David picture

DAVID POSADA

Full Professor, Genetics.
Departamento de Bioquímica, Genética e Inmunología.
Facultad de Biología, Campus Universitario, Universidad de Vigo, Vigo 36310, Spain.
Phone: +34 986 812038. Fax: +34 986 812556.


Places

  • 1989-1994 BA Biology. University of Santiago de Compostela (Spain)
  • 1994-1997 MS Biology, University of Vigo (Spain)
  • 1997-2001 PhD Zoology, Brigham Young University (Utah, USA)
  • 2000 Visiting Scientist, Oxford University (UK)
  • 2001-2003 Senior Scientist, Variagenics, Inc (Boston, USA)
  • 2002 Visiting Scientist, MIT (Boston, USA)
  • 2003-2007. Ramón and Cajal Research Fellow. University of Vigo (Spain)
  • 2007-2011. Associate Professor, Genetics. University of Vigo (Spain)
  • 2011-pres. Full Professor, Genetics. University of Vigo (Spain)

Publications

Articles

  1. Posada D and Crandall KA 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (9): 817-818. pdf
  2. Crandall KA, Vasco DL, Posada D and Imamichi H 1999. Advances in understanding the evolution of HIV. AIDS 13: (suppl A): S39-S47. pdf
  3. Crandall KA, Posada D and Vasco Dl 1999. Effective population sizes: missing measures and missing concepts. Animal Conservation 2 (4): 317-319. pdf
  4. Vilá C, Amorim IR, Leonard JA, Posada D, Castroviejo J, Petrucci-Fonseca F, Crandall KA, Ellegre H and Wayne RK. 1999. Mitochondrial DNA phylogeography and population history of the Gray Wolf Canis lupus. Molecular Ecology 8(12): 2089-2103. pdf
  5. Posada D, Crandall KA, Nguyen M, Demma JC and Viscidi RP. 2000. Population genetics of the porB gene of Neisseria gonorrheae. Molecular Biology and Evolution 17(3): 423-436. pdf
  6. Posada D, Crandall KA and Templeton AR. 2000. GeoDis: A program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Molecular Ecology 9(4): 487-488. pdf
  7. Schwenk K, Posada D and Hebert PDN. 2000. Molecular systematics of european Hyalodaphnia: The role of contemporary hybridization in ancient species . Proceedings of the Royal Society London B 267: 1833-1842 pdf
  8. Clement M, Posada D and Crandall KA. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9 (10): 1657-1660. pdf
  9. Posada D and Crandall KA. 2001. Intraspecific phylogenetics: Trees grafting into networks. Trends in Ecology and Evolution 16(1): 37-45. pdf
  10. Posada D and Crandall KA. 2001. Simple (wrong) models for complex trees: Empirical example from retroviral sequences. Molecular Biology and Evolution 18(2): 271-275. pdf
  11. Posada D and Crandall KA. 2001. Selecting models of nucleotide substitution: An application to the human immunodeficiency virus 1 (HIV-1). Molecular Biology and Evolution 18(6): 897-906. pdf
  12. Posada D 2001. The effect of branch length variation on the selection of models of molecular evolution. Journal of Molecular Evolution 52: 434-444. pdf
  13. Posada D 2001. Unveiling the molecular clock in the presence of recombination. Molecular Biology and Evolution 18: 1976-1978. pdf
  14. Posada D and Crandall KA. 2001. Selecting the best-fit model of nucleotide substitution. Systematic Biology 50: 580-601. pdf
  15. Tarjuelo I, Posada D, Crandall KA, Pascual M, Turón X. 2001. Cryptic species of Clavelina (Ascidiacea) in two different habitats: harbours and rocky littoral zones in the northwestern Mediterranean. Marine Biology 139:455-462 pdf
  16. Posada D and Crandall KA. 2001. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proceedings of the National Academy of Sciences USA 98: 13757-13762. pdf
