PUBLICATIONS
(peer-reviewed)
2024
Submitted
• João P. Marques, Paulo C. Alves, Isabel R. Amorim, Ricardo J. Lopes, Mónica Moura, Eugene W. Myers, Manuela Sim-Sim, Carla Sousa Santos et (al including Rui Faria). Building a Portuguese Coalition for Biodiversity Genomics. (submitted)
• Anja M Westram, Hernán E. Morales, Kerstin Johannesson, Roger Butlin, Rui Faria. Understanding the adaptive role of chromosomal inversions across large geographical scales: The potential of pool-seq data. (submitted)
• Diego Garcia Castillo, Nick Barton, Rui Faria, Jenny Larsson, Sean Stankowski, Roger Butlin, Kerstin Johannesson. Anja Marie Westram. Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails (submitted)
Accepted
• Roger K. Butlin, Rui Faria. Local adaptation and reproductive isolation: when does speciation start? Evolutionary Journal of the Linnean Society (in press)
• Aurélien De Jode, Rui Faria, Giulio Formenti, Ying Sims, Timothy P. Smith, Alan Tracey, Jonathan M. D. Wood, Zuzanna B. Zagrodzka, Kerstin Johannesson, Roger K. Butlin, Erica H Leder. Chromosome-scale genome assembly of the rough periwinkle Littorina saxitilis. Genome Biology and Evolution (in press)
• Alan Le Moan, Sean Stankowski, Marina Rafajlovic, Olga Ortega-Martinez, Rui Faria, Roger K Butlin, Kerstin Johannesson. Coupling of twelve chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes. Evolution Letters (in press)
• Pierre Barry, Alfonso Balmori-de la Puente, Isabel Monral, Rui Faria#. Evolutionary processes in marine environments. eLS (in press)
• Andrade P, Alves JM, Pereira P, Rubin Carl-Johan, Silva E, Grace-Sprehn C, Enbody E, Afonso S, Faria R, Zhang Y, Duckwortn JA, Garreau H, Letnic M, Strive T, Thulin C-G, Queney G, Villafuerte R, Jiggins FM, Ferrand N, Andersson L, Carneiro M. Selection against domestication alleles in introduced rabbit populations. Nature Ecology and Evolution (in press)
Published
• Johannesson K , Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S (2024) Diverse pathways to speciation revealed by marine snails. Trends in Genetics. DOI: https://doi.org/10.1016/j.tig.2024.01.002
• da Fonseca RR, Campos PF, Rey-Iglesia A, Barroso GV, Bergeron LA, Nande M, Tuya F, Abidli S, Pérez M, Riveiro I, Carrera P, Jurado-Ruzafa A, Santamaria MTG, Faria R, Machado AM, Fonseca MM, Froufe E, Castro LFC (2024) Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia. Genes, 15(2), 170.
2023
• Reeve J, Butlin R, Koch E, Stankowski S, Faria R (2023). Locating chromosomal inversions across species ranges of the rough periwinkles (Littorina saxatilis and L. arcana)'. Molecular Ecology, https://onlinelibrary.wiley.com/doi/full/10.1111/mec.17160.
• Berdan E, Barton N, Butlin RK, Charlesworth B, Faria R, Fragata I, Gilbert K, Jay P, Kapun M, Lotterhos K, Mérot C, Durmaz E, Pascual M, Peichel C, Rafajlović M, Westram AM, Schaeffer S, Johannesson K, Flatt T (2023). How chromosomal inversions reorient the evolutionary process. Journal of Evolutionary Biology 36, 1761-1782.
• Carvalho C, Morales HE, Faria R, Butlin RK, Sousa VC (2023). Integrating Pool-seq uncertainties into demographic inference. Molecular Ecology Resources 23 (7), 1737-1755.
• Carvalho J, Faria R, Butlin RK, Sousa VC (2023). PoolHelper: An R package to help in designing Pool-Seq studies. Methods in Ecology and Evolution 14 (9), 2189-2510.
