Perfil profesional
Publicaciones
Proyectos
Perfil profesional
My main research interests lie in understanding complex diversification processes. For that, I develop new inferential methods using bayesian and and machine learning techniques applied for population genetics, species delimitation, biogeography, phylogenetic and diversification analyses of epidemiological and macroevolutionary datasets.
My specific research topics include: (i) species delimitation, phylogeography and population genetics approaches for species with recent diversification; (ii) machine learning approaches applied to phylogenetic information of epidemiological and macroevolutionary datasets; (iii) development of genomic resources in non-model species; (iv) assessment of climate change impacts on the conservation of endangered species.
Publicaciones
Artículos científicos
Capítulos de libros
Artículos científicos
| # | FECHA | PUBLICACIÓN |
|---|---|---|
| 2026 | Sassi, F.M.C., de Souza, F.H.S., Perez, M.F., Shams, F., Ezaz, T., Deon, G.A., Liehr, T., Xu, L., Cioffi, M.B. (2026). Rapid turnover of sex chromosomes is associated with speciation in Neotropical armored catfish Harttia (Siluriformes, Loricariidae). Biology Direct 21(1):211. Open Access | |
| 2026 | Perez, M.F., Gascuel, O. (2026). PhyloCNN: Improving Tree Representation and Neural Network Architecture for Deep Learning from Trees in Phylodynamics and Diversification Studies. Systematic Biology 75(4):776–795. Open Access |
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| 2021 | Sassi, F.M.C., Perez, M.F., Silva, M.A., Kavalco, K.F., Pasa, R. (2021). Can geometric morphometrics work for species clusterization on the armored catfish Hypostomus (Siluriformes, Loricariidae)?. Biodiversity Journal 12 4):147-153. Open Access | |
| 2011 | Perez, M.F., Téo, M.F., Zappi, D.C., Taylor, N.P., Moraes, E.M. (2011). Isolation, characterization, and cross-species amplification of polymorphic microsatellite markers for Pilosocereus machrisii (Cactaceae). American Journal of Botany 98(8):e204-e206. Open Access | |
| 2012 | Moraes, E.M., Perez, M.F., Téo, M.F., Zappi, D.C., Taylor, N.P., MacHado, M.C. (2012). Cross-species amplification of microsatellites reveals incongruence in the molecular variation and taxonomic limits of the Pilosocereus aurisetus group (Cactaceae). Genetica 140(7-9):277-285. DOI | |
| 2014 | Bonatelli, I.A.S., Perez, M.F., Peterson, A.T., Taylor, N.P., Zappi, D.C., MacHado, M.C., Koch, I., Pires, A.H.C., Moraes, E.M. (2014). Interglacial microrefugia and diversification of a cactus species complex: Phylogeography and palaeodistributional reconstructions for Pilosocereus aurisetus and allies. Molecular Ecology 23(12):3044-3063. DOI | |
| 2015 | Garrick, R.C., Bonatelli, I.A.S., Hyseni, C., Morales, A., Pelletier, T.A., Perez, M.F., Rice, E., Satler, J.D., Symula, R.E., Thomé, M.T.C., Carstens, B.C. (2015). The evolution of phylogeographic data sets. Molecular Ecology 24(6):1164-1171. Open Access | |
| 2015 | Peres, E.A., Sobral-Souza, T., Perez, M.F., Bonatelli, I.A.S., Silva, D.P., Silva, M.J., Solferini, V.N. (2015). Pleistocene niche stability and lineage diversification in the subtropical spider Araneus omnicolor (Araneidae). PLOS ONE 10(4):e0121543. Open Access | |
| 2016 | Perez, M.F., Carstens, B.C., Rodrigues, G.L., Moraes, E.M. (2016). Anonymous nuclear markers reveal taxonomic incongruence and long-term disjunction in a cactus species complex with continental-island distribution in South America. Molecular Phylogenetics and Evolution 95:11-19. Open Access | |
| 2016 | Perez, M.F., Carstens, B.C., Rodrigues, G.L., Moraes, E.M. (2016). Anonymous nuclear markers data supporting species tree phylogeny and divergence time estimates in a cactus species complex in South America. Data in Brief 6:456-460. Open Access | |
| 2016 | Perez, M.F., Bonatelli, I.A.S., Moraes, E.M., Carstens, B.C. (2016). Model-based analysis supports interglacial refugia over long-dispersal events in the diversification of two South American cactus species. Heredity 116(6):550-557. Open Access | |