  17. Posada D and Crandall KA. 2002. The effect of recombination on the accuracy of phylogeny reconstruction. Journal of Molecular Evolution 54: 396-402.pdf
  18. Posada D 2002. Evaluation of methods for detecting recombination from DNA sequences: real data. Molecular Biology and Evolution 19(5): 708-717 pdf
  19. Pfenninger M and Posada D. 2002. Phylogeographic history of the land snail Candidula unifasciata (Poiret 1801) (Helicellinae, Stylommatophora): fragmentation, corridor migration and secondary contact. Evolution 56(9): 1776-1788. pdf
  20. Posada D, Crandall KA and Holmes EC. 2002. Recombination in evolutionary genomics. Annual Review of Genetics 36: 75-97 pdf
  21. Posada D and Wiuf C. 2003. Simulating haplotype blocks in the human genome. Bioinformatics 19: 289-290. pdf
  22. Wiuf C. and Posada D. 2003. A coalescent model of recombination hotspots. Genetics 164: 407-417. pdf
  23. Pfenninger M, Posada D, Frederic Magnin. 2003. Evidence for survival of Pleistocene climatic changes in Northern refugia by the land snail Trochoidea geyeri (Soos 1926) (Helicellinae, Stylommatophora). BMC Evolutionary Biology 3:8. pdf
  24. Miadlikowska J, Lutzoni F, Goward T, Zoller S and Posada D. 2003. New approach to an old problem: incorporating gap-rich regions from ITS and rDNA large subunit into phylogenetic analyses to solve the Peltigera canina species complex. Mycologia 95: 1181-1203. pdf
  25. Rambaut A, Posada D, Crandall KA and Holmes EC. 2004. The causes and consequences of HIV evolution. Nature Reviews Genetics 5: 52-61. pdf
  26. Chasman, DI, Posada D, Subrahmanyan L, Cook NR, Stanton VP and Ridker PM. 2004. A pharmacogenetic study of statin therapy and cholesterol reduction. Journal of the American Medical Association 291: 2821-2827. pdf
  27. Tarjuelo I, Posada D, Crandall KA, Pascual M, Turón X. 2004. Phylogeography and speciation of colour morphs in Pseudodistoma crucigaster (Ascidiacea: Polyclinidae). Molecular Ecology 13: 3125-3136. pdf
  28. Posada D and Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Systematic Biology 53: 793-808. pdf
  29. Bos D, Posada D. Using models of nucleotide evolution to build phylogenetic trees. 2005. Developmental and Comparative Immunology 29: 211-227. pdf
  30. Martin, DP, Williamson C, Posada, D. 2005. RDP2: Recombination detection and analysis from sequence alignments. Bioinformatics 21: 260-262. pdf
  31. Martin, DP, Posada, D, Crandall KA, Williamson C. 2005. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS research and Human Retroviruses 21: 98-102. pdf
  32. Templeton AR, Maxwell T, Posada D, Stengård JH, Boerwinkle E, Sing CF. 2005. Tree scanning: a method for using haplotype trees in genotoype/phenotype association studies. Genetics 169: 441-453. pdf
  33. Tsaousis AD, Martin DP, Ladoukakis ED, Posada D, Zouros E. 2005. Widespread recombination in published animal mtDNA sequences. Molecular Biology and Evolution 22: 925-933. pdf
  34. Abascal F, Zardoya R, Posada, D. 2005. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105. pdf
  35. Posada D, Maxwell TJ, Templeton AR. 2005. TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees. Bioinformatics 21: 2130-2132. pdf
  36. Novoa B, Posada D, Figueras A. 2005. Polymorphisms in the sequences of Marteilia internal transcribed spacer region of the ribosomal RNA genes (ITS-1) in Spain: genetic types are not related with bivalve hosts. Journal of Fish Diseases 28: 331-338. pdf
  37. Thomson MM, Casado G, Posada D, Sierra M, Nájera R. 2005. Identification of a novel HIV-1 complex circulating recombinant form of central african origin in cuba. AIDS 19: 1155-1163. pdf
