The pairwise distance distributions within humans, as well as between humans and Neandertals, are closer and overlap more extensively for more recent Neandertals (p < 0.001) than for the Scladina specimen (Figure 2). While the diversity of the more recent Neandertals is similar to that of modern humans worldwide, the sequence from Scladina reveals that more divergent Neandertal haplotypes existed before 42,000 years ago. This could suggest that Neandertals experienced genetic drift as demographic bottlenecks eliminated the phylogenetically more recent (i.e. less expanded) haplotypes from populations. Consequently, the most likely conserved Neandertal haplotypes could also be the phylogenetically most ancient (i.e. the most closely related to the common ancestor of modern humans and Neandertals). This could explain the shift towards modern human pairwise distributions observed between 100,000 and 40,000 years ago. Whatever this shift should be related to cohabitation, climatic changes, or any subdivision of populations, the Scladina sequence has revealed that the genetic diversity of Neandertals has been underestimated. Thus, more Neandertal sequences than the six presently available and longer than 100 bp are needed to fully understand the extent of the past diversity of Neandertals.
Current Biology Volume 16, Issue 11 , June 2006, Pages R400-R402
Revisiting Neandertal diversity with a 100,000 year old mtDNA sequence
Ludovic Orlando et al.