Publications
A full list of publications is available on Google Scholar
Research highlights
We found exceptional resolution for relationships within the largest family of marine fishes. We explored how assessing conflict from biological and non-biological signals can uncover support for alternative hypotheses.
LC Hughes, CM Nash, WT White, MW Westneat
Genomic ddRAD data uncovers a hybrid zone between marine and freshwater silversides in the Mar Chiquita estuary, Argentina. Check out a summary of this paper in English and Spanish here!
M González-Castro, YP Cardoso, LC Hughes, G Ortí
Lead by PhD Candidate Chloe M. Nash at University of Chicago, we investigated the evolutionary history of goatfishes and found that they emerged surprisingly recently! Most goatfish species evolved within the past 5 million years, but have relatively conserved morphology.
CM Nash, LL Lungstrom, LC Hughes, MW Westneat
Molecular Phylogenetics & Evolution (2022)
Ancient evolutionary radiations with rapid branching at the base of the tree are difficult problems in phylogenetics. We show how different measures of branch support compare in resolving these difficult clades. * These authors contributed equally to this article.
D Arcila*, LC Hughes*, F Meléndez-Vazquez, CC Baldwin, WT White, KE Carpenter, JT Williams, MD Santos, JJ Pogonoski, M Miya, G Ortí, R Betancur-R
We developed seven probe sets for sequence capture of ~1,100 single-copy exons, to advance the phylogenomics of ray-finned fishes. A tutorial of our bioinformatics pipeline is available on GitHub.
LC Hughes, G Ortí, H Saad, C Li, WT White, CC Baldwin, KA Crandall, D Arcila, R Betancur-R
Molecular Ecology Resources (2021)
Genomic data uncover the evolutionary history of Odontesthes silversides, revealing three transitions from marine to freshwater habitats, and different patterns of hybridization in eastern and western South America.
LC Hughes, YP Cardoso, JA Sommer, R Cifuentes, M Cuello, GM Somoza, M González-Castro, LR Malabarba, V Cussac, EM Habit, R Betancur-R, G Ortí
The tree of life of ray-finned fishes inferred from over 300 genomes and transcriptomes - one of the largest analyses of its kind to date.
LC Hughes, G Ortí, Y Huang, Y Sun, CC Baldwin, AW Thompson, D Arcila, R Betancur-R, C Li, L Becker, N Bellora, X Zhao, X Li, M Wang, C Fang, B Xie, Z Zhou, H Huang, S Chen, B Venkatesh, Q Shi
Proceedings of the National Academy of Sciences (2018)
Comparing gill transcriptomes between marine and freshwater silversides uncovers genes that may be involved in adaptation to these different habitats, and also suggests differences in their microbiomes.
LC Hughes, GM Somoza, BN Nguyen, JP Bernot, M González-Castro, JMD de Astarloa, G Ortí
All publications - L.C. Hughes
Phylogenomic and comparative genomic analyses support a single evolutionary origin of flatfish asymmetry
E Duarte-Ribeiro, U Rosas-Puchuri, M Friedman, GC Woodruff, LC Hughes, KE Carpenter, WT White, JJ Pogonoski, M Westneat, JM Diaz de Astarloa, JT Williams, MD Santos, O Domínguez-Domínguez, G Ortí, D Arcila, R Betancur-R
Nature Genetics (2024)
Concordance and discordance in the phylogenomics of wrasses and parrotfishes (Teleostei:Labridae)
LC Hughes, CM Nash, WT White, MW Westneat
Systematic Biology (2023)
Hybridization is strongly constrained by salinity during secondary contact between silverside fishes (Odontesthes, Atheriniformes)
M González-Castro, YP Cardoso, LC Hughes, G Ortí
Heredity (2022)
The impact of paleoclimatic changes on body size evolution in marine fishes
EM Troyer, R Betancur-R, LC Hughes, M Westneat, G Carnevale, WT White, JJ Pogonoski, JC Tyler, CC Baldwin, G Ortí, A Brinkworth, J Clavel, D Arcila
