Recent and Historical Determinants of Genomic Erosion by Structural Variation and SNPs Across a Pan-Holarctic Superspecies

Recent and Historical Determinants of Genomic Erosion by Structural Variation and SNPs Across a Pan-Holarctic Superspecies | 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 Recent and Historical Determinants of Genomic Erosion by Structural Variation and SNPs Across a Pan-Holarctic Superspecies Gabriel David, Patrik Rödin-Mörch, Kristinn Pétur Magnússon, Jacob Höglund This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8176843/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Despite disproportionate fitness impacts imposed by deleterious structural variants (SVs) and associated transposable elements, few studies have yet examined their relative contribution to genomic erosion. To examine the role of both recent and ancient population history in the accumulation of deleterious SVs relative to single nucleotide polymorphisms (SNPs), the rock and willow ptarmigan (Lagopus spp.) superspecies form an ideal pan-Holarctic system, harbouring a broad range of historical effective population sizes increasingly threatened by fragmentation and climate change. By contrasting diversity ratios for non-synonymous SNPs and non- neutral SVs across 99 individuals from 12 island and mainland populations, we find that purifying selection against most putatively deleterious SVs appears insufficient to prevent their long-term accumulation in small populations, conforming with classic nearly-neutral dynamics. Likewise, proportions of realised (homozygous), masked (heterozygous) and fixed drift load due to putative highly and mildly deleterious SVs mirrored SNPs in mostly accumulating as a function of increased homozygosity in smaller populations. However, population-specific differences in the accrual of drift debt due to SVs did not reflect historical Ne alone: elevated realised load but reduced drift load in the Pyrenees (relative to the smallest population; Svalbard) indicate that the effects of recent fragmentation-induced inbreeding have yet to fully manifest. Our findings highlight the need to account for recent population decline and fragmentation, rather than solely relying on historical Ne to predict outcomes of genomic erosion— especially given the potential for disproportionate drift debt imposed by deleterious SVs. Biological sciences/Evolution/Population genetics/Genetic variation/Structural variation Biological sciences/Evolution/Molecular evolution Full Text Additional Declarations There is NO Competing Interest. Supplementary Files SupplementaryMaterials.pdf Supplementary Materials for "Recent and Historical Determinants of Genomic Erosion by Structural Variation and SNPs Across a Pan-Holarctic Superspecies" r3.pdf Reporting Summary Cite Share Download PDF Status: Under Review 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. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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-8176843","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":569734026,"identity":"e0899e81-471f-48de-8be8-6bba4e32f9a8","order_by":0,"name":"Gabriel David","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA00lEQVRIiWNgGAWjYDACCQYDIMnMwMDeAKQNLEjRwnMApEWCFC0SCRAuQSAf3bztwcc91nLmks+vbvhRIMHA396dgFeL4Z1j5YYznqUbW87OKbvZA3SYxJmzG/BrmZFjJs1z4HDihts5aTd4gFoMJHKJ01K/4eaZtJt/iNEiLwHRkmBwg/3YbaJsMZA5ViY540C64YYzOWy3ZQwkeAj6RX528zaJDwes5Q2OH392880fGzn+9l4CthyAM3kMwCRe5WBbGuBM9gcEVY+CUTAKRsHIBACc+kkzb9uBZgAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0009-0007-2935-3335","institution":"Uppsala universitet","correspondingAuthor":true,"prefix":"","firstName":"Gabriel","middleName":"","lastName":"David","suffix":""},{"id":569734027,"identity":"b5357b89-d261-4bf3-a6f9-235fac748459","order_by":1,"name":"Patrik Rödin-Mörch","email":"","orcid":"","institution":"Uppsala University","correspondingAuthor":false,"prefix":"","firstName":"Patrik","middleName":"","lastName":"Rödin-Mörch","suffix":""},{"id":569734028,"identity":"2fc633be-46fd-4325-8052-c4ab3ece6700","order_by":2,"name":"Kristinn Pétur Magnússon","email":"","orcid":"","institution":"University of Akureyri","correspondingAuthor":false,"prefix":"","firstName":"Kristinn","middleName":"Pétur","lastName":"Magnússon","suffix":""},{"id":569734029,"identity":"f1b78e7e-5dd9-4195-9d38-33537e1f6d7c","order_by":3,"name":"Jacob Höglund","email":"","orcid":"https://orcid.org/0000-0002-5840-779X","institution":"Uppsala University","correspondingAuthor":false,"prefix":"","firstName":"Jacob","middleName":"","lastName":"Höglund","suffix":""}],"badges":[],"createdAt":"2025-11-21 22:45:13","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8176843/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8176843/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":99603926,"identity":"27d2fd07-4ae3-4ff3-9b74-2704fb63f9ea","added_by":"auto","created_at":"2026-01-06 11:03:34","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":1589810,"visible":true,"origin":"","legend":"","description":"","filename":"GenomicErosionbySVsMBEMainText.