  38. Martin DP, van der Walt E, Posada D, Rybicki EP. 2005. The evolutionary value of recombination is constrained by genome modularity. PLoS Genetics 1(4): e51. pdf html
  39. Coulthart MB, Posada D, Crandall KA, Dekaban, GA. 2006. On the Phylogenetic Placement of Human T Cell Leukemia Virus Type 1 Sequences Associated with an Andean Mummy. Infection, Genetics and Evolution 6: 91-96. pdf
  40. Carvajal-Rodríguez A, Crandall KA, Posada D. 2006. Recombination estimation under complex evolutionary models with the coalescent composite likelihood method. Molecular Biology and Evolution 23: 817-827. pdf
  41. Abascal F, Posada D, Knight RD, Zardoya R. 2006. Parallel evolution of the genetic code in arthropod mitochondrial genomes. PloS Biology 4(5):e127. pdf html
  42. Gestal C, Novoa B, Posada D, Figueras A, Azevedo C. 2006. Perkinsoide chabelardi n. gen., a protozoan parasite with an intermediate evolutionary position: possible cause of the decrease of sardine fisheries? Environmental Microbiology 8(6): 1105-1114. pdf
  43. Posada D. 2006. ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. Nucleic Acids Research 34: W700-W703. pdf html
  44. Abascal F, Zardoya R, Posada D. 2006. GenDecoder: genetic code prediction for metazoan mitochondria. Nucleic Acids Research 34: W389-W393. pdf html
  45. Campos JL, Posada D, Morán P. 2006. Genetic variation at MHC, mitochondrial and microsatellite loci in isolated populations of Brown trout (Salmo trutta). Conservation Genetics 7: 515-530. pdf
  46. Posada D, Crandall KA, Templeton AR. 2006. Nested Clade Analysis statistics. Molecular Ecology Notes 6: 590-593. pdf
  47. Jobes DV, Daoust M, Nguyen VT, Padua A, Sinangil F, Pérez-Losada M, Crandall KA, Oliphant T, Posada D, Rambaut A, Fuchs J, Berman PW. 2006. Longitudinal population analysis of dual infection with recombination in two strains of HIV-1 subtype B in an individual from a phase 3 HIV vaccine efficacy trial. AIDS Research and Human Retroviruses 22: 968-978.pdf
  48. Kosakovsky-Pond SL, Posada D, Gravenor MB, Woelk CH, Frost S. 2006. Automated phylogenetic detection of recombination using a genetic algorithm. Molecular Biology and Evolution 23: 1891-1901. pdf
  49. Kosakovsky-Pond SL, Posada D, Gravenor MB, Woelk CH, Frost S. 2006. GARD: A Genetic Algorithm for Recombination Detection. Bioinformatics 22: 3096-3098. pdf
  50. Abascal F, Posada D, Zardoya R. 2007. MtArt: A new model of amino acid replacement for Arthropoda. Molecular Biology and Evolution 24: 1-5. pdf
  51. Campos JL, Posada D, Morán P. 2007. Spatio-temporal genetic variability in sea trout (Salmo trutta) populations from northwestern Spain. Freshwater Biology 52: 510-524. pdf
  52. Rocha S, Posada D, Carretero MA, Harris DJ. 2007. Phylogenetic affinities of Comoroan and East African day geckos (genus Phelsuma): multiple natural colonisations, introductions and island radiations. Molecular Phylogenetics and Evolution 43: 685-692. pdf
  53. Bello G, Casado C, Garcia S, Rodriguez C, Romero J, Carvajal-Rodriguez A, Posada D, Lopez-Galindez C. 2007. Lack of temporal structure in the short term HIV-1 evolution within asymptomatic naïve patients. Virology 362: 294-303. pdf
  54. Sierra M, Thomson MM, Posada D, Pérez L Aragonés C, González Z, Pérez J, Casado G, Nájera R. 2007. Identification of three phylogenetically-related HIV-1 BG intersubtype circulating recombinant forms in Cuba. Journal of Acquired Immune Deficiency Syndromes 45: 151-160. pdf
