I have written to Dr. Goodwin regarding this set of dates but have not yet received clarification regarding his methods. However, I do think that an earlier article on establishing the DNA sequence of Neanderthals ("DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen" at http://www.pnas.org/cgi/content/full/96/10/5581) provides important information on the methods used. This article says :
The date of divergence between the mtDNAs of the Neandertal and contemporary humans is estimated to 465,000 years before the present, with confidence limits of 317,000 and 741,000 years. Taken together, the results support the concept that the Neandertal mtDNA evolved separately from that of modern humans for a substantial amount of time and lends no support to the idea that they contributed mtDNA to contemporary modern humans.
Dates of Divergences. For the estimation of the ages of MRCAs [Most Recent Common Ancestors] of different groups of mtDNAs, the observed nucleotide differences were corrected for multiple substitutions by using the Tamura-Nei algorithm. The resulting genetic distances and the estimated age of the modern human-chimpanzee split of 4-5 million years were used to calculate the substitution rate of 0.94 × 10 7 substitutions per site per year per lineage with 5.92 × 10 8 and 1.38 × 10 7 as the lower and upper confidence limits. These estimates are in reasonable agreement with previous rate estimations for the mtDNA control region. Using these rates, the age of the MRCA of the Neandertal and modern human mtDNAs was estimated to be 465,000 years, with confidence limits of 317,000 and 741,000 years. This age is significantly older than that of the MRCA of modern human mtDNAs, which, by the same procedure, was determined to be 163,000 years, with 111,000 and 260,000 years as confidence limits. Finally, the age of the MRCA of the mtDNAs of the seven chimpanzees and the two bonobos was calculated as 2,844,000 years (confidence limits: 1,940,000 and 4,534,000 years).
However, mtDNA sequences from more Neandertal individuals are needed to obtain a better understanding of the extent of separation between the mtDNA gene pools of Neandertals and modern humans.