Allele frequency fluctuations are associated with demographic cycling in Icelandic rock ptarmigan

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The study investigated genomic consequences of multi-annual demographic cycling in a northeastern Iceland population of rock ptarmigan using whole-genome sequences from 91 individuals sampled over 11 years, spanning population peaks (2010, 2018) and troughs (2007, 2013). Applying a simulation-based framework, the authors identified 22,399 SNPs showing patterns consistent with strong fluctuating selection that tracked fluctuating, density-dependent demography, with top candidate regions overlapping many candidate genes. The strongest candidate locus, CTNNA2, was highlighted for links to startle response and anxiety-like behaviors relevant to predator avoidance, while other candidates included genes such as GUCY2C and TRAF2, framed in relation to host–parasite conflict. The preprint caveat is that the work is based on a simulation-based inference of fluctuating selection signals from temporal genomic data, without direct measurement of the underlying selective pressures. This paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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Abstract

Abstract Understanding how natural populations adapt to recurring environmental changes, such as demographic cycles, is a central question in evolutionary biology. Multi-annual population cycles impose fluctuating selective pressures, yet disentangling the resulting genomic signals from those of long-term directional selection and genetic drift has been challenging due to a lack of high-resolution temporal data. Here, we investigate the genomic consequences of demographic cycling in a population of rock ptarmigan ( Lagopus muta ) from northeastern Iceland. We analyzed whole-genome sequences from 91 individuals sampled over an 11-year period, encompassing two population peaks (in 2010 and 2018) and two troughs (in 2007 and 2013). Using a simulation-based framework, we identified 22,399 single-nucleotide polymorphisms (SNPs) exhibiting patterns of strong fluctuating selection. These patterns were highly correlated with fluctuating demography, consistent with density-dependent selection. The strongest fluctuating sites overlapped with numerous candidate genes that may be important in the context of density-depending selection. The most significant candidate, CTNNA2 (Catenin Alpha-2), is associated with startle response and anxiety-like behaviors that may be associated with predator avoidance. We also found candidate genes such as GUCY2C and TRAF2 , whose functions may intersect with key stages of host-parasite conflicts. Our findings suggest that multi-annual demographic cycles are a powerful evolutionary force driving rapid and widespread genomic changes, with density-dependent selection on traits potentially playing a key role in adaptation. This study highlights the significance of temporal genomics in clarifying the interplay between demography and natural selection in wild populations.
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Allele frequency fluctuations are associated with demographic cycling in Icelandic rock ptarmigan | 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 Allele frequency fluctuations are associated with demographic cycling in Icelandic rock ptarmigan Theodore Squires, Alexandre Rego, Wanyi Wei, Patrik Rödin-Mörch, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8090944/v1 This work is licensed under a CC BY 4.0 License Status: Under Revision Version 1 posted 10 You are reading this latest preprint version Abstract Understanding how natural populations adapt to recurring environmental changes, such as demographic cycles, is a central question in evolutionary biology. Multi-annual population cycles impose fluctuating selective pressures, yet disentangling the resulting genomic signals from those of long-term directional selection and genetic drift has been challenging due to a lack of high-resolution temporal data. Here, we investigate the genomic consequences of demographic cycling in a population of rock ptarmigan ( Lagopus muta ) from northeastern Iceland. We analyzed whole-genome sequences from 91 individuals sampled over an 11-year period, encompassing two population peaks (in 2010 and 2018) and