Modelling tree shape and structure in viral phylodynamics
Open Access
- 19 March 2013
- journal article
- research article
- Published by The Royal Society in Philosophical Transactions Of The Royal Society B-Biological Sciences
- Vol. 368 (1614), 20120208
- https://doi.org/10.1098/rstb.2012.0208
Abstract
Epidemiological models have highlighted the importance of population structure in the transmission dynamics of infectious diseases. Using HIV-1 as an example of a model evolutionary system, we consider how population structure affects the shape and the structure of a viral phylogeny in the absence of strong selection at the population level. For structured populations, the number of lineages as a function of time is insufficient to describe the shape of the phylogeny. We develop deterministic approximations for the dynamics of tips of the phylogeny over evolutionary time, the number of ‘cherries’, tips that share a direct common ancestor, and Sackin's index, a commonly used measure of phylogenetic imbalance or asymmetry. We employ cherries both as a measure of asymmetry of the tree as well as a measure of the association between sequences from different groups. We consider heterogeneity in infectiousness associated with different stages of HIV infection, and in contact rates between groups of individuals. In the absence of selection, we find that population structure may have relatively little impact on the overall asymmetry of a tree, especially when only a small fraction of infected individuals is sampled, but may have marked effects on how sequences from different subpopulations cluster and co-cluster.Keywords
This publication has 41 references indexed in Scilit:
- Rates of coalescence for common epidemiological models at equilibriumJournal of The Royal Society Interface, 2011
- Inference for Nonlinear Epidemiological Models Using Genealogies and Time SeriesPLoS Computational Biology, 2011
- Three roads diverged? Routes to phylogeographic inferenceTrends in Ecology & Evolution, 2010
- Viral phylodynamics and the search for an ‘effective number of infections’Philosophical Transactions Of The Royal Society B-Biological Sciences, 2010
- The genomic and epidemiological dynamics of human influenza A virusNature, 2008
- Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population DynamicsMolecular Biology and Evolution, 2008
- Generation interval contraction and epidemic data analysisMathematical Biosciences, 2008
- Comparative Study of Methods for Detecting Sequence Compartmentalization in Human Immunodeficiency Virus Type 1Journal of Virology, 2007
- Unifying the Epidemiological and Evolutionary Dynamics of PathogensScience, 2004
- Inferring Evolutionary Process from Phylogenetic Tree ShapeThe Quarterly Review of Biology, 1997