Publications 2011 - Current

2017

  • Calvo-Martín, J. M., Papaceit, M. & Segarra, C. 2017 Evidence of neofunctionalization after the duplication of the highly conserved Polycomb group gene Caf1-55 in the obscura group of Drosophila. Sci. Rep. 7, 40536. (doi:10.1038/srep40536)
  • Fukushima, K. et al. 2017. The pitcher plant Cephalotus genome reveals genetic changes associated with carnivory. Nature Ecol. Evol. 1: XXX-XXX.
  • Guirao‐Rico, S., Sánchez‐Gracia, A. and Charlesworth, D. 2017. Sequence diversity patterns suggesting balancing selection in partially sex‐linked genes of the plant Silene latifolia are not generated by demographic history or gene flow. Mol. Ecol. 26: XXX-XXX. doi:10.1111/mec.13969.
  • Vizueta, J., Frías-López, C., Macías-Hernández, N., Arnedo, M. A., Sánchez-Gracia, A. and Rozas, J. 2017. Evolution of chemosensory gene families in arthropods: Insight from the first inclusive comparative transcriptome analysis across spider appendages. Genome Biol. Evol. 9: XXX-XXX. doi:10.1093/gbe/evw296.

2016

  • Bidegaray-Batista, L., Sánchez-Gracia, A., Santulli, G., Maiorano, L., Guisan, A., Vogler, A. and Arnedo, M. A. 2016. Imprints of multiple glacial refugia in the Pyrenees revealed by phylogeography and palaeodistribution modelling of an endemic spider. Mol. Ecol. 25: 2046-2064. doi: 10.1111/mec.13585.
  • Clifton, B. D. et al. 2016. Rapid Functional And Sequence Differentiation of a Tandemly-Repeated Species-Specific Multigene Family in Drosophila. Mol. Biol. Evol. XX: YYY-YYY. doi: 10.1093/molbev/msw212.
  • Donaire, L., Rozas, J. and Ayllón, M. A. 2016. Molecular characterization of Botrytis ourmia-like virus, a mycovirus close to the plant pathogenic genus Ourmiavirus.Virology 489: 158-164. doi: 10.1016/j.virol.2015.11.027.
  • Frías-López, C., Sánchez-Herrero, J. F., Guirao-Rico, S., Mora, E., Arnedo, M. A., Sánchez-Gracia, A. and Rozas, J. 2016. DOMINO: Development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms. Bioinformatics 32: 3753-3759. doi:10.1093/bioinformatics/btw534.
  • Gulia-Nuss, M. et al. 2016. Genomic insights into the Ixodes scapularis tick vector of Lyme disease. Nature Commun. 7: 10057. doi: 10.1038/ncomms10507.
  • Kanost, M. R. et al. 2016. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. Insect Biochemistry and Molecular Biololgy 76: 118-147. doi: 10.1016/j.ibmb.2016.07.005.
  • Librado, P. and Rozas, J. 2016. Weak polygenic selection drives the rapid adaptation of the Drosophila chemosensory system: lessons from the upstream regions of the major gene families. Genome Biol. Evol.8: 2493-2504. doi: 10.1093/gbe/evw191.
  • Torres-Oliva, M., Almeida, F. C., Sánchez-Gracia, A. and Rozas, J. 2016. Comparative genomics uncovers unique gene turnover and evolutionary rates in a gene family involved in the detection of insect cuticular pheromones. Genome Biol. Evol. 8: 1734-1747. doi:10.1093/gbe/evw108.

2015

  • Blanco, I. et al. Assessing Associations between the AURKA-HMMR-TPX2-TUBG1 Functional Module and Breast Cancer Risk in BRCA1/2 Mutation Carriers. PLoS ONE 10: e0120020. doi: 10.1371/journal.pone.0120020.
  • Calvo-Martín J.M., Librado P., Aguadé M., Papaceit M., Segarra C. Adaptive selection and coevolution at the proteins of the Polycomb repressive complexes in Drosophila. Heredity. doi: 10.1038/hdy.2015.91
  • Carretero-Paulet, L., Chang, T.-H., Librado, P., Ibarra-Laclette, E., Herrera-Estrella, L., Rozas, J. and Albert, V. A. Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba. Genome Biol. Evol. 7: 444-456.
  • Carretero-Paulet, L., Librado, P., Chang, T.-H., Ibarra-Laclette, E., Herrera-Estrella, L., Rozas, J. and Albert, V. A. High Gene Family Turnover Rates and Gene Space Adaptation in the Compact Genome of the Carnivorous Plant Utricularia gibba. Mol. Biol. Evol. 32: 1284-1295.
  • Frías-López, C., Almeida, F. C., Guirao-Rico, S., Vizueta, J., Sánchez-Gracia, A., Arnedo, M. A., Rozas, J. Comparative analysis of tissue-specific transcriptomes in the funnel-web spider Macrothele calpeiana (Araneae, Hexathelidae) PeerJ 3: e1064. doi: 10.7717/peerj.1064.
  • Kornobis, E., Cabellos, L., Aguilar, F., Frías-López, C., Rozas, J., Marco, J. and Zardoya, R. 2015. TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing. Evolutionay Bioinformatics. 11: 97-104.
  • Orengo D.J., Puerma E., Papaceit M., Segarra C, Aguadé M. A molecular perspective on a complex polymorphic inversion system with cytological evidence of multiply reused breakpoints. Heredity. 114: 610-8. PMID 25712227 DOI: 10.1038/hdy.2015.4
  • Pratdesaba R., Segarra C., Aguadé M. Inferring the demographic history of Drosophila subobscura from nucleotide variation at regions not affected by chromosomal inversions. Molecular Ecology. 24: 1729-41. PMID 25776124 DOI: 10.1111/mec.13155
  • Romero-Hernández, B., Tedim, A. P., Sánchez-Herrero, J. F., Librado, P., Rozas, J., Muñoz, G., Baquero, F., Cantón, R., Campo, R. D. Streptococcus gallolyticus subsp. gallolyticus from Human and Animal Origins: Genetic Diversity, Antimicrobial Susceptibility, and Characterization of a Vancomycin-Resistant Calf Isolate Carrying a VanA-Tn1546-Like Element. Antimicrob. Agents Chemother. 59: 2006-2015.
  • Solà, E., Alvarez-Presas, M., Frías-López, C., Littlewood, T. J., Rozas, J., Riutort, M. 2015. Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms. PLoS ONE 10: e0120081. doi: 10.1371/journal.pone.0120081.