two troughs (in 2007 and 2013). Using a simulation-based framework, we identified 22,399 single-nucleotide polymorphisms (SNPs) exhibiting patterns of strong fluctuating selection. These patterns were highly correlated with fluctuating demography, consistent with density-dependent selection. The strongest fluctuating sites overlapped with numerous candidate genes that may be important in the context of density-depending selection. The most significant candidate, CTNNA2 (Catenin Alpha-2), is associated with startle response and anxiety-like behaviors that may be associated with predator avoidance. We also found candidate genes such as GUCY2C and TRAF2 , whose functions may intersect with key stages of host-parasite conflicts. Our findings suggest that multi-annual demographic cycles are a powerful evolutionary force driving rapid and widespread genomic changes, with density-dependent selection on traits potentially playing a key role in adaptation. This study highlights the significance of temporal genomics in clarifying the interplay between demography and natural selection in wild populations. Biological sciences/Genetics/Evolutionary biology Biological sciences/Evolution/Population genetics Biological sciences/Ecology/Ecological genetics Biological sciences/Evolution/Evolutionary genetics Biological sciences/Ecology/Population dynamics Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Full Text Additional Declarations There is no duality of interest Table 1 is available in the Supplementary Files section. Supplementary Files Table1.tif Table 1 TableS1.tif Table S1. Top twenty genes and corresponding gene card information for candidate sites after accounting for strongly fluctuating variants as calculated by CAF. TableS2.tif Table S2. Top fifty gene terms and corresponding information from a g:Profiler enrichment analysis on genes encompassed by all 22,399 candidate SNPs . SupplementaryS1.tif Figure S1. LD-decay among all SNPs as a function of physical distance showing a steep increase in average r 2 for sites with a genomic distance below 10kb. Trends are shown for each population cohort independently and largely align. SupplementaryS2.tif Figure S2. Genetic diversity (π) of each sampling year and the genetic differentiation (F ST ) between different groups. The circles represent collection years and the sizes indicate the π value, coloured by collection years. The values on each line represent the F ST value between each two groups (2007, n = 26; 2010, n = 20; 2013, n = 24; 2018, n = 21). SupplementaryS3.tif Figure S3. Temporal SNP frequency shifts of windows with the top 10 ZF ST windows between trough years, i.e. 2007 and 2013, and peak years, 2010 and 2018. Each line represents a SNP and is coloured by whether it is within the respective gene region. Overlap of these SNPs with top 5% of frequency change scoring sites is shown in green. Here you can see that the SNPs picked up by the outlier CAF scores were also present in outlier ZF ST windows. SupplementaryS4.tif Figure S4. Allele frequency change of candidates SNPs showing significant (p < 0.05) changes across all three time points in explicitly fluctuating patterns (n=22,399). The average allele frequency change is indicated in red. The allele shown (either reference or alternate) was chosen to ensure consistent directionality within the cluster. Cite Share Download PDF Status: Under Revision Version 1 posted Editorial decision: revise 30 Jan, 2026 Review # 3 received at journal 27 Jan, 2026 Review # 2 received at journal 19 Dec, 2025 Reviewer # 3 agreed at journal 18 Dec, 2025 Reviewer # 2 agreed at journal 10 Dec, 2025 Review # 1 received at journal 08 Dec, 2025 Reviewer # 1 agreed at journal 04 Dec, 2025 Reviewers invited by journal 27 Nov, 2025 Editor assigned by journal 11 Nov, 2025 First submitted to journal 11 Nov, 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. 