| 2017 | Franco, F.F., Jojima, C.L., Perez, M.F., Zappi, D.C., Taylor, N.P., Moraes, E.M. (2017). The xeric side of the Brazilian Atlantic Forest: The forces shaping phylogeographic structure of cacti. Ecology and Evolution 7(22):9281-9293. Open Access | |
| 2017 | Miño, C.I., Avelar, L.H.D.S., da Silva, F.M., Perez, M.F., Menezes, L.F., del Lama, S.N. (2017). Genetic differentiation and historical demography of wood stork populations in Brazilian wetlands: Implications for the conservation of the species and associated ecosystems. Aquatic Conservation: Marine and Freshwater Ecosystems 27(6):1313-1324. DOI | |
| 2017 | Khan, G., Godoy, M.O., Franco, F.F., Perez, M.F., Taylor, N.P., Zappi, D.C., MacHado, M.C., Moraes, E.M. (2017). Extreme population subdivision or cryptic speciation in the cactus Pilosocereus jauruensis? A taxonomic challenge posed by a naturally fragmented system. Systematics and Biodiversity 16(2):188-199. DOI | |
| 2018 | Khan, G., Ribeiro, P.M., Bonatelli, I.A.S., Perez, M.F., Franco, F.F., Moraes, E.M. (2018). Weak population structure and no genetic erosion in Pilosocereus aureispinus: A microendemic and threatened cactus species from eastern Brazil. PLOS ONE 13(4):e0195475. Open Access | |
| 2018 | Perez, M.F., Franco, F.F., Bombonato, J.R., Bonatelli, I.A.S., Khan, G., Romeiro-Brito, M., Fegies, A.C., Ribeiro, P.M., Silva, G.A.R., Moraes, E.M. (2018). Assessing population structure in the face of isolation by distance: Are we neglecting the problem?. Diversity and Distributions 24(12):1883-1889. Open Access | |
| 2019 | Cioffi, M.B., Ráb, P., Ezaz, T. et al. (2019). Deciphering the Evolutionary History of Arowana Fishes (Teleostei, Osteoglossiformes, Osteoglossidae): Insight from Comparative Cytogenomics. International Journal of Molecular Sciences 20(17):4296. Open Access | |
| 2019 | Souza, F.H.S., Perez, M.F., Bertollo, L.A.C., Oliveira, E.A., Lavoué, S., Gestich, C.C., Ráb, P., Ezaz, T., Liehr, T., Viana, P.F., Feldberg, E., Cioffi, M.B. (2019). Interspecific Genetic Differences and Historical Demography in South American Arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum). Genes 10(9):693. Open Access | |
| 2019 | Souza, A.S.D., Dias Júnior, E.A., Perez, M.F., Cioffi, M.B., Bertollo, L.A.C., García-Machado, E., Vallinoto, M.N.S., Galetti, P.M., Molina, W.F. (2019). Phylogeography and Historical Demography of Two Sympatric Atlantic Snappers: Lutjanus analis and L. jocu. Frontiers in Marine Science 6:545. Open Access | |
| 2020 | Oliveira, E.A., Perez, M.F., Bertollo, L.A.C., Gestich, C.C., Ráb, P., Ezaz, T., Souza, F.H.S., Viana, P.F., Feldberg, E., Oliveira, E.H.C., Cioffi, M.B. (2020). Historical demography and climate driven distributional changes in a widespread Neotropical freshwater species with high economic importance. Ecography 43(9):1291-1304. Open Access | |
| 2021 | Sassi, F.D.M.C., Perez, M.F., Oliveira, V.C.S., Deon, G.A., de Souza, F.H.S., Ferreira, P.H.N., Oliveira, E.A., Hatanaka, T., Liehr, T., Bertollo, L.A.C., Cioffi, M.B. (2021). High genetic diversity despite conserved karyotype organization in the giant trahiras from genus hoplias (Characiformes, erythrinidae). Genes 12(2):252. Open Access | |
| 2021 | Fegies, A.C., Carmignotto, A.P., Perez, M.F., Guilardi, M.D., Lessinger, A.C. (2021). Molecular Phylogeny of Cryptonanus (Didelphidae: Thylamyini): Evidence for a recent and complex diversification in South American open biomes. Molecular Phylogenetics and Evolution 162:107213. Open Access | |
| 2021 | Sember, A., Nguyen, P., Perez, M.F., Altmanová, M., Ráb, P., Cioffi, M.B. (2021). Multiple sex chromosomes in teleost fishes from a cytogenetic perspective: State of the art and future challenges. Philosophical Transactions of the Royal Society B: Biological Sciences 376(1833):20200098. Open Access | |
| 2020 | Oliveira, E.A., Sassi, F.D.M.C., Perez, M.F., Bertollo, L.A.C., Ráb, P., Ezaz, T., Hatanaka, T., Viana, P.F., Feldberg, E., Oliveira, E.H.C., Cioffi, M.B. (2020). Comparative cytogenetic survey of the giant bonytongue arapaima fish (Osteoglossiformes: Arapaimidae), across different Amazonian and Tocantins/Araguaia River Basins. Neotropical Ichthyology 18(4):e200055. Open Access | |
