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We expected the order of elements in this sequence to depart more drastically from randomness in models with migration.
However, shared polymorphisms in populations with lower levels of divergence have a stronger clustering of S sites than models with migration.
We predict that values of run statistics (i.e. number of runs, R F and R S ) will be lower under models with migration than under models of pure divergence.
The distinct behaviour of the R F statistic under the isolation model and the models with migration indicates that it can be used to tackle the problem in hand under a large range of conditions.
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In the present study we investigate this question theoretically in a mainland-island model with migration from mainland to island.
A modification of our model with migration from the start does not change the results qualitatively as long as migration is below the critical migration rate.
We also simulated data under a simple Wright Fisher model with migration (Appendix III2) using a simplified version of previously described algorithms [10], [13].
In the third scenario (MDN), allele count data were also simulated for L = 1,000 independent bi-allelic neutral SNPs in P random mating populations evolving under a Wright Fisher model with migration.
M0 assumes an isolation model without migration, and M1 and M2 assume an isolation model with migration.
In the population split model with migration, the same outlier loci were detected as in the per species models (Table S5 and Table S6).
We consider a discrete-time version of a model with migration and selection at two biallelic loci (Bürger and Akerman 2011).
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