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-8090944","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":551869190,"identity":"ad61bf3b-3dd2-4160-b759-e9b18b2b1e06","order_by":0,"name":"Theodore Squires","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABCUlEQVRIiWNgGAWjYDACCSDmgXESgJgfwcUOeDC0SDaQpAUEDA4Q0GIv3XzwwZuKe3IM/Ie3STzcY2NvfLz34AfGtsMM8u0N2G2ROZZsOOdMsTGDRFqZRMKztMRtZ84lS4C0GJw5gMNhOWbSvG0JiQ0SPGYSCQcOJ5jdyDFjAGuRSMChJf8bSEt9A/8ZkJb/9sbz30C0yM9/gMsWNpAWoIE5IC0HGDcArQNrYbiB3fs8N9KMgX5JMGyTSCu2SDiQnDjjTF6yRMK5dB6DM9gdxj4j+SEwxBLk+fkPb7z544CdPX/72YMfPpRZy8m3Y/c+HLABYwTBS2AglAYgwICwklEwCkbBKBiRAACSOlde0As/pgAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0003-3185-4749","institution":"University of Akureyri","correspondingAuthor":true,"prefix":"","firstName":"Theodore","middleName":"","lastName":"Squires","suffix":""},{"id":551869191,"identity":"7cbd66e6-6c8b-4f2b-bd05-f6885f5923c7","order_by":1,"name":"Alexandre Rego","email":"","orcid":"","institution":"Uppsala University","correspondingAuthor":false,"prefix":"","firstName":"Alexandre","middleName":"","lastName":"Rego","suffix":""},{"id":551869192,"identity":"756c5c31-c9d0-4a3c-89a3-bba5bfd28d26","order_by":2,"name":"Wanyi Wei","email":"","orcid":"","institution":"University of Oslo","correspondingAuthor":false,"prefix":"","firstName":"Wanyi","middleName":"","lastName":"Wei","suffix":""},{"id":551869193,"identity":"ef9f0c8e-d9b7-4e53-a300-16762f892f4e","order_by":3,"name":"Patrik Rödin-Mörch","email":"","orcid":"https://orcid.org/0000-0001-6737-1488","institution":"Uppsala University","correspondingAuthor":false,"prefix":"","firstName":"Patrik","middleName":"","lastName":"Rödin-Mörch","suffix":""},{"id":551869194,"identity":"10f11402-f393-447d-917c-caf346dc643b","order_by":4,"name":"Jacob Höglund","email":"","orcid":"https://orcid.org/0000-0002-5840-779X","institution":"Uppsala University","correspondingAuthor":false,"prefix":"","firstName":"Jacob","middleName":"","lastName":"Höglund","suffix":""},{"id":551869195,"identity":"a0f0d295-4413-4d15-9555-bb8282a97f3b","order_by":5,"name":"Kristinn Magnússon","email":"","orcid":"https://orcid.org/0000-0003-4528-6826","institution":"University of Akureyri","correspondingAuthor":false,"prefix":"","firstName":"Kristinn","middleName":"","lastName":"Magnússon","suffix":""}],"badges":[],"createdAt":"2025-11-12 01:45:42","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8090944/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8090944/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":97131308,"identity":"3160a2b1-99f8-4cef-900a-bd0181fe73d0","added_by":"auto","created_at":"2025-12-01 08:42:30","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":1083822,"visible":true,"origin":"","legend":"\u003cp\u003eRelief map showing the years and locations of Rock Ptarmigan used in the present study from around northeastern Iceland approximately between Husavík and Reykjahlíð. Number of individuals from the various years are 2007, n = 26 (light yellow); 2010, n = 20 (orange); 2013, n = 24 (dark orange); and 2018, n = 21 (red).\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-8090944/v1/e1feef5080ef78bd9ebd74e9.png"},{"id":97131306,"identity":"f4096354-2385-4bce-93f5-c6aaf8bbb1a7","added_by":"auto","created_at":"2025-12-01 08:42:30","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":186380,"visible":true,"origin":"","legend":"\u003cp\u003eOverview of spring population census data from rock ptarmigan counted in the Northeastern Region (\u003cem\u003eNorðurland eystra\u003c/em\u003e) of Iceland between 2005 and 2023 as collected by the Natural Science Institute of Iceland (methods detailed in Ferrarini and Nielsen 2025). Our sampling years are highlighted with bold red points. This figure was developed from data previously reported by Johnson and Nielsen (2024) and made available in their dryad repository (https://doi.org/10.5061/dryad.c59zw3rg3).\u003c/p\u003e","description":"","filename":"Figure2.png","url":"https://assets-eu.researchsquare.com/files/rs-8090944/v1/1465b53b132b8b219503d8e8.png"},{"id":97131307,"identity":"c9877084-5977-49f9-a7ad-ee6e5364e105","added_by":"auto","created_at":"2025-12-01 08:42:30","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":2227861,"visible":true,"origin":"","legend":"\u003cp\u003eDifferentiation (ZF\u003csub\u003eST\u003c/sub\u003e) among SNP:s in 10 kB sliding windows between A) peak (2010\u0026nbsp; and 2018) and trough years (2007 and 2013) and B) between the start (2007) and end (2018) year among the first 28 rock ptarmigan autosomes cut for visual clarity. Protein coding genes in the ten top outlier windows are indicated and the red line indicates the cutoff for 5% genome wide outliers (above the line).