Rapid evolution of a large highly-divergent haplotype region during a bacterial epidemic

Rapid evolution of a large highly-divergent haplotype region during a bacterial epidemic | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Rapid evolution of a large highly-divergent haplotype region during a bacterial epidemic Eric Dexter, Pascal Angst, Peter Fields, Fabian Scheuber, Marlon Henseler, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6422822/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 24 Nov, 2025 Read the published version in Heredity → Version 1 posted 8 You are reading this latest preprint version Abstract The field of population genetics is primarily focused on simple genetic variants such as single nucleotide polymorphisms (SNPs), small insertions or deletions (INDELs), and copy-number variants (CNVs). However, large-scale genomic variants are beginning to undergo increased scrutiny as new sequencing methods facilitate their discovery. Here, we report an unusually large and highly variable structural feature in the Daphnia magna genome that is strongly associated with immune function. Alternative forms of this genomic structure encompass 2-5 Mb non-homologous regions that contain largely non-overlapping sets of genes. One highly divergent haplotype (HDH-5-1.1) shows a near-perfect correlation with susceptibility to a common strain of the virulent bacterial, Pasteuria ramosa, which is a common and widespread parasite of D. magna. Rapid selection against HDH-5-1.1 was observed during a natural P. ramosa epidemic, coinciding with a strong population-wide increase in resistance. Despite recurrent episodes of strong selection against Pasteuria susceptibility, we observe evidence of balancing selection at this hyper-divergent region - suggesting counter selection against the resistant form by a yet unidentified mechanism. Biological sciences/Genetics/Genomics/Comparative genomics Biological sciences/Genetics/Genomics/Genome evolution Biological sciences/Evolution/Evolutionary genetics Biological sciences/Genetics/Population genetics/Genetic variation/Structural variation Biological sciences/Genetics/Genome/Genetic variation/Structural variation Daphnia Pasteuria supergene coevolution immunity highly-diverged haplotype Full Text Additional Declarations There is no duality of interest Cite Share Download PDF Status: Published Journal Publication published 24 Nov, 2025 Read the published version in Heredity → Version 1 posted Editorial decision: revise 18 Jul, 2025 Review # 2 received at journal 08 Jul, 2025 Reviewer # 2 agreed at journal 20 Jun, 2025 Review # 1 received at journal 23 May, 2025 Reviewer # 1 agreed at journal 07 May, 2025 Reviewers invited by journal 02 May, 2025 Editor assigned by journal 10 Apr, 2025 First submitted to journal 10 Apr, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6422822","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":451223537,"identity":"581c0e18-9d75-4053-837f-386a3143949a","order_by":0,"name":"Eric 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