2024

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Peñalba, J. V., Runemark, A., Meier, J. I., Singh, P., Woogan, G. O. U., Sánchez-Guillén, R., Mallet, J., Rometsch, S. J., Menon, M., Seehausen, O., Kulmuni, J., Pereira, R. J.#* 2024 The Role of Hybridization in Species Formation and Persistence. Cold Spring Harbor Perspectives in Speciation. https://cshperspectives.cshlp.org/cgi/collection/speciation

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Coelho, J. F. R., Mendes, L. D. F., Di Dario, F., Carvalho, P. H., Dias, R. M., Lima, S. M. Q., ... & Pereira, R. J. (2024). Integration of genomic and ecological methods inform management of an undescribed, yet highly exploited, sardine species. Proceedings of the Royal Society B, 291(2018), 20232746.

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2023​​

Bein, B., Lima, F. D., Lazzarotto, H., Rocha, L. A., Leite, T. S., Lima, S. M. Q., Pereira, R. J.#* Population genomics of an Octopus species identify oceanographic barriers and inbreeding patterns. Mar. Biol. 170, 161 (2023). https://doi.org/10.1007/s00227-023-04307-z

Verba, J. T., Stow, A., Bein, B., Pennino, M. G., Lopes, P. F. M., Ferreira, B. P., Mortier, M., Lima, S. M. Q., & Pereira, R. J.# 2023. Low population genetic structure is consistent with high habitat connectivity in a commercially important fish species (Lutjanus jocu). Marine Biology, 170(1), 5. https://doi.org/10.1007/s00227-022-04149-1​​​​​​

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2022

Borges, R., Boussau, B., Höhna, S., Pereira, R. J., & Kosiol, C. 2022. Polymorphism-aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13980

Rollins, R. E., Sato, K., Nakao, M., Tawfeeq, M. T., Herrera-Mesías, F., Pereira, R. J., Kovalev, S., Margos, G., Fingerle, V., Kawabata, H., & Becker, N. S. 2022. Out of Asia? Expansion of Eurasian Lyme borreliosis causing genospecies display unique evolutionary trajectories. Molecular Ecology. https://doi.org/10.1111/mec.16805

Hawlitschek, O., E. M. Ortiz, S. Noori, K. C. Webster, M. Husemann, R. J. Pereira#. 2022. Transcriptomic data reveals nuclear-mitochondrial discordance in Gomphocerinae grasshoppers (Insecta: Orthoptera: Acrididae). Molecular Phylogenetics and Evolution. doi: 10.1016/j.ympev.2022.107439

Hagberg, L., E. Celemín, I. Irisarri, O. Hawlitschek, J. L. Bella, T. Mott, and R. J. Pereira#*. 2022. Extensive introgression at late stages of species formation: Insights from grasshopper hybrid zones. Molecular Ecology; doi: https://doi.org/10.1111/mec.16406

Pereira, R. J.*, and S. Singhal. 2022. A lizard with two tales: What diversification within Sceloporus occidentalis teaches us about species formation. Molecular Ecology 31, 407– 410. https://doi.org/10.1111/mec.16321​​​​​

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2021

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 127, 323–333 (2021). https://doi.org/10.1038/s41437-021-00455-4

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. 30: 6403– 6416. https://doi.org/10.1111/mec.15985

Pereira, R. J.*, 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. J Zool Syst Evol Res. 2021; 59: 635– 645. https://doi.org/10.1111/jzs.12446

Antunes, B., 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. 126, 776–789. https://doi.org/10.1038/s41437-021-00405-0​​​

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2020

Nolen, Z. J., 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. Mol Ecol. 29: 4985– 5002. https://doi.org/10.1111/mec.15695

Neves, J. M. M., 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. J Zool Syst Evol Res. 59: 163– 178. https://doi.org/10.1111/jzs.12421

Neves, J. M. M., 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. doi: https://doi.org/10.1080/14772000.2020.1729892

Almeida, J. P. F. A., 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. DOI: https://doi.org/10.1080/14772000.2020.1783716

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2017

Pereira, R. J.*, 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. https://doi.org/10.1098/rspb.2017.0236​​​​​

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2016

Neves, J. M. M., 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: https://doi.org/10.1371/journal.pone.0157472

da Fonseca, R. R., 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: https://doi.org/10.1016/j.margen.2016.04.012

Pereira, R. J., 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. https://doi.org/10.1111/mec.13575

Pereira, R. J.*, 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.  https://doi.org/10.1111/mec.13579. Highlighted by a “Perspectives” article in Molecular Ecology

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2015

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

Barreto, F. S., R. J. Pereira, R. S. Burton. 2015. Hybrid dysfunction and physiological compensation in gene expression. Molecular Biology and Evolution 32 (3): 613-622. https://doi.org/10.1093/molbev/msu321

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2014

Carneiro, M., 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. https://doi.org/10.1371/journal.pgen.1003519

Tarroso, P., 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. https://doi.org/10.1111/mec.12671

Pereira, R. J.*, 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. https://doi.org/10.1111/evo.12254​

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2013

Burton, R. S., R. J. Pereira, and F. S. Barreto. 2013. Cytonuclear Genomic Interactions and Hybrid Breakdown. Annual Review of Ecology, Evolution, and Systematics 44: 281-302. https://doi.org/10.1146/annurev-ecolsys-110512-135758

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2012

Monahan, W. B., 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; https://doi.org/10.1186/1741-7007-10-20. Highlighted by a “Commentary” article in BMC Biology

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2011

Pereira, R. J.*, 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: https://doi.org/10.1186/1471-2148-11-194.

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2009

Goncalves, H., 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. doi: https://doi.org/10.1111/j.1365-294X.2009.04426.x

Pereira, R. J.*, and D. B. Wake. 2009. Genetic leakage after adaptive and non-adaptive divergence in the Ensatina eschscholtzii ring species. Evolution 63: 2288-2301. https://doi.org/10.1111/j.1558-5646.2009.00722.x. Rated “Exceptional” in Faculty of 1000 Biology

Devitt, T. J., 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. https://doi.org/10.1111/j.1755-0998.2009.02518.x

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2005

Gonçalves, H., 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 5: 767-769. doi: https://doi.org/10.1111/j.1471-8286.2005.01057.x

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2004

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