Excel was used to generate figures for comparisons among all markers: Supplementary Table S4 includes the contingency table, formulas and description of the routine. Supporting Information Figure S1 The groups identified by Johnson et al. (2007) [16] based on African elephant mtDNA CYTB sequences largely overlap the mtDNA diversity reported by Debruyne (2005) [12]. Panel descriptions are shown in the figure. (PDF) Figure S2 Comparison of mtDNA sequences across studies of African elephant genetics: (A) Diagram illustrating mtDNA regions sequenced by different researchers, showing overlapping and non-overlapping regions across studies. Positions follow those of the elephant reference mtDNA genome (Genbank accession number NC_000934) [85]. (B) Corresponding clade designations for representative elephant sequences across studies. Relevant sequences that proved identical or matched closely across studies are indicated. The ND4-tRNAGLU sequences of Lei et al. (2008) [13] were used in a Blast query to retrieve the overlapping ND5 sequences Roca et al. (2005) [4]. The CYTB sequences of the same individual elephant (same ‘‘sample ID’’) of Lei et al. (2008) [13] was also used to retrieve matching CYTB and control region (CR) sequences of Debruyne (2005) [12] and CYTB sequences of Johnson et al. (2007) [16]. Through a Blast query using the retrieved Debruyne (2005) [12] sequence, matching mtDNA hypervariable region (HVR) sequences of Johnson et al. (2007) [16] were also obtained. Using this system, designations for the equivalent clades across studies were identified. (PDF) Figure S3 Map and list of locations of elephants sampled and sequenced for mtDNA across genetic studies [4,12,13,15,16,36,37]. (PDF) References 1. Roca AL, Georgiadis N, O’Brien SJ (2007) Cyto-nuclear genomic dissociation and the African elephant species question. Quaternary International 169–170: 4–16. 2. 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