Mammoth mitochondrial DNA cladograms. (a) WM lineages (blue) are summarized from previous studies [9–11] with clades indicated and haplogroups labeled at the tips. Hypothetical CM lineage positions (green) are expected positions derived from strict interpretations of paleontological models that posit the two species were separate since the early Pleistocene. The multiple node positions reflect the general uncertainty surrounding the chronology and identity of the WM lineage common ancestor. The position of WM haplogroup B is poorly resolved, exhibiting deep common ancestry with the other haplogroups. Haplogroups A and C are endemic to Eurasia and North America, respectively; haplogroups B, D, and E occur on both continents. Radiocarbon chronologies indicate that haplogroup A went extinct approximately 35,000 14Cya, and clade I by approximately 3,200 14Cya. Calculated MRCA ages for all nodes yield wide confidence intervals. (b) Our estimated mtDNA cladograms of haplogroup C are depicted using two datasets: the black cladogram and associated scale and posterior probabilities (parameter set 1b, Figure S4 in Additional file 3) are estimated from 743 bp for which several dozen mammoths have been sequenced, whereas the red cladogram and associated scale and posterior probabilities (parameter set 4b, Figure S8 in Additional file 3) are estimated from full mitochondrial genomes, for which only one other haplogroup C mammoth has been sequenced. Each tip in the black cladogram represents a haplotype. M. columbi (haplotype C32) as represented by the Huntington Mammoth is indicated with a yellow star. Scale units are substitutions per site.