Extended Data Fig. 4. Phylogenetic placement of Elephantidae mitochondrial reads within mastodons (Mammut americanum), using Elephas maximus as outgroup, including transitions and transversion SNPs.

(Please note that the NCBI taxonomy includes the Mammut genus within Elephantidae). The reference dataset consisted of mitochondria from mastodons (Mammut americanum) only and one Elephas maximus as an outgroup. Reads have been merged from all layers and sites. The green numbers on each edge represent the number of supporting (+) SNPs, whereas the red numbers indicate conflicting (−) SNPs in the ancient Elephantidae environmental mitochondrial genome overlapping the reference SNPs assigned to the respective edge. There is a placement for the ancient Elephantidae environmental mitochondrial genome on the edge marked +2/−1, identifying it as basal to the mastodon (Mammut americanum) clade, which contains most of all mastodon reference mitochondrial genomes. Please note that this placement is based on two transition SNPs with a read depth of three reads per SNP.