  55. Boni MF, Posada D, Feldman MW. 2007. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176: 1035-1047. pdf
  56. Carvajal-Rodríguez A, Crandall KA, Posada D. 2007. Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy. Infection, Genetics and Evolution 7: 476-483. pdf
  57. Quesada H, Posada D, Caballero A, Morán P, Rolán-Álvarez E. 2007. Phylogenetic evidence for multiple sympatric ecological diversification in a marine snail. Evolution 61: 1600-1612. pdf
  58. Sotelo G, Morán P, Posada D. 2007. Identification and characterization of microsatellite loci in the spiny spider crab Maja brachydactyla. Conservation Genetics 8: 245-247. pdf
  59. Arenas M, Posada D. 2007. Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics 8: 458. pdf
  60. Campos JL, Posada D, Morán P. 2008. Introgression and genetic structure in northern Spanish Atlantic salmon (Salmo salar L.) populations according to mtDNA data. Conservation Genetics 9: 157-169. pdf
  61. Sotelo G, Morán P, Posada D. 2008. Genetic identification of the northeastern Atlantic spiny spider crab as Maja brachydactyla. Journal of Crustacean Biology 28: 76-81.pdf
  62. Carvajal-Rodríguez A, Posada D, Pérez-Losada M, Keller E, Abrams EJ, Viscidi RP, Crandall KA. 2008. Disease progression and evolution of the HIV-1 env gene in 24 infected infants. Infection, Genetics and Evolution 8: 110-120. pdf
  63. Woolley SM, Posada D, Crandall KA. 2008. A Comparison of Phylogenetic Network Methods using Computer Simulation. PLoS ONE 3: e1913. pdf html
  64. Fonseca MM, Posada D, Harris DJ. 2008. Inverted replication of vertebrate mitochondria. Molecular Biology and Evolution 25: 805-808. pdf
  65. Posada D. 2008. jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution 25: 1253-1256. pdf
  66. Sotelo G, Morán P, Fernández L, Posada D. 2008. Genetic variation of the spiny spider crab Maja brachydactyla in the northeastern Atlantic. Marine Ecology Progress Series 362:211-223. pdf
  67. Arenas M, Valiente G, Posada D. 2008. Characterization of reticulate networks based on the coalescent. Molecular Biology and Evolution 25: 2517-2520. pdf
  68. Sotelo G, Posada D, Morán P. 2009. Low mitochondrial diversity and lack of structure in the velvet swimming crab Necora puber along the Galician coast. Marine Biology 156: 1039-1048. pdf
  69. Abrantes J, Posada D, Guillon P, Esteves PJ, Le Pendu J. 2009. Widespread gene conversion of alpha-2-fucosyltransferase genes in mammals. Journal of Molecular Evolution 69: 22-31. pdf
  70. Rocha S, Vences M, Glaw F, Posada D, Harris DJ. 2009. Multigene phylogeny of Malagasy day geckos of the genus Phelsuma. Molecular Phylogenetics and Evolution 52: 530-537. pdf
  71. Perez-Losada M, Posada D, Arenas M, Jobes DV, Sinangil F, Berman PW and Crandall KA. 2009. Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial. Retrovirology 2009, 6:67 html
  72. Sotelo G, Morán, P, Posada D. 2009. Molecular phylogeny and biogeographic history of the European Maja spider crabs (Decapoda, Majidae). Molecular Phylogenetics and Evolution 53: 314-319.
  73. Iglesias MJ, Morán P, Posada D. 2009. Are the sexual, somatic and genetic characters enough to solve nomenclatural problems in lumbricid taxonomy?". Soil Biology & Biochemistry: Soil Biology & Biochemistry 41: 2257-2271.
  74. Kosakovsky Pond SL, Posada D, Stawiski S, Chappey C, Poon AFY, Hughes G, Fearnhill E, Gravenor MB, Leigh Brown AJ and Frost SDW. 2009. An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Computational Biology 5(11):e1000581.
