Faria R, Perdomo-Sabogal A, Overduin B, Bleidorn C, Santana CI, Langenberger D, Triant D, Dall’Olio G, Indrischek H, Aerts J, Engelhardt J, Engelken J, Liebal K, Fasold M, Robb S, Grath S, Kolora SR, Carvallho T, Salzburger W, Jovanovic V, Nowick K. Ten Simple Rules for Running an Extended Introductory Bioinformatics Training Course.

Sabatino SJ, Faria R, Alexandrino P. Genetic structure and diversity in Alosa alosa and A. fallax: Implications for conservation.



Jackson B, Butlin R, Navarro A, Faria R (2016). The role of chromosomal rearrangements in speciation.



Carvalho J, Sotelo G, Galindo J, Faria R (2016). Genetic characterization of flat periwinkles (Littorinidae) from the Iberian Peninsula reveals interspecific hybridization and different degrees of differentiation. doi: 10.1111/bij.12762.

Kolora SR, Faria R, Weigert A, Nowick K, Schaffer S, Grimm A, Henle K, Sahyon A, Stadler P, Bleidorn C, Schlegel M (2015). The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. viridis. Mitochondrial DNA 28, 1-3.

Carvalho J, Pereira C, Sotelo G, Costa D, Galindo J, Faria R (2015) De novo isolation of 17 microsatellite loci for flat periwinkles (Littorina fabalis and L. obtusata) and their application for species discrimination and hybridization studies. Journal of Molluscan Studies 81 (3), 421-425.

Sotelo G, Andree KB, López MA, Alexandrino P, Gisbert E, Faria R (2014) The puzzling demographic history and genetic differentiation of the twaite shad (Alosa fallax) in the Ebro River. Conservation Genetics 15, 1037-1052.

Navarro A, Faria R (2014) Pool and conquer: new tricks for (c)old problems. Molecular Ecology, 23, 1653-1655.

Faria R, Renaut S, Galindo J, Pinho C, Melo-Ferreira J, Melo M, Jones F, Salzburger W, Schluter D, Butlin R (2014) Advances in Ecological Speciation: an integrative approach. Molecular Ecology, 23, 513-521.

Nowick K, Carneiro M, Faria R (2013) A prominent role of KRAB-ZNF transcription factors in mammalian speciation? Trends in Genetics, 29: 130-139.

Faria R, Weiss S, Alexandrino P (2012) Comparative phylogeography and demographic history of European shads (Alosa alosa and A. fallax) inferred from mitochondrial DNA. BMC Evolutionary Biology, 12:194. doi:10.1186/1471-2148-12-194

Elias M, Faria R, Gompert Z, Hendry A (2012) Factors influencing progress toward ecological speciation. International Journal of ecology. doi:10.1155/2012/235010

Faria R, Pinheiro A, Gabaldon T, Weiss S, Alexandrino P (2011) Molecular tools for species discrimination and detection of hybridization between two closely related Clupeid fishes Alosa alosa and A. fallax. Journal of applied Ichthyology, 27(s3), 16-20.

Saura M, Faria R (2011) Genetic tools for restoration of fish populations. Journal of applied Ichthyology. Journal of applied Ichthyology, 27(s3), 5-15.

Andree KB,  Lopéz MA, Alexandrino P, Faria R, Gisbert E (2011) A preliminary genetic analysis of a recently rediscovered population of the Twaite shad (Alosa fallax) in the Ebro river, Spain (Western Mediterranean). Journal of applied Ichthyology, 27(s3), 21-23.

Faria R, Neto, S, Noor, MAF, Navarro, A (2011) Role of Natural Selection in Chromosomal Speciation. Encyclopedia Life Sciences. In: eLS 2011, John Wiley & Sons, Ltd:Chichester. [DOI: 10.1002/9780470015902.a0022850]

The Orang-utan Genome Consortium (Including R. Faria) (2011) Comparative and demographic analysis of orang-utan genomes. Nature, 469, 529-533.

