An island model of migration is used to study the effects of subdivision wi
thin populations and species on sample genealogies and on between-populatio
n or between-species measures of genetic variation. The model assumes that
the number of demes within each population or species is large. When popula
tions (or species), connected either by gene flow or historical association
, are themselves subdivided into demes, changes in the migration rate among
demes alter both the structure of genealogies and the time scale of the co
alescent process. The time scale of the coalescent is related to the effect
ive size of the population, which depends on the migration rate among demes
. When the migration rate among demes within populations is low, isolation
(or speciation) events seem more recent and migration rates among populatio
ns seem higher because the effective size of each population is increased.
This affects the probability of reciprocal monophyly of two samples, the ch
ance that a gene tree of a sample marches the species tree, and relative li
kelihoods of different types of polymorphic sites. It can also have a profo
und effect on the estimation of divergence times.