inferring epidemiological processes from genetic data
The landscape genetics of infectious disease emergence and spread
The spread of parasites is inherently a spatial process often embedded in physically complex landscapes. It is therefore not surprising thatinfectious disease researchers are increasingly taking a landscape genetics perspective to elucidate mechanisms underlying basicecological processes driving infectious disease dynamics and to understand the linkage between spatially dependent populationprocesses and the geographic distribution of genetic variation within both hosts and parasites. The increasing availability of geneticinformation on hosts and parasites when coupled to their ecological interactions can lead to insights for predicting patterns of diseaseemergence, spread and control. Here, we review research progress in this area based on four different motivations for the application oflandscape genetics approaches: (i) assessing the spatial organization of genetic variation in parasites as a function of environmentalvariability, (ii) using host population genetic structure as a means to parameterize ecological dynamics that indirectly influence parasitepopulations, for example, gene flow and movement pathways across heterogeneous landscapes and the concurrent transport of infectiousagents, (iii) elucidating the temporal and spatial scales of disease processes and (iv) reconstructing and understanding infectious diseaseinvasion. Throughout this review, we emphasize that landscape genetic principles are relevant to infection dynamics across a range ofscales from within host dynamics to global geographic patterns and that they can also be applied to unconventional ‘landscapes’ such asheterogeneous contact networks underlying the spread of human and livestock diseases. We conclude by discussing some general considerations and problems for inferring epidemiological processes from genetic data and try to identify possible future directions andapplications for this rapidly expanding field.
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