Santaquiteria, A., Miller, E. C., Rosas-Puchuri, U., Pedraza-Marrón, C. D. R., Troyer, E. M., Westneat, M. W., Carnevale, G., Arcila, D., & Betancur-R., R. (2025). Colonization Dynamics Explain the Decoupling of Species Richness and Morphological Disparity in Syngnatharian Fishes across Oceans. The American Naturalist, E000–E000. https://doi.org/10.1086/733931

Miller, E. C., Faucher, R., Hart, P. B., Rincón-Sandoval, M., Santaquiteria, A., White, W. T., Baldwin, C. C., Miya, M., Betancur-R, R., Tornabene, L., Evans, K., & Arcila, D. (2024). Reduced evolutionary constraint accompanies ongoing radiation in deep-sea anglerfishes. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-024-02586-3

Rincon-Sandoval, M., De-Kayne, R., Shank, S. D., Pirro, S., Ko’ou, A., Abueg, L., Tracey, A., Mountcastle, J., O’Toole, B., Balacco, J., Formenti, G., Jarvis, E. D., Arcila, D., Kosakovsky Pond, S. L., Davis, A., Bloom, D. D., & Betancur-R, R. (2024). Ecological diversification of sea catfishes is accompanied by genome-wide signatures of positive selection. Nature Communications, 15(1), 10040. https://doi.org/10.1038/s41467-024-54184-3

Troyer, E. M., Evans, K. M., Goatley, C. H. R., Friedman, M., Carnevale, G., Nicholas, B., Kolmann, M., Bemis, K. E., & Arcila, D. (2024). Evolutionary innovation accelerates morphological diversification in pufferfishes and their relatives. Evolution, qpae127. https://doi.org/10.1093/evolut/qpae127

Duarte-Ribeiro, E., Rosas-Puchuri, U., Friedman, M., Woodruff, G. C., Hughes, L. C., Carpenter, K. E., White, W. T., Pogonoski, J. J., Westneat, M., Diaz De Astarloa, J. M., Williams, J. T., Santos, M. D., 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. https://doi.org/10.1038/s41588-024-01784-w

Egan, J. P., Simons, A. M., Alavi-Yeganeh, M. S., Hammer, M. P., Tongnunui, P., Arcila, D., Betancur-R, R., & Bloom, D. D. (2024). Phylogenomics, Lineage Diversification Rates, and the Evolution of Diadromy in Clupeiformes (Anchovies, Herrings, Sardines, and Relatives). Systematic Biology, syae022. https://doi.org/10.1093/sysbio/syae022

Mihalič, F., Arcila, D., Pettersson, M. E., Farkhondehkish, P., Andersson, E., Andersson, L., Betancur-R, R., & Jemth, P. (2024). Conservation of affinity rather than sequence underlies a dynamic evolution of the motif-mediated p53/MDM2 interaction in ray-finned fishes. Molecular Biology and Evolution, msae018. https://doi.org/10.1093/molbev/msae018

Drabeck, D. H., Wiese, J., Gilbertson, E., Arroyave, J., Stiassny, M. L. J., Alter, S. E., Borowsky, R., Hendrickson, D. A., Arcila, D., & McGaugh, S. E. (2024). Gene loss and relaxed selection of plaat1 in vertebrates adapted to low-light environments. Proceedings of the Royal Society B: Biological Sciences, 291(2024), 20232847. https://doi.org/10.1098/rspb.2023.2847

Heiple, Z., Huie, J. M., Medeiros, A. P. M., Hart, P. B., Goatley, C. H. R., Arcila, D., & Miller, E. C. (2023). Many ways to build an angler: diversity of feeding morphologies in a deep-sea evolutionary radiation. Biology Letters, 19(6). https://doi.org/ARTN 20230049 10.1098/rsbl.2023.0049

Arcila, D., Rincon-Sandoval, M., Hanson, W., Hart, P. B., González, V. L., Betancur-R, R., & Bichuette, M. E. (2023). Transcriptomic analysis of the Brazilian blind characid, Stygichthys typhlops, reveals convergent selection with Astyanax mexicanus and other cavefishes. Frontiers in Ecology and Evolution, 11, 1076756. https://doi.org/10.3389/fevo.2023.1076756

Baldwin, C. C., Arcila, D., Robertson, D. R., & Tornabene, L. (2023). Description of the First Species of Polylepion (Teleostei: Labridae) from the Atlantic Ocean with Analysis of Evolutionary Relationships of the New Species. Ichthyology & Herpetology, 111(2). https://doi.org/10.1643/i2022075

Collins, Q. P., Grunsted, M. J., Arcila, D., Xiong, Y., & Barmchi, M. P. (2023). Transcriptomic analysis provides insight into the mechanism of IKKβ-mediated suppression of HPV18E6-induced cellular abnormalities. G3-Genes Genomes Genetics, 13(4). https://doi.org/10.1093/g3journal/jkad020