\u003c/p\u003e","description":"","filename":"Figure3.png","url":"https://assets-eu.researchsquare.com/files/rs-8090944/v1/1337d7e82849a5b8ffed0d13.png"},{"id":97141808,"identity":"e71bf330-218f-4fef-ba86-0f9fc9344241","added_by":"auto","created_at":"2025-12-01 10:07:03","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":385203,"visible":true,"origin":"","legend":"\u003cp\u003eTemporal SNP frequency shifts of windows with the top 10 ZF\u003csub\u003eST\u003c/sub\u003e windows in different comparisons. A) Comparisons between trough years, i.e. 2007 and 2013, and peak years, 2010 and 2018. B) Comparisons between the earliest year, 2007, and the latest year, 2018. Each line represents a SNP and coloured by whether it is within the respective gene region. Overlap of these SNPs with top 5% of frequency change scoring sites is shown in Fig. S3. Fluctuating protein coding genes found in windows are indicated though some windows may include multiple other genes.\u003c/p\u003e","description":"","filename":"Figure4.png","url":"https://assets-eu.researchsquare.com/files/rs-8090944/v1/1194d3b6425a43afb7ec1936.png"},{"id":97142204,"identity":"90466602-686f-4110-9417-e3ee7260dc46","added_by":"auto","created_at":"2025-12-01 10:07:25","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":678577,"visible":true,"origin":"","legend":"\u003cp\u003eClusters of allele frequency changes in putatively selected loci. Individual frequency trajectories are shown in grey, the mean allele frequency of the cluster is in red, and the census trend is shown in blue. The percentage of SNPs contained within each cluster is shown (of the 56,307 candidate SNPs which showed p \u0026lt; 0.001 in any time interval), as well as the mean absolute correlation and standard deviation between allele frequency and census size. Note that nearly all clusters exhibit patterns of fluctuating selection of some form (i.e., non-linear patterns of allele frequency change). Within each cluster, the allele shown (either reference or alternate) was chosen to ensure consistent directionality within the cluster. Regional census data as previously reported in Fig 2.\u003c/p\u003e","description":"","filename":"Figure5.png","url":"https://assets-eu.researchsquare.com/files/rs-8090944/v1/cd14dd4b6e8e7cae9a992587.png"},{"id":97248411,"identity":"2cfbec43-a259-4da6-a7d5-f2053477c656","added_by":"auto","created_at":"2025-12-02 12:57:42","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1592021,"visible":true,"origin":"","legend":"","description":"","filename":"MainManuscriptAnonymized.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8090944/v1_covered_335690b8-a5d0-44ef-a372-40078d40e33f.pdf"},{"id":97131309,"identity":"88d7f6f2-1151-42b8-828b-2f21000762ae","added_by":"auto","created_at":"2025-12-01 08:42:30","extension":"tif","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":103236,"visible":true,"origin":"","legend":"Table 1","description":"","filename":"Table1.tif","url":"https://assets-eu.researchsquare.com/files/rs-8090944/v1/e2c1cd865f0220634bbd35c5.tif"},{"id":97131311,"identity":"a0644849-d06e-4fcf-b1d6-06c52920aee9","added_by":"auto","created_at":"2025-12-01 08:42:30","extension":"tif","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":562124,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eTable S1.\u003c/strong\u003e Top twenty genes and corresponding gene card information for candidate sites after accounting for strongly fluctuating variants as calculated by CAF.\u003c/p\u003e","description":"","filename":"TableS1.tif","url":"https://assets-eu.researchsquare.com/files/rs-8090944/v1/17b7e242fb3d2630938d5e6e.tif"},{"id":97131313,"identity":"99792569-f28f-4a55-80ba-ecc85cdf7da2","added_by":"auto","created_at":"2025-12-01 08:42:30","extension":"tif","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":518118,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eTable S2.\u003c/strong\u003e Top fifty gene terms and corresponding information from a g:Profiler enrichment analysis on genes encompassed by all 22,399 candidate SNPs .\u003c/p\u003e","description":"","filename":"TableS2.tif","url":"https://assets-eu.researchsquare.com/files/rs-8090944/v1/37f77b312b8977a06f35b2d8.tif"},{"id":97131317,"identity":"2229e11a-a047-48f4-b527-668b7427d7e5","added_by":"auto","created_at":"2025-12-01 08:42:30","extension":"tif","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":2295392,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eFigure S1.