INFERRING THE POPULATION HISTORY OF AN EPIDEMIC FROM A PHYLOGENETIC TREE

Phylogenetic or family trees reconstructed from a sample of individual s belonging to a population or species can be used to infer population dynamic history. A method for making such inferences involves visual inspection of the graphs of the numbers of lineages in the phylogeny p lotted against the times when they occur. One transformation of the li neages axis often produces a linear lineages-through-time plot if the population has been growing exponentially. However, that transformatio n is known to fail under certain circumstances. We report a series of simulation studies designed to determine the conditions under which th e transformation fails. As long as the sample represents less than 0.5 % of individuals in the total population, the Type 1 error rate is acc eptable. This means that studies of virus populations are likely not t o suffer from transformation failure, so long as a random sample from the population is represented. When the transformation does fail, the resultant lineages-through-time plot is very similar to a two-stage ep idemic process. (C) 1996 Academic Press Limited