• Sean Stankowski, Zuzanna B Zagrodzka, Juan Galindo, Mauricio Montaño-Rendón, Rui Faria, Natalia Mikhailova, April M H Blakeslee, Einar Arnason, Thomas Broquet, Hernán E Morales, John W Grahame, Anja M Westram, Kerstin Johannesson, Roger K Butlin (2023). Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society 2(1), kzad002.
• Berdan EL, Aubier TG, Cozzolino S, Faria R, Feder JL, Giménez MD, Joron M, Searle JB, Mérot C (2023). Structural Variants and Speciation: Multiple Processes at Play. Cold Spring Harbor Perspectives in Biology.
https://cshperspectives.cshlp.org/content/early/2023/12/05/cshperspect.a041446.abstract
• Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R# (2023). The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution. Cold Spring Harbor Perspectives in Biology. https://cshperspectives.cshlp.org/content/early/2023/08/21/cshperspect.a041447.full.pdf+html
• Theissinger K, Fernandes C, Formenti G, et al (including Rui Faria as part of The European Reference Genome Atlas Consortium) (2023). How genomics can help biodiversity conservation. Trends in Genetics, 39, 545-559.
• Le Moan A, Panova M, De Jode A, Ortega-Martinez O, Duvetorp M, Faria R, Butlin R, Johannesson K (2023) An allozyme polymorphism is associated with a large chromosomal inversion in the marine snail Littorina fabalis. Evolutionary Applications, 16, 542-559.
2022
• Hearn KE, Koch EL, Stankowski S, Butlin RK1, Faria R1, Johannesson K1, Westram AM1 (2022). Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters 6, 358-374. https://doi.org/10.1002/evl3.295
• Anja M. Westram, Rui Faria, Kerstin Johannesson, Roger Butlin, Nick Barton (2022). Inversions and parallel evolution. Phil. Trans. R. Soc. B 377: 20210203. https://doi.org/10.1098/rstb.2021.0203
• Aurélien De Jode, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja Marie Westram, Roger K. Butlin, Marina Rafajlović, Christelle Fraïsse (2022) Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. https://doi.org/10.1111/eva.13428.
• Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Claudio Ciofi, Angelica Crottini, José A. Godoy, Jacob Höglund, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsbøll, Christophe Pampoulie, María J. Ruiz-López, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Camila J. Mazzoni, Erich D. Jarvis, Miklós Bálint and The European Reference Genome Atlas (ERGA) Consortium (including Faria R). The era of reference genomes in conservation genomics. Trends in Ecology and Evolution 37, 197-202. https://doi.org/10.1016/j.tree.2021.11.008
• Sabatino S, Faria R, Alexandrino P (2021) Genetic structure, diversity, and connectivity in anadromous and freshwater Alosa alosa and A. fallax. Marine Biology 169, 2. https://doi.org/10.1007/s00227-021-03970-4
2021
• Kolora R, Gysi D, Schaffer S, Grimm-Seyfarth A, Szabolcs M, Faria R, Henle K, Stadler PF, Schlegel M, Nowick N (2021) Accelerated evolution of tissue-specific genes mediates divergence amidst gene flow in European green lizards. Genome Biology and Evolution 13, evab109. https://doi.org/10.1093/gbe/evab109
• E.L. Koch, H. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin (2021) Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters 5, 96-213.
https://doi.org/10.1002/evl3.227
• M. Rafajlović, J. Rambla, J. Feder, A. Navarro, R. Faria (2021) Assessing the role of inversions in maintaining genomic differentiation after secondary contact: local adaptation, genetic incompatibilities, and drift. Evolution 75, 1288-1303. https://doi.org/10.1111/evo.14223
• Westram AM, Faria R, Butlin RK, Johannesson K (2021) Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Molecular Ecology 30, 3797-3814.
• Faria R#, Johannesson, J, Stankowski S (2021) Speciation in marine environments: diving under the surface. Journal of Evolutionary Biology 4-15.