\u003c/strong\u003e LD-decay among all SNPs as a function of physical distance showing a steep increase in average r\u003csup\u003e2\u003c/sup\u003e for sites with a genomic distance below 10kb. Trends are shown for each population cohort independently and largely align.\u003c/p\u003e","description":"","filename":"SupplementaryS1.tif","url":"https://assets-eu.researchsquare.com/files/rs-8090944/v1/7b3630e3408b0f4c98b6de4b.tif"},{"id":97131316,"identity":"7d624c7d-203f-4754-89c2-b184237f5295","added_by":"auto","created_at":"2025-12-01 08:42:30","extension":"tif","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":2292444,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eFigure S2.\u003c/strong\u003e Genetic diversity (π) of each sampling year and the genetic differentiation (F\u003csub\u003eST\u003c/sub\u003e) between different groups. The circles represent collection years and the sizes indicate the π value, coloured by collection years. The values on each line represent the F\u003csub\u003eST\u003c/sub\u003e value between each two groups (2007, n = 26; 2010, n = 20; 2013, n = 24; 2018, n = 21).\u003c/p\u003e","description":"","filename":"SupplementaryS2.tif","url":"https://assets-eu.researchsquare.com/files/rs-8090944/v1/0c02a62f9316c3425815f8c0.tif"},{"id":97142202,"identity":"a129238b-13be-40dd-acd7-db74724c6b7e","added_by":"auto","created_at":"2025-12-01 10:07:25","extension":"tif","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":3328418,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eFigure S3.\u003c/strong\u003e Temporal SNP frequency shifts of windows with the top 10 ZF\u003csub\u003eST\u003c/sub\u003e windows between trough years, i.e. 2007 and 2013, and peak years, 2010 and 2018. Each line represents a SNP and is coloured by whether it is within the respective gene region. Overlap of these SNPs with top 5% of frequency change scoring sites is shown in green. Here you can see that the SNPs picked up by the outlier CAF scores were also present in outlier ZF\u003csub\u003eST\u003c/sub\u003e windows.\u003c/p\u003e","description":"","filename":"SupplementaryS3.tif","url":"https://assets-eu.researchsquare.com/files/rs-8090944/v1/32a097609699b00e1a3d4626.tif"},{"id":97131314,"identity":"ce060607-7f0f-444f-83cd-002eb3aba20b","added_by":"auto","created_at":"2025-12-01 08:42:30","extension":"tif","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":724384,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eFigure S4\u003c/strong\u003e. Allele frequency change of candidates SNPs showing significant (p \u0026lt; 0.05) changes across all three time points in explicitly fluctuating patterns (n=22,399). The average allele frequency change is indicated in red. The allele shown (either reference or alternate) was chosen to ensure consistent directionality within the cluster.\u003c/p\u003e","description":"","filename":"SupplementaryS4.tif","url":"https://assets-eu.researchsquare.com/files/rs-8090944/v1/d6d8471b122dae53cd000ea7.tif"}],"financialInterests":"\u003cp\u003eThere is no duality of interest\u003c/p\u003e\n\u003cp\u003eTable 1 is available in the Supplementary Files section.\u003c/p\u003e","formattedTitle":"Allele frequency fluctuations are associated with demographic cycling in Icelandic rock ptarmigan","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"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":"heredity","isNatureJournal":false,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"hdy","sideBox":"Learn more about [Heredity](http://www.nature.com/hdy/)","snPcode":"41437","submissionUrl":"https://mts-hdy.nature.com/cgi-bin/main.plex","title":"Heredity","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-8090944/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8090944/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eUnderstanding how natural populations adapt to recurring environmental changes, such as demographic cycles, is a central question in evolutionary biology. Multi-annual population cycles impose fluctuating selective pressures, yet disentangling the resulting genomic signals from those of long-term directional selection and genetic drift has been challenging due to a lack of high-resolution