ArticleMolecular biology and evolution2006
Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method.
Article in Molecular biology and evolution, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 42 citations in OpenAlex.
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- Short branch attraction in phylogenomic inference under the multispecies coalescent.Frontiers in ecology and evolution · 2023Article
- ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation.Bioinformatics (Oxford, England) · 2021Article
- Quantifying the dynamics of viral recombination during free virus and cell-to-cell transmission in HIV-1 infection.Virus evolution · 2021Article
- CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation.Molecular biology and evolution · 2015Article
- Simulation of genome-wide evolution under heterogeneous substitution models and complex multispecies coalescent histories.Molecular biology and evolution · 2014Article
- Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation.Heredity · 2014Article
- Simulation of molecular data under diverse evolutionary scenarios.PLoS computational biology · 2012Article
- The evolution of HIV: inferences using phylogenetics.Molecular phylogenetics and evolution · 2012Review
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- Coalescent simulation of intracodon recombination.Genetics · 2010Article
- The tempo and mode of evolution of transposable elements as revealed by molecular phylogenies reconstructed from mosquito genomes.Evolution; international journal of organic evolution · 2009Article
- Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression.PLoS computational biology · 2008Article
- GENOMEPOP: a program to simulate genomes in populations.BMC bioinformatics · 2008Article
- Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography.BMC bioinformatics · 2007Article
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- Evidence of recombination within human alpha-papillomavirus.Virology journal · 2007Article
- Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.PLoS computational biology · 2007Article
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3 authors at 1 institution in 1 country.
Funding
Abstract
The composite-likelihood estimator (CLE) of the population recombination rate considers only sites with exactly two alleles under a finite-sites mutation model (McVean, G. A. T., P. Awadalla, and P. Fearnhead. 2002. A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160:1231-1241). While in such a model the identity of alleles is not considered, the CLE has been shown to be robust to minor misspecification of the underlying mutational model. However, there are many situations where the putative mutation and demographic history can be quite complex. One good example is rapidly evolving pathogens, like HIV-1. First we evaluated the performance of the CLE and the likelihood permutation test (LPT) under more complex, realistic models, including a general time reversible (GTR) substitution model, rate heterogeneity among sites (Gamma), positive selection, population growth, population structure, and noncontemporaneous sampling. Second, we relaxed some of the assumptions of the CLE allowing for a four-allele, GTR + Gamma model in an attempt to use the data more efficiently. Through simulations and the analysis of real data, we concluded that the CLE is robust to severe misspecifications of the substitution model, but underestimates the recombination rate in the presence of exponential growth, population mixture, selection, or noncontemporaneous sampling. In such cases, the use of more complex models slightly increases performance in some occasions, especially in the case of the LPT. Thus, our results provide for a more robust application of the estimation of recombination rates.
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