  75. Perez-Losada M, Jobes DV, Sinangil F, Crandall KA, Posada D and Berman PW. 2010. Phylodynamics of HIV-1 from a Phase III AIDS vaccine trial in North America. Molecular Biology and Evolution 27:417-425.
  76. Arenas M, Posada D. 2010. Coalescent simulation of intracodon recombination. Genetics 184: 429-437.
  77. Rocha S, Rösler H, Gehring PS, Glaw F, Posada D, Harris DJ, Vences M. 2010. Phylogenetic systematics of day geckos, genus Phelsuma based on molecular and morphological data (Squamata: Gekkonidae). Zootaxa 2429: 1-28.
  78. Glez-Peña D, Gómez-Blanco D, Reboiro-Jato M, Fdez-Riverola F, Posada D. 2010. ALTER: program-oriented conversion of DNA and protein alignments. Nucleic Acids Research (Web server issue) 2010: 1-5. pdf html
  79. Arenas M, Posada D. 2010. The effect of recombination on the reconstruction of ancestral sequences. Genetics 184: 1133-1139.
  80. Arenas M, Patricio M, Posada D, Valiente G. 2010. Characterization of Phylogenetic Networks with NetTest. BMC Bioinformatics 11: 268-272. html
  81. Pascual S, Villalba A, Abollo E, Garci M, González AF, Nombela MA, Posada D and Guerra A. 2010. The mussel Xenostrobus securis: a well-established alien invader in the Ria de Vigo (Spain, NE Atlantic). Biological Invasions 7: 2091-2103.
  82. Martin DP, Lemey P, Lott M, Moulton V, Posada D and Lefeuvre P. 2010. RDP3: A flexible and fast computer program for analysing recombination. Bioinformatics 26: 2462-2463.
  83. Arenas M, Posada D. 2010. Computational design of centralized HIV-1 genes. Current HIV Research 8: 613-621.
  84. Romero A, Dios D, Poisa-Beiro L, Costa MM, Posada D, Figueras A, Novoa B. 2011. Individual sequence variability and functional activities of fibrinogen-related proteins (FREPs) in the Mediterranean mussel (Mytilus galloprovincialis) suggest ancient and complex immune recognition models in invertebrates. Developmental & Comparative Immunology 35: 334-344.
  85. Perez-Losada M, Jobes DV, Sinangil F, Crandall KA, Arenas M, Posada D and Berman PW. 2011. Phylodynamics of HIV-1 from a Phase III AIDS vaccine trial in Bangkok, Thailand. PLoS ONE 6(3): e16902.
  86. Tazi L, Imamichi H, Hirschfeld S, Metcalf JA, Orsega S, Pérez-Losada M, Posada D, Lane HC and Crandall KA. 2011. HIV-1 Infected Monozygotic Twins: A Tale of Two Outcomes. BMC Evolutionary Biology 11: 62.
  87. Darriba D, Taboada GL, Doallo R, Posada D. 2011. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27: 1164-1165.
  88. Arbiza L, Patricio M, Dopazo H, Posada D. 2011. Genome-wide heterogeneity of nucleotide substitution model-fit. Genome Biology and Evolution 3:896-908.
  89. Martin DP, Lemey P, Posada D. 2011. Analysing recombination in nucleotide sequences. Molecular Ecology Resources 11: 943-955.
  90. Rocha S, Harris DJ, Posada D. 2011. Cryptic diversity within the endemic Prehensile-tailed gecko Urocotyledon inexpectata across the Seychelles Islands: patterns of phylogeographic structure and isolation at the multilocus level. Biological Journal of the Linnean Society 104: 177-191.
  91. Moreira R, Balseiro P, Romero A, Dios S, Posada D, Novoa B, Figueras A. 2012. Gene expression analysis of clams Ruditapes philippinarum and Ruditapes decussatus following bacterial infection yields molecular insights into pathogen resistance and immunity. Developmental and Comparative Immunology 36: 140-149.
  92. Abascal F, Posada D, Zardoya R. In press. The evolution of the mitochondrial genetic code in arthropods revisited. mtDNA.


