Between a rock and a hard polytomy: phylogenomics of the rock-dwelling mbuna cichlids of Lake Malawi

Whole genome sequences are beginning to revolutionise our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure the phylogenetic history of the group. To overcome such challenges, one emerging strategy is to integrate results across different methods. Most such approaches have been implemented on reduced representation genomic datasets, but whole genomes should provide the maximum possible evidence approach. Here, we test the ability of SNPs extracted from whole genome resequencing data, implemented in an integrative genomic approach, to resolve key nodes in the phylogeny of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomise the phylogenetic intractability that often accompanies explosive lineage diversification. This monophyletic radiation has diversified a...