Quills of Confusion! Genomic insight into the evolution and morphology of sea pens (Octocorallia: Scleralcyonacea: Pennatuloidea)

Quills of Confusion! Genomic insight into the evolution and morphology of sea pens (Octocorallia: Scleralcyonacea: Pennatuloidea) | 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 Quills of Confusion! Genomic insight into the evolution and morphology of sea pens (Octocorallia: Scleralcyonacea: Pennatuloidea) Upasana Ganguly, Scott C. France This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6866112/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 Background: Sea pens, Superfamily Pennatuloidea (Ehrenberg 1832), are a group of colonial octocorals so named because of the resemblance of some species to quill pens. These octocorals were grouped together due to their ability to live anchored in soft-sedimented sea floors using the peduncle. A modification of the peduncle in the species of one genus allow them to attach onto hard rocky substrates. Diverse colony morphology is seen among the sea pens, and some taxa have polyp-bearing secondary leaf-like extensions arising from the main axis (rachis). A few phylogenetic studies have investigated the evolutionary history of this group; however, this is the first genomic-scale investigation, in the form of Ultra Conserved Elements (UCEs), focused on Pennatuloidea. A mtMutS phylogeny with wider taxon sampling has also been constructed and compared to the UCE tree to address questions regarding the diversification of the different groups of sea pens. We also investigated the evolution of diverse colony morphology in sea pens by conducting ancestral state reconstruction analyses. Results: We found evidence that the sea pen lineage spilts into two major clades, which is not reflected in their current taxonomy. Our results show that most families of sea pens are not monophyletic and require reclassification. We also found that colony morphology has a complex evolutionary history, with at least seven independent origins of colonies bearing leaf-like extensions ("branches") arising from the main axis. Conclusion: Our results demonstrate incongruence among morphology, taxonomy, and phylogeny in most families of sea pens. We were able to confirm the monophyly of only 4 out of the 16 extant families. This incongruence is also evident in the presence of leaf-like extensions from which secondary polyps arise. sea pens phylogenomics Ultra Conserved Elements (UCEs) phylogenetics mtMutS colony morphology Full Text Additional Declarations No competing interests reported. Cite Share Download PDF Status: Under Revision Version 1 posted Editorial decision: Revision requested 21 Jul, 2025 Reviews received at journal 06 Jul, 2025 Reviews received at journal 24 Jun, 2025 Reviewers agreed at journal 18 Jun, 2025 Reviewers agreed at journal 18 Jun, 2025 Reviewers invited by journal 18 Jun, 2025 Editor assigned by journal 18 Jun, 2025 Editor invited by journal 18 Jun, 2025 Submission checks completed at journal 17 Jun, 2025 First submitted to journal 17 Jun, 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-6866112","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":473334798,"identity":"e5eaac52-b965-48e9-ae83-8d4f3673e3df","order_by":0,"name":"Upasana Ganguly","email":"data:image/png;base64,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","orcid":"","institution":"University of Louisiana at Lafayette","correspondingAuthor":true,"prefix":"","firstName":"Upasana","middleName":"","lastName":"Ganguly","suffix":""},{"id":473334799,"identity":"a730e0c3-02b0-4d19-87c2-851cec5e79fa","order_by":1,"name":"Scott C. 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Genomic insight into the evolution and morphology of sea pens (Octocorallia: Scleralcyonacea: Pennatuloidea)","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":"bmc-ecology-and-evolution","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"evob","sideBox":"Learn more about [BMC Ecology and Evolution](http://bmcevolbiol.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/evob/default.aspx","title":"BMC Ecology and Evolution","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"sea pens, phylogenomics, Ultra Conserved Elements (UCEs), phylogenetics, mtMutS, colony morphology","lastPublishedDoi":"10.21203/rs.3.rs-6866112/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6866112/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eSea pens, Superfamily Pennatuloidea (Ehrenberg 1832), are a group of colonial octocorals so named because of the resemblance of some species to quill pens. 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