Book chapters

  1. Posada D, Crandall KA and Hillis D. 2001. Phylogenetics of HIV. In Computational and evolutionary analysis of HIV molecular sequences. (Rodrigo, A.G. and Learn, J., eds.). Kluwer Academic Publishers, Norwell, MA. pp. 121-160. pdf
  2. Crandall KA and Posada D. 2002. Phylogenetic approaches to molecular epidemiology. In The Molecular Epidemiology of Human Viruses. Thomas Leitner, ed. Kluwer Academic press. pp. 25-40. pdf
  3. Posada D. 2003. Using Modeltest and PAUP* to select a model of nucleotide substitution. Current Protocols in Bioinformatics (Baxevanis et al. eds). John Wiley & Sons. 6.5.1-6.5.14 pdf
  4. Posada D. 2003. Selecting models of evolution. In The Phylogenetic Handbook. Vandemme AM, Salemi M (eds).Cambridge University press. pp. 256-282. pdf
  5. Lewis-Oritt N, Crandall KA, Posada D. 2004. Evolutionary analysis of genetic recombination. In "Dynamical Genetics", edited by Valerio Parisi, Valeria De Fonzo and Filippo Aluffi-Pentini. Research Signpost (India). pp. 49-78. pdf
  6. Posada D. 2009. Selecting Models of Molecular Evolution. In "The Phylogenetic Handbook", 2nd Edition. Vandamme AM, Salemi M, Lemey P (eds). Cambridge University Press. pp. 345-361.
  7. Lemey P, Posada D. 2009. Molecular clock analysis. In "The Phylogenetic Handbook", 2nd Edition. Vandamme AM, Salemi M, Lemey P (eds). Cambridge University Press. pp. 362-380.
  8. Lemey P, Posada D. 2009. Introduction to recombination detection. In "The Phylogenetic Handbook", 2nd Edition. Vandamme AM, Salemi M, Lemey P (eds). Cambridge University Press. pp. 493-518.
  9. Posada D. 2009. Selection of models of DNA evolution with jModelTest. In "Bioinformatic analysis of DNA sequences". Posada D (ed.). Methods in Molecular Biology Series. Humana Press. pp. 93-112.
  10. Abascal F, Zardoya R, Posada D. 2009. Genetic code prediction for metazoan mitochondria with GenDecoder. In "Bioinformatic analysis of DNA sequences". Posada D (ed.). Methods in Molecular Biology Series. Humana Press. pp. 233-242.
  11. Buhay J, Crandall KA, Posada D. 2009. Nested clade phylogeographic analysis for conservation genetics. In "Population Genetics for Animal Conservation". Bertorelle G. et al. (eds.) Cambridge University Press. pp. 80-103.
  12. Posada D. 2009. Selección de modelos de evolución molecular. En "Adaptación y Evolución : 150 años después del Origen de las Especies" (Navarro A and Dopazo H, eds.). Sociedad Española de Biología Evolutiva (SESBE).
  13. Abascal F, Patricio M, Zardoya R, Posada D. 2011. Deciphering the evolution of the mitochondrial genetic code in arthropods. In Encyclopedia of Life Sciences 2011, John Wiley & Sons, Ltd: Chichester http://www.els.ne
  14. Arenas M and Posada D, In press. Simulation of Coding Sequence Evolution. In "Codon Evolution: Mechanisms and Models". (Cannarozzi GM and Schneider A., eds.). Oxford University Press.
  15. Posada D. In press. Reconstrucción de árboles filogenéticos. En "El árbol de la vida: sistemática y evolución de los seres vivos" (Vargas P, Zardoya R, eds.). Reverté.


Comments

  1. Posada D 2000. How does recombination affect phylogeny estimation?. Trends in Ecology and Evolution 15(12): 489-490 pdf
  2. Carvajal-Rodríguez A, Crandall KA, Posada D. 2005. Caracterización y modelado computacional de la recombinación en secuencias de ADN en el virus del SIDA (VIH-1). Biojournal 2. pdf


This document last modified Wednesday December 28, 2011