Fig. 4

Phylogenetic reconstruction of UCE generated SNPs. The consensus topology inferred using the 2707 SNPs that had a minor allele frequency greater than 2% is presented. The bootstrap values of the 2707 SNP dataset are shown above the branches subtending nodes, and bootstraps from the data set limited to a single SNP per locus are shown below the branches. There is evidence for the monophyly, shown with a bar dissecting the branch that subtends their last common ancestor, of the hypertrophied lip species Eclectochromis ornatus, Placidochromis “Mbenji fatlip”, Placidochromis milomo, and Cheilochromis euchilus as well as the non-hypertrophied lip species Chilotilapia rhoadesii. This group is highlighted with a red bar behind the species names. Also, Lichnochromis acuticeps, which has somewhat hypertrophied lips, groups with these taxa greater than 50% of the time in the 2707 SNP dataset