last 5 years

In press

  • Escalona M, Rocha S, Posada D. 2018. NGSphy: phylogenomic simulation of next-generation sequencing data. Bioinformatics, bty146,
  • Duchemin W, Guillaume G, Arigon AM, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davín A, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, Posada D, Scornavacca C, Szöllosi G, Zhang L, Tannier E, Daubin V. 2018. RecPhyloXML – a format for reconciled gene trees. Bioinformatics: in press.
  • Arenas M. 2019. Applications of the Coalescent for the Evolutionary Analysis of Genetic Data. In Encyclopedia of Bioinformatics and Computational Biology. Eds, Ranganathan S, Gribskov M, Nakai K, Schönbach C. Elsevier. Pp. 746–758.
  • Bastolla U, Arenas M. 2019. The Influence of Protein Stability on Sequence Evolution: Applications to Phylogenetic Inference. In Computational Methods in Protein Evolution. Ed, Sikosek T. Springer. Pp. 215–231.
  • Vicens A, Vinuesa P, Arenas M, Treviño CL. 2019. Analyzing the functional divergence of Slo1 and Slo3 channel subfamilies. Molecular Phylogenetics and Evolution, 133: 33–41.
  • Negredo A, Habela MA, Ramírez de Arellano E, Diez F, Lasala F, López P, Sarria A, Labiod N, Calero-Bernal R, Arenas M, Tenorio A, Estrada A, Sánchez-Seco MP. 2019. Follow up of a Crimean-Congo hemorrhagic Fever enzootic focus in Spain (2011-2015). Emerging Infectious Diseases. In press.
  • Pascual-Garcia A, Arenas M, Bastolla U. 2019. The molecular clock in the evolution of protein structures. Systematic Biology. In press.
  • Arenas M, Bastolla U. 2019. ProtASR2: Ancestral Reconstruction of Protein Sequences accounting for Folding Stability. Methods in Ecology and Evolution. In press.



  • Vicens A, Posada D. 2018. Selective Pressures on Human Cancer Genes along the Evolution of Mammals. Genes, 9(582).
  • Branco C, Velasco M, Benguigui M, Currat M, Ray N, Arenas M. 2018. Consequences of Diverse Evolutionary Processes on American Genetic Gradients of Modern Humans. Heredity, 121(6): 548–556.
  • Branco C, Arenas M. 2018. Selecting among Alternative Scenarios of Human Evolution by Simulated Genetic Gradients. Genes, 9(10), 506.
  • Jimenez-Santos MJ, Arenas M, Bastolla U. 2018. Influence of mutation bias and hydrophobicity on the substitution rates and sequence entropies of protein evolution. PeerJ, 6:e5549.
  • Oliveira M, Arenas M, Lage O, Cunha M, Amorim MI. 2018. Epiphytic fungal community in Vitis vinifera of the Portuguese wine regions. Letters in Applied Microbiology, 66:93–102.
  • Ramirez-Amaro S, Picornell A, Arenas M, Castro JA, Massutí E, Ramon MM, Terrasa B. 2018. Contrasting evolutionary patterns in populations of demersal sharks throughout the western Mediterranean. Marine Biology. 165:3.
  • Jimenez MJ, Arenas M, Bastolla U. 2018. Substitution rates predicted by stability-constrained models of protein evolution are not consistent with empirical data. Molecular Biology and Evolution, 35(3):743–755.
  • Oliveira M, Arenas M, Amorim, A. 2018. New Trends in Microbial Epidemiology: Can An Old Dog Learn New Tricks?. Annals of Microbiology and Immunology, 1(1):1004.
  • Perez-Losada M, Arenas M, Castro-Nallar E. 2018. Microbial sequence typing in the genomic era. Infection, Genetics and Evolution, 63:346-359.
  • Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Perez-Losada M. 2018. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. Infection, Genetics and Evolution, 63:295-306.
  • Alves JA, Posada D. 2018. Sensitivity to sequencing depth in single-cell cancer genomics. Genome Medicine 10: 29.



