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The Vertebrate Genomes Project Phase I: A global reference genome resource. bioRxiv. 2026 Jun 25.
Formenti G, Absolon DE, Abueg LAL, Ackerman F, Al-Ajli FO, Aleixo A, Antunes A, Arcila D, Audet JN, Balacco JR, Beavan AJS, Belov K, Betancur-R R, Bidwell SL, Biegler MT, Bista I, Blaxter M, Boyer K, Braasch I, Bradbury IR, Brajuka N, Bronikowski AM, Brown T, Butler G, Cao S, Charvel E, Chen Y, Ciofi C, Clawson HM, Collins JC, Correard S, Corrigan S, Couture M, Crawford AJ, D'Alessandre ND, da Conceicao HB, da Fonseca RR, Daigavane M, Dalapicolla J, de Bruyn M, de Jong E, De Panis DN, Detrich HW, Scott CD, Diekhans M, Duarte E, Durbin R, Escalona M, Eschenbrenner M, Fedrigo O, Fenn J, Flannery P, Forde N, Gable SM, Galante PA, Ganesan R, Gardiner A, Garrison E, Gemmell NJ, Gilbert MTP, Giudicelli F, Gonçalves TM, Guardia GDA, Guarracino A, Gupta A, Haase B, Hays D, Hickey G, Hiller M, Hime PM, Hogg CJ, Horan KM, Howe K, Jackson D, Jain N, Kang L, Kliver S, Ko BJ, Koepfli KP, Komissarov A, Komoroske LM, Koo B, Koren S, Korlach J, Kovacic I, Krasheninnikova K, Kuderna LF, Langlois RA, Lariviere D, Larkin DM, Lee C, Lee YH, Lewin HA, Lim D, Lou RN, Mak SS, Makova KD, Marín-Gual L, Marques-Bonet T, Martin FJ, Mathers TC, Mazzoni CJ, McCaffrey K, McCarthy SA, Medico JA, Mercuri RLV, Meyer A, Michalak P, Mirarab S, Morin PA, Mountcastle J, Murphy RW, Murphy TD, Myers EW, Naylor GJ, Near T, Nekrutenko A, Ning Z, Novak BJ, O'Brien MF, O'Connell MJ, O'Toole BP, Paez S, Paten B, Paulini M, Pelan SE, Pennell M, Pfenning AR, Phillippy AM, Pinto B, Pippel M, Popova M, Prylutskyi M, Rhie A, Crollius HR, Ruiz-Herrera A, Ryder O, Safonova Y, Santos CA, Schatz MC, Secomandi S, Shaffer HB, Shalmiyev L, Shapiro B, Smith JJ, Sollitto M, Sotero-Caio CG, Steiner CC, Sudmant PH, Sweeney DJ, Talbot SC, Taylor CH, Teeling EC, Thibaud-Nissen F, Tilley T, Timoshevskaya N, Traore P, Turakhia Y, Uliano-Silva M, Venditti C, Venkatesh B, Vernes SC, Warren WC, Whelan CV, Wilson MA, Winkler S, Wood JM, Zhang G, Zhao G, Jarvis ED, Vertebrate Genomes Project Consortium Phase I. PMID: 42395566; PMCID: PMC13320880.
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Global adaptation to climate change in the twilight zone revealed by shared signals of selection in mesopelagic lanternfishes. bioRxiv. 2026 May 26.
Cama B, Tian D, Siu N, Frable B, Prado X, Yalisove M, Smith L, Dowlin A, Johnsen S, Salvanes AGV, Tseng ZJ, Correa A, Arcila D, Martin CH. PMID: 42244678; PMCID: PMC13232121.
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Ecological and genomic signatures of the convergent evolution of planktivory in fossil and living reef fishes over deep time. Nat Commun. 2026 May 22; 17(1).
Santaquiteria A, Arcila D, Carnevale G, Rincon-Sandoval M, Melendez-Vazquez F, White WT, Baldwin CC, Westneat MW, Ortí G, Tyler JC, Betancur-R R. PMID: 42173838.
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Phylogenomics of poachers (Agonidae) and the evolution of armor in cottoid fishes (Perciformes: Cottoidei). Mol Phylogenet Evol. 2026 Apr; 217:108552.
Vandenberg ML, Heiple Z, Kolmann MA, Buser T, Summers AP, Meléndez-Vazquez F, Arcila D, Maslenikov KP, Tornabene L. PMID: 41581679.
