Evolutionary Biology

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Scientific Publications

Neves, J. M. M., Z. J. Nolen, N. N. Fabré, T. Mott, and R. J. Pereira. 2021. Genomic methods reveal independent demographic histories despite strong morphological conservatism in fish species. Heredity 1–11. Springer US.

Pereira, R. J., T. G. Lima, N. T. Pierce-Ward, L. Chao, and R. S. Burton. 2021. Recovery from hybrid breakdown reveals a complex genetic architecture of mitonuclear incompatibilities. Molecular Ecology, doi: 10.1111/mec.15985. John Wiley & Sons, Ltd.

R. J. Pereira, F. J. Ruiz-Ruano, C. J. E. Thomas, M. Pérez-Ruiz, M. Jiménez-Bartolomé, S. Liu, J. de la Torre, J. L. Bella. 2021. Mind the numt: finding informative mitochondrial markers in a giant grasshopper genome. Journal of Zoological Systematics and Evolutionary Research. In press.

B. Antunes, G. Velo-Antón, D. Buckley, R. J. Pereira, I. Martínez-Solano. 2021. Physical and ecological isolation contribute to maintain genetic differentiation between fire salamander subspecies. Heredity. In press.

Z. J. Nolen, B. Yildirim, I. Irisarri, S. Liu, C. Groot Crego, D. B. Amby, F. Mayer, M. T. P. Gilbert, R. J. Pereira. 2020. Historical isolation facilitates species radiation by sexual selection: Insights from Chorthippus grasshoppers. Molecular Ecology. 29:4985–5002.

J. M. M. Neves, A. Perez, N. N. Fabré, R. J. Pereira, T. Mott. 2020. Integrative taxonomy reveals extreme morphological conservatism in sympatric Mugil species from the Tropical Southwestern Atlantic. Journal of Zoological Systematics and Evolutionary Research. 2008:1–16.

J. M. M. Neves, J. P. F. A. Almeida, M. J. Sturaro, N. N. Fabré, R. J. Pereira, T. Mott. 2020. Deep genetic divergence and paraphyly in cryptic species of Mugil fishes (Actinopterygii: Mugilidae). Systematics and Biodiversity 18 (2): 116-128.

J. P. F. A. Almeida, M. T. Thomé, M. J. Sturaro, R. J. Pereira, T. Mott. 2020. The relative role of glacial refugia and longstanding barriers in the diversification of a fossorial squamate. Systematics and Biodiversity 18 (5): 447-463.

R. J. Pereira, M. C. Sasaki, R. S. Burton. 2017. Adaptation to latitudinal temperature gradient within a widespread copepod species: the contribution of genetic divergence and phenotypic plasticity. Proceedings for the Royal Society of London B 280(1768): 1–9.

J. M. M. Neves, S. M. Q. Lima, L. F. Mendes, R. A. Torres, R. J. Pereira, T. Mott. 2016. Population Structure of the Rockpool Blenny Entomacrodus vomerinus Shows Source-Sink Dynamics Among Ecoregions in the Tropical Southwestern Atlantic. PLoS ONE 11(6): e0157472. doi: 10.1371/journal.pone.0157472

R. R. da Fonseca, A. Albrechtsen, G. E. Themudo, J. R. Madrigal, J. A. Sibbesen, L. Maretty, M. L. Zepeda-Mendoza, P. F. Campos, R. Heller, R. J. Pereira. 2016. Next-generation biology: Sequencing and data analysis approaches for non-model organisms. Marine Genomics. doi:10.1016/j.margen.2016.04.012

R. J. Pereira, I. Martínez-Solano, D. Buckley. 2016. Hybridization during altitudinal range shifts: nuclear introgression leads to extensive cyto-nuclear discordance in the fire salamander. Molecular Ecology 25 (7): 1551-1565.

R. J. Pereira, F. S. Barreto, N. T. Pierce, M. Carneiro, R. S. Burton. 2016. Transcriptome-wide patterns of divergence during allopatric evolution. Molecular Ecology 25 (7): 1478-1493.

