Contacts Centre for Environmental Biology


Assistant Professor

CBA research group(s):

Computational Biology and Population Genomics

Personal webpage

Team webpage

Octávio Paulo

Main Research Interests

My main research interests are inthe study of current genetic patterns at the intraspecific level and the mechanism that generated and maintained that patterns. Secondly the study of the adaptive genetic process of populations and the consequent recommendations for conservation of the genetic variability and adaptability.


Academic Qualifications

- 2001 PhD in Ecology (Queen Mary and Westfield College, University of London)

- 1988 5-year college graduation in Biology (Faculty of Sciences, University of Lisbon)

Recent Publications

Modesto I.S.,  Miguel C., Pina-Martins F.,  Glushkova M.,  Veloso M., Paulo O.P. & Batista D. 2014. Identifying signatures of natural selection in cork oak (Quercus suber L.) genes through SNP analysis. Tree Genetics & Genomes. (in press)

Pereira-Leal J.B., Abreu I.A., Alabaça C.S., Almeida M.H., Almeida P., Almeida T., Amroim M.I., araújo S., Azevedo H., Badia A., Batista D., Bohn A., Capote T., Carrasquinho I., Chaves I., Coelho A.C., Ribeiro Costa M.M., Costa R., Cravador A., Egas C., Faro C., Fortes A.M., Fortunato A.S., Gaspar M.J., Gonçalves S., Graça J., Horta H., Inácio V., Leitão J.M., Lino-Neto T., Marum L., Matos J., Mendonça D., Miguel A., Miguel C.M., Morais-Cecílio L., Neves I., Nóbrega F., Oliveira M.M., Oliveira R., Pais M.S., Paiva J.A., Paulo O.S., Pinheiro M., Raimundo J.A.P., Ramalho J.C., Ribeiro A.I., Ribeiro T., Rocheta M., Rodrigues A.I., Rodrigues J.C., Saibo N.J.M., Santo T.E., Santos A.M., Sá-Pereira P., Sebastiana M., Simões F., Sobral R.S., Tavares R., Teixeira R., Varela C., Veloso M.M. & Ricardo C.P.P. 2014. A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing. BMC Genomics 15:371.

Rodrigues A.S.B., Silva S.E., Marabuto E., Silva D.N., Wilson M.R., Thompson V., Yurtsever S., Halkka A., Borges P.A.V, Quartau J.A., Paulo O.S. & Seabra S.G. 2014. New mitochondrial and nuclear evidences support recent demographic expansion and an atypical phylogeographic pattern in the spittlebug Philaenus spumarius (Hemiptera, Aphrophoridae). PLoS One 9(6):e98375.

Sebastiana M., Vieira B., Lino-Neto T., Monteiro F., Figueiredo A., Sousa L., Pais M.S., Tavares R. & Paulo O. 2014. Oak Root Response to Ectomycorrhizal Symbiosis Establishment: RNA-Seq Derived Transcript Identification and Expression Profiling. PLoS ONE 9(5):e98376.

Dourado C.G., Duarte M.A., Grosso A.R., Bastos-Silveira C., Marrero P., Oliveira P., Paulo O.S. & Dias D. 2014. Phylogenetic origin of the endemic pigeons from Madeira (Columba trocaz) and Azores Islands (Columba palumbus azorica). Journal of Ornithology 155:71-82.

Nunes V.L., Mendes R., Marabuto E., Novais B.M., Hertach T., Quartau J.A., Seabra S.G., Paulo O.S. & Simões P.C. 2014. Conflicting patterns of DNA barcoding and taxonomy in the cicada genus Tettigettalna from southern Europe (Hemiptera: Cicadidae). Molecular Ecology Resources 14(1):27-38.

Talhinhas P., Azinheira H.G., Vieira B., Loureiro A., Tavares S., Batista D., Morin E., Petitot A.S., Paulo O.S., Poulain J., Da Silva C., Duplessis S., Silva M.D. & Fernandez D. 2014. Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix with an emphasis on early stages of infection. Frontiers in Plant Science 5(88):1-17.