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Second record and range extension of the one-jaw eel, Monognathus jesse, from the northeastern Pacific Ocean (Anguilliformes: Monognathidae). J Fish Biol. 2026 Jun; 108(6):1712-1716.
Frable BW, Arcila D, Choy CA. PMID: 41546465.
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Parallel shifts in differential gene expression reveal convergent miniaturization in fishes. Proc Natl Acad Sci U S A. 2025 Oct 28; 122(43):e2512299122.
Troyer EM, White WT, Betancur-R R, Arcila D. PMID: 41123994; PMCID: PMC12582303.
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Genome-wide phylogeny reshapes our understanding of the evolution of deep-sea dragonfishes, bristlemouths, viperfishes, and allies (Stomiiformes). BMC Ecol Evol. 2025 Oct 21; 25(1):111.
Chang S, Heiple Z, Hays D, Melendez-Vazquez F, Lee C, Frable BW, Pogonoski J, Martinez CM, Betancur-R R, Arcila D. PMID: 41120872; PMCID: PMC12542184.
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Ancient climate changes and relaxed selection shape cave colonization in North American cavefishes. Proc Biol Sci. 2025 Jul; 292(2051):20242516.
Hart PB, Rincon-Sandoval M, Melendez-Vazquez F, Armbruster JW, Troyer EM, Bierstein OM, Gough BJ, Betancur-R R, Niemiller ML, Arcila D. PMID: 40669076.
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Ecological interactions and genomic innovation fueled the evolution of ray-finned fish endothermy. Sci Adv. 2025 Jun 27; 11(26):eads8488.
Melendez-Vazquez F, Lucaci AG, Selberg A, Clavel J, Rincon-Sandoval M, Santaquiteria A, White WT, Drabeck D, Carnevale G, Duarte-Ribeiro E, Miya M, Westneat MW, Baldwin CC, Hughes LC, Ortí G, Kosakovsky Pond SL, Betancur-R R, Arcila D. PMID: 40561012; PMCID: PMC12190012.
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The complete genome sequences of 12 species of Percopsiformes. Biodivers Genomes. 2025; 2025.
Niemiller ML, Hart PB, Pirro S, Arcila D. PMID: 40256647; PMCID: PMC12007890.
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Colonization Dynamics Explain the Decoupling of Species Richness and Morphological Disparity in Syngnatharian Fishes across Oceans. Am Nat. 2025 Mar; 205(3):E80-E99.
Santaquiteria A, Miller EC, Rosas-Puchuri U, Pedraza-Marrón CDR, Troyer EM, Westneat MW, Carnevale G, Arcila D, Betancur-R R. PMID: 39965231.
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Reduced evolutionary constraint accompanies ongoing radiation in deep-sea anglerfishes. Nat Ecol Evol. 2025 Mar; 9(3):474-490.
Miller EC, Faucher R, Hart PB, Rincón-Sandoval M, Santaquiteria A, White WT, Baldwin CC, Miya M, Betancur-R R, Tornabene L, Evans K, Arcila D. PMID: 39604701.
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Ecological diversification of sea catfishes is accompanied by genome-wide signatures of positive selection. Nat Commun. 2024 11 20; 15(1):10040.
Rincon-Sandoval M, De-Kayne R, Shank SD, Pirro S, Ko'ou A, Abueg L, Tracey A, Mountcastle J, O'Toole B, Balacco J, Formenti G, Jarvis ED, Arcila D, Kosakovsky Pond SL, Davis A, Bloom DD, Betancur-R R. PMID: 39567489; PMCID: PMC11579386.
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Evolutionary innovation accelerates morphological diversification in pufferfishes and their relatives. Evolution. 2024 10 28; 78(11):1869-1882.
Troyer EM, Evans KM, Goatley CHR, Friedman M, Carnevale G, Nicholas B, Kolmann M, Bemis KE, Arcila D. PMID: 39258573.
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Phylogenomics, Lineage Diversification Rates, and the Evolution of Diadromy in Clupeiformes (Anchovies, Herrings, Sardines, and Relatives). Syst Biol. 2024 10 25; 73(4):683-703.
Egan JP, Simons AM, Alavi-Yeganeh MS, Hammer MP, Tongnunui P, Arcila D, Betancur-R R, Bloom DD. PMID: 38756097.
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Gene loss and relaxed selection of plaat1 in vertebrates adapted to low-light environments. Proc Biol Sci. 2024 06; 291(2024):20232847.
Drabeck DH, Wiese J, Gilbertson E, Arroyave J, Stiassny MLJ, Alter SE, Borowsky R, Hendrickson DA, Arcila D, McGaugh SE. PMID: 38864338; PMCID: PMC11285778.
