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In a classic case of a trophically polymorphic cichlid fish (\n                    <jats:italic>Herichthys minckleyi<\/jats:italic>\n                    ), 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 (\n                    <jats:italic>H. cyanoguttatus<\/jats:italic>\n                    ) to dissect the genetic architecture of this dental polymorphism. Then, using whole genome resequencing across the small Cuatro Ci\u00e9negas valley where\n                    <jats:italic>H. minckleyi<\/jats:italic>\n                    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 (\n                    <jats:italic>IRX<\/jats:italic>\n                    ) gene cluster associated with\n                    <jats:italic>H. minckleyi<\/jats:italic>\n                    \u2019s dental divergence. Interspecific introgression in this genomic region appears negligible, suggesting the genomic basis of the polymorphism likely arose within cichlids confined to Cuatro Ci\u00e9negas. Because\n                    <jats:italic>H. minckleyi<\/jats:italic>\n                    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.\n                  <\/jats:p>","DOI":"10.1038\/s42003-026-09689-6","type":"journal-article","created":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T15:54:59Z","timestamp":1771689299000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Divergence at the IRX gene cluster underlies extreme trophic polymorphism in a cichlid fish (Herichthys minckleyi)"],"prefix":"10.1038","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9653-6728","authenticated-orcid":false,"given":"C. 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