Scientists have the approximate rate at which the bases in the mtDNA mutate thus they can estimate how long ago H.sapiens and H.neanderthalensis diverged by counting the base mutations.

An average coalescence time is 600KYA. It is important to note that genes differentiate prior to any visible population differentiation. This means that differences in the mtDNA were developing inside a common ancestor of the two clades. The date of 600KYA is when the first evidence of Homo heidelbergensis appears. Homo heidelbergensis is stated as the most recent common ancestor to H.sapiens and H.neanderthalensis, considering that they are indeed two different species.

Figure 12 outlines the test results for a polymerase chain reaction test. The test is designed to amplify and remove many small sections of the Neanderthal mtDNA and then overlap the sections to create a sequence. The overlap is applied to recreate the sequence with minimal error (evident in columns 5, 6, 7, 11, 12). The bases shown in red indicate a distinct deviance from the reference sequence (a modern mtDNA sample).

Figure 12: Results of mtDNA PCR test.