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3 Fields:
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Phylogenomic and comparative genomic analyses support a single evolutionary origin of flatfish asymmetry. Nat Genet. 2024 Jun; 56(6):1069-1072.
Duarte-Ribeiro E, Rosas-Puchuri U, Friedman M, Woodruff GC, Hughes LC, Carpenter KE, White WT, Pogonoski JJ, Westneat M, Diaz de Astarloa JM, Williams JT, Santos MD, Domínguez-Domínguez O, Ortí G, Arcila D, Betancur-R R. PMID: 38802566.
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3 Fields:
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Conservation of Affinity Rather Than Sequence Underlies a Dynamic Evolution of the Motif-Mediated p53/MDM2 Interaction in Ray-Finned Fishes. Mol Biol Evol. 2024 02 01; 41(2).
Mihalic F, Arcila D, Pettersson ME, Farkhondehkish P, Andersson E, Andersson L, Betancur-R R, Jemth P. PMID: 38301272; PMCID: PMC10901556.
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Gene loss and relaxed selection of plaat1 in vertebrates adapted to low-light environments. bioRxiv. 2023 Dec 13.
Drabeck DH, Wiese J, Gilbertson E, Arroyave J, Arcila D, Alter SE, Borowsky R, Hendrickson D, Stiassny M, McGaugh SE. PMID: 38168154; PMCID: PMC10760033.
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Many ways to build an angler: diversity of feeding morphologies in a deep-sea evolutionary radiation. Biol Lett. 2023 06; 19(6):20230049.
Heiple Z, Huie JM, Medeiros APM, Hart PB, Goatley CHR, Arcila D, Miller EC. PMID: 37376854; PMCID: PMC10300507.
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4 Fields:
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Transcriptomic analysis provides insight into the mechanism of IKKβ-mediated suppression of HPV18E6-induced cellular abnormalities. G3 (Bethesda). 2023 04 11; 13(4).
Collins QP, Grunsted MJ, Arcila D, Xiong Y, Padash Barmchi M. PMID: 36722216; PMCID: PMC10085804.
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Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds. bioRxiv. 2023 Mar 16.
McLaughlin JF, Aguilar C, Bernstein JM, Navia-Gine WG, Cueto-Aparicio LE, Alarcon AC, Alarcon BD, Collier R, Takyar A, Vong SJ, López-Chong OG, Driver R, Loaiza JR, De León LF, Saltonstall K, Lipshutz SE, Arcila D, Brock KM, Miller MJ. PMID: 36993716; PMCID: PMC10055050.
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Phylogenomics of Bony-Tongue Fishes (Osteoglossomorpha) Shed Light on the Craniofacial Evolution and Biogeography of the Weakly Electric Clade (Mormyridae). Syst Biol. 2022 08 10; 71(5):1032-1044.
Peterson RD, Sullivan JP, Hopkins CD, Santaquiteria A, Dillman CB, Pirro S, Betancur-R R, Arcila D, Hughes LC, Ortí G. PMID: 35041001.
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9 Fields:
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The impact of paleoclimatic changes on body size evolution in marine fishes. Proc Natl Acad Sci U S A. 2022 07 19; 119(29):e2122486119.
Troyer EM, Betancur-R R, Hughes LC, Westneat M, Carnevale G, White WT, Pogonoski JJ, Tyler JC, Baldwin CC, Ortí G, Brinkworth A, Clavel J, Arcila D. PMID: 35858316; PMCID: PMC9308125.
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11 Fields:
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Molecular and morphological evidence revalidates Acrobrycontarijae (Characiformes, Characidae) and shows hidden diversity. Zookeys. 2022; 1091:99-117.
Briñoccoli YF, Bogan S, Arcila D, Rosso JJ, Mabragaña E, Delpiani SM, de Astarloa JMD, Cardoso YP. PMID: 35586022; PMCID: PMC9005463.
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Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria). Syst Biol. 2021 10 13; 70(6):1123-1144.
Arcila D, Hughes LC, Meléndez-Vazquez B, Baldwin CC, White WT, Carpenter KE, Williams JT, Santos MD, Pogonoski JJ, Miya M, Ortí G, Betancur-R R. PMID: 33783539.
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11 Fields:
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Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences. Syst Biol. 2021 10 13; 70(6):1145-1162.
Santaquiteria A, Siqueira AC, Duarte-Ribeiro E, Carnevale G, White WT, Pogonoski JJ, Baldwin CC, Ortí G, Arcila D, Ricardo BR. PMID: 33892493.
