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Genomes and Genes | D PosadaSummaryAffiliation: Brigham Young University Country: USA Publications
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Publications
The effect of recombination on the accuracy of phylogeny estimationDavid Posada
Department of Zoology, Brigham Young University, Provo, UT 84602, USA
J Mol Evol 54:396-402. 2002..In this case, when the recombinational breakpoint divided the alignment in two regions of similar length, a phylogeny that was different from any of the true phylogenies underlying the data was inferred...- Recombination in evolutionary genomicsDavid Posada
Variagenics Inc Cambridge, Massachusetts 02139, USA
Annu Rev Genet 36:75-97. 2002..We conclude by highlighting a number of areas for future development of tools to help quantify the role of recombination in genomic evolution... - Evaluation of methods for detecting recombination from DNA sequences: empirical dataDavid Posada
Department of Zoology, Brigham Young University, Provo, Utah, USA
Mol Biol Evol 19:708-17. 2002..This finding might have serious implications on vaccine development and on the reliability of previous inferences of HIV-1 evolutionary history and dynamics... 
Evaluation of methods for detecting recombination from DNA sequences: computer simulationsD Posada
Department of Zoology, Brigham Young University, Provo, UT 84602, USA
Proc Natl Acad Sci U S A 98:13757-62. 2001..Results shown here will provide some guidance in the selection of the most appropriate method/s for the analysis of the particular data at hand...- Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1)D Posada
Department of Zoology, Brigham Young University, Provo, UT 84602 5255, USA
Mol Biol Evol 18:897-906. 2001..The importance of models in evolutionary analyses and their repercussions on the derived conclusions are discussed... - The effect of branch length variation on the selection of models of molecular evolutionD Posada
Department of Zoology, Brigham Young University, Provo, UT 84602 5255, USA
J Mol Evol 52:434-44. 2001..A specific hierarchy of LRTs, which starts from a simple model of evolution, performed overall better than other possible LRT hierarchies, or than the AIC or BIC... - Selecting the best-fit model of nucleotide substitutionD Posada
Department of Zoology, Brigham Young University, Provo, Utah 84602 5255, USA
Syst Biol 50:580-601. 2001..We show here that a best-fit model can be readily identified. Consequently, given the relevance of models, model fitting should be routine in any phylogenetic analysis that uses models of evolution... - MODELTEST: testing the model of DNA substitutionD Posada
Department of Zoology, Brigham Young University, 574 WIDB, Provo, UT 84602 5255, USA
Bioinformatics 14:817-8. 1998..AVAILABILITY: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html... - Population genetics of the porB gene of Neisseria gonorrhoeae: different dynamics in different homology groupsD Posada
Department of Zoology, Brigham Young University, Provo, Utah 84602 5255, USA
Mol Biol Evol 17:423-36. 2000..The molecular evolution of Neisseria gonorrhoeae seems to be driven by the simultaneous action of selection and recombination, but under different rates and selection pressures for the PIA and PIB homology groups... - Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapyAntonio Carvajal-Rodriguez
Department of Microbiology and Molecular Biology, Brigham Young University, 84602 Provo, UT, USA
Infect Genet Evol 7:476-83. 2007..Our results suggest that recombination plays an important role in the evolution of drug resistance in HIV-1 under various realistic scenarios. These findings could be taken into account in order to develop optimal HIV-1 drug treatments... - Recombination estimation under complex evolutionary models with the coalescent composite-likelihood methodAntonio Carvajal-Rodriguez
Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
Mol Biol Evol 23:817-27. 2006..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... - Identification of 3 phylogenetically related HIV-1 BG intersubtype circulating recombinant forms in CubaMaria Sierra
Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
J Acquir Immune Defic Syndr 45:151-60. 2007..These results allow us to identify 3 new BG intersubtype circulating recombinant forms in Cuba derived from a common recombinant ancestor, which originated from B and G subtype parental strains circulating in Cuba... - Parallel evolution of the genetic code in arthropod mitochondrial genomesFederico Abascal
