Coalescent simulation of intracodon recombination.

Genetics
Miguel Arenas, David Posada

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, r...Continue Reading

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Citations

Mar 5, 2011·BMC Bioinformatics·Giltae SongWebb Miller
Mar 5, 2011·BMC Bioinformatics·Laxmi ParidaAsif Javed
Jun 14, 2012·PLoS Computational Biology·Miguel Arenas
Feb 4, 2010·Genetics·Miguel Arenas, David Posada
Jun 8, 2014·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Renana Sabi, Tamir Tuller
Oct 8, 2016·Microbial Genomics·Thomas BrownNicola De Maio
Dec 30, 2014·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Marcos Pérez-LosadaFernando González-Candelas
Nov 26, 2014·Genome Medicine·Michael InouyeKathryn E Holt
Oct 1, 2014·Scientific Reports·Cheong Xin ChanMark A Ragan
Sep 12, 2015·Molecular Phylogenetics and Evolution·Miguel ArenasCecilio Lopez-Galindez
Jun 11, 2015·Statistical Applications in Genetics and Molecular Biology·Peter B ChiVladimir N Minin
May 12, 2012·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Dániel CadarAttila Cságola
Oct 18, 2005·BMC Bioinformatics·Thomas MailundLeif Schauser
Jul 10, 2008·PloS One·Leonardo de Oliveira MartinsHirohisa Kishino
May 6, 2016·PLoS Computational Biology·Jerome KelleherGilean McVean
Mar 10, 2018·Evolution; International Journal of Organic Evolution·Joel SharbroughMaurine Neiman
Aug 19, 2015·Evolutionary Bioinformatics Online·Insung AhnHyeon Seok Son
May 14, 2011·Molecular Ecology Resources·Miguel NavascuésBrent C Emerson
Nov 19, 2015·Frontiers in Genetics·Miguel Arenas
May 15, 2013·G3 : Genes - Genomes - Genetics·Daniel James WhiteNeil John Gemmell
Nov 9, 2017·Nature Communications·Wei ZhangMarcus R Kronforst
Feb 14, 2020·Nature Communications·Sara Silva PereiraAndrew P Jackson
May 20, 2011·Molecular Ecology Resources·Darren P MartinDavid Posada
Jan 26, 2017·Frontiers in Genetics·Zane A Goodwin, Cristina de Guzman Strong
Mar 5, 2017·Genetics·Nicola De Maio, Daniel J Wilson
Sep 27, 2018·Frontiers in Genetics·Paola Andrea Camargo-AyalaManuel A Patarroyo
Feb 11, 2021·International Journal of Molecular Sciences·Laura Alejandra Ricaurte-ContrerasManuel Alfonso Patarroyo
Jan 23, 2021·Briefings in Bioinformatics·Roberto Del AmparoMiguel Arenas

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