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14 Fields:
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Exon-capture data and locus screening provide new insights into the phylogeny of flatfishes (Pleuronectoidei). Mol Phylogenet Evol. 2022 01; 166:107315.
Atta CJ, Yuan H, Li C, Arcila D, Betancur-R R, Hughes LC, Ortí G, Tornabene L. PMID: 34537325.
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2 Fields:
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Evolutionary determinism and convergence associated with water-column transitions in marine fishes. Proc Natl Acad Sci U S A. 2020 12 29; 117(52):33396-33403.
Rincon-Sandoval M, Duarte-Ribeiro E, Davis AM, Santaquiteria A, Hughes LC, Baldwin CC, Soto-Torres L, Acero P A, Walker HJ, Carpenter KE, Sheaves M, Ortí G, Arcila D, Betancur-R R. PMID: 33328271; PMCID: PMC7777220.
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13 Fields:
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Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics. Mol Ecol Resour. 2021 Apr; 21(3):816-833.
Hughes LC, Ortí G, Saad H, Li C, White WT, Baldwin CC, Crandall KA, Arcila D, Betancur-R R. PMID: 33084200.
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10 Fields:
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Life history, distribution and molecular phylogenetics of the Upward-Mouth Spikefish Atrophacanthus japonicus (Teleostei: Tetraodontiformes: Triacanthodidae). J Fish Biol. 2019 Apr; 94(4):578-584.
Bemis KE, Tyler JC, Arcila D. PMID: 30734929.
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Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes. Evolution. 2019 02; 73(2):329-345.
Betancur-R R, Arcila D, Vari RP, Hughes LC, Oliveira C, Sabaj MH, Ortí G. PMID: 30426469.
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22 Fields:
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Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proc Natl Acad Sci U S A. 2018 06 12; 115(24):6249-6254.
Hughes LC, Ortí G, Huang Y, Sun Y, Baldwin CC, Thompson AW, 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, Venkatesh B, Shi Q. PMID: 29760103; PMCID: PMC6004478.
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245 Fields:
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Mass extinction in tetraodontiform fishes linked to the Palaeocene-Eocene thermal maximum. Proc Biol Sci. 2017 Nov 15; 284(1866).
Arcila D, Tyler JC. PMID: 29118135; PMCID: PMC5698648.
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Trophic evolution in African citharinoid fishes (Teleostei: Characiformes) and the origin of intraordinal pterygophagy. Mol Phylogenet Evol. 2017 08; 113:23-32.
Lavoué S, Arnegard ME, Rabosky DL, McIntyre PB, Arcila D, Vari RP, Nishida M. PMID: 28478196.
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Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life. Nat Ecol Evol. 2017 Jan 13; 1(2):20.
Arcila D, Ortí G, Vari R, Armbruster JW, Stiassny MLJ, Ko KD, Sabaj MH, Lundberg J, Revell LJ, Betancur-R R. PMID: 28812610.
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Erratum to: Molecular phylogeny of the subfamily Stevardiinae Gill, 1858 (Characiformes: Characidae): classification and the evolution of reproductive traits. BMC Evol Biol. 2015 Dec 03; 15:269.
Thomaz AT, Arcila D, Ortí G, Malabarba LR. PMID: 26634700; PMCID: PMC4669599.
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Molecular phylogeny of the subfamily Stevardiinae Gill, 1858 (Characiformes: Characidae): classification and the evolution of reproductive traits. BMC Evol Biol. 2015 Jul 21; 15:146.
Thomaz AT, Arcila D, Ortí G, Malabarba LR. PMID: 26195030; PMCID: PMC4509481.
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12 Fields:
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An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae). Mol Phylogenet Evol. 2015 Jan; 82 Pt A:131-45.
Arcila D, Alexander Pyron R, Tyler JC, Ortí G, Betancur-R R. PMID: 25462998.
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42 Fields:
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The tree of life and a new classification of bony fishes. PLoS Curr. 2013 Apr 18; 5.
Betancur-R R, Broughton RE, Wiley EO, Carpenter K, López JA, Li C, Holcroft NI, Arcila D, Sanciangco M, Cureton Ii JC, Zhang F, Buser T, Campbell MA, Ballesteros JA, Roa-Varon A, Willis S, Borden WC, Rowley T, Reneau PC, Hough DJ, Lu G, Grande T, Arratia G, Ortí G. PMID: 23653398; PMCID: PMC3644299.
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