Proceedings of the National Academy of Sciences (2022)
Phylogenomics and body shape morphometrics reveal recent origin and diversification in the goatfishes (Syngnatharia: Mullidae)
CM Nash, LL Lungstrom, LC Hughes, MW Westneat
Molecular Phylogenetics & Evolution (2022)
Phylogenomics of Bony-Tongue Fishes (Osteoglossomorpha) Shed Light on the Craniofacial Evolution and Biogeography of the Weakly Electric Clade (Mormyridae)
RD Peterson, JP Sullivan, CD Hopkins, A Santaquiteria, CB Dillman, S Pirro, R Betancur-R, D Arcila, LC Hughes, G Ortí
Systematic Biology (2022)
Exon-capture data and locus screening provide new insights into the phylogeny of flatfishes (Pleuronectoidei)
CJ Atta, H Yuan, C Li, D Arcila, R Betancur-R, LC Hughes, G Ortí, L Tornabene
Molecular Phylogenetics and Evolution (2022)
Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei:Pelagiaria)
D Arcila*, LC Hughes*, F Meléndez-Vazquez, CC Baldwin, WT White, KE Carpenter, JT Williams, MD Santos, JJ Pogonoski, M Miya, G Ortí, R Betancur-R
Systematic Biology (2021)
Phylogenomics of Piranhas and Pacus (Serrasalmidae) Uncovers How Dietary Convergence and Parallelism Obfuscate Traditional Morphological Taxonomy
MA Kolmann, LC Hughes, LP Hernandez, D Arcila, R Betancur-R, MH Sabaj, H López-Fernández, G Ortí
Systematic Biology (2021)
Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics
LC Hughes, G Ortí, H Saad, C Li, WT White, CC Baldwin, KA Crandall, D Arcila, R Betancur-R
Molecular Ecology Resources (2021)
Evolutionary determinism and convergence associated with water-column transitions in marine fishes
M Rincon-Sandoval, E Duarte-Ribeiro, AM Davis, A Santaquiteria, LC Hughes, CC Baldwin, L Soto-Torres, A Acero, HJ Walker, KE Carpenter, M Sheaves, G Ortí, D Arcila, R Betancur-R
Proceedings of the National Academy of Sciences (2020)
Biogeography, habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data
LC Hughes, YP Cardoso, JA Sommer, R Cifuentes, M Cuello, GM Somoza, M González-Castro, LR Malabarba, V Cussac, EM Habit, R Betancur-R, G Ortí
Molecular Ecology (2020)
Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: The monophyly of characiform fishes
R Betancur-R, D Arcila, RP Vari, LC Hughes, C Oliveira, MH Sabaj ,G Ortí
Evolution (2019)
Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data
LC Hughes, G Ortí, Y Huang, Y Sun, CC Baldwin, AW Thompson, D Arcila, R Betancur-R, C Li, L Becker, N Bellora, X Zhao, X Li, M Wang, C Fang, B Xie, Z Zhou, H Huang, S Chen, B Venkatesh, Q Shi
Proceedings of the National Academy of Sciences (2018)
Transcriptomic differentiation underlying marine-to-freshwater transitions in the South American silversides Odontesthes argentinensis and O. bonariensis (Atheriniformes)
LC Hughes, GM Somoza, BN Nguyen, JP Bernot, M González-Castro, JMD de Astarloa, G Ortí
Ecology and Evolution (2017)
Kisspeptin system in pejerrey fish (Odontesthes bonariensis). Characterization and gene expression pattern during early developmental stages
MOT Bohórquez, AS Mechaly, LC Hughes, D Campanella, G Ortí, LF Canosa, GM Somoza
Comparative Biochemistry and Physiology Part A - Molecular & Integrative Physiology (2017)
Multi-locus fossil-calibrated phylogeny of Atheriniformes (Teleostei, Ovalentaria)
D Campanella, LC Hughes, PJ Unmack, DD Bloom, KR Piller, G Ortí
Molecular Phylogenetics and Evolution (2015)
Can ecotypic differences in male courtship behaviour be explained by visual cues provided by female threespine stickleback?
LC Hughes, SA Foster, JA Baker
Evolutionary Ecology Research (2013)