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Finally, we estimated migration since lineages A, B and C split using the isolation with migration model implemented in the program IMa2 [ 64].

I used the comparative DNA sequence data and the Isolation with Migration model implemented in IM [ 28] to infer historical rates of between-species gene flow.

We analyzed ten nuclear loci using the "isolation with migration" model implemented in the IM program, finding evidence for introgression from L. intermedia towards L. whitmani in three loci.

The Isolation with Migration model implemented in IMa has several assumptions that may be violated in empirical data sets, including: no intralocus recombination, no gene flow with an unsampled species/population, no linkage among loci, no selection and no population structure in the ancestral population.

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We inferred the colonisation history of each clade separately by using isolation with migration models implemented in the program IMa [19], [20].

Finally, modern and ancestral effective population sizes were also inferred under the isolation-with-migration model implemented in the software IM v. 31 July 2006 [23], [49], [50].

Modern and ancestral effective population sizes were also inferred for the same 20-locus autosomal dataset under the isolation-with-migration model implemented by Jody Hey and colleagues [23].

Migration rate (m), effective population size, and divergence time between populations were estimated using the coalescent-based isolation-with-migration model implemented in IMa [ 75].

An additional analysis of migration rates within each river was conducted based on an isolation-with-migration model implemented in IMa2 (Hey and Nielsen 2007) applying a geometric heating scheme for 10 steps after a burn-in period of 10.

Lastly, we used the Isolation-with-Migration model implemented in the software IMa2 [ 85] to test the hypothesis that the pattern observed in Wirth and Bernatchez [ 39] results from varying gene flow rates between European and American populations as opposed to ancestral polymorphism due to incomplete lineage sorting.

We reconstructed evolutionary relationships among the sampled gibbon taxa using coalescent species tree analysis employed in the program *BEAST and we further applied the isolation-with-migration (IM) model implemented in the program IMa2 to assess the possibility of gene flow between closely related species.

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