We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades,~1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the ^14C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.
Sympatric just means there was a spatial overlap between the lineages (see Figure 1 in the paper). I don't particular care much about the specific inferences being made here; I just think it's really cool that this sort of work can be performed on an extinct lineage of organisms. Of course, mammoth and mtDNA are optimal targets for this sort of research. Mammoth are big, widespread and were extant across a region where there is a high likelihood of preservation (low temperatures and permafrost), while mtDNA is relatively copious and so a greater likelihood exists of usable quantities remaining even after eons of degradation. But ultimately time is probably the biggest factor, mammoth were around relatively recently in terms of natural historical scales.