| 2022 | Perez, M.F., Bonatelli, I.A.S., Romeiro-Brito, M., Franco, F.F., Taylor, N.P. , Zappi, D.C., Moraes, E.M. (2022). Coalescent-based species delimitation meets deep learning: Insights from a highly fragmented cactus system. Molecular Ecology Resources 22(3):1016-1028. DOI |
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| 2022 | Souza, F.H.D., Sassi, F.D.M., Ferreira, P.H., Bertollo, L.A., Ezaz, T., Liehr, T., Perez, M.F., Cioffi, M.B. (2022). Integrating Cytogenetics and Population Genomics: Allopatry and Neo-Sex Chromosomes May Have Shaped the Genetic Divergence in the Erythrinus erythrinus Species Complex (Teleostei, Characiformes). Biology 11(2):315. Open Access | |
| 2022 | Ferreira, P.H., Souza, F.H.D., Moraes, R.L.R., Perez, M.F., Sassi, F.D.M., Viana, P.F., Feldberg, E., Ezaz, T., Liehr, T., Bertollo, L.A., Cioffi, M.B. (2022). The genetic differentiation of Pyrrhulina (Teleostei, Characiformes) species is likely influenced by both geographical distribution and chromosomal rearrangements. Frontiers in Genetics 13:869073.. Open Access | |
| 2023 | Romeiro-Brito, M., Khan, G., Perez, M. F., Zappi, D.C., Taylor, N.P., Olsthoorn G., Franco, F.F., Moraes, E.M. (2023). Revisiting phylogeny, systematics, and biogeography of a Pleistocene radiation. American Journal of Botany 110(3):e16134. Open Access | |
| 2023 | Lauterbur, M.E., Cavassim, M.I.A., Gladstein, A.L. et al. (2023). Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations. eLife 12: RP84874. Open Access | |
| 2024 | Souza, F. H., Perez, M.F., Ferreira, P. H., Bertollo, L. A., Ezaz, T., Charlesworth, D., Cioffi, M. B. (2024). Multiple karyotype differences between populations of the Hoplias malabaricus (Teleostei; Characiformes), a species complex in the gray area of the speciation process. Heredity 133(4): 216-226. DOI | |
| 2025 | Crilly, A., Malivert, A., Jørgensen, A.C.S., Heaney, C.E., Vera Gonzalez, G.I., Ghosh, M., Perez, M.F., Mieskolainen, M.M., Azzouzi, M., Li, Z. (2025). Ten simple rules for navigating AI in science. PLOS Computational Biology 21:e1013259. Open Access | |
| 2024 | Rincón Barrado, M., Perez, M.F., Villaverde, T., García-Verdugo, C., Caujapé-Castells, J., Riina, R., Sanmartín, I. (2024). Phylogenomics and phylogeographic model testing using convolutional neural networks reveal a history of recent admixture in the Canarian Kleinia neriifolia. Molecular Ecology 33(21):e17537. Open Access | |
| 2024 | Rincón-Barrado, M., Villaverde, T., Perez, M.F., Sanmartín,I., Riina, R. (2024). The sweet tabaiba or there and back again: phylogeographical history of the Macaronesian Euphorbia balsamifera. Annals of Botany 133(5-6)::883-903. Open Access | |
| 2022 | Kirschner, P., Perez, M.F., Záveská, E., Sanmartín, I., Marquer, L., Schlick-Steiner, B.C., Álvarez, N., Steiner, F.M., Schönswetter, P., STEPPE Consortium (2022). Congruent evolutionary responses of European steppe biota to late Quaternary climate change. Nature communications 13(1):1921. Open Access |
Capítulos de libros
| # | FECHA | PUBLICACIÓN |
|---|---|---|
| 2023 | Perez, M.F., Toma, G.A., Souza, F.H.S., Ferreira, P.N., Ráb, P., Cioffi, M.B. (2023). Integrating Genomic and Cytogenetic Data to Study the Evolutionary History of Arapaimas and Arowanas in the Neotropics. In: Galetti Jr., P.M. (eds) Conservation Genetics in the Neotropics. Springer, Cham. pp. 523–537. DOI |
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| 2023 | Machado, C.B., Perez, M.F. (2023). Phylogeography for Neotropical Species Conservation: Lineages Through Time and Space. In: Galetti Jr., P.M. (eds) Conservation Genetics in the Neotropics. Springer, Cham. pp. 119-143. DOI |
Proyectos
Integración de la micro y la macroevolución en la biología evolutiva mediante inteligencia artificial. Web del proyecto
2025-2029. Proyecto 2024-T1/ECO-31482 financiado a través de la Convocatoria de Ayudas destinadas a la Atracción de Talento Investigador ‘César Nombela’ (2024) de la Comunidad de Madrid .IP: Manolo Fernandez Perez.
