The extraordinary number of species of cichlid fishes (Teleostei: Cichlidae) of the African great lakes Malawi, Tanganyika and Victoria are a classic evolutionary mystery, and biologists have long wondered how so many species could have evolved over short time periods. In the case of Lake Malawi, the estimated geological age of the lake is 4–5 million years, but the lake probably dried out at times, perhaps as recently as 570,000 years ago (Delvaux, 1996).

A complicating factor for phylogenetic and population genetic investigations of the Lake Malawi cichlids is that species tend to share much of their genetic variation, which has been seen with allozymes (Kornfield, 1978; McKaye et al., 1982, 1984), mitochondrial haplotype data (Moran and Kornfield, 1993; Parker and Kornfield, 1997), microsatellite or short-tandem repeat (STR) loci (Kornfield and Parker, 1997), and nuclear DNA sequences (Hey et al., 2004). The fact of shared variation means that neither allelic nor haplotypic data from individual loci (or from a small number of loci) can provide phylogenetic resolution (Kornfield and Parker, 1997; Moran and Kornfield, 1993; Parker and Kornfield, 1997), and in recent years investigators have had to turn to using very large numbers of amplified fragment-length polymorphism markers to estimate phylogenies (Albertson et al., 1999; Allender et al., 2003).

Shared genetic variation also raises important, albeit difficult, population genetic questions. The extensive sharing of genetic variation by closely related cichlid species has traditionally been attributed to the simple persistence of variation that was present in ancestral species (Albertson et al., 1999; Moran and Kornfield, 1993; Parker and Kornfield, 1997). However, shared variation and low levels of divergence between cichlid species have also been interpreted as evidence of ongoing low levels of gene flow (Danley and Kocher, 2001). Direct evidence of interspecies gene flow comes from hybrids and hybrid populations (Smith et al., 2003; Stauffer et al., 1996; Streelman et al., 2004). If cichlid species are diverging in the presence of gene flow, then it is also necessary to consider the role that natural selection plays, either in driving divergence and/or limiting gene flow.

Hey et al. (2004) developed the use of compound loci that have a low-mutation rate component and a high-mutation rate component and then analyzed the data by using a recently developed parameter-rich model of population divergence (Fig. 10.1). Here we extend this approach to a larger set of loci and species. In addition, we include dated outgroup sequences that allow us to estimate the actual times and effective population sizes associated with speciation events.