D Posada

Summary

Affiliation: Brigham Young University
Country: USA

Publications

  1. ncbi The effect of recombination on the accuracy of phylogeny estimation
    David Posada
    Department of Zoology, Brigham Young University, Provo, UT 84602, USA
    J Mol Evol 54:396-402. 2002
  2. ncbi Recombination in evolutionary genomics
    David Posada
    Variagenics Inc Cambridge, Massachusetts 02139, USA
    Annu Rev Genet 36:75-97. 2002
  3. ncbi Evaluation of methods for detecting recombination from DNA sequences: empirical data
    David Posada
    Department of Zoology, Brigham Young University, Provo, Utah, USA
    Mol Biol Evol 19:708-17. 2002
  4. pmc Evaluation of methods for detecting recombination from DNA sequences: computer simulations
    D Posada
    Department of Zoology, Brigham Young University, Provo, UT 84602, USA
    Proc Natl Acad Sci U S A 98:13757-62. 2001
  5. ncbi 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
  6. ncbi The effect of branch length variation on the selection of models of molecular evolution
    D Posada
    Department of Zoology, Brigham Young University, Provo, UT 84602 5255, USA
    J Mol Evol 52:434-44. 2001
  7. ncbi Selecting the best-fit model of nucleotide substitution
    D Posada
    Department of Zoology, Brigham Young University, Provo, Utah 84602 5255, USA
    Syst Biol 50:580-601. 2001
  8. ncbi MODELTEST: testing the model of DNA substitution
    D Posada
    Department of Zoology, Brigham Young University, 574 WIDB, Provo, UT 84602 5255, USA
    Bioinformatics 14:817-8. 1998
  9. ncbi Population genetics of the porB gene of Neisseria gonorrhoeae: different dynamics in different homology groups
    D Posada
    Department of Zoology, Brigham Young University, Provo, Utah 84602 5255, USA
    Mol Biol Evol 17:423-36. 2000
  10. pmc Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy
    Antonio Carvajal-Rodriguez
    Department of Microbiology and Molecular Biology, Brigham Young University, 84602 Provo, UT, USA
    Infect Genet Evol 7:476-83. 2007

Collaborators

Detail Information

Publications41

  1. ncbi The effect of recombination on the accuracy of phylogeny estimation
    David 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...
  2. ncbi Recombination in evolutionary genomics
    David 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...
  3. ncbi Evaluation of methods for detecting recombination from DNA sequences: empirical data
    David 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...
  4. pmc Evaluation of methods for detecting recombination from DNA sequences: computer simulations
    D 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...
  5. ncbi 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...
  6. ncbi The effect of branch length variation on the selection of models of molecular evolution
    D 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...
  7. ncbi Selecting the best-fit model of nucleotide substitution
    D 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...
  8. ncbi MODELTEST: testing the model of DNA substitution
    D Posada
    Department of Zoology, Brigham Young University, 574 WIDB, Provo, UT 84602 5255, USA
    Bioinformatics 14:817-8. 1998
    ..The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data...
  9. ncbi Population genetics of the porB gene of Neisseria gonorrhoeae: different dynamics in different homology groups
    D 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...
  10. pmc Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy
    Antonio 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...
  11. pmc Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method
    Antonio 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...
  12. ncbi Identification of 3 phylogenetically related HIV-1 BG intersubtype circulating recombinant forms in Cuba
    Maria 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...
  13. pmc Parallel evolution of the genetic code in arthropod mitochondrial genomes
    Federico 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...
  14. ncbi Lack of temporal structure in the short term HIV-1 evolution within asymptomatic naïve patients
    Gonzalo 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...
  15. ncbi GARD: a genetic algorithm for recombination detection
    Sergei 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...
  16. ncbi ProtTest: selection of best-fit models of protein evolution
    Federico 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...
  17. pmc Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography
    Miguel 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...
  18. ncbi Automated phylogenetic detection of recombination using a genetic algorithm
    Sergei 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...
  19. pmc 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 trial
    David 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...
  20. ncbi The causes and consequences of HIV evolution
    Andrew Rambaut
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    Nat Rev Genet 5:52-61. 2004
  21. ncbi Simulating haplotype blocks in the human genome
    David Posada
    Variagenics Inc, 60 Hampshire St, Cambridge, MA 02139 1548, USA
    Bioinformatics 19:289-90. 2003
    ..The samples generated can be very useful to better understand the architecture of the human genome and to investigate its impact in association studies searching for disease genes...
  22. pmc A comparison of phylogenetic network methods using computer simulation
    Steven M Woolley
    Computational Biology Program, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS ONE 3:e1913. 2008
    ....
  23. doi Using MODELTEST and PAUP* to select a model of nucleotide substitution
    David 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...
  24. ncbi Phylogenetic affinities of Comoroan and East African day geckos (genus Phelsuma): multiple natural colonisations, introductions and island radiations
    Sara Rocha
    CIBIO, Centro de Investigacao em Biodiversidade e Recursos Geneticos, Campus Agrário de Vairão, 4485 661 Vairão, Portugal
    Mol Phylogenet Evol 43:685-92. 2007
  25. doi jModelTest: phylogenetic model averaging
    David 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...
  26. pmc An exact nonparametric method for inferring mosaic structure in sequence triplets
    Maciej F Boni
    Stanford Genome Technology Center, Palo Alto, California 94304, USA
    Genetics 176:1035-47. 2007
    ....
  27. ncbi Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail
    Humberto 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...
  28. doi Disease progression and evolution of the HIV-1 env gene in 24 infected infants
    Antonio 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...
  29. ncbi MtArt: a new model of amino acid replacement for Arthropoda
    Federico Abascal
    Mol Biol Evol 24:1-5. 2007
    ....
  30. pmc 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...
  31. pmc A coalescent model of recombination hotspots
    Carsten Wiuf
    Variagenics, Cambridge, Massachusetts 02139, USA
    Genetics 164:407-17. 2003
    ..A number of new analytical results about the model are derived...
  32. pmc Tree scanning: a method for using haplotype trees in phenotype/genotype association studies
    Alan 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...
  33. ncbi Using models of nucleotide evolution to build phylogenetic trees
    David 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...
  34. ncbi TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees
    David Posada
    Variagenics, Inc, Cambridge, MA 02139, USA
    Bioinformatics 21:2130-2. 2005
    ..We present the software implementation of the tree scanning method to detect associations between genetic haplotypes and quantitative traits, utilizing the evolutionary history of the haplotypes, in samples of unrelated individuals...
  35. ncbi Identification of a novel HIV-1 complex circulating recombinant form (CRF18_cpx) of Central African origin in Cuba
    Michael M Thomson
    Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
    AIDS 19:1155-63. 2005
    ..Analysis of partial pol and env sequences have indicated a high diversity of HIV-1 genetic forms in Cuba, including two potential novel circulating recombinant forms (CRF): U/H and D/A...
  36. pmc The evolutionary value of recombination is constrained by genome modularity
    Darren P Martin
    Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
    PLoS Genet 1:e51. 2005
    ....
  37. pmc On the phylogenetic placement of human T cell leukemia virus type 1 sequences associated with an Andean mummy
    Michael 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...
  38. ncbi 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...
  39. ncbi Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests
    David 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)...
  40. pmc GenDecoder: genetic code prediction for metazoan mitochondria
    Federico 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...
  41. ncbi Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact
    Markus 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...