Bradnam K. R., Fass J. N., Alexandrov A., Baranay P., Bechner M., Birol I., Boisvert S., Chapman J.A., Chapuis G., Chikhi R., Chitsaz H., Chou W.C., Corbeil J., Del Fabbro C., Docking T.R., Durbin R., Earl D., Emrich S., Fedotov P., Fonseca N.A., Ganapathy G., Gibbs R.A., Gnerre S., Godzaridis E., Goldstein S., Haimel M., Hall G., Haussler D., Hiatt J.B., Ho I. Y., Howard J., Hunt M., Jackman S.D., Jaffe D.B., Jarvis E.D., Jiang H., Kazakov S., Kersey P.J., Kitzman J.O., Knight J.R., Koren S., Lam T.W., Lavenier D., Laviolette F., Li Y., Li Z., Liu B., Liu Y., Luo R., Maccallum I., Macmanes M. D., Maillet N., Melnikov S., Naquin D., Ning Z., Otto T. D., Paten B., Paulo O.S., Phillippy A.M., Pina-Martins F., Place M., Przybylski D., Qin X., Qu C., Ribeiro F.J., Richards S., Rokhsar D.S., Ruby J.G., Scalabrin S., Schatz M. C., Schwartz D. C., Sergushichev A., Sharpe T., Shaw T.I., Shendure J., Shi Y., Simpson J.T., Song H., Tsarev F., Vezzi F., Vicedomini R., Vieira B. M., Wang J., Worley K.C., Yin S., Yiu S.M., Yuan J., Zhang G., Zhang H., Zhou S. & Korf I.F. 2013. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience 2(1):10.

Martins R.F., Zina V., da Silva E.B., Rebelo M.T., Figueiredo E., Mendel Z., Paulo O.S., Franco J.C. & Seabra S.G. 2012. Isolation and characterization of fifteen polymorphic microsatellite loci for the citrus mealybug, Planococcus citri (Hemiptera: Pseudococcidae), and cross-amplification in two other mealybug species. Journal of Genetics 91(2):e75-8.

Miraldo A., Hewitt G.M., Dear P.H., Paulo O.S. & Emerson B.C. 2012. Numts help to reconstruct the demographic history of the ocellated lizard (Lacerta lepida) in a secondary contact zone. Molecular Ecology 21:1005-1018.

Nunes V.L., Beaumont M.A., Butlin R.K. & Paulo O.S. 2012. Challenges and pitfalls in the characterization of anonymous outlier AFLP markers in non-model species: lessons from an ocellated lizard genome scan. Heredity 109(6):340-348.

Silva D.N., Talhinhas P., Cai L., Luzolo M., Guichuru E.K., Loureiro A., Várzea V., Paulo O.S. & Batista D. 2012. Host-jump drives rapid and contemporary ecological speciation of the emergent fungal pathogen Colletotrichum kahawae. Molecular Ecology 21(11):2655-2670.

Silva D.N., Talhinhas P., Várzea V., Cai L., Paulo O.S. & Batista D. 2012. Application of the Apn2/MAT locus to improve the systematics of the Colletotrichum gloeosporioides complex: An example from coffee (Coffea spp.) hosts. Mycologia 104(2):396-409.

Vieira A., Talhinhas P., Loureiro A., Thürich J., Duplessis S., Fernandez D., Silva M.C., Paulo O.S. & Azinheira H.G. 2012. Expression profiling of genes involved in the biotrophic colonisation of Coffea arabica leaves by Hemileia vastatrix. European Journal of Plant Pathology 133(1):261-277.

Costa J., Miguel C., Almeida H., Oliveira M., Matos J., Simoes F., Veloso M., Ricardo P., Paulo O.S. & Batista D. 2011. Genetic divergence in Cork Oak based on cpDNA sequence data. BMC Proceedings 5(Suppl 7):13.

Miraldo A., Hewitt G.M., Paulo O.S. & Emerson B.C. 2011. Phylogeography and demographic history of Lacerta lepida in the Iberian Peninsula: multiple refugia, range expansions and secondary contact zones. BMC Evolutionary Biology 11:170.

Nunes V.L., Beaumont M.A., Butlin R.K. & Paulo O.S. 2011. Multiple approaches to detect outliers in a genome scan for selection in ocellated lizards (Lacerta lepida) along an environmental gradient. Molecular Ecology 20(2):193-205.

Nunes V.L., Miraldo A., Beaumont M.A., Butlin R.K. & Paulo O.S. 2011. Association of Mc1r variants with ecologically relevant phenotypes in the European ocellated lizard, Lacerta lepida. Journal of Evolutionary Biology 24(10):2289-2298.