Peterson, R. D., Sullivan, J. P., Hopkins, C. D., Santaquiteria, A., Dillman, C. B., Pirro, S., Betancur-R, R., Arcila, D., Hughes, L. C., & Ortí, G. (2022). Phylogenomics of Bony-Tongue Fishes (Osteoglossomorpha) Shed Light on the Craniofacial Evolution and Biogeography of the Weakly Electric Clade (Mormyridae). Systematic Biology, 71(5), 1032–1044. https://doi.org/10.1093/sysbio/syac001

Troyer, E. M., Betancur-R, R., Hughes, L. C., Westneat, M., Carnevale, G., White, W. T., Pogonoski, J. J., Tyler, J. C., Baldwin, C. C., Ortí, G., Brinkworth, A., Clavel, J., & Arcila, D. (2022). The impact of paleoclimatic changes on body size evolution in marine fishes. Proceedings of the National Academy of Sciences of the United States of America, 119(29). https://doi.org/ARTN e2122486119 10.1073/pnas.2122486119

Briñoccoli, Y. F., Bogan, S., Arcila, D., Rosso, J. J., Mabragaña, E., Delpiani, S. M., de Astarloa, J. M. D., & Cardoso, Y. P. (2022). Molecular and morphological evidence revalidates Acrobrycon tarijae (Characiformes, Characidae) and shows hidden diversity. Zookeys, 1091, 99–117. https://doi.org/10.3897/zookeys.1091.73446

Arcila, D., & Orti, G. (2022). Phylogenetic Systematics of Fishes. In S. Midway, C. Hasler, & P. Chakrabarty (Eds.), Methods for Fish Biology, 2nd edition (2nd ed.). American Fisheries Society.

Santaquiteria, A., Siqueira, A. C., Duarte-Ribeiro, E., Carnevale, G., White, W. T., Pogonoski, J. 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 Factors Driving Uncertainty in Biogeographic Inferences. Systematic Biology, 70(6), 1145–1162. https://doi.org/10.1093/sysbio/syab028

Arcila, D., Hughes, L. C., Meléndez-Vazquez, B., Baldwin, C. C., White, W. T., Carpenter, K. E., Williams, J. T., Santos, M. D., Pogonoski, J. J., Miya, M., Ortí, G., & Betancur-R, R. (2021). Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria). Systematic Biology, 70(6), 1123–1144. https://doi.org/10.1093/sysbio/syab018

Atta, C. J., Yuan, H., Li, C. H., Arcila, D., Betancur-R, R., Hughes, L. C., Ortí, G., & Tornabene, L. (2021). Exon-capture data and locus screening provide new insights into the phylogeny of flatfishes (Pleuronectoidei). Molecular Phylogenetics and Evolution, 166. https://doi.org/https://doi.org/10.1016/j.ympev.2021.107315

Rincon-Sandoval, M., Duarte-Ribeiro, E., Davis, A. M., Santaquiteria, A., Hughes, L. C., Baldwin, C. C., Soto-Torres, L., Acero, A., Walker, H. J., Carpenter, K. E., Sheaves, M., Orti, G., Arcila, D., & Betancur-R, R. (2020). Evolutionary determinism and convergence associated with water-column transitions in marine fishes. Proceedings of the National Academy of Sciences of the United States of America, 117(52), 33396–33403. https://doi.org/10.1073/pnas.2006511117

Hughes, L. C., Ortí, G., Saad, H., Li, C. H., White, W. T., Baldwin, C. C., Crandall, K. A., Arcila, D., & Betancur, R. (2020). Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics. Mol Ecol Resour, 21(3), 816–833. https://doi.org/10.1111/1755-0998.13287

Kolmann, M. A., Hughes, L. C., Hernandez, L. P., Arcila, D., Betancur-R, R., Sabaj, M. H., López-Fernández, H., & Ortí, G. (2020). Phylogenomics of Piranhas and Pacus (Serrasalmidae) Uncovers How Dietary Convergence and Parallelism Obfuscate Traditional Morphological Taxonomy. Systematic Biology, 70(3), 576–592. https://doi.org/10.1093/sysbio/syaa065

Meléndez-Vazquez, F., Olmeda-Saldaña, M., Cruz, J., Arcila, D., & Betancur, R. (2019). Effects of Hurricane Maria in hamlet communities (Serranidae: spp.) in Puerto Rico. Ecological Indicators, 107. https://doi.org/ARTN 105591 10.1016/j.ecolind.2019.105591

Bemis, K. E., Tyler, J. C., & Arcila, D. (2019). Life history, distribution and molecular phylogenetics of the Upward-Mouth Spikefish Atrophacanthus japonicus (Teleostei: Tetraodontiformes: Triacanthodidae). Journal of Fish Biology, 94(4), 578–584. https://doi.org/10.1111/jfb.13923