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8176843/v1/371d9143e02f47328c226a54.pdf"},{"id":99603924,"identity":"825ad25f-7bae-4624-adad-11c6116b92a6","added_by":"auto","created_at":"2026-01-06 11:03:34","extension":"json","order_by":1,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":6178,"visible":true,"origin":"","legend":"","description":"","filename":"NCOMMS2594464.json","url":"https://assets-eu.researchsquare.com/files/rs-8176843/v1/396563928dd9e7873c2d47e2.json"},{"id":99603927,"identity":"c8924a6f-b5d6-4593-be7a-7eee344dec29","added_by":"auto","created_at":"2026-01-06 11:03:34","extension":"pdf","order_by":2,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":1541614,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryMaterials.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8176843/v1/9b9964b3437197ebdc1a3dfe.pdf"},{"id":99804485,"identity":"71485068-81d0-4c54-a20c-a91eed5f4156","added_by":"auto","created_at":"2026-01-08 14:13:35","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":880225,"visible":true,"origin":"","legend":"Article File","description":"","filename":"GenomicErosionbySVsMBEMainText.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8176843/v1_covered_6a45d84b-8578-433c-9e38-8a1336f7d80f.pdf"},{"id":99792444,"identity":"f6761e7c-4315-40ba-bb1b-4d4acf1a5ddc","added_by":"auto","created_at":"2026-01-08 13:19:58","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":1541614,"visible":true,"origin":"","legend":"Supplementary Materials for \"Recent and Historical Determinants of Genomic Erosion by Structural Variation and SNPs Across a Pan-Holarctic Superspecies\"","description":"","filename":"SupplementaryMaterials.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8176843/v1/f9237606cea3bb85e6d70161.pdf"},{"id":99794467,"identity":"01d34bca-1fcd-4059-99e2-ac54234ac470","added_by":"auto","created_at":"2026-01-08 13:35:03","extension":"pdf","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":154721,"visible":true,"origin":"","legend":"Reporting Summary","description":"","filename":"r3.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8176843/v1/b45e70d2123db0bec8a3f0bc.pdf"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"Recent and Historical Determinants of Genomic Erosion by Structural Variation and SNPs Across a Pan-Holarctic Superspecies","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-8176843/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8176843/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Despite disproportionate fitness impacts imposed by deleterious structural variants (SVs) and associated transposable elements, few studies have yet examined their relative contribution to genomic erosion. To examine the role of both recent and ancient population history in the accumulation of deleterious SVs relative to single nucleotide polymorphisms (SNPs), the rock and willow ptarmigan (Lagopus spp.) superspecies form an ideal pan-Holarctic system, harbouring a broad range of historical effective population sizes increasingly threatened by fragmentation and climate change. By contrasting diversity ratios for non-synonymous SNPs and non- neutral SVs across 99 individuals from 12 island and mainland populations, we find that purifying selection against most putatively deleterious SVs appears insufficient to prevent their long-term accumulation in small populations, conforming with classic nearly-neutral dynamics. Likewise, proportions of realised (homozygous), masked (heterozygous) and fixed drift load due to putative highly and mildly deleterious SVs mirrored SNPs in mostly accumulating as a function of increased homozygosity in smaller populations. However, population-specific differences in the accrual of drift debt due to SVs did not reflect historical Ne alone: elevated realised load but reduced drift load in the Pyrenees (relative to the smallest population; Svalbard) indicate that the effects of recent fragmentation-induced inbreeding have yet to fully manifest. Our findings highlight the need to account for recent population decline and fragmentation, rather than solely relying on historical Ne to predict outcomes of genomic erosion— especially given the potential for disproportionate drift debt imposed by deleterious SVs.","manuscriptTitle":"Recent and Historical Determinants of Genomic Erosion by Structural Variation and SNPs Across a Pan-Holarctic Superspecies","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-01-06 11:03:30","doi":"10.21203/rs.3.rs-8176843/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-communications","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"NCOMMS","sideBox":"Learn more about [Nature Communications](http://www.nature.com/ncomms/)","snPcode":"","submissionUrl":"https://mts-ncomms.nature.com/","title":"Nature Communications","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Communications","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"61895560-f147-4f62-a312-30b65089d202","owner":[],"postedDate":"January 6th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":60621698,"name":"Biological sciences/Evolution/Population genetics/Genetic variation/Structural variation"},{"id":60621699,"name":"Biological sciences/Evolution/Molecular evolution"}],"tags":[],"updatedAt":"2026-02-17T11:45:12+00:00","versionOfRecord":[],"versionCreatedAt":"2026-01-06 11:03:30","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8176843","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8176843","identity":"rs-8176843","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}