Evolutionary dynamics of gene and isoform regulation underlying rapid and parallel adaptive radiations

Evolutionary dynamics of gene and isoform regulation underlying rapid and parallel adaptive radiations | 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 Research Article Evolutionary dynamics of gene and isoform regulation underlying rapid and parallel adaptive radiations Pooja Singh This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6705667/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract While the contribution of gene expression (GE) to adaptive evolution is widely accepted, the role of alternative splicing (AS) remains less understood. Here, we investigate AS and GE across three iconic adaptive radiations of African cichlid fishes that evolved within < 16,000 to 3.8 million years. We show that AS evolves faster than GE, with both sources of variation being ‘fine-tuned’ over evolutionary time to become species-specific and clade-specific, respectively. Ecologically divergent species from younger radiations exhibit greater differences in splicing than those from older radiations. Most of these differentially spliced isoforms arose from standing variation, which was also present at low levels in non-radiating species, and increased in frequency during the adaptive radiation process. We identified several novel isoforms of craniofacial remodelling genes that emerged within each lake radiation and were differentially incorporated in the jaws of herbivorous vs. carnivorous species. Our findings indicate that a complex temporal interplay of GE and AS underlies adaptive radiation, with ancestral splice variation enabling rapid ecological diversification at early stages of speciation. Evolutionary Biology Evolutionary Genetics Marine and Freshwater Ecology gene regulation speciation convergent evolution trophic adaptation morphology Full Text Additional Declarations The authors declare no competing interests. Supplementary Files st26jawsuppinformation.pdf Cite Share Download PDF Status: Posted Version 1 posted 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. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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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-6705667","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":459195035,"identity":"179c62c6-e728-4ba6-9ed2-d69054bf61e9","order_by":0,"name":"Pooja Singh","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA/klEQVRIiWNgGAWjYJACAyDmAaEDHyqATGbmBqK1MD6ccQakhZGwFijgYTbmbQMxCGgxZ28+UPCDoU7GnH/tMWneebXR/O1ALT8qtuHUYtlzLMGwh+Ewj+WMd2mSc7cdz51xmLGBsefMbdz+uJFjYAD0OI/BjTNmEm+3HcttAGphZmzDr8XwD0MdRAvvnGO584nRYszDwMxjcL7H2JC3oSZ3AyEtIL8YyxgcBtrCY/hwxrEDuRuBWg7i8wswxI4Zvqmoszc4f8bgwIeautx55w8ffPCjAo/DGBjYDMCRKZEA4h8Gix7AqR6ihfkBmMUPVleHT/EoGAWjYBSMUAAAU+tcq7AebKYAAAAASUVORK5CYII=","orcid":"","institution":"University of Bern","correspondingAuthor":true,"prefix":"","firstName":"Pooja","middleName":"","lastName":"Singh","suffix":""}],"badges":[],"createdAt":"2025-05-20 08:49:17","currentVersionCode":1,"declarations":{"humanSubjects":false,"vertebrateSubjects":true,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":true},"doi":"10.21203/rs.3.rs-6705667/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6705667/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":83245256,"identity":"f6d6d72c-fe57-4791-bba1-ff07faeb0560","added_by":"auto","created_at":"2025-05-21 16:54:56","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1815976,"visible":true,"origin":"","legend":"","description":"","filename":"st26jawparallelismNatGensubmission.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6705667/v1_covered_c8962d60-251f-4821-a32d-fb9fe82d8de5.pdf"},{"id":83242904,"identity":"1afb576d-4cc7-4c60-9f49-940010068383","added_by":"auto","created_at":"2025-05-21 16:22:53","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":1706505,"visible":true,"origin":"","legend":"","description":"","filename":"st26jawsuppinformation.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6705667/v1/9113b9ce07681209c3068332.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003eEvolutionary dynamics of gene and isoform regulation underlying rapid and parallel adaptive radiations\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"University of Bern","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":true,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"gene regulation, speciation, convergent evolution, trophic adaptation, morphology","lastPublishedDoi":"10.21203/rs.3.rs-6705667/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6705667/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eWhile the contribution of gene expression (GE) to adaptive evolution is widely accepted, the role of alternative splicing (AS) remains less understood. Here, we investigate AS and GE across three iconic adaptive radiations of African cichlid fishes that evolved within \u0026lt;\u0026thinsp;16,000 to 3.8\u0026nbsp;million years. We show that AS evolves faster than GE, with both sources of variation being \u0026lsquo;fine-tuned\u0026rsquo; over evolutionary time to become species-specific and clade-specific, respectively. Ecologically divergent species from younger radiations exhibit greater differences in splicing than those from older radiations. Most of these differentially spliced isoforms arose from standing variation, which was also present at low levels in non-radiating species, and increased in frequency during the adaptive radiation process. We identified several novel isoforms of craniofacial remodelling genes that emerged within each lake radiation and were differentially incorporated in the jaws of herbivorous vs. carnivorous species. 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