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portions of the compound loci were typically ≈300,000 times higher than the mutation rate per site in the flanking sequence. If the mutation rate in the flanking sequence is 2 × 10−9 per site per generation (i.e., the per site per year estimate based on the outgroup divergence × 2 years per generation), then our estimate of the STR mutation rate would be 300,000 times higher than this, or ≈6 × 10−4 per generation, which is a fairly typical rate (Goldstein and Schlötterer, 1999). The IM analyses suggest that populations and species have been exchanging genes, particularly from T. tropheops and T. broad mouth into populations of T. gracilior. However the estimated densities of migration parameters are mostly flat, and there is little resolution of migration rates in most cases. In recent years several authors have argued that some gene flow between species is probably occurring (Markert et al., 2001; Seehausen, 2004; Smith and Kornfield, 2002; Smith et al., 2003), and in particular Kocher and colleagues (Danley and Kocher, 2001; Danley et al., 2000) have argued in support of the “divergence with gene flow” model of speciation (Endler, 1973; Rice and Hostert, 1993) for Malawi cichlids. In such models, two populations may diverge in parapatry or sympatry because of selective forces, even in the presence of gene flow. These models differ fundamentally from strictly allopatric models of speciation in that they directly entail a role for divergent natural selection as a cause of species diversity (Rice and Hostert, 1993).

Although the use of dated outgroup sequences and a parameter-rich model of divergence allows us to address difficult questions about the divergence of Malawi cichlids, there are clear limitations to these interpretations. Necessarily, the divergence process has been viewed through the lens of the IM model, and it is not yet clear how the picture would change if we were able to consider more than two populations simultaneously or could better assess the impact of assuming the stepwise mutation model for the STR portions of loci. The consistently very large estimates for ancestral population sizes do suggest that our samples contain variation that arose not just in single ancestral populations but in a wider array of partly intermingled populations. This interpretation is consistent with the evidence for recent gene exchange among populations and species.


We thank Jeff Markert and Matt Arnegard for help collecting samples; Richard Zatha, Daniel Phiri, and David Mwafulirwe for providing valuable field assistance; and Aggrey Ambali (Molecular Biology and Ecology Research Unit, University of Malawi, Zomba, Malawi) for helping to facilitate the collecting trip and for the use of the Molecular Biology and

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