Genomic DNA Extraction and Sequencing from Lake Malawi Cichlids

We extracted genomic DNA, from fin clips of 22 male individuals^{62 (link)} (Qiagen DNeasy, Cat #69504), from 8 rock dwelling and 14 sand dwelling Lake Malawi species (Supplementary Table S2) representing broad diversity across the rock and sand lineages in Lake Malawi. We made libraries using the Illumina Nextera Library prep kit and performed paired-end sequencing on the Illumina Hi-Seq 2500 at Georgia Tech. The Metriaclima zebra reference genome version MZ_UMD2a^{34 (link)} was used for genome alignment, variant discovery and annotation using standard BWA^{63 (link)} and GATK practices^{64 (link)}. The maximum likelihood tree in Fig. 1A was constructed using SNPhylo^{65 (link)}, from variant data.