Supplemental Material for Kitchen et al., 2019

The R code used to perform the DFCA and generate Figure 6 is provided in File S1. Table S1 is the alignment summary statistics for all samples. Table S2 is the discriminant factorial correspondence analysis results for the microsatellite and SNV markers. Table S3 provides the location, SNV, primers and enzymes for the SNV markers and Table S4 provides their gene annotation. Table S5 is the summary of the gene models identified in the two highest scoring genomic intervals. Figure S1 is the genome coverage of the 21 Acropora cervicornis samples. Figure S2 is a phylogenetic tree and identity-by-state analysis of the Acropora samples based on high-quality SNVs. Figure S3 present the locations of mitochondrial variants. Figures S4- S6 and S10 are protein alignments highlighting variants between corals and human orthologue. Figure S7 is an image of the sequence coverage of the 12-bp deletion of STRADa protein. Figure S8 and S9 are protein models of STRADa and ABCB1, respectively. Figure S11 highlights the conservation in ATP-binding cassette sub-family D member 2 in vertebrates. Figure S12 is a comparison of the nucleotide diversity, and relative and absolute divergence between the two species for the genomic islands of divergence. Figure S13 is a gel electrophoresis of RFLP results for two fixed SNV loci.