Detecting Evolutionary Change-Points with Branch-Specific Substitution Models and Shrinkage Priors

Detecting Evolutionary Change-Points with Branch-Specific Substitution Models and Shrinkage Priors | 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 Detecting Evolutionary Change-Points with Branch-Specific Substitution Models and Shrinkage Priors Xiang Ji, Benjamin Redelings, Shuo Su, Hongcun Bao, Wu-Min Deng, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6926809/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 Branch-specific substitution models are popular for detecting evolutionary change-points, such as shifts in selective pressure. However, applying such models typically requires prior knowledge of change-point locations on the phylogeny or faces scalability issues with large data sets. To address both limitations, we integrate branch-specific substitution models with shrinkage priors to automatically identify change-points without prior knowledge, while simultaneously estimating distinct substitution parameters for each branch. To enable tractable inference under this high-dimensional model, we develop an analytical gradient algorithm for the branch-specific substitution parameters where the computational time is linear in the number of parameters. We apply this gradient algorithm to infer selection pressure dynamics in the evolution of the BRCA1 gene in primates and mutational dynamics in viral sequences from the recent mpox epidemic. Our novel algorithm enhances inference efficiency, achieving up to a 90-fold speedup per iteration in maximum likelihood optimization when compared to central difference numerical gradient method and up to a 360-fold improvement in computational performance within a Bayesian framework using Hamiltonian Monte Carlo sampler compared to conventional univariate random walk sampler. Biological sciences/Evolution/Phylogenetics Biological sciences/Computational biology and bioinformatics linear-time gradient algorithm branch-specific substitution model Bayesian infer36 ence maximum likelihood natural selection Full Text Additional Declarations There is NO Competing Interest. 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. 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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-6926809","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":473496996,"identity":"81e4390f-04ba-4d84-b05f-d5d9dbd9d2f4","order_by":0,"name":"Xiang Ji","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAv0lEQVRIiWNgGAWjYFCCgw0GHxgYZCAcNiK1FM5IYOAhRQsDw2cekrQYHDzcuNn2x2Ee/tnNBxg+lB0mrEWy4WCzcU7CYR6JO8cSGGecI0ILP8PBNrAWhhs5Bsy8bURoYWM42P7bAqhF/kb+B+a/xGgB2tJgzADUYnAjh4GZkRgtQL80GPakpfMY3kgzONhzLp2wFoMbxx8Y/LCxlpO7kfzwwY8ya8JaGCQOINgHcClCBfwNxKkbBaNgFIyCEQwAODI+PAdEcT4AAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0002-7243-0865","institution":"Tulane University","correspondingAuthor":true,"prefix":"","firstName":"Xiang","middleName":"","lastName":"Ji","suffix":""},{"id":473496997,"identity":"501a751f-1789-41b1-bbc2-fd70aef72e8a","order_by":1,"name":"Benjamin Redelings","email":"","orcid":"","institution":"Duke University","correspondingAuthor":false,"prefix":"","firstName":"Benjamin","middleName":"","lastName":"Redelings","suffix":""},{"id":473496998,"identity":"e55e2b82-cfaf-4d11-ac20-a73eeb1a6a25","order_by":2,"name":"Shuo Su","email":"","orcid":"","institution":"","correspondingAuthor":false,"prefix":"","firstName":"Shuo","middleName":"","lastName":"Su","suffix":""},{"id":473496999,"identity":"7bd77537-f76e-4112-92ed-af181ee57057","order_by":3,"name":"Hongcun Bao","email":"","orcid":"","institution":"Tulane University","correspondingAuthor":false,"prefix":"","firstName":"Hongcun","middleName":"","lastName":"Bao","suffix":""},{"id":473497000,"identity":"a17dd071-d82a-409b-847e-cdf438487262","order_by":4,"name":"Wu-Min Deng","email":"","orcid":"","institution":"Tulane University","correspondingAuthor":false,"prefix":"","firstName":"Wu-Min","middleName":"","lastName":"Deng","suffix":""},{"id":473497001,"identity":"220acb8e-bfe9-4f39-8db1-070d33c7edb5","order_by":5,"name":"Samuel Hong","email":"","orcid":"https://orcid.org/0000-0001-6354-4943","institution":"KU Leuven","correspondingAuthor":false,"prefix":"","firstName":"Samuel","middleName":"","lastName":"Hong","suffix":""},{"id":473497002,"identity":"7e4c9cc0-3e40-491a-9b67-38a37f8a0757","order_by":6,"name":"Guy Baele","email":"","orcid":"https://orcid.org/0000-0002-1915-7732","institution":"Rega Institute for Medical Research, KU Leuven","correspondingAuthor":false,"prefix":"","firstName":"Guy","middleName":"","lastName":"Baele","suffix":""},{"id":473497003,"identity":"40020f52-a1ac-4c2f-b0dc-48cdbef7d99b","order_by":7,"name":"Philippe Lemey","email":"","orcid":"https://orcid.org/0000-0003-2826-5353","institution":"KU Leuven","correspondingAuthor":false,"prefix":"","firstName":"Philippe","middleName":"","lastName":"Lemey","suffix":""},{"id":473497004,"identity":"5bb07076-0115-4806-885c-c4dff2d9a417","order_by":8,"name":"Marc Suchard","email":"","orcid":"https://orcid.org/0000-0001-9818-479X","institution":"Department of Human Genetics David Geffen School of Medicine University of California; 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