47. Rosas-Puchuri, U., E. Duarte-Ribeiro, S. Khanmohammadi, D. Arcila, G. Ortí & R. Betancur-R. Dissecting factors underlying phylogenetic uncertainty using machine learning models. Under review.

46. Troyer, E., White, W.T., Betancur-R, R., Arcila, D.  Parallel shifts in differential gene expression reveal convergent miniaturization in fishes. Under review.

45. Chang, S., Heiple, Z., Hays, D., Melendez-Vazquez, F., Lee, C., Pogonoski, J., Martinez, C.M., Betancur-R, R., Arcila, D. Genome-wide phylogeny reshapes our understanding of the evolution of deep-sea dragonfishes, bristlemouths, viperfishes, and allies (Stomiiformes). Under review.

44. **Hart, P., Rincon-Sandoval, M., Melendez-Vazquez, F., Armbruster, J., Troyer, E.M., Bierstein, O.M., Gough, B.J., Betancur-R, R., Niemiller, M. & D. Arcila. Ancient climate changes and relaxed selection shape cave colonization in North American cavefishes. Accepted.

43. Souto-Santos, I.C.A., E. Mejia, D. Arcila, P.A. Buckup. Disentangling the Phalloceros harpagos species complex: morphological and molecular evidence for a widespread, undescribed species of livebearing fishes (Poeciliidae). Accepted

42. **Melendez-Vazquez, F., A. Lucaci, A. Selberg, J. Clavel, M. Rincon-Sandoval, A. Santaquiteria, W. White, D. Drabeck, G. Carnevale, E. Duarte-Ribeiro, M. Miya, M. Westneat, C. Baldwin, L. Hughes, G. Ortí, S. Kosakovsky Pond, R. Betancur-R. & D. Arcila. Ecological interactions and genomic innovations fueled evolution of fish endothermy. Accepted.

41. Miller, E.C., R. Faucher, P.B. Hart, M. Rincon-Sandoval, A. Santaquiteria, W.T. White, C.C. Baldwin, M. Miya, R. Betancur-R., L. Tornabene, K. Evans & D. Arcila. 2024. Phylogenomics reveals the deep ocean as an accelerator for evolutionary diversification in anglerfishes. Nature Ecology & Evolution. Accepted. Biorxiv preprint.

40. Troyer, E.M. K.M. Evans, C. Goatley, M.Friedman, G. Carnevale, B. Nicholas, M. Kolmann, K.E. Bemis, D. Arcila. 2024. Evolutionary innovation accelerates morphological diversification in pufferfishes and their relatives. Evolution. qpae127

39. **M. Rincon-Sandoval, R.  De-Kayne, S.D. Shank, S. Pirro, A. Ko’oue, L. Abueg, A. Tracey, J. Mountcastle, B. O'Toole, J. Balacco, G. Formenti, E.D.  Jarvis, D. Arcila, S.L.K. Pond, A.  Davis, D.D. Bloom &  R. Betancur-R. Ecological diversification of sea catfishes is accompanied by genome-wide signatures of positive selection. Nature Communications (2024)15:10040. PDF. 

38. **Santaquiteria, A., E. Miller, U. Rosas-Puchuri, C. Pedraza-Marrón, E. Troyer, M. Westneat, G. Carnevale, D. Arcila & R. Betancur-R. 2024. Colonization dynamics explain the decoupling of species richness and morphological disparity in syngnatharian fishes across oceans. The American Naturalist. 

37. Mihalič, F., D. Arcila, M. E. Pettersson, P. Farkhondehkish, E. Andersson, L. Andersson, R. Betancur-R. & P. Jemth. 2024. Conservation of affinity rather than sequence underlies a dynamic evolution of the motif-mediated p53/MDM2 interaction in teleosts. Molecular Biology and Evolution 41(2):msae018. PDF.

36. **Drabeck, D.H, J. Wiese, E. Gilbertson, J. Arroyave, S.E. Alter, R. Borowsky, A. Gluesenkamp, D. Hendrickson, D. Arcila, & S.E. McGaugh. 2024. Gene loss and relaxed selection of plaat1 in vertebrates adapted to low light environments. Proceedings of the Royal Society B.

35. **Duarte-Ribeiro, E., U. Rosas-Puchuri, M. Friedman, G.C. Woodruff, L.C. Hughes, K.E. Carpenter, O. Domínguez-Domínguez, G. Ortí, D. Arcila & R. Betancur.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. PDF. Press releases: NY Times (by Carl Zimmer) & Why Evolution is True blog (by Jerry Coyne).

34. Egan, J. P., A. M. Simons, M. Sadegh Alavi-Yeganeh, M. P. Hammer, P. Tongnunui, D. Arcila, R. Betancur-R. & D. Bloom. 2024. Phylogenomics, lineage diversification rates, and the evolution of diadromy in Clupeiformes (anchovies, herrings, sardines, and relatives). Systematic Biology.

33. Arcila, D.A. & R. Betancur-R. Scientist spotlights: Dahiana Arcila & Ricardo Betancur-R. Ichthyology and Herpetology 111, No. 2, 2023, 331–334. PDF. 