Departamento de Bioquimica, Genetica, e Inmunología, Universidad de Vigo, Vigo, Spain
PLoS Biol 4:e127. 2006..These rather simple mutations, together with a low usage of the AGG codon, might explain the recurrence of the AGG reassignments... - Lack of temporal structure in the short term HIV-1 evolution within asymptomatic naïve patientsGonzalo Bello
Centro Nacional de Microbiología CNM, Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
Virology 362:294-303. 2007..These results support the existence of distinct patterns of env evolution in untreated HIV-1-infected patients... - GARD: a genetic algorithm for recombination detectionSergei L Kosakovsky Pond
Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
Bioinformatics 22:3096-8. 2006..The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments... - ProtTest: selection of best-fit models of protein evolutionFederico Abascal
Department of Biochemistry, Genetics and Immunology, Universidad de Vigo, Spain
Bioinformatics 21:2104-5. 2005..We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment. AVAILABILITY: ProtTest is available under the GNU license from http://darwin.uvigo.es.. - Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demographyMiguel Arenas
Departamento de Bioquimica, Genética e Inmunología, Universidad de Vigo, 36310 Vigo, Spain
BMC Bioinformatics 8:458. 2007..To date, no single coalescent program is able to simulate codon sequences sampled from populations with recombination, migration and growth... - Automated phylogenetic detection of recombination using a genetic algorithmSergei L Kosakovsky Pond
Department of Pathology, University of California San Diego, USA
Mol Biol Evol 23:1891-901. 2006..Finally, we demonstrate that prescreening alignments with our method allows one to analyze recombinant sequences for positive selection... - Longitudinal population analysis of dual infection with recombination in two strains of HIV type 1 subtype B in an individual from a Phase 3 HIV vaccine efficacy trialDavid V Jobes
VaxGen, Inc, South San Francisco, California 94080, USA
AIDS Res Hum Retroviruses 22:968-78. 2006..Our results suggest significant differences on the evolutionary dynamics of these strains. We then discuss the implications of these results for vaccine development... - The causes and consequences of HIV evolutionAndrew Rambaut
Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
Nat Rev Genet 5:52-61. 2004 - Simulating haplotype blocks in the human genomeDavid Posada
Variagenics Inc, 60 Hampshire St, Cambridge, MA 02139 1548, USA
Bioinformatics 19:289-90. 2003..AVAILABILITY: The SNPsim package is available at http://www.evolgenics.com/software.. - A comparison of phylogenetic network methods using computer simulationSteven M Woolley
Computational Biology Program, Washington University School of Medicine, St Louis, Missouri, United States of America
PLoS ONE 3:e1913. 2008.... - Using MODELTEST and PAUP* to select a model of nucleotide substitutionDavid Posada
Universidad of de Vigo, Vigo, Spain
Curr Protoc Bioinformatics . 2003..An example data file is analyzed and the interpretation of the results is discussed. Some background theory on model selection and a discussion of the relevance of models is included at the end of the unit... - Phylogenetic affinities of Comoroan and East African day geckos (genus Phelsuma): multiple natural colonisations, introductions and island radiationsSara Rocha
CIBIO, , , , Portugal
Mol Phylogenet Evol 43:685-92. 2007 - jModelTest: phylogenetic model averagingDavid Posada
Mol Biol Evol 25:1253-6. 2008..The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es... - An exact nonparametric method for inferring mosaic structure in sequence tripletsMaciej F Boni
Stanford Genome Technology Center, Palo Alto, California 94304, USA
Genetics 176:1035-47. 2007.... - Phylogenetic evidence for multiple sympatric ecological diversification in a marine snailHumberto Quesada
Departamento de Bioquimica, Genética e Inmunología, Facultad de Biologia, Universidad de Vigo, Campus As Lagoas Marcosende, 36310 Vigo, Spain
Evolution 61:1600-12. 2007..Thus, divergent selection occurring independently in different populations has produced the marine equivalent of host races, which may represent the first step in speciation... 
