title: Eight challenges in phylodynamic inference.
abstract: The field of phylodynamics, which attempts to enhance our understanding of infectious disease dynamics using pathogen phylogenies, has made great strides in the past decade. Basic epidemiological and evolutionary models are now well characterized with inferential frameworks in place. However, significant challenges remain in extending phylodynamic inference to more complex systems. These challenges include accounting for evolutionary complexities such as changing mutation rates, selection, reassortment, and recombination, as well as epidemiological complexities such as stochastic population dynamics, host population structure, and different patterns at the within-host and between-host scales. An additional challenge exists in making efficient inferences from an ever increasing corpus of sequence data.
authors.affiliation: Department of Veterinary Medicine, University of Cambridge, Cambridge, UK; Institute of Public Health, University of Cambridge, Cambridge, UK. Electronic address: sdf22@cam.ac.uk.
authors.forename: Simon D W
authors.initials: SD
authors.lastname: Frost
authors.affiliation: Department of Zoology, University of Oxford, Oxford, UK.
authors.forename: Oliver G
authors.initials: OG
authors.lastname: Pybus
authors.affiliation: Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK.
authors.forename: Julia R
authors.initials: JR
authors.lastname: Gog
authors.affiliation: Fogarty International Center, National Institutes of Health, Bethesda, USA.
authors.forename: Cecile
authors.initials: C
authors.lastname: Viboud
authors.affiliation: Institute of. Integrative Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Bonhoeffer
authors.affiliation: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, USA.
authors.forename: Trevor
authors.initials: T
authors.lastname: Bedford
mesh_terms: D005075:Biological Evolution; D003141:Communicable Diseases / Q000453:epidemiology* / Q000235:genetics / Q000276:immunology; D014644:Genetic Variation / Q000235:genetics; D054884:Host-Pathogen Interactions / Q000235:genetics; D006801:Humans; D015233:Models, Statistical; D010802:Phylogeny; D011157:Population Dynamics; D011995:Recombination, Genetic / Q000235:genetics; D012641:Selection, Genetic / Q000235:genetics; D013269:Stochastic Processes
keywords: Coalescent models; Phylodynamics; Recombination; Selection
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