Dr. Ricardo J. Pereira

Profilbild Ricardo Pereira

Junior Research Group Leader

Hybridization and Speciation


+49 (0) 711 / 8936-181
+49 (0) 711 / 8936-100

Research interests

How are species formed and how do they persist in a changing environment? 

Understanding how lineages split through time to result in the biodiversity patterns that we observe today – Darwin’s “mystery of mysteries” – is a longstanding question in evolutionary biology. Likewise, it is unclear how such lineages (species, subspecies, ecotypes, or populations) persist in the face of environmental change. Although these evolutionary processes are hard to infer from well-differentiated species, their action can be directly observed in closely related taxa that remain distinct in nature, despite ongoing hybridization.

Over the past 15 years, I developed an interdisciplinary research program that uses a diversity of natural hybridization systems (e.g. amphibians, reptiles, fishes, cephalopods, insects) combined with novel molecular tools to understand:

  1. how the current patterns of biodiversity resulted from past climate cycles, 
  2. how such diversity persists today, and 
  3. how current patterns of genetic diversity within species might help respond to future environmental change. 




  • 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.#* 2024The Role of Hybridization in Species Formation and Persistence. Cold Spring Harbor Perspectives in Speciation.https://cshperspectives.cshlp.org/cgi/collection/speciation


  • 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


  • 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


  • 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


  • 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:10.1080/14772000.2020.1729892


  • 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


  • 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: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: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


  • Pereira, R. J.*, 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
  • 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


  • 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



  • 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


  • 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:10.1186/1471-2148-11-194.


  • 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: 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
  • 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


  • 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:10.1111/j.1471-8286.2005.01057.


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