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Transposable elements (TEs) represent an underestimated source of genetic variation in eukaryotic genomes. By integrating 516 whole\u2010genome resequencing datasets and 236 transcriptomes from common carp (\n                    <jats:italic>Cyprinus carpio<\/jats:italic>\n                    ), a representative allotetraploid fish, we constructed the first population\u2010scale landscape of TE insertions in teleosts. TE insertions are widespread in the carp genome and preferentially associated with stress\u2010responsive genes, with DNA transposons as major contributors. Relaxed purifying selection and TE burst events coexist, generating abundant variation for subsequent subspecies differentiation. Compared with a closely related diploid species, carp exhibits more exonic TE insertions and shorter TE\u2013gene distances, and multiple TE superfamilies expanded during tetraploidization. Genome\u2010wide association analyses uncovered intragenic TE variants underlying domesticated traits missed by SNPs, including DNA transposon deletions associated with scale reduction and altered body shape. Notably, lighter\u2010colored individuals harbor homozygous deletions of LTR and DNA transposons within\n                    <jats:italic>mdfic2<\/jats:italic>\n                    , whose knockout in zebrafish reduces pigmentation. Most trait\u2010associated variants reflect lineage\u2010specific loss of ancient TE insertions rather than recent transposition. Overall, these findings highlight the distinct role of TEs in polyploid genome evolution and phenotypic diversification, providing new insights into TE dynamics in vertebrates.\n                  <\/jats:p>","DOI":"10.1002\/advs.77790","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T05:17:51Z","timestamp":1789622271000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Transposable Element Dynamics Drive the Genomic Evolution and Phenotypic Diversification of Allotetraploid Common Carp"],"prefix":"10.1002","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5913-2102","authenticated-orcid":false,"given":"Shuimu","family":"Hu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Mariculture Breeding, College of Ocean and Earth Sciences Xiamen University Xiamen China"},{"name":"Fujian Key Laboratory of Genetics and Breeding of Marine Organisms College of Ocean and 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