Special issue edited by Rui Faria, Kerstin Johannesson, and Sean Stankowski (2021)
on Speciation in Marine Environments for the Journal of Evolutionary Biology.
Journal Cover
• Galindo J, Carvalho J, Sotelo G, Duvetorp M, Costa D, Kemppainen K, Panova M, Kaliontzopoulou A, Johannesson K, Faria R#. (2021) Genetic and morphological divergence between Littorina fabalis ecotypes in Northern Europe. Journal of Evolutionary Biology 34, 97-113.
2020
• Estévez D, Kozminsky E, Carvajal-Rodríguez A. Caballero A, Faria R, Galindo J & Rolán-Alvarez E. (2020) Frequency-dependent sexual selection contributes to the maintenance of shell colour polymorphism in a marine snail by means of mate choice. Frontiers in Marine Science 7:614237. doi: 10.3389/fmars.2020.614237
• Westram AM, Faria R, Butlin R, Johannesson J. (2020) Inversions and evolution. In: Encyclopedia Life Sciences - eLS, John Wiley & Sons, Ltd: Chichester. https://doi.org/10.1002/9780470015902.a0029007
• Marques JP, Sotelo G, Galindo J, Chaube P, Costa D, Afonso S, Panova M, Nowick K, Butlin R, Hollander J, Faria R#. (2020) Transcriptomic resources for evolutionary studies in flat periwinkles and related species. Scientific Data 7. https://doi.org/10.1038/s41597-020-0408-8
• Moutinho AF, Serén N, Paupério J, Silva TL, Martínez-Freiría F, Sotelo G, Faria R, Mappes T, Alves PC, Brito JC, Boratyński Z. (2020) Evolutionary history of two cryptic species of Northern African jerboas. BMC Evolutionary Biology 20, https://doi.org/10.1186/s12862-020-1592-z
• Costa D, Sotelo G, Kaliontzopoulou A, Carvalho J, Butlin Roger, Hollander J, Faria R# (2020) Hybridization patterns between two marine snails, Littorina fabalis and L. obtusata. Ecology and Evolution 10, 1158-1179.
• Sotelo G, Duvetorp M, Costa D, Panova M, Johannesson K, Faria R#. (2020) Phylogeographic history of flat periwinkles, Littorina fabalis and L. obtusata. BMC Evolutionary Biology 30, DOI: 10.1186/s12862-019-1561-6
• Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. (2020) Is embryo abortion an intrinsic postzygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology 33, 342–351. DOI: 10.1111/jeb.13570
2019
• Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin JK. (2019) Genomic architecture of parallel ecological divergence: beyond a single environmental contrast. Science Advances 5, eaav9963
• Faria R, Johannesson K, Butlin R, Westram A. (2019) Evolving inversions. Trends in Ecology and Evolution 34, 239-248
(authors listed alphabetically)
• Faria R#, Chaube P, Morales H, Larsson T, Lemmon AR, Lemmon EM, Rafajlovic M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. (2019) Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology 28, 1375-1393
• Kolora R, Tech M, Weigert A, Saffari A, Kehr S, Costa M, Spröer C, Indrischek H, Chintalapati M, Doose G, Bunk B, Overmann J, Lohse K, Bleidorn C, Henle K, Nowick K, Faria R, Stadler P, Schlegel M. (2019) Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata and implications for speciation. GigaScience 8(2), giy160. doi: 10.1093/gigascience/giy160
2018
• García-Souto D, Alonso S, Costa D, Eirín-López JM, Rolán-Álvarez E, Faria R, Galindo J, Pasantes JJ. (2018) Karyotype characterization of nine periwinkle species (Gastropoda, Littorinidae). Genes 9, 517.
• Westram AM, Rafajlovic M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R (2018) Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evolution Letters 2, 297-309.
