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Here, we examine the largely unexplored genetic architecture of internal bone microstructural variation between marine and freshwater stickleback. Micro-computed tomography X-ray analysis revealed differences in the porosity, bone thickness, and bone volume fraction within armor plates and vertebrae from a marine and freshwater stickleback. Quantitative trait locus mapping in F2 progeny from a marine \u00d7 freshwater stickleback cross identified a significant locus on chromosome 4 influencing multiple aspects of armor plate internal microstructure. This locus overlaps the well-characterized Eda region previously known to control armor plate number and size. Co-mapping of bone microstructure could be due to pleiotropic effects of Eda on multiple aspects of plate development or to changes in closely linked genes including Itm2a, which also plays a role in bone formation. Most bone microstructure traits in vertebrae showed weak or no genetic signal, consistent with a polygenic architecture. However, we identified a highly significant locus on chromosome 17 that is strongly associated with abnormally thickened \u201civory vertebrae\u201d that occurred in 8.4% of F2 offspring. This phenotype resembles Paget\u2019s disease in humans, and the major locus region contains Tnfrsf1b, the stickleback ortholog of a human Paget\u2019s disease susceptibility gene TNFRSF11A. Together, our findings identify genetic loci underlying natural variation in bone microstructure in wild fish and reveal a candidate gene associated with a disease-like skeletal phenotype, highlighting stickleback as a model for studying both evolutionary and pathological bone biology.<\/jats:p>","DOI":"10.1093\/g3journal\/jkag164","type":"journal-article","created":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T17:59:33Z","timestamp":1791482373000},"source":"Crossref","is-referenced-by-count":0,"title":["Genetic analysis of bone morphometry and ivory vertebrae in threespine stickleback"],"prefix":"10.1093","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2006-9350","authenticated-orcid":false,"given":"Veronica C","family":"Behrens","sequence":"first","affiliation":[{"name":"Department of Developmental Biology, Stanford University School of Medicine , Stanford, CA 94305 ,","place":["United 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