  • Arenas M, Weber CC, Liberles D, Bastolla U. 2017. ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability. Systematic Biology, 66(6):1054–1064.
  • Castelhano N, Araujo NM, Arenas M. 2017. Heterogeneous recombination among Hepatitis B virus genotypes. Infection, Genetics and Evolution. 54:486–490.
  • Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A. 2017. Forensic genetics and genomics: Much more than just a human affair. PLoS Genetics. 13(9): e1006960.
  • Pimenta J, Lopes AM, Comas D, Amorim A, Arenas M. 2017. Evaluating the Neolithic Expansion at Both Shores of the Mediterranean Sea. Molecular Biology and Evolution, 34(12):3232–3242.
  • Alves JA, Prieto T, Posada D. 2017. Multiregional tumor trees are not phylogenies. Trends in Cancer: Cancer 3: 546-550.
  • Maley C, Aktipis A, Graham T, Sottoriva A, Boddy A, Janiszewska M, Silva A, Gerlinger M, Yuan Y, Pienta K, Anderson K, Gatenby R, Swanton C, Posada D, Wu C-I, Schiffman J, Hwang S, Polyak K, Anderson A, Brown J, Greaves M, Shibata D. 2017. Classifying the Evolutionary and Ecological Features of Neoplasms. Nature Reviews Cancer 17: 605-619.
  • Martins LO, Posada D. 2017. Species Tree Estimation from Genome-wide Data with Guenomu. In Bioinformatics Vol I. 2º ed. Keith JM ed. Methods in Molecular Biology 1525: 461-478. Springer. ISBN 978-1-4939-6620-2; doi:10.1007/978-1-4939-6622-6; ISBN 978-1-4939-6622-6 (eBook).



  • Soliman T, Takama O, Fernandez-Silva I, Reimer JD. 2016. Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan. PeerJ 4:e2410.
  • Escalona M, Rocha S, Posada D. 2016. A comparison of tools for the simulation of genomic NGS data. Nature Reviews Genetics 17: 459-469.
  • Mallo D, Posada D. 2016. Multilocus inference of species trees and DNA barcoding. Philosophical Transactions of the Royal Society B 371: 20150335.
  • Rocha S, Perera A, Silva A, Posada D, Harris J. 2016. Evolutionary history of Trachylepis skinks from the Seychelles islands: introgressive hybridization, morphological evolution and geographic structure. Biological Journal of the Linnean Society 119: 15-36.
  • Posada D. 2016. Phylogenomics for Systematic Biology. Systematic Biology 65: 353-356.
  • Martins LO, Mallo D, Posada D. 2016. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction. Systematic Biology 65: 397-416.
  • Martins LO, Posada D. 2016. Infinitely Long Branches and an Informal Test of Common Ancestry. Biology Direct 11: 19.
  • Murgarella M, Puiu D, Novoa B, Figueras A, Posada DCanchaya C. 2016. A first insight into the genome of the filter-feeder mussel Mytilus galloprovincialisPLoS ONE 11(3): e0151561. doi:10.1371/journal.pone.0151561
  • Gulia Nuss et al (includes Jose Tubio). 2016. Genomic insights into the Ixodes scapularis tick vector of Lyme disease. Nature communications 7:10507.
  • Mallo D, Martins LO, Posada D. 2016. SimPhy: Phylogenomic Simulation of Gene, Locus and Species Trees. Systematic Biology 65: 334-344.
  • Rodríguez-Pascual M, Kanellopoulos C, Rubio-Montero AJ, Darriba D, Prnjat O, Posada D, Mayo-García R. 2016. Adapting Reproducible Research Capabilities to Resilient Distributed Calculations. International Journal of Grid and High Performance Computing 8: 58-69.
  • Prieto T, Alves JM, Posada D. 2016. NGS analysis of somatic mutations in cancer genomes. In Big Data Analytics in Genomics. Ed Wong KC. Pp 357-372.Springer. ISBN 978-3-319-41278-8
DOI 10.1007/978-3-319-41279-5.



  • Posada D. Cancer molecular evolution. 2015. Journal of Molecular Evolution 81: 81-83.
  • Moreira R, Pereiro P, Canchaya CPosada D, Figueras A, Novoa B. 2015. RNA-Seq in Mytilus galloprovincialis: Comparative transcriptomics and expression profiles among different tissues. BMC Genomics 16:728..
  • Arenas M, Lopes JS, Beaumont MA, Posada D. 2015. CodABC: A Computational Framework to Coestimate Recombination, Substitution and Molecular Adaptation rates by approximate Bayesian computation. Molecular Biology and Evolution 32: 1109-1112.
  • Palopoli MF, Fergus DJ, Minot S, Pei DT, Simison WB, Fernandez-Silva I, Thoemmes MS, Dunn RR, Trautwein M. 2015. Global divergence of the human follicle mite Demodex folliculorum: Persistent associations between host ancestry and mite lineages. Proceedings of the National Academy of Sciences 112: 15958-15963.



