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MHC diversity, driven by pathogen-mediated selection, is vital for species survival and is characterized by high genetic diversity in many taxa, namely at the sequence, allelic and haplotype levels. Chondrichthyans, the most basal jawed vertebrates with an adaptive immune system, exhibit a high diversity of MHC gene lineages conservatively organized in a compact region of the genome. Such genomic architecture suggests linkage among MHC genes, where alleles from different genes possibly co-segregate together. Such condition may have major implications on immune response, individual fitness and evolution. In this study, we examine MHC II\u03b2 haplotype diversity in a model shark species, the small spotted catshark,\n                    <jats:italic>Scyliorhinus canicula.<\/jats:italic>\n                    Making use of pedigree data, we reconstructed MHC II\u03b2 haplotypes to understand allele transmission from parent to offspring. Results indicate allele co-segregation consistent with tight linkage among MHC II\u03b2 genes, suggesting the presence of functional stable haplotypes inherited from parents to offspring. The reconstructed haplotypes suggested extensive haplotype diversity characterized by variable allele numbers and allelic lineage composition, as well as marked allelic divergence, consistent with previous population-level data on this species. These findings underscore the complexity of MHC genetics (and of MHC evolution) in chondrichthyans. Accurate reconstruction of MHC haplotypes and assessment of its functional significance are crucial for better understanding adaptive immune responses and MHC evolutionary dynamics in chondrichthyans.\n                  <\/jats:p>","DOI":"10.1007\/s00251-025-01376-w","type":"journal-article","created":{"date-parts":[[2025,4,2]],"date-time":"2025-04-02T23:41:29Z","timestamp":1743637289000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Allele co-segregation and haplotype diversity of MHC II\u03b2 genes in the small-spotted catshark Scyliorhinus canicula"],"prefix":"10.1007","volume":"77","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-3428-8838","authenticated-orcid":false,"given":"Alessia","family":"Rota","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3396-9822","authenticated-orcid":false,"given":"Ana","family":"Ver\u00edssimo","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2176-1488","authenticated-orcid":false,"given":"Arnaud","family":"Gaigher","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,3,31]]},"reference":[{"key":"1376_CR1","doi-asserted-by":"publisher","first-page":"892","DOI":"10.4049\/jimmunol.1901025","volume":"204","author":"T Almeida","year":"2020","unstructured":"Almeida T, Esteves PJ, Flajnik MF et al (2020) An ancient, MHC-linked, nonclassical class I lineage in Cartilaginous fish. 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