Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference.

ABSTRACT: Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this task formulates an observed sequence data likelihood exploiting a coalescent model for the sampled individuals' genealogy and then integrating over all possible genealogies via Monte Carlo or, less efficiently, by conditioning on one genealogy estimated from the sequence data. However, when analyzing sequences sampled serially through time, current methods implicitly assume either that sampling times are fixed deterministically by the data collection protocol or that their distribution does not depend on the size of the population. Through simulation, we first show that, when sampling times do probabilistically depe

SUBMITTER: Karcher MD 

PROVIDER: S-EPMC4777449 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature