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. Under Review. Phylogenomics reveals the deep ocean as an accelerator for evolutionary diversification in anglerfishes. Accepted with revision. Nature Ecology and Evolution. Biorxiv preprint.

**Santaquiteria, A., E. Miller, U. Rosas-Puchuri, C. Pedraza-Marrón, E. Troyer, M. Westneat, G. Carnevale, D. Arcila & R. Betancur-R. Under review. Early colonizations explain the high species richness of syngnatharian fishes in the Indo-Pacific but morphological similarities persist across marine realms. Under revision. The American Naturalist.

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. Molecular Phylogenetics and Evolution. 

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. Accepted. Phylogenomics, lineage diversification rates, and the evolution of diadromy in Clupeiformes (anchovies, herrings, sardines, and relatives). Systematic Biology.

**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.* Accepted with revision. Phylogenomic and comparative genomic analyses support a single evolutionary origin of flatfish asymmetry. Nature Genetics.

**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