  • Arenas M and Posada D. 2014. The influence of recombination on the estimation of selection from coding sequence alignments. In “Natural Selection: Methods and Applications” (Fares MA, ed.). CRC Press/Taylor & Francis. Pp. 112-125.
  • Mallo D, Martins LO, Posada D. 2014. Estimation of Species Trees. In Encyclopedia of Life Sciences 2014, John Wiley & Sons, Ltd: Chichester.
  • Mallo D, Martins LO, Posada D. 2014. Unsorted Homology within Locus and Species Trees. Systematic Biology 63: 988-992.
  • Fonseca MM, Harris DJ, Posada D. 2014. The inversion of the control region in three mitogenomes provides further evidence for an asymmetric model of vertebrate mtDNA replication. PLoS ONE: e106654.
  • Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy JP, Pépin J, Posada D, Peeters M, Pybus OG, Lemey P. 2014. The early spread and epidemic ignition of HIV-1 in human populations. Science 364: 56-61.
  • Martins LO, Posada D. 2014. Testing for Universal Common Ancestry. Systematic Biology 63: 838-842.
  • Forn-Cuní G, Reis ES, Dios S, Posada D, Lambris JD, Figueras A, Novoa B. 2014. The Evolution and Appearance of C3 Duplications in Fish Originate an Exclusive Teleost c3Gene Form with Anti-Inflammatory Activity. PLoS ONE 9(6): e99673.
  • Arenas MPosada D. 2014. Simulation of Genome-wide Evolution under Heterogeneous Substitution models and Complex Multispecies Coalescent Histories. Molecular Biology and Evolution 31: 1295-1301.
  • Lopes JS, Arenas M, Posada D, Beaumont MA. 2014. Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation. Heredity 112: 255-264.
  • Darriba D, Taboada GL, Doallo R, Posada D. 2014. HPC Selection of Models of DNA Substitution for Multicore Clusters. International Journal of High Performance Computing 28: 112-125.
  • Santorum JM, Taboada GL, Darriba D, Posada D. 2014. selection of nucleotide substitution models on the cloud. Bioinformatics 30: 1312-1313.
  • Fonseca MM, Harris DJ, Posada D. 2014. Origin and length distribution of unidirectional prokaryotic overlapping genes. G3: Genes, Genomes, Genetics 4: 19-27



  • Rocha S, Posada D, Harris DJ. 2013. Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands. BMC Evolutionary Biology 13: 3. doi:10.1186/1471-2148-13-3
  • Martins LO, Mallo D, Posada D. 2013. Phylogenetic Likelihood. In Encyclopedia of Life Sciences 2013, John Wiley & Sons, Ltd: Chichester. doi:10.1002/9780470015902.a0005141
  • Bizinoto MC, Yabe S, Leal E, Kishino H, Martins LO, Lima ML, Morais ER, Diaz RS, Janini LM. 2013. Codon pairs of the HIV-1 vif gene correlate with CD4+ T cell count. BMC Infectious Diseases 13:173. doi:10.1186/1471-2334-13-173.
  • Lima A, Harris D.J., Rocha S., Miralles A, Glaw F, Vences M. 2013. Phylogenetic relationships of Trachylepis skink species from Madagascar and the Seychelles (Scincidae: Lygosominae). Molecular Phylogenetics and Evolution 67: 615-629. doi: 10.1016/j.ympev.2013.02.001.
  • Posada D. 2013. Phylogenetic Models of Molecular Evolution: Next-Generation Data, Fit, and Performance. Journal of Molecular Evolution 76: 351-352. doi: 10.1007/s00239-013-9566-z
  • Arenas M, Dos Santos HG, Posada D, Bastolla U. 2013. Protein Evolution along Phylogenetic Histories under Structurally Constrained Substitution Models. Bioinformatics 29: 3020-3028. doi:10.1093/bioinformatics/btt530.



  • 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.
  • Abascal F, Posada D, Zardoya R. 2012. The evolution of the mitochondrial genetic code in arthropods revisited. mtDNA 23: 84-91.
  • Martins LO, Posada D. 2012.Proving universal common ancestry with similar sequences. Trends in Evolutionary Biology 4:e5.
  • Fonseca MM, Rocha S, Posada D. 2012. Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes. PLoS One 7: e36605.
  • Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772.
  • Coulthart MB, Andonov A, Crandall KA, Pérez-Losada M, Posada D, Padmore R, Giulivi A, Oger JJ, Peters AA, Dekaban GA. 2012. Insights into origins of Human T-cell Lymphotropic Virus Type 1 based on new strains from aboriginal people of Canada. Infection, Genetics and Evolution 8:1822-1830.
  • Arenas M and Posada D. 2012. Simulation of Coding Sequence Evolution. In “Codon Evolution: Mechanisms and Models”. (Cannarozzi GM and Schneider A., eds.). Oxford University Press. 978-0-19-960116-5.
  • Posada D. 2012. Selection of Phylogenetic Models of Molecular Evolution. In Encyclopedia of Life Sciences 2012, John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0022845.
  • Posada D. 2012. Reconstrucción de árboles filogenéticos. En “El árbol de la vida: sistemática y evolución de los seres vivos” (Vargas P, Zardoya R, eds.). Madrid, 617 pp.


For older please publications look at the personal web pages.