2014

  • Almeida, F. C., Sánchez-Gracia, A., Campos, J. L. and Rozas, J. Family Size Evolution in Drosophila Chemosensory Gene Families: A Comparative Analysis with a Critical Appraisal of Methods.Genome Biol. Evol. 61669-1682.

  • Alvarez-Presas, M., Sánchez-Gracia, A., Carbayo F., Rozas, J. and Riutort, M. Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hotspot: A statistical phylogeographic study using a low-dispersal organism. Heredity 112: 656-665.

  • Carretero-Paulet, L., Chang, T.-H., Librado, P., Ibarra-Laclette, E., Herrera-Estrella, L., Rozas, J. and Albert, V. A. Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba. Genome Biol. Evol. 7: 444-456.

  • Chipman, A. D. et al. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima. PLoS Biol. 12: e1002005.

  • Denoeud, F. et al. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 345: 1181-1184.

  • Librado, P., Vieira, F. G., Sánchez-Gracia, A., Kolokotronis, S.-O. and Rozas, J. Mycobacterial Phylogenomics: An Enhanced Method for Gene Turnover Analysis Reveals Uneven Levels of Gene Gain and Loss among Species and Gene Families. Genome Biol. Evol. 6: 1454-1465.

  • Puerma E., Orengo D.J., Aguadé M. Evidence for a gene involved in multiple and diverse rearrangements in the Drosophila genus. Molecular Biology and Evolution. 31: 2998-3001. doi: 10.1093/molbev/msu239
  • Puerma E., Orengo D.J., Salguero D., Papaceit M., Segarra C., Aguadé M. Characterization of the breakpoints of a polymorphic inversion complex detects strict and broad breakpoint reuse at the molecular level. Molecular Biology and Evolution. 31: 2331-41. doi: 10.1093/molbev/msu177
  • Rozas, J. and Sánchez-Gracia, A. Nucleotide Variability Analysis and Intraespecific phylogenies. In Vargas, P. and Zardoya, R. (eds.). The tree of life. P. Vargas and R. Zardoya (eds.). Sinauer.

2013

  • ALVAREZ-PONCE, D., AGUADÉ, M. and ROZAS, J. 
    Comment on: 'The Molecular Evolutionary Patterns of the Insulin/FOXO Signaling Pathway'.
    Evol. Bioinformatics (in press).
  • GUIRAO-RICO, S. and AGUADÉ, M.
    Patterns of nucleotide diversity at the regions encompassing the Drosophila insulin-like peptide (dilp) genes: demography vs. positive selection in Drosophila melanogaster.
    PLoS One. 8:e53593. doi: 10.1371/journal.pone.0053593.
  • PAPACEIT, M., SEGARRA, C. and AGUADÉ, M.
    Structure and population genetics of the breakpoints of a polymorphic inversion in Drosophila subobscura.
    Evolution 67:66-79. doi: 10.1111/j.1558-5646.2012.01731.x.
  • PUERMA, E. and AGUADÉ, M.
    Polymorphism at genes involved in salt tolerance in Arabidopsis thaliana (Brassicaceae).
    Am. J. Bot. 100:384-390. doi: 10.3732/ajb.1200332.
  • ROZAS, J. and SÁNCHEZ-GRACÍA, A. 
    Nucleotide Variability Analysis and Intraespecific phylogenies.
    In The tree of life. P. Vargas and R. Zardoya (eds.). Sinauer (in press).