Marigorta U, Lao O, Casals F, Calafell F, Morcillo-Suárez C, Faria R, Bosch E, Serra F, Dopazo H, Bertranpetit J, Navarro A (2011) Recent human evolution has shaped geographical differences in susceptibility to disease. BMC Genomics, 12, 55.

Faria R, Navarro A (2010) “Chromosomal speciation” revisited: rearranging theory with pieces of evidence. Trends in Ecology and Evolution, 25, 660-669.

Faria R, & Navarro A (2009) On the role of natural selection in chromosomal speciation. In: Hernani Dopazo and Arcadi Navarro. Evolución y Adaptación.150 años después del Origen de las Especies. Sociedad Española de Biología Evolutiva. 123-132. (book chapter, peer-reviewed).

Faria R, Weiss S, Alexandrino P (2006) A molecular phylogenetic perspective on the evolutionary history of Alosa spp. (Clupeidae). Molecular Phylogenetics and Evolution, 40, 298-304.

Alexandrino P, Faria R, Linhares D, Castro F, Le Corre M, Sabatié R, Baglinière JL, Weiss S (2006) Interspecific differentiation and intraspecific substructure in two closely related clupeids with extensive hybridization, Alosa alosa and A. fallax. Journal of Fish Biology, 69, 242-259.

Santos NP, Fontaínhas-Fernandes A, Faria R, Torres-Castro L-F, Cortes R,  Alexandrino P (2006) Genetic introgression between wild and stocked brown trout (Salmo trutta) in the Northern of Portugal, Folia Zoologica, 55, 433-443.

Correia AT, Faria R, Alexandrino P, Antunes C, Isidro EJ,  Coimbra J (2006) Evidence for genetic differentiation in the European conger eel Conger conger based on mitochondrial DNA analysis. Fisheries Science, 72, 20-27.

Antunes A, Faria R, Johnson WE, Guyomard R, Alexandrino P (2006) Life on the Edge: The Long-Term Persistence and Contrasting Spatial Genetic Structure of Distinct Brown Trout Life Histories at Their Ecological Limits. Journal of Heredity, 97, 193-205.

Faria R, Wallner B, Weiss S, Alexandrino, P (2004) Isolation and characterization of eight dinucleotide microsatellite loci from two closely related clupeid species (Alosa alosa and A. fallax). Molecular Ecology Notes, 4, 586-588.

Antunes A, Faria R, Weiss S, Alexandrino, P (2001) Complex evolutionary history in the brown trout: insights on the recognition of conservation units. Conservation Genetics, 2, 337-347.


2007  Faria, R. “Study of evolutionary processes and phylogeography in European species of the genus Alosa based on molecular markers”. PhD dissertation (University of Porto, Portugal).

2002  Faria, R. “Genetic diversity in Portuguese populations of trout Salmo trutta, L., based on allozymes and microsatellites: comparative analysis of genetic diversity and population substructure”. Graduation thesis (University of Porto, Portugal).


Marianne Elias, Rui Faria, Zachariah Gompert, and Andrew Hendry (2012). Ecological Speciation. International Journal of ecology. Hindawi Publishing Corporation. (Guest co-editor of a special issue in ecological speciation –

Other publications

Afonso D, Faria R. Darwinismo social. In Campos R (ed.). Um livro sobre evolução. CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos. Porto, Portugal. Pp 115-118. (Portuguese and Spanish edition– for general public)

Santos NP, Faria R, Carrola J, Castro L, Cortes R, Alexandrino P (2002) Avaliação Genética da Eficácia de Repovoamentos com Truta (Salmo trutta)- Resultados Preliminares. Proceedings of the XII Congresso de Zootecnia- Universidade de Trás dos Montes e Alto Douro (UTAD), Vila Real, Novembro de 2002. (in portuguese)