32. Heiple, Z. J.M., Huie, A. Medeiros, P. Hart, C. Goatley, D. Arcila, E.C. Miller. 2023. Many ways to build an angler: An analysis of feeding morphologies in deep-sea anglerfishes (Ceratioidei: Lophiiformes). Biology Letters.

31. Arcila D., M. Rincon-Sandoval, W. Hanson,  P.B.  Hart, V.L. González, R. Betancur-R. & M.E. Bichuette. 2023. Transcriptomic Analysis of the Brazilian Blind Characid, Stygichthys typhlops, Reveals Convergent Selection with Astyanax mexicanus and Other Cavefishes. Frontiers in Ecology and Evolution 2023 (11). PDF.

30. Baldwin, C., D. Arcila., D.R. Robertson & L. Tornabene. 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): 182–190. PDF

29. Collis, Q., M. Grunstead, D. Arcila, Y. Xiong & M.P. Barmchi. 2023. Transcriptomic analysis provides insight into the mechanism of IKKβ-mediated suppression of HPV18E6-induced cellular abnormalities. G3: Genes| Genomes|Genetics. 10.1093/g3journal/jkad020. 

**28. Troyer, E.M., R. Betancur-R., L.C. Hughes, M. Westneat, G. Carnevale, W. White, J. Pogonoski, J.C. Tyler, C.C. Baldwin, G. Ortí, A. Brinkworth, J. Clavel & D. Arcila. 2022. The impact of paleoclimatic changes on body size evolution in marine fishes. Proceedings of the National Academy of Sciences 119 (29) e2122486119. PDF. Press releases: PNAS News.

27. Arcila D. & G. Ortí. 2022 Phylogenetic Systematics of Fishes. In Midway S., C. Hasler, & P. Chakrabarty, editors. Methods for Fish Biology, Second edition. American Fisheries Society, Bethesda, Maryland, USA.

26.  Peterson, R. D., J. P. Sullivan, C. D. Hopkins, A. Santaquiteria, C. B. Dillman, S. Pirro, R. Betancur-R., D. Arcila, L. C. Hughes, G. Ortí. 2022. Convergent Craniofacial Evolution and Biogeography of Weakly Electric 1 Mormyrids and Bonytongue Fishes (Osteoglossomorpha). Systematic Biology. PDF.

25. Briñoccoli, Y.F., S. Bogan, D. Arcila, J.J. Rosso, E. Mabragaña, S.M. Delpiani, J.M. Díaz de Astarloa, Y.P. Cardoso. 2022. Molecular and taxonomic evidence unmask hidden species diversity in the genus Acrobrycon (Characiformes: Characidae). ZooKeys

24. Atta, C., H. Yuan, C. Li, D. Arcila, R. Betancur-R., L. Hughes, G. Orti & L. Tornabene. 2022. Exon-capture data and locus screening provide new insights into the phylogeny of flatfishes (Pleuronectoidei). Molecular Phylogenetics and Evolution 166, 107315. PDF.

23. Santaquiteria, A., A. C. Siqueira, E. Duarte-Ribeiro, G. Carnevale, W. White, J. Pogonoski, C. C. Baldwin, G. Ortí, D. Arcila & R. Betancur-R. 2021. Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences 70 (6):1145–1162. PDF. See comment about the paper in MarineBio.

22. Arcila, D*., L. C  Hughes*, F. Melendez, C. C. Baldwin, W. White, K. Carpenter, J. T.  Williams, D. M. Santos, J. Pogonoski, M. Miya, G. Ortí & R. Betancur-R. 2021. Testing the utility of alternative metrics of branch support to resolve the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria). Systematic Biology 70 (6):1123–1144. *Equal contribution. PDF.

**21. Rincon-Sandoval, M.*, E. Duarte-Ribeiro*, A. M. Davis, A. Santaquiteria, L. C. Hughes, C. C.  Baldwin, L. Soto-Torres, A. Acero P., H. J. Walker, K. E. Carpenter, M. Sheaves, G. Ortí, D. Arcila &  R. Betancur-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. PDF. Press releases: Eureka Alert, OU, GWU.

20. Hughes, L.C. , G. Ortí, H. Saad, C. Li , W.T. White, C. Baldwin, D. Arcila & R. Betancur-R. 2020. Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics. Molecular Ecology Resources 21(3): 816-833. PDF.

