiency virus 1 coding data sets.
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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.