Betancur-R, R., Arcila, D., Vari, R. P., Hughes, L. C., Oliveira, C., Sabaj, M. H., & Ortí, G. (2019). Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes. Evolution, 73(2), 329–345. https://doi.org/10.1111/evo.13649

Hughes, L. C., Ortí, G., Huang, Y., Sun, Y., Baldwin, C. C., Thompson, A. W., Arcila, D., Betancur, R. R., Li, C., Becker, L., Bellora, N., Zhao, X., Li, X., Wang, M., Fang, C., Xie, B., Zhou, Z., Huang, H., Chen, S., … Shi, Q. (2018). Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proc Natl Acad Sci U S A, 115(24), 6249–6254. https://doi.org/10.1073/pnas.1719358115

Arcila, D., Petry, P., & Ortí, G. (2018). Phylogenetic relationships of the family Tarumaniidae (Characiformes) based on nuclear and mitochondrial data. Neotropical Ichthyology, 16(3). https://doi.org/Artn 180016 10.1590/1982-0224-20180016

Arcila, D., & Tyler, J. C. (2017). Mass extinction in tetraodontiform fishes linked to the Palaeocene-Eocene thermal maximum. Proceedings of the Royal Society B-Biological Sciences, 284(1866). https://doi.org/ARTN 20171771 10.1098/rspb.2017.1771

Lavoué, S., Arnegard, M. E., Rabosky, D. L., McIntyre, P. B., Arcila, D., Vari, R. P., & Nishida, M. (2017). Trophic evolution in African citharinoid fishes (Teleostei: Characiformes) and the origin of intraordinal pterygophagy. Molecular Phylogenetics and Evolution, 113, 23–32. https://doi.org/https://doi.org/10.1016/j.ympev.2017.05.001

Arcila, D., Orti, G., Vari, R., Armbruster, J. W., Stiassny, M. L. J., Ko, K. D., Sabaj, M. H., Lundberg, J., Revell, L. J., & Betancur, R. (2017). Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life. Nature Ecology & Evolution, 1(2). https://doi.org/ARTN 0020 10.1038/s41559-016-0020

Bannikov, A. F., Tyler, J. C., Arcila, D., & Carnevale, G. (2017). A new family of gymnodont fish (Tetraodontiformes) from the earliest Eocene of the Peri-Tethys (Kabardino-Balkaria, northern Caucasus, Russia). Journal of Systematic Palaeontology, 15(2), 129–146. https://doi.org/10.1080/14772019.2016.1149115

Thomaz, A. T., Arcila, D., Ortí, G., & Malabarba, L. R. (2015). Molecular phylogeny of the subfamily Stevardiinae Gill, 1858 (Characiformes: Characidae): classification and the evolution of reproductive traits. Bmc Evolutionary Biology, 15. https://doi.org/ARTN 146 10.1186/s12862-015-0403-4

Arcila, D., Pyron, R. A., Tyler, J. C., Ortí, G., & Betancur-R, R. (2015). An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae). Molecular Phylogenetics and Evolution, 82, 131–145. https://doi.org/10.1016/j.ympev.2014.10.011

Arcila, D., Vari, R. P., & Menezes, N. A. (2013). Revision of the Neotropical Genus (Ostariophysi: Characiformes: Characidae) with Description of Two New Species. Copeia, 4, 604–611. https://doi.org/10.1643/Ci-13-009

Betancur-R, R., Broughton, R. E., Wiley, E. O., Carpenter, K., López, J. A., Li, C. H., Holcroft, N. I., Arcila, D., Sanciangco, M., Cureton, J. C., Zhang, F. F., Buser, T., Campbell, M. A., Ballesteros, J. A., Roa-Varon, A., Willis, S., Borden, W. C., Rowley, T., Reneau, P. C., … Ortí, G. (2013). The Tree of Life and a New Classification of Bony Fishes. Plos Currents-Tree of Life. https://doi.org/10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288

Rom√°n-Valencia, C., & Arcila-Mesa, D. K. (2010). Five new species of Hemibrycon (Characiformes: Characidae) from the Rio Magdalena basin, Colombia. Revista de BiologÌa Tropical, 58, 339+.

Román- Valencia, C., & Arcila, D. (2009). Two new species of Hemibrycon (Characiformes, Characidae) from the Magdalena River, Colombia. Animal Biodiversity and Conservation, 32. https://doi.org/10.32800/abc.2009.32.0077

Román-Valencia, C., Arcila-Mesa, D. K., & Hurtado T, H. (2009). Variación morfológica de los peces Hemibrycon boquiae y Hemibrycon rafaelense (Characiformes: Characidae) en el Río Cauca, Colombia. Revista de BiologÌa Tropical, 57(3), 541–556.

Román- Valencia, C., & Arcila, D. (2008). Hemibrycon rafaelense n. sp. (Characiformes, Characidae), a new species from the upper Cauca River, with keys to Colombian species. Animal Biodiversity and Conservation, 31. https://doi.org/10.32800/abc.2008.31.0067