Estimating Effective Population Size and Migration Rates From Genetic Samples Over Space and Time

Corresponding author: Jinliang Wang, Zoological Society of London, Regent's Park, London NW1 4RY, United Kingdom., jinliang.wang{at}ioz.ac.uk (E-mail)

Communicating editor: J. B. WALSH

In the past, moment and likelihood methods have been developed to estimate the effective population size (N_e) on the basis of the observed changes of marker allele frequencies over time, and these have been applied to a large variety of species and populations. Such methods invariably make the critical assumption of a single isolated population receiving no immigrants over the study interval. For most populations in the real world, however, migration is not negligible and can substantially bias estimates of N_e if it is not accounted for. Here we extend previous moment and maximum-likelihood methods to allow the joint estimation of N_e and migration rate (m) using genetic samples over space and time. It is shown that, compared to genetic drift acting alone, migration results in changes in allele frequency that are greater in the short term and smaller in the long term, leading to under- and overestimation of N_e, respectively, if it is ignored. Extensive simulations are run to evaluate the newly developed moment and likelihood methods, which yield generally satisfactory estimates of both N_e and m for populations with widely different effective sizes and migration rates and patterns, given a reasonably large sample size and number of markers.

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