temporal data. Here, we investigate the genomic consequences of demographic cycling in a population of rock ptarmigan (\u003cem\u003eLagopus muta\u003c/em\u003e) from northeastern Iceland. We analyzed whole-genome sequences from 91 individuals sampled over an 11-year period, encompassing two population peaks (in 2010 and 2018) and two troughs (in 2007 and 2013). Using a simulation-based framework, we identified 22,399 single-nucleotide polymorphisms (SNPs) exhibiting patterns of strong fluctuating selection. These patterns were highly correlated with fluctuating demography, consistent with density-dependent selection. The strongest fluctuating sites overlapped with numerous candidate genes that may be important in the context of density-depending selection. The most significant candidate, \u003cem\u003eCTNNA2\u003c/em\u003e(Catenin Alpha-2), is associated with startle response and anxiety-like behaviors that may be associated with predator avoidance. We also found candidate genes such as \u003cem\u003eGUCY2C\u003c/em\u003e and \u003cem\u003eTRAF2\u003c/em\u003e, whose functions may intersect with key stages of host-parasite conflicts. Our findings suggest that multi-annual demographic cycles are a powerful evolutionary force driving rapid and widespread genomic changes, with density-dependent selection on traits potentially playing a key role in adaptation. This study highlights the significance of temporal genomics in clarifying the interplay between demography and natural selection in wild populations.\u003c/p\u003e","manuscriptTitle":"Allele frequency fluctuations are associated with demographic cycling in Icelandic rock ptarmigan","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-12-01 08:42:25","doi":"10.21203/rs.3.rs-8090944/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"revise","date":"2026-01-30T08:40:27+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"This content is not available.","date":"2026-01-27T07:46:42+00:00","index":3,"fulltext":"This content is not available."},{"type":"editorInvitedReview","content":"This content is not available.","date":"2025-12-19T09:57:08+00:00","index":2,"fulltext":"This content is not available."},{"type":"reviewerAgreed","content":"This content is not available.","date":"2025-12-19T04:37:38+00:00","index":3,"fulltext":"This content is not available."},{"type":"reviewerAgreed","content":"This content is not available.","date":"2025-12-10T14:40:24+00:00","index":2,"fulltext":"This content is not available."},{"type":"editorInvitedReview","content":"This content is not available.","date":"2025-12-08T14:30:56+00:00","index":1,"fulltext":"This content is not available."},{"type":"reviewerAgreed","content":"This content is not available.","date":"2025-12-04T16:17:50+00:00","index":1,"fulltext":"This content is not available."},{"type":"reviewersInvited","content":"","date":"2025-11-27T16:13:22+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-11-12T01:42:52+00:00","index":"","fulltext":""},{"type":"submitted","content":"Heredity","date":"2025-11-12T01:42:51+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"heredity","isNatureJournal":false,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"hdy","sideBox":"Learn more about [Heredity](http://www.nature.com/hdy/)","snPcode":"41437","submissionUrl":"https://mts-hdy.nature.com/cgi-bin/main.plex","title":"Heredity","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"1a113c1c-a71d-43cf-b921-e0c3567c265b","owner":[],"postedDate":"December 1st, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"in-revision","subjectAreas":[{"id":58728436,"name":"Biological sciences/Genetics/Evolutionary biology"},{"id":58728437,"name":"Biological sciences/Evolution/Population genetics"},{"id":58728438,"name":"Biological sciences/Ecology/Ecological genetics"},{"id":58728439,"name":"Biological sciences/Evolution/Evolutionary genetics"},{"id":58728440,"name":"Biological sciences/Ecology/Population dynamics"}],"tags":[],"updatedAt":"2026-01-30T08:45:13+00:00","versionOfRecord":[],"versionCreatedAt":"2025-12-01 08:42:25","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8090944","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8090944","identity":"rs-8090944","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}

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