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

Pedraza-Marrón, C.D.R., O. Domínguez-Domínguez, S. Jarjoura, L. Benestan, B.C. Victor, A. Acero P., R. Robertson, C.C. Baldwin, P.A. Hastings & R. Betancur-R. Geographic breaks and seascape features shape evolutionary divergence in cryptobenthic reef fishes. Under review. 

**Helkampf, M., F. Coulmance, M. Heckwolf, A. Acero P., A. Balard, I. Bista, O. Dominguez Dominguez, P. Frandsen, M. Torres-Oliva, A. Santaquiteria, J. Tavera Vargas, B. Victor, D. R. Robertson, R. Betancur-R., W. O. McMillan & O. Puebla. Radiation with reproductive isolation in the near-absence of phylogenetic signal. Science Advances. Under revision.

**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. Science Advances. Under revision. 

**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.

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. PDF.

**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.* 2024. Ecological diversification of sea catfishes is accompanied by genome-wide signatures of positive selection. Nature Communications (2024)15:10040. PDF. *Equal contribution.

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 205(3). PDF.

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 ray-finned fishes. Molecular Biology and Evolution 41(2):msae018. PDF.

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, syae022.

**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).

**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.

Medeiros, A. P.*, B. A. Santos & R. Betancur-R.* 2022. Does genome size increase with water depth in marine fishes? Evolution 76 (7): 1578-1589.  PDF. *Equal contribution.

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

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. PDF.

**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.

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.

Hughes, L.C., Y. Cardozo, J. Sommer, R. Cifuentes, M. Cuello, G.M. Somoza, M. González-Castro, L.R. Malabaraba, V. Cussac, E.M. Habit, R. Betancur-R. & G. Ortí. 2020. Biogeography, habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data. Molecular Ecology 2020 (00):1–14. PDF.

Rincon-Sandoval, M.*, Betancur-R., R.* & J. Maldonado-Ocampo. 2019. Comparative phylogeography of trans-Andean freshwater fishes based on genome-wide nuclear and mitochondrial markers. 2019. Molecular Ecology 28 (5): 1096-1115. *Equal contribution. PDF.

**Pedraza-Marrón, C.R.* R. da Silva, J. Deeds, S.M. Van Belleghem, A. Mastretta-Yanes, O. Domínguez-Domínguez, R.A. Rivero-Vega, L. Lutackas, D. Murie, D. Parkyn, L. Bullock, K. Foss, H. Ortiz-Zuazaga, J. Narváez-Barandica, A. Acero, G. Gomes & Betancur-R., R.* 2019. Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation. Proceedings of the Royal Society B 286 (1900). *Equal contribution. PDF.

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.

**Ribeiro, E.D., A. Davis, R. A. Rivero-Vega, G. Ortí, & R. Betancur-R. 2018. Post-Cretaceous bursts of evolution along the benthic-pelagic axis in marine fishes. Proceedings of the Royal Society B: 285, 20182010. 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.

Betancur-R., R., E. O. Wiley, G. Arratia, A. Acero, N. Bailly, M. Miya, G. Lecointre & G. Ortí. 2017. Phylogenetic classification of bony fishes. BMC Evolutionary Biology 17(162): DOI: 10.1186/s12862-017-0958-3. PDF. Get the actual figures: Fig 1 & Fig 2.

**Davis, A. & R. Betancur-R. 2017. Widespread ecomorphological convergence in multiple fish families spanning the marine-freshwater interface. Proceedings of the Royal Society series B**. 284(1854). PDF. Featured in PNAS "Journal Club" analysis.

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. 

A. Davis, P. Unmack, R. Vari & R. Betancur-R. 2016. Herbivory promotes dental disparification and macroevolutionary dynamics in grunters (Teleostei: Terapontidae), a freshwater adaptive radiation. The American Naturalist 187(3): 320-333. PDF

**R. Betancur-R., G. Ortí & A. Pyron. 2015. Fossil-based comparative analyses reveal ancient marine ancestry erased by extinction in ray-finned fishes. Ecology Letters 18: 441–450. PDF. Blog discussing the paper.

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

Betancur-R., R. , G. Naylor & G. Ortí. 2014. Conserved genes, sampling error, and phylogenomic inference. Systematic Biology 63(2): 257-262. PDF

Betancur-R., R., C. Li, T. A Munroe, J. A. Ballesteros & G. Ortí. 2013. Addressing gene-tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes). Systematic Biology 62(5):763–785. PDF

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.

**Betancur-R., R., G. Ortí, A. M. Stein, A. P. Marceniuk & R. A. Pyron. 2012. Apparent signal of competition limiting diversification after ecological transitions from marine to freshwater habitats. Ecology Letters 15(8): 822-830. PDF & other files.

Betancur-R., R.,  A. Hines, A. Acero P., G. Ortí, A.E. Wilbur & D.W. Freshwater. 2011. Reconstructing the lionfish invasion: insights into Greater Caribbean biogeography. Journal of Biogeography 38: 1281-1293. PDF. Press release in Frontiers in Ecology and the Environment 2011 9(6). PDF

Betancur-R., R., A. Acero P., H. Duque-Caro & S. R. Santos. 2010. Phylogenetic and morphological analyses of a coastal fish reveal a marine biogeographic break of terrestrial origin in the Southern Caribbean. PLoS ONE 5(7): e11566. doi:10.1371/journal.pone.0011566.  PDF

Betancur-R., R. 2010. Molecular phylogenetics supports multiple evolutionary transitions from marine to freshwater habitats in ariid catfishes. Molecular Phylogenetics and Evolution 55(1): 249-258. PDF

Betancur-R., R. & J.W. Armbruster. 2009. Molecular clocks provide new insights into the evolutionary history of galeichthyine sea catfishes. Evolution 63(5): 1232-1243. PDF. Missing Appendix A from article here.

Betancur-R., R. 2009. Molecular phylogenetics and evolutionary history of ariid catfishes revisited: a comprehensive sampling. BMC Evolutionary Biology 2009 9: 175. Highly accessed paper. PDF