Modeling the velocity of evolving lineages and predicting dispersal patterns

• 成果类型: Article
• 署名作者: Bastide, Paul; Rocu, Pauline; Wirtz, Johannes; Hassler, Gabriel W.; Chevenet, Francois; Fargette, Denis; Suchard, Marc A.; Dellicour, Simon; Lemey, Philippe; Guindon, Stephane
• 署名单位: Centre National de la Recherche Scientifique (CNRS); Universite de Montpellier; Centre National de la Recherche Scientifique (CNRS); Universite Paris Cite; Centre National de la Recherche Scientifique (CNRS); CNRS - Institute for Information Sciences & Technologies (INS2I); Universite Paul-Valery; Universite Perpignan Via Domitia; Universite de Montpellier; Universite PSL; Ecole Pratique des Hautes Etudes (EPHE); Institut Agro; Montpellier SupAgro; CIRAD; Centre National de la Recherche Scientifique (CNRS); Institut de Recherche pour le Developpement (IRD); Universite Paul-Valery; Universite de Montpellier; RAND Corporation; Rand Health; Institut de Recherche pour le Developpement (IRD); Universite de Montpellier; Centre National de la Recherche Scientifique (CNRS); Universite de Montpellier; CIRAD; INRAE; Institut de Recherche pour le Developpement (IRD); University of California System; University of California Los Angeles; University of California System; University of California Los Angeles; University of California Los Angeles Medical Center; David Geffen School of Medicine at UCLA; University of California System; University of California Los Angeles; University of California Los Angeles Medical Center; David Geffen School of Medicine at UCLA; Universite Libre de Bruxelles; KU Leuven
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-10411
• DOI: 10.1073/pnas.2411582121
• 发表日期: 2024-11-19
• 关键词: random-walk; EVOLUTION; inference; coalescent

摘要

Accurate estimation of the dispersal velocity or speed of evolving organisms is no mean feat. In fact, existing probabilistic models in phylogeography or spatial population genetics generally do not provide an adequate framework to define velocity in a relevant manner. For instance, the very concept of instantaneous speed simply does not exist under one of the most popular approaches that models the evolution of spatial coordinates as Brownian trajectories running along a phylogeny. Here, we introduce a use Gaussian processes to explicitly model the velocity of evolving lineages instead of focusing on the fluctuation of spatial coordinates over time. We describe the properties of these models and show an increased accuracy of velocity estimates compared to previous approaches. Analyses of West Nile virus data in the United States indicate that PIV models provide sensible predictions of the dispersal of evolving pathogens at a one-year time horizon. These results demonstrate the feasibility and relevance of predictive phylogeography in monitoring epidemics in time and space.