• Faria R#, Triant D, Perdomo Sabogal A, Overduin B, Bleidorn C, Santana C, Langenberger D, Dall’Olio G, Indrischek H, Aerts J, et al. (2018) Introducing evolutionary biologists to the analysis of big data: guidelines to organize extended bioinformatics training courses. Evolution: Education and Outreach 11:8.
• Gazda MA, Andrade P, Afonso S, Dilyte J, Archer JP, Lopes RJ, Faria R, Carneiro M (2018) Signatures of Selection on Standing Genetic Variation Underlie Athletic and Navigational Performance in Racing Pigeons. Molecular Biology and Evolution 35, 1176–1189.
Journal Cover
2017
< 2016
2016
• Ravinet M, Faria R, Butlin RK, Galindo J, Bierne N, Rafajlovic M, Noor MAF, Mehlig B, Westram AM. Interpreting the genomic landscape of speciation: finding barriers to gene flow. Journal of Evolutionary Biology 30, 1450– 1477.
Target Review (cover)
• Marques JP, Sotelo G, Larsson T, Johannesson K, Panova M, Faria R# (2017) Comparative mitogenomic analysis of three species of periwinkles: Littorina fabalis, L. obtusata and L. saxatilis. Marine Genomics 32, 41-47.
• Kolora SR, Faria R, Weigert A, Nowick K, Schaffer S, Grimm A, Henle K, Sahyon A, Stadler P, Bleidorn C, Schlegel M (2017). The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. viridis. Mitochondrial DNA 28, 13.
• 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. Biological Journal of the Linnean Society 118, 503-519.
• Pinho C, Faria R (2016). Magadi tilapia ecological specialization: filling the early gap in the speciation continuum. Molecular Ecology 25, 1420-1422. (News and Views)
• Jackson B, Butlin R, Navarro A, Faria R# (2016) Chromosomal Rearrangements and Speciation. pp. 149-158. In: Encyclopedia of Evolutionary Biology (Editors: R. Kliman & D. OrtizBarrientos), Elsevier. (Book chapter)
• 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. doi: 10.1093/mollus/eyv014.
• 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.
• Elias M, Faria R, Gompert Z, Hendry A (2012) Factors influencing progress toward ecological speciation: a special issue. International Journal of Ecology. doi:10.1155/2012/235010.
Special issue edited by Marianne Elias, Rui Faria, Zachariah Gompert, and Andrew Hendry (2012). Ecological Speciation. International Journal of Ecology.
Hindawi Publishing Corporation.
• 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.
• Faria R#, Neto S, Noor MAF, Navarro A (2011) Role of Natural Selection in Chromosomal Speciation. In: Encyclopedia Life Sciences - eLS, John Wiley & Sons, Ltd: Chichester http://www.els.net/ [doi:10.1002/9780470015902.a0022850]. (book/encyclopedia chapter)
• 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.
• The Orang-utan Genome Consortium (Including Faria R) (2011) Comparative and demographic analysis of orang-utan genomes. Nature 469, 529-533.
(Journal Cover)
• 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. Evolución y Adaptación.150 años después del Origen de las Especies (ed. by H. Dopazo and A. Navarro), pp. 123-132. Sociedad Española de Biología Evolutiva (book chapter)
• 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.
• 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.
• 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.
• 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.
# Corresponding author
OTHER PUBLICATIONS
• Afonso D, Faria R (2013) Darwinismo social. In Campos R (ed.). Um livro sobre evolução. CIBIO, Porto, Portugal. Pp 115-118. (Book chapter for the general public, in Portuguese)
• Faria R, Navarro A (2009) On The Role of Natural Selection in Chromosomal Speciation. Evolución y Adaptación.150 años después del Origen de las Especies (ed. by H. Dopazo and A. Navarro), pp. 123-132. Sociedad Española de Biología Evolutiva.
• 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. XII Congresso de Zootecnia – Univ. of Trás dos Montes e Alto Douro (UTAD), Vila Real, Portugal. (Conference proceedings, in Portuguese)