2012

  • AGUADÉ, M., BERTRANPETIT, J. and PERETÓ, J.
    Genòmica i Evolució. En Cent anys de la Societat Catalana de Biologia (Piferrer F., ed.).
    Treballs de la Societat Catalana de Biologia 63:101-122.
  • ALVAREZ-PONCE, D., GUIRAO-RICO, S., ORENGO, DJ., SEGARRA, C., ROZAS, J. and AGUADÉ, M.
    Molecular population genetics of the insulin/TOR signal transduction pathway: a network-level analysis in Drosophila melanogaster.
    Mol. Biol. Evol. 29:123-132.
  • EIRÍN-LÓPEZ, J. M., REBORDINOS, L., ROONEY, A. P. and ROZAS, J.
    The birth-and-death evolution of multigene families revisited.
    Pp. 170-196. In Garrido-Ramos, M. A. (ed.). Repetitive DNA. Genome Dynamics, Vol. 7. Karger Pub. Basel
  • KHADEM M, MUNTÉ A, CAMACHO R, AGUADÉ, M. and SEGARRA C.
    Multilocus analysis of nucleotide variation in Drosophila madeirensis, an endemic species of the Laurisilva forest in Madeira.
    J. Evol. Biol. 25:726-39
  • LIBRADO, P., VIEIRA, F. G. and ROZAS, J.
    BadiRate: Estimating Family Turnover Rates by Likelihood-Based Methods.
    Bioinformatics 28:279-281.
  • MACKAY, T. F. C. et al.
    The Drosophila melanogaster Genetic Reference Panel.
    Nature 482:173-178.
  • RAMIA, M., LIBRADO, P., CASILLAS, S., ROZAS, J. and BARBADILLA, A. 
    PopDrowser: the Population Drosophila Browser
    Bioinformatics 28:595-596.
  • ROZAS, J.
    Análisis de la variabilidad genética y filogenias intraespecíficas.
    Pp. 553-561. In Vargas, P. and Zardoya, R. (eds.). El árbol de la vida: sistemática y evolución de los seres vivos. Madrid.
  • SÁNCHEZ-GRACIA, A. and CASTRESANA, J.
    Impact of Deep Coalescence on the Reliability of Species Tree Inference from Different Types of DNA Markers in Mammals
    PLoS ONE 7:e30239.
  • VIEIRA, F. G., FORÊT, S., HE, X., ROZAS, J., FIELD, L. M. and ZHOU, J.-J.
    Unique features of odorant-binding proteins of the parasitoid wasp Nasonia vitripennis
    revealed by genome annotation and comparative analyses.
    PLoS ONE  7:e43034. doi:10.1371/journal.pone.0043034.
  • YEH, S.-D., DO, T., CHAN, C., CORDOVA, A., CARRANZA, F., YAMAMOTO, E. A., ABBASSI, M., 
    GANDASETIAWAN, K. A., LIBRADO, P., DAMIA, E., DIMITRI, P., ROZAS, J., HARTL, D. L., ROOTE, J. and RANZ, J. M..
    Functional evidence that a recently evolved Drosophila sperm-specific gene boosts sperm competition.
    Proc. Natl. Acad. Sci. USA. 109:2043-2048..

2011

  • ALVAREZ-PONCE, D., AGUADÉ, M. and ROZAS, J.
    Comparative genomics of the vertebrate insulin/TOR signal transduction pathway: A network-level analysis of selective pressures.
    Genome Biol. Evol. 3:87-101.
  • ALVAREZ-PRESAS, M., CARBAYO, F., ROZAS, J. and RIUTORT, M.
    Land planarians (Platyhelminthes) as a model organism for fine-scale phylogeographic studies: Understanding patterns of biodiversity in the Brazilian Atlantic Forest hotspot.
    J. Evol. Biol. 24:887-896.
  • CONCEIÇÃO, IC. and AGUADÉ, M.
    Odorant receptor (Or) genes: polymorphism and divergence in the D. melanogaster and D. pseudoobscura lineages.
    PLoS One. 5:e13389.
  • GUIRAO-RICO, S. and AGUADÉ, M.
    Molecular evolution of the ligands of the insulin-signaling pathway: dilp genes in the genus drosophila.
    Mol Biol Evol. 28:1557-1560.
  • POWELL, JR., DION, K., PAPACEIT, M., AGUADÉ, M., VICARIO, S. and GARRICK, RC.
    Nonrecombining genes in a recombination environment: the Drosophila "dot" chromosome.
    Mol Biol Evol. 28:825-833.
  • SÁNCHEZ-GRACIA, A. and ROZAS, J.
    Molecular population genetics of the Odorant-Binding Protein 83 genomic region in Drosophila subobscura and D. guanche: Contrasting the effects of natural selection and gene arrangement expansion in the patterns of nucleotide variation.
    Heredity 106:191-201.
  • SÁNCHEZ-GRACIA, A., VIEIRA, F. G., ALMEIDA, F. C. and ROZAS, J.
    Comparative Genomics of the Major Chemosensory Gene Families in Arthropods.
    In Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester.
  • VIEIRA, F. G. and ROZAS, J.
    Comparative genomics of the Odorant-Binding and Chemosensory Protein gene families across the Arthropoda: Origin and evolutionary history of the chemosensory system.
    Genome Biol. Evol. 3:476-490.
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