Disease progression and evolution of the HIV-1 env gene in 24 infected infantsAntonio Carvajal-Rodriguez
Department of Biology, Brigham Young University, 84602 Provo, UT, USA
Infect Genet Evol 8:110-20. 2008..Overall, the results obtained confirm that viral adaptation in the C2V3C3 region of the env gene is related to disease progression, although the statistical characterization of such pattern seems rather difficult...- MtArt: a new model of amino acid replacement for ArthropodaFederico Abascal
Mol Biol Evol 24:1-5. 2007.... - Evidence for survival of Pleistocene climatic changes in Northern refugia by the land snail Trochoidea geyeri (Soós 1926) (Helicellinae, Stylommatophora)Markus Pfenninger
IMEP URA CNRS 1152 Case 451, Faculté des Sciences et Techniques de St, Jerome, F 13997 Marseille Cedex 20, France
BMC Evol Biol 3:8. 2003..Fossil evidence suggests that current populations of T. geyeri are relicts of a much more widespread distribution during more favourable climatic periods in the Pleistocene... - A coalescent model of recombination hotspotsCarsten Wiuf
Variagenics, Cambridge, Massachusetts 02139, USA
Genetics 164:407-17. 2003..A number of new analytical results about the model are derived... - Tree scanning: a method for using haplotype trees in phenotype/genotype association studiesAlan R Templeton
Department of Biology, Washington University, St Louis, Missouri 63130 4899, USA
Genetics 169:441-53. 2005..Overall, tree scanning is a simple, powerful, and flexible method for using haplotype trees to detect phenotype/genotype associations at candidate loci... - Using models of nucleotide evolution to build phylogenetic treesDavid H Bos
School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
Dev Comp Immunol 29:211-27. 2005..Statistical model selection strikes a balance between the bias introduced by some models and the increased variance of parameter estimates that results from using other models... - TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype treesDavid Posada
Variagenics, Inc, Cambridge, MA 02139, USA
Bioinformatics 21:2130-2. 2005..AVAILABILITY: The program is available free of charge, under the GNU General Public License. A package including C source code, a Makefile, and Windows (DOS) and Macintosh binaries, can be downloaded from http://darwin.uvigo.es.. - Identification of a novel HIV-1 complex circulating recombinant form (CRF18_cpx) of Central African origin in CubaMichael M Thomson
, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
AIDS 19:1155-63. 2005..CONCLUSIONS: A novel HIV-1 complex circulating recombinant form (CRF18_cpx) has been identified that is circulating in Cuba and Central Africa... - The evolutionary value of recombination is constrained by genome modularityDarren P Martin
Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
PLoS Genet 1:e51. 2005.... - On the phylogenetic placement of human T cell leukemia virus type 1 sequences associated with an Andean mummyMichael B Coulthart
Host Genetics and Prion Diseases Program, National Microbiology Laboratory, Health Canada, Winnipeg, MB, Canada R3E 3R2
Infect Genet Evol 6:91-6. 2006..However, one of these placements for the other mummy sequence category falls very close to the root of the Cosmopolitan clade, consistent with an ancient origin for both this mummy sequence and the Cosmopolitan clade... - Perkinsoide chabelardi n. gen., a protozoan parasite with an intermediate evolutionary position: possible cause of the decrease of sardine fisheries?Camino Gestal
Department of Cell Biology, Institute of Biomedical Sciences, ICBAS, University of Porto, Largo Prof Abel Salazar no 2, 4099 003 Porto, Portugal
Environ Microbiol 8:1105-14. 2006..This protozoan parasite caused the death of all the infected sardine eggs, and therefore a high impact in the recruitment of this fishery in the Atlantic coast is expected... - Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio testsDavid Posada
Departamento de Bioquimica, Genética e Inmunología, Facultad de Biologia, Universidad de Vigo, Vigo 36200, Spain
Syst Biol 53:793-808. 2004..To illustrate some of these points, we have applied AIC-based model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus(genus Carabus) ground beetles described by Sota and Vogler (2001)... - GenDecoder: genetic code prediction for metazoan mitochondriaFederico Abascal
Departamento de Bioquimica, Genetica, e Inmunología, Universidad de Vigo, 36310 Vigo, Spain
Nucleic Acids Res 34:W389-93. 2006..Overall, the method is highly precise (99%), although highly divergent organisms such as platyhelminths are more problematic. The GenDecoder web server is freely available from http://darwin.uvigo.es/software/gendecoder.html... - Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contactMarkus Pfenninger
Abteilung Okologie und Evolution, Zoologisches Institut der J W Goethe Universitat, Frankfurt Main, Germany
Evolution 56:1776-88. 2002..unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal...