Phylodynamics of Pepino mosaic virus in Spain P. Gómez & R. N. Sempere & M. A. Aranda & S. F. Elena Accepted: 31 May 2012 / Published online: 22 June 2012 # KNPV 2012 Abstract Pepino mosaic virus (PepMV) is an emerg- ing pathogen that causes severe economic losses in tomato crops in the Northern hemisphere. After its first identification, the new viral strain PepMV-CH2 has been isolated in several countries worldwide. In order to further understand the evolutionary dynamics of PepMV before and after PepMV-CH2 emergence, we analyzed a collection of PepMV isolates from southeastern Spain, estimating the rate of PepMV molecular evolution and the coalescence process for the effective number of PepMV infections using a Bayesian phylogenetic approach. Our results show that the rate of PepMV molecular evolution was 5.570×10 -3 substitutions/site/year, a value which is approximately an order of magnitude higher than the rates recently reported for other plant RNA viruses. Moreover, PepMV-CH2 was estimated to have origi- nated in 2000, coincident with the onset of PepMV- CH2 infections in southeastern Spain, its population following now an expansion process. This further illustrates that genetic and ecological interactions among different viral strains can modulate the evolu- tionary dynamics of PepMV and determine its epide- miological profile. Keywords Evolutionary dynamics . Molecular epidemiology . PepMV . Rate of molecular evolution . Tomato disease . Virus evolution Despite the implementation of permanent surveillance and prevention programs, Pepino mosaic virus (PepMV) represents a serious threat to tomato crops in many temperate regions in America, Africa, Asia, and Europe (Gómez et al. 2012). PepMV was initially identified in Peru, in 1974, as the agent responsible for a previously uncharacterized disease affecting pepino Eur J Plant Pathol (2012) 134:445–449 DOI 10.1007/s10658-012-0019-0 Electronic supplementary material The online version of this article (doi:10.1007/s10658-012-0019-0) contains supplementary material, which is available to authorized users. P. Gómez (*) : R. N. Sempere : M. A. Aranda Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario de Espinardo, Apdo. Correos 164, 30100 Espinardo, Murcia, Spain e-mail: p.gomez-lopez@exeter.ac.uk S. F. Elena Instituto de Biología Molecular y Celular de Plantas (IBMCP). CSIC-UPV, 46022 València, Spain S. F. Elena The Santa Fe Institute, Santa Fe NM 87501, USA Present Address: P. Gómez Centre for Ecology and Conservation, School of Biosciences, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK Present Address: R. N. Sempere Bioprodin SL, Edificio CEEIM, Campus de Espinardo s/n, 30100 Espinardo, Murcia, Spain