Hierarchical mode of evolution in freshwater SAR11 driven by species dispersal and lake history

Hierarchical mode of evolution in freshwater SAR11 driven by species dispersal and lake history | 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 Hierarchical mode of evolution in freshwater SAR11 driven by species dispersal and lake history Michaela Salcher, Clafy Fernandes, Yusuke Okazaki This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8206985/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 Microorganisms dominate aquatic ecosystems, yet the evolutionary forces shaping their biogeography remain poorly understood. Freshwater habitats, acting as “isolated islands", may generate distinct evolutionary patterns in contrast to globally connected marine systems. Here, we investigated the globally abundant freshwater SAR11 genus Fontibacterium using a comparative population genomics framework. We analysed genome-wide single nucleotide variants (SNVs) from three species with contrasting dispersal capacities: an African endemic ( F. africanum ), a temperate specialist ( F. temperatum ), and a cosmopolitan species ( F. commune ). All species exhibited significant lake-specific population structure, but the scale of differentiation was constrained by their dispersal potential, ranging from complete genetic isolation between ancient lakes in the endemic species to transcontinental cohesion in the cosmopolitan one. Notably, the cosmopolitan species showed near-complete genetic cohesion between antipodal populations (Japan and Brazil) suggesting stochastic long-distance dispersal without geographic barriers. Furthermore, population genetic signatures varied among lake systems, especially elevated nucleotide diversity and pN/pS ratios in ancient African lakes suggesting relaxed purifying selection; a pattern that may reflect their unique evolutionary history. These findings support a hierarchical model where a species' dispersal capacity sets the broad-scale potential for gene flow, while local lake history determines the fine-scale genetic structure of its populations. Biological sciences/Microbiology/Environmental microbiology/Water microbiology Biological sciences/Microbiology/Bacteria/Bacterial genomics Earth and environmental sciences/Limnology Biological sciences/Evolution/Evolutionary genetics Biological sciences/Microbiology/Microbial communities/Metagenomics Full Text Additional Declarations There is NO Competing Interest. Supplementary Files FernandesSupplemetaryData.xlsx Supplementary Data 1 to 10 FernandesSupplementaryInformation.pdf Supplementary Information 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-8206985","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":555361327,"identity":"74aa227d-0102-4231-921f-18c0834ed7b4","order_by":0,"name":"Michaela 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Freshwater habitats, acting as “isolated islands\", may generate distinct evolutionary patterns in contrast to globally connected marine systems. Here, we investigated the globally abundant freshwater SAR11 genus \u003ci\u003eFontibacterium\u003c/i\u003e using a comparative population genomics framework. We analysed genome-wide single nucleotide variants (SNVs) from three species with contrasting dispersal capacities: an African endemic (\u003ci\u003eF. africanum\u003c/i\u003e), a temperate specialist (\u003ci\u003eF. temperatum\u003c/i\u003e), and a cosmopolitan species (\u003ci\u003eF. commune\u003c/i\u003e). All species exhibited significant lake-specific population structure, but the scale of differentiation was constrained by their dispersal potential, ranging from complete genetic isolation between ancient lakes in the endemic species to transcontinental cohesion in the cosmopolitan one. 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