title: Host ecology determines the dispersal patterns of a plant virus.
abstract: Since its isolation in 1966 in Kenya, rice yellow mottle virus (RYMV) has been reported throughout Africa resulting in one of the economically most important tropical plant emerging diseases. A thorough understanding of RYMV evolution and dispersal is critical to manage viral spread in tropical areas that heavily rely on agriculture for subsistence. Phylogenetic analyses have suggested a relatively recent expansion, perhaps driven by the intensification of agricultural practices, but this has not yet been examined in a coherent statistical framework. To gain insight into the historical spread of RYMV within Africa rice cultivations, we analyse a dataset of 300 coat protein gene sequences, sampled from East to West Africa over a 46-year period, using Bayesian evolutionary inference. Spatiotemporal reconstructions date the origin of RMYV back to 1852 (1791-1903) and confirm Tanzania as the most likely geographic origin. Following a single long-distance transmission event from East to West Africa, separate viral populations have been maintained for about a century. To identify the factors that shaped the RYMV distribution, we apply a generalised linear model (GLM) extension of discrete phylogenetic diffusion and provide strong support for distances measured on a rice connectivity landscape as the major determinant of RYMV spread. Phylogeographic estimates in continuous space further complement this by demonstrating more pronounced expansion dynamics in West Africa that are consistent with agricultural intensification and extensification. Taken together, our principled phylogeographic inference approach shows for the first time that host ecology dynamics have shaped the historical spread of a plant virus.
authors: Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium.
authors: Nídia Sequeira
authors: NS
authors: Trovão
authors: Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium.
authors: Guy
authors: G
authors: Baele
authors: Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium.
authors: Bram
authors: B
authors: Vrancken
authors: Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium.
authors: Filip
authors: F
authors: Bielejec
authors: Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 0095-1766, USA,; Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA 0095-1766, USA and.
authors: Marc A
authors: MA
authors: Suchard
authors: Institut de Recherches pour le Développement (IRD), UMR IPME (IRD, CIRAD, Université de Montpellier), 34394 Montpellier, France.
authors: Denis
authors: D
authors: Fargette
authors: Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium.
authors: Philippe
authors: P
authors: Lemey
keywords: Bayesian inference; RYMV; disease ecology; phylogeography; plant virus; viral evolution