R. J. Pereira, and D. B. Wake. 2015. Ring species as demonstrations of the continuum of species formation. Molecular Ecology 24: 5312–5314. doi:10.1111/mec.13412

F. S. Barreto, R. J. Pereira, R. S. Burton. 2015. Hybrid dysfunction and physiological compensation in gene expression. Molecular Biology and Evolution 32 (3): 613-622.

M. Carneiro, F. W. Albert, S. Afonso, R. J. Pereira, R. Campos, J. Melo-Ferreira, J. A. Blanco-Aguiar, R. Villafuerte, M. W. Nachman, J. M. Good, and N. Ferrand. 2014. The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit. Plos Genetics 10(8): e1003519.

P. Tarroso, R. J. Pereira, F. Martínez-Freiría, R. Godinho, and J. C. Brito. 2014. Hybridization at an ecotone: ecological and genetic barriers between three Iberian vipers. Molecular Ecology 23: 1108-1123.

R. J. Pereira, F. S. Barreto, R. S. Burton. 2014. Ecological novelty by hybridization: experimental evidence for increased thermal tolerance by transgressive segregation in Tigriopus californicus. Evolution 68: 204-215.

R. S. Burton, R. J. Pereira, and F. S. Barreto. 2013. Cytonuclear Genomic Interactions and Hybrid Breakdown. Annual Review of Ecology, Evolution, and Systematics 44: 281-302.

W. B. Monahan, R. J. Pereira, and D. B. Wake. 2012. Ring distributions leading to species formation: a global topographic analysis of geographic barriers associated with ring species. BMC Biology 10:20; doi:10.1186/1741-7007-10-20.

· Highlighted by a “Commentary” article in BMC Biology

R. J. Pereira, B. W. Monahan, and D. B. Wake. 2011. Predictors for reproductive isolation in a ring species complex following genetic and ecological divergence. BMC Evolutionary Biology 11:194; doi:10.1186/1471-2148-11-194.

H. Goncalves, I. Martinez-Solano, R. J. Pereira, M. Garcia-Paris and N. Ferrand. 2009. High levels of population subdivision in a morphologically conserved Mediterranean toad (Alytes cisternasii) result from recent, multiple refugia: evidence from mtDNA, microsatellites and nuclear genealogies. Molecular Ecology 18: 5143-5160.

R. J. Pereira, and D. B. Wake. 2009. Genetic leakage after adaptive and non-adaptive divergence in the Ensatina eschscholtzii ring species. Evolution 63: 2288-2301.

T. J. Devitt, R. J. Pereira, L. Jakkula, J. Alexandrino, C. Bardeleben, and C. Moritz. 2009. Isolation and characterization of 19 polymorphic microsatellites in the Plethodontid salamander Ensatina eschscholtzii. Molecular Ecology Resources 9: 966-969.

H. Gonçalves, R. J. Pereira, G. Rowe, T. Beebee, N. Ferrand. 2005. Isolation and characterization of two dinucleotide and four tetranucleotide polymorphic microsatellite loci in the Iberian midwife toad Alytes cisternasii. Molecular Ecology Notes 3: 152-154.

R. J. Pereira, and Sara Rocha. 2004. Two-headed larva of Chioglossa lusitanica. The Herpetological Bulletin 87: 29-30.


Outreach Publications

Martinez-Solano, I., D. Buckley and R. J. Pereira. 2009. Darwin, las especies… y su origen: ejemplos actuales de especiación (Darwin, species… and their origen: recent examples of speciation). Quercus 16: 16-23. Published in Spanish.

Pereira, R. J., R. Ribeiro, and S. Rocha. 2005. Guia de Anfíbios e Répteis das Minas do Braçal (Guide of Amphibian and Reptiles from the Braçal mines). Vertigem, Leiria. Published in Portuguese, English and French.


Book chapters

Pereira, R. J. 2014. Convergent evolution. in R. Campos (Ed.), A book on Evolution (pp. 164). Porto, Portugal. Book published in Portuguese and Spanish.

Pereira, R. J. 2014. Evolution of flightless birds. in R. Campos (Ed.), A book on Evolution (pp. 164). Porto, Portugal. Book published in Portuguese and Spanish.