Publications
Preface
My work has helped advance our understanding of the evolutionary dynamics and genetic mechanisms that shape the Fish Tree of Life. By combining genomic data with phylogenetic methods, I’ve addressed key uncertainties in fish evolution, explored how evolutionary convergence drives body plan evolution and uncovered the molecular basis of important adaptive traits. These findings have not only helped resolve long-standing questions in fish evolution but also provided new insights into the genetic basis of complex traits, creating a comprehensive framework for studying macroevolutionary patterns in vertebrates. Below you will find a curated and updated list of my publications.
Most Significant Publications
Duarte-Ribeiro E., Rosas U., Friedman M., Woodruff G. C., Hughes L. C., Carpenter K. E, Domínguez-Domínguez O., Ortí G., Arcila D., Betancur-R, R. (2024). Phylogenomic and comparative genomic analyses support a single evolutionary origin of flatfish asymmetry. Nature Genetics, 56, 1069–1072. DOI: 10.1038/s41588-024-01784-w
This publication addressed the origins of the asymmetric body plan in flatfishes. By accounting for lineage-specific variations in base composition, we challenged the notion of convergent evolution and instead supported a simpler hypothesis of a single origin for flatfish asymmetry. This research garnered significant attention, including a piece by Carl Zimmer in The New York Times.
Rincon-Sandoval, M.*, Duarte-Ribeiro E.*, Davis, A. M., Santaquiteria, A., Hughes, L. C., Baldwin, C. C., Betancur-R, R.* (2020). Evolutionary determinism and convergence associated with water-column transitions in marine fishes. Proceedings of the National Academy of Sciences, 117(52), 33396-33403. *Equal contribution. DOI: 10.1073/pnas.2006511117 PDF
A fundamental question in biology concerns whether evolutionary outcomes are predictable, governed by natural laws, or contingent upon unpredictable historical events, such as environmental catastrophes. This publication presented links between incursions into the water column and evolutionary convergence in pelagic fish body plan, supporting the notion of deterministic evolution along this ecological gradient.
Ribeiro, E. D., Davis, A. M., Rivero-Vega, R. A., Ortí, G., & Betancur-R, R. (2018). Post-Cretaceous bursts of evolution along the benthic-pelagic axis in marine fishes. Proceedings of the Royal Society B, 285(1893), 20182010. DOI: 10.1098/rspb.2018.2010 PDF
This publication highlighted the importance of increased ecological opportunities following the Cretaceous-Paleogene (K-Pg) mass extinction, which ignited a series of adaptive radiations now recognized as the onset of "the modern age of fishes."
Additional Publications
In Press
Melendez-Vazquez, F., Lucaci, A., Selberg, A., Clavel, J., Rincon, S. Santaquiteria, A., White, W., Drabeck, D., Carnevale, G., Duarte-Ribeiro E., Miya, M., Westneat, M., Baldwin, C., Hughes, L., Orti, G., Pond, S., Betancur-R, R., Arcila, D. Interactions with cetaceans fueled the evolution of fish endothermy. Science Advances (in press).
Rosas U., Duarte-Ribeiro E., Khanmohammadi S., Arcila D., Ortí G. Betancur-R. R., Dissecting Factors Underlying Phylogenetic Uncertainty Using Machine Learning Models. Molecular Phylogenetics and Evolution (in press).
2021
Santaquiteria A., Siqueira A.C., Duarte-Ribeiro E., Carnevale G., White W., Pogonoski J, Baldwin C. C., Ortí G., Arcila D., Betancur-R R. (2021). Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing the Factors Driving Uncertainty in Biogeographic Inferences. Systematic Biology, 70(6), 1145-1162. DOI: 10.1093/sysbio/syab028 PDF
Loera-Padilla, F. J., Piñeros, V. J., Baldwin, C. C., Cox, C. E., Simoes, N., Duarte-Ribeiro, E., Domínguez-Domínguez, O. (2021). Phylogeography, population connectivity and demographic history of the Stoplight parrotfish, Sparisoma viride (Teleostei: Labridae), in the Greater Caribbean. Coral Reefs, 1-13. DOI: 10.1007/s00338-020-02036-z PDF
2018
Collins, R. A., Bifi, A. G., de Oliveira, R. R., Ribeiro, E. D., Lujan, N. K., Rapp Py-Daniel, L. H., & Hrbek, T. (2018). Biogeography and species delimitation of the rheophilic suckermouth catfish genus Pseudolithoxus (Siluriformes: Loricariidae), with the description of a new species from the Brazilian Amazon. Systematics and Biodiversity, 16(6), 538-550. DOI: 10.1080/14772000.2018.1468362 PDF
2015
Collins, R. A., Ribeiro, E. D., Machado, V. N., Hrbek, T., & Farias, I. P. (2015). A preliminary inventory of the catfishes of the lower Rio Nhamundá, Brazil (Ostariophysi, Siluriformes). Biodiversity Data Journal, (3). DOI: 10.3897/BDJ.3.e4162 PDF
2014
Da Silva, M., Ribeiro, E. D., Matoso, D. A., Sousa, L. M., Hrbek, T., Py-Daniel, L. R., & Feldberg, E. (2014). Chromosomal polymorphism in two species of Hypancistrus (Siluriformes: Loricariidae): an integrative approach for understanding their biodiversity. Genetica, 142(2), 127-139. DOI: 10.1007/s10709-014-9760-y
2013
Ribeiro, E. D., & Molina, W. F. (2013). Marcada diferenciação cariotípica entre as "manjubas" Atherinella blackburni e A. brasiliensis (Atheriniformes). Biota Amazônia, 3(2), 40-52. DOI: 10.18561/2179-5746/biotaamazonia.v3n2p40-52 PDF