Abstract
The origin of the extensive phenotypic divergence characterizing adaptive radiation could often be geographically localized and genetically simple. In a classic case of a trophically polymorphic cichlid fish (Herichthys minckleyi), we investigated alternative genomic processes that could have produced its extreme within-population variation in pharyngeal jaw tooth size. First, we generated a high-quality reference genome for its close relative (H. cyanoguttatus) to dissect the genetic architecture of this dental polymorphism. Then, using whole genome resequencing across the small Cuatro Ciénegas valley where H. minckleyi is endemic, we found substantial micro-geographic subdivision and effectively no genetic structure due to pharyngeal morphotype. We also employed quantitative trait loci mapping and genome wide association to pinpoint a single peak in an Iroquois-related (IRX) gene cluster associated with H. minckleyi’s dental divergence. Interspecific introgression in this genomic region appears negligible, suggesting the genomic basis of the polymorphism likely arose within cichlids confined to Cuatro Ciénegas. Because H. minckleyi tooth size disparity is comparable to that found in all Central American cichlids, this offers a striking example of how genomic divergence at a single locus could produce a punctuated burst of eco-morphological divergence that generates phenotypic breadth comparable to a highly diverse cichlid adaptive radiation.
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Data availability
The Herichthys cyanogutattus genome assembly, the genomic data used to build and scaffold the contigs (PacBio HiFi long reads, 10x chromium synthetic long reads, Hi-C short reads, and Bionano optical map), and the transcriptomic data used to annotate the protein-coding genes in the genome have been deposited into the NCBI database under BioProject PRJNA1163081. The ddRAD data of the two parents and the 193 F2 individuals used to produce the linkage map and perform QTL mapping of the tooth area have been deposited into the NCBI database under BioProject PRJNA1165996. The WGS data of the 70 individuals, including the two parents of the QTL cross, used to analyze population structure, gene flow, and carry out GWAS, have been deposited into the NCBI database under BioProject PRJNA1167894. The Herichthys cyanogutattus protein-coding gene annotation123 has been deposited into FigShare.
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Acknowledgements
The Mexican government provided permits for collection of fish used in this study (Permiso de Pesca de Fomento 230401-613-03, 2-130409-0961, DAN-01202, and DAN-02939). The LongRead Project of the Max-Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) provided funding and expertise as part of the DcGC Dresden-concept Genome Center, a core facility of the CMCB and Technology Platform of the TUD Dresden University of Technology. The National Geographic Society to CDH, US National Science Foundation (NSF IOS-0919459) to CDH, and Deutsche Forschungsgemeinschaft Taxonomics SPP 1991 and grant (DFG 447185000) to CDH and AM provided funding for this study.
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Conception and Design: C.D.H., P.F., P.M. F.J.G.L., A.M. Data Analysis: C.D.H., P.F., P.M., A.F.K., G. M.-S., M.P., F.J.G.L., E.M. Initial Drafting of Manuscript: C.D.H. Critical Review and Editing of the Manuscript: All authors contributed to the critical review and editing of the manuscript.
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Hulsey, C.D., Franchini, P., Masonick, P. et al. Divergence at the IRX gene cluster underlies extreme trophic polymorphism in a cichlid fish (Herichthys minckleyi). Commun Biol (2026). https://doi.org/10.1038/s42003-026-09689-6
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DOI: https://doi.org/10.1038/s42003-026-09689-6
