We introduce a conceptual bridge between the previously unlinked fields of phylogenetics and mathematical spatial ecology, which enables the spatial parameters of an emerging epidemic to be directly estimated from sampled pathogen genome sequences. By using phylogenetic history to correct for spatial autocorrelation, we illustrate how a fundamental spatial variable, the diffusion coefficient, can be estimated using robust nonparametric statistics, and how heterogeneity in dispersal can be readily quantified. We apply this framework to the spread of the West Nile virus across North America, an important recent instance of spatial invasion by an emerging infectious disease. We demonstrate that the dispersal of West Nile virus is greater and far more variable than previously measured, such that its dissemination was critically determined by rare, long-range movements that are unlikely to be discerned during field observations. Our results indicate that, by ignoring this heterogeneity, previous models of the epidemic have substantially overestimated its basic reproductive number. More generally, our approach demonstrates that easily obtainable genetic data can be used to measure the spatial dynamics of natural populations that are otherwise difficult or costly to quantify.phylogeny | phylogeography | transmission T he explanation of spatial patterns of infectious disease, particularly those of emerging pathogens, has remained a central problem of epidemiology since its inception (1). The existence and nature of traveling waves of infection were first explained in theoretical models (2, 3) and later quantified in empirical studies of rabies and the Black Death (4, 5). These and other studies highlighted the fundamental problem of spatial autocorrelation: observations of infection are statistically dependent due to transmission among proximate individuals, greatly complicating the analysis of spatiotemporal incidence. Consequently, many recent analyses of spatial epidemic behavior use detailed mathematical models of spatial structure to account for autocorrelation (6). Entirely independently, in the field of evolutionary biology there has developed a separate body of work, now termed phylogeography, which focuses on reconstructing past movement events from the genome sequences of sampled organisms (7-10). However, these evolutionary tools typically generate descriptive results that, though informative, remain divorced from epidemiological theory. Crucially neither approach can be considered complete when applied to rapidly evolving viruses, whose spatial, epidemic, and evolutionary dynamics occur on the same timescale (11), necessitating the development of methods that consider all these processes together.Here we introduce a unique approach that integrates the disciplines of spatial epidemiology and phylogenetics. To illustrate the utility of this approach, we show how, from pathogen genomes alone, it can estimate the diffusion coefficient (D) of an epidemic as well as variation in the process of spatial spread. D is...