Figure 6

Placing the DNA from Layer V within the Cervidae mtDNA diversity. (a) Reconstruction of a partial consensus mtDNA genome sequence, using the alignment to the Cervus elaphus reference mitochondrial genome (bottom). Blue dots indicate the positions at which bases could be called (middle). At each position, the coverage (green) and the support for the majority base (orange) is shown (top). The minimum thresholds for these parameters are shown in dashed lines. (b) Maximum Likelihood phylogenetic tree based on the partial mtDNA genome sequence reconstructed from sample SP5773 (shown in red) and 380 previously-sequenced Cervidae mtDNA genomes. Branch lengths are scaled based on the number of substitutions per site, and the support for each branch is based on 500 bootstrap replications. Only the part of the tree containing the Sefunim sample is shown, with the full tree presented in Supplementary Fig. S2. The phylogenetic tree was plotted in MEGA X⁸⁴ (https://www.megasoftware.net/).