Effect of an unsampled population on the estimation of a population size

An Isolation-with-Migration (IM) model is used to estimate extant population sizes, the splitting time of populations split away from their common ancestral populations, and migration rates between the extant populations. An evolutionary model such as IM models is estimated by analyzing DNA sequences sampled from the extant populations in the model. When a true model includes an unsampled 'ghost' population without data, the unsampled population is often ignored from the evolutionary model to infer. In this paper, we conduct a simulation study to investigate the effect of an unsampled population on the estimation of the size of the sampled population. When there exists an unsampled population that shares migrations with the sampled population, the size estimation of the sampled population was biased. However, the size estimation was improved if an evolutionary model, including the unsampled population, was estimated.