The heterogeneous selection landscape of genome evolution in prokaryotes

The heterogeneous selection landscape of genome evolution in prokaryotes | 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 The heterogeneous selection landscape of genome evolution in prokaryotes Eugene Koonin, Sofiya Garushyants, Svetlana Karamycheva, Nash Rochman, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8216272/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 Evolution of prokaryote genomes appears to be defined by the interplay of selection for genome streamlining, deletion bias and selection for functional diversification. The previously observed overall positive correlation between the strength of selection, measured as the ratio of non-synonymous to synonymous nucleotide substitutions (dN/dS), points to diversification as the primary factor of prokaryote genome evolution. Here, we investigated the interplay between genome size and selection pressure by analyzing an expanded collection of closely related prokaryotic genomes, evaluating genome-wide selection by measuring dN/dS by using an accurate, phylogeny-based method and decomposing the resulting values into lineage-specific and gene-specific components. These analyses reveal a pronounced heterogeneity in the relationship between genome size and the strength of selection across the diversity of prokaryotes. Most bacteria display a positive correlation consistent with selection for diversification, whereas all analyzed archaeal lineages show strong negative correlation which is the signature of streamlining. These findings indicate that the selection regimes broadly vary across the diversity of prokaryotes rather than following a single, universal pattern. Genome streamlining, selection for functional diversity and drift in small populations are all important factors of evolution, their relative contributions depending on the population genetics and ecology of a given lineage. Biological sciences/Evolution/Evolutionary genetics Biological sciences/Microbiology/Microbial genetics Full Text Additional Declarations There is NO Competing Interest. Supplementary Files KogaySupplement.pdf Supplementrary material 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. 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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-8216272","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":558891481,"identity":"b2b50614-b443-4e6b-92b3-91c50870048d","order_by":0,"name":"Eugene 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