Romeiras M., Paulo O.S., Duarte M.C., Pina-Martins F., Cotrim H.C., Carine M. & Pais M.S. 2011. Origin and diversification of the genus Echium (Boraginaceae) in the Cape Verde archipelago. Taxon 60(5):1375-1385.

Vieira A., Talhinhas P, Loureiro A., Duplessis S., Fernandez D., Silva M.D., Paulo O.S. & Azinheira H.G. 2011. Validation of RT-qPCR reference genes for in planta expression studies in Hemileia vastatrix, the causal agent of coffee leaf rust. Fungal Biology 115(9):891-901.

Pereira C.M., Rosado J., Seabra S.G., Pina-Martins F., Paulo O.S. & Fonseca P.J. 2010. Conus pennaceus: a phylogenetic analysis of the Mozambican molluscan complex. African Journal of Marine Science 32(3):591–599.

Seabra S.G., Pina-Martins F., Marabuto E., Yurtsever S., Halkka O., Quartau J.A. & Paulo O.S. 2010. Molecular phylogeny and DNA barcoding in the meadow-spittlebug Philaenus spumarius (Hemiptera, Cercopidae) and its related species. Molecular Phylogenetics and Evolution 56(1):462-467.

Batista D., Nunes V.L., Gomes-Laranjo J., Paulo O.S. & Costa R. 2009. Segregation of SSR and AFLP Loci in Chestnut F-1 Hybrids (Castanea sativa x C. crenata/C. mollissima). Iv International Chestnut Symposium 844:249-255.

Fonseca M.M., Brito J.C., Paulo O.S., Carretero M.A. & Harris D.J. 2009. Systematic and phylogeographical assessment of the Acanthodactylus erythrurus group (Reptilia: Lacertidae) based on phylogenetic analyses of mitochondrial and nuclear DNA. Molecular Phylogenetics and Evolution 51:131-142.

Batista D., Valdiviesso T., Santos L., Costa R., Paulo O.S. & Gomes-Laranjo J. 2008. Genotyping Castanea sativa x C. crenata and C-sativa x C-mollissima F1 hybrids using nuclear SSRs. Proceedings of the Second Iberian Congress on Chestnut. C. G. P. F. P. G. J. Abreu:107-112.

Fonseca P.J., Serrão E.A., Pina-Martins F., Silva P., Mira S., Quartau J.A., Paulo O.S. & Cancela L. 2008. The evolution of cicada songs contrasted with the relationships inferred from mitochondrial DNA (Insecta, Hemiptera). Bioacoustics 18(1):17-34.

Paulo O.S., Pinheiro J., Miraldo A., Bruford M.W., Jordan W.C. & Nichols R.A. 2008. The role of vicariance vs. dispersal in shaping genetic patterns in ocellated lizard species in the western Mediterranean. Molecular Ecology 17(6):1535-1551.

Pina-Martins F. & Paulo O.S. 2008. Concatenator: Sequence data matrices handling made easy. Molecular Ecology Resources (Formerly Molecular Ecology Notes) 8:1254-1255.

Moreira P.L., Nunes V.L., Martín J. & Paulo O.S. 2007. Copulatory plugs do not assure high first male fertilisation success: sperm displacement in a lizard. Behavioral Ecology and Sociobiology 62:281-288.

Miraldo A., Pinto I., Pinheiro J., Rosario I., Maymone M. & Paulo O.S. 2005. Distribution and conservation of the common chameleon, Chamaeleo chamaeleon, in Algarve, southern Portugal. Israel Journal of Zoology 51(2):157-164.

Ongoing Projects

  • Cork oak ESTs Consortium - Polymorphism detection and validation (SOBREIRO/0036/2009)
  • Adaptive significance and genetic basis of a balanced colour-polymorphism (PTDC/BIA-BEC/098783/2008)
  • Assessment of the adaptive genetic variation of natural populations (PTDC/AGR-AAM/104966/2008)
  • Has tiger-fly a rolei n biological control of protected crops? (PTDC/AGR-AAM/099723/2008)


Other Information

Member of the following Scientific organizations: European Society for Evolutionary Biology; Society of Molecular Biology and Evolution; British Genetic Society; Sociedade Espanhola de Herpetologia.