{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T18:06:37Z","timestamp":1789236397354,"version":"build-2803163510"},"posted":{"date-parts":[[2026,9,10]]},"group-title":"Evolutionary Biology","reference-count":98,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T00:00:00Z","timestamp":1788998400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R35GM151348"],"award-info":[{"award-number":["R35GM151348"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,10]]},"abstract":"<jats:p>The genomic architecture of immunoglobulin (IG) loci in birds has received remarkably little attention, despite their relevance to infectious disease susceptibility. One of the few exceptions is the domestic chicken, which has been found to use a completely different mechanism to generate a diverse IG repertoire than most vertebrates; rather than relying on V(D)J recombination, chickens primarily use somatic gene conversion. Whether this is true of all birds has remained unknown and untestable at scale until now. And importantly, it is not known how this alternative mechanism for antibody generation shapes, and is shaped by, genome evolution in birds. Leveraging IG locus annotations from 122 bird species generated through the Vertebrate Genomes Project and 17 species from the California Conservation Genomics Project, we show that avian IGH loci display a striking, previously unreported architecture of recurrent inverted duplications that generate direct and inverted copies of the same repeat unit, found in no other vertebrate lineage. Inversion density varies considerably across species, and population-level analyses reveal that these inversions evolve rapidly. We propose a model in which these inversions are actively maintained because they continuously replenish a pool of highly similar pseudogenes that serve as donors for somatic gene conversion, substituting for the large functional V gene repertoires other vertebrates use to generate IG diversity. This model makes a direct prediction: IGH loci should harbor few functional genes and many pseudogenes, while IGL loci, which typically lack this inversion architecture, should show the opposite pattern. Our cross-species analysis confirms this. To test the model at the level of the expressed repertoire, we generated paired whole-genome and Iso-seq data from a single wild-caught Red-winged Blackbird. Consistent with our predictions, a single terminal IGLV gene is diversified through gene conversion from surrounding pseudogenes, while IGH carries a large donor pool at which we also detect gene conversion. Together, these findings reveal that the molecular evolution of IG in birds is governed by fundamentally different constraints and processes than in the rest of known vertebrates.<\/jats:p>","DOI":"10.64898\/2026.09.05.749481","type":"posted-content","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T02:15:11Z","timestamp":1789092911000},"source":"Crossref","is-referenced-by-count":0,"title":["Gene conversion facilitates rapid evolution of inversions across avian immunoglobulin loci"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-7211-328X","authenticated-orcid":false,"given":"Katalin","family":"Voss","sequence":"first","affiliation":[{"name":"Department of Computational Biology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-0101-6313","authenticated-orcid":false,"given":"Daniel","family":"Hardesty","sequence":"additional","affiliation":[{"name":"Homer Senior High School, NY, USA"},{"name":"Binghamton University, Binghamton, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5402-1796","authenticated-orcid":false,"given":"Anton","family":"Zamyatin","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, Cornell University, Ithaca, NY, USA"},{"name":"Computer Science and Engineering Department, Pennsylvania State University, State College, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5810-3382","authenticated-orcid":false,"given":"Mariia","family":"Pospelova","sequence":"additional","affiliation":[{"name":"Computer Science and Engineering Department, Pennsylvania State University, State College, PA, USA"},{"name":"Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4257-462X","authenticated-orcid":false,"given":"Yixin","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9647-3627","authenticated-orcid":false,"given":"Maria Recuerda","family":"Carrasco","sequence":"additional","affiliation":[{"name":"Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0609-9542","authenticated-orcid":false,"given":"Anton","family":"Bankevich","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, Cornell University, Ithaca, NY, USA"},{"name":"Computer Science and Engineering Department, Pennsylvania State University, State College, PA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8408-8553","authenticated-orcid":false,"given":"Leonardo","family":"Campagna","sequence":"additional","affiliation":[{"name":"Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, NY, USA"},{"name":"Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9634-4216","authenticated-orcid":false,"given":"Yana","family":"Safonova","sequence":"additional","affiliation":[{"name":"Computer Science and Engineering Department, Pennsylvania State University, State College, PA, USA"},{"name":"Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA"},{"name":"Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2886-3970","authenticated-orcid":false,"given":"Matt","family":"Pennell","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, Cornell University, Ithaca, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026091210550946000_2026.09.05.749481v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/302575a0"},{"key":"2026091210550946000_2026.09.05.749481v1.2","unstructured":"Abbas AK , Lichtman AH , Pillai S , Baker DL . 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