19. Kolmann, M., L. Hughes, P. Hernandez, D. Arcila, R. Betancur-R., M.H. Sabaj, H. Lopez-Fernandez & G. Ortí. 2020. Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how dietary convergence and parallelism obfuscate traditional morphological taxonomy. Systematic Biology. PDF

18. Meléndez-Vazquez, F., M. Olmeda-Saldaña, J. Cruz, D. Arcila & R. Betancur-R. 2019. Effects of Hurricane Maria in hamlet (Serranidae: Hypoplectrus) communities in Puerto Rico. Ecological Indicators 107 (2019) 105591. PDF

17. Arcila, D. & Cartwright S. 2019. Ichthyology Collection of The Sam Noble Oklahoma Museum of Natural History. Boletim Sociedade Brasileira de Ictiologia 2019(129): 113-116. PDF

16. Bemis, K.E. Tyler, J.C. & D. Arcila. 2019. Life history, distribution, and molecular phylogenetics of the Upward-Mouth Spikefishes, Atrophacanthus japonicus (Teleostei: Tetraodontiformes: Triacanthodidae). Journal of Fish Biology 2019: 1-7. PDF

15. Betancur-R., R.*, D. Arcila*, R. Vari, L. Hughes, C. Oliveira, M. Sabaj & G. Ortí. 2019. Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: the monophyly of characiform fishes. *Equal contribution. PDF. Evolution Digest article on the study by Montero-Mendieta and Dheer (2019) here. Also featured in ANSP news.

14. Arcila D., P. Petry & G. Ortí. 2018. Phylogenetic relationships of the family Tarumaniidae (Characiformes) based on nuclear and mitochondrial data. Neotropical Ichthyology 16(3): e180016. PDF

**13. Hughes, L.C., G. Ortí, Y. Huang, Y. Sun, C.C. Baldwin, A.W. Thompson, D. Arcila, R. Betancur-R., C. Li, L. Becker et al. 2018. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proceedings of the National Academy of Sciences, 201719358. PDF, Supplement. PNAS comment by M. Alfaro.

**12. Arcila, D. & J. Tyler. 2017. Mass extinction in tetraodontiform fishes linked to the Palaeocene–Eocene thermal maximum. Proceedings of the Royal Society of London B 284 (1866): 20171771. PDF

11. Lavoue, S., M. Arnegard, D. Rabosky, P. McIntyre, D. Arcila, R. Vari & M. Nishida. 2017. Trophic evolution in African citharinoid fishes (Teleostei: Characiformes) and the origin of intraordinal pterygophagy. Molecular Phylogenetics and Evolution 113, 23-32. PDF

10. Arcila, D., G. Ortí, R. Vari, J. W. Armbruster, M. Stiassny, K. D. Ko, M. H. Sabaj, J. Lundberg, L. J. Revell & R. Betancur-R. 2017. Genome-wide interrogation advances resolution of recalcitrant groups in the Tree of Life. Nature Ecology & Evolution 1: 0020. PDF & Supplement. Featured in "News and Views" about the paper by S. Mirarab, news outlet, in Spanish, El Tiempo, Ciencia PR, and "Behind the Paper" post. For a GGI tutorial see here. 

9. Bannikov, A.F., G. Carnevale, D. Arcila & J.C. Tyler. 2016. 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, 1-18. PDF.  Featured in NatGeo.

8. Thomaz, A*., D. Arcila*, G. Ortí & L.R. Malabarba. 2015. Molecular phylogeny of the subfamily Stevardiinae Gill, 1858 (Characiformes: Characidae): classification and the evolution of reproductive traits. BMC Evolutionary Biology 15, 146. PDF. *Equal contribution. 

7. Arcila, D.*, A. Pyron, J. Tyler, G. Ortí & R. Betancur-R. 2015. An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes. Molecular Phylogenetics and Evolution 82(2015): 131-145. *Equal contribution. PDF

6. Betancur-R., R., R.E. Broughton, E.O. Wiley, K. Carpenter, J.A. Lopez, C. Li, N.I. Holcroft, D. Arcila, M. Sanciangco, J. Cureton, F. Zhang, T. Buser, M. Campbell, T. Rowley, J.A. Ballesteros, G. Lu, T. Grande, G. Arratia & G. Ortí. 2013. The tree of life and a new classification of bony fishes. PLoS Currents Tree of Life. Pub Med Version. Press releases: Science Daily, e! Science News, GWU, PLoS Blogs.

5. Arcila, D., R.P. Vari & N. Menezes. 2013. Revision of the neotropical genus Acrobrycon (Ostariophysi: Characiformes) with description of two new species. Copeia 4, 604-611. PDF

4. Román-Valencia, C. & D. Arcila*. 2010. Five new species Hemibrycon (Characiformes: Characidae) from the Rio Magdalena basin, Colombia. Revista de Biología Tropical 58, 339-356. *Undergraduate student. PDF

3. Román-Valencia, C.,  D. Arcila* & R. Ruiz-C. 2009. Two new species of Hemibrycon (Characiformes: Characidae) from the Magdalena river, Colombia. Animal Biodiversity and Conservation 32.2, 77-87. *Undergraduate student. PDF 

2. Román-Valencia, C., D. Arcila*, H. Hurtado. 2009. Variación morfológica de las poblaciones de Hemibrycon boquiae y H. rafaelense (Characiformes: Characidae) en el río Cauca, Colombia. Revista de Biología Tropical 57, 541-556. *Undergraduate student. PDF

1. Román-Valencia, C. & D. Arcila*. 2008 Hemibrycon rafaelense n. sp. (Characiformes: Characidae), a new species from the upper Cauca River, with keys to Colombian species. Animal Biodiversity and Conservation 31.1, 67-75. *Undergraduate student. PDF