Inferring pandemic growth rates from sequence data

de Silva, Eric; Ferguson, Neil M.; Fraser, Christophe

More specifically, coalescent analysis starts from the straightforward observation that for the Wright -Fisher model, the probability that two randomly selected individuals from one generation share a parent is equal to 1/N, where N is the population size. Taking the definition of the effective population size, N e , to be the size of a Wright -Fisher model population that would give an observed level of diversity, we can then observe for an arbitrary panmictic population, the probability that two lineages in one generation have a common ancestor lineage in the previous generation is equal to 1/N e . Applying this observation to a phylogenetic tree, which encodes the ancestral probability distribution of all coalescent event times in the population, provides estimates of the changing effective population size throughout the history of the population up to the TMRCA.