Lalueza-Fox and colleagues (2005) report on the recovery of endogenous mtDNA from a Neandertal specimen from El Sidrón cave, in northern Spain. The fossil specimen (El Sidrón 441) was dated by AMS to a calibrated 43,129 +/- 129 years. Only a very limited amount of sequence could be recovered, amounting to only two short fragments of under a hundred base pairs total. This area of HVR-1 contains a number of distinctive mutations in other Neandertal sequences, however, and the El Sidrón reconstructed sequence is identical to the Feldhofer 1 (but not Feldhofer 2) and the two Vindija sequences over at least its short length.
The authors push two interpretations of this variation. The first focuses on the fact that the Spanish specimen shares its sequence with the Vindija specimens of a similar age. These individuals had the length of Europe between them, and may have belonged to populations that inhabited different refugia during glaciations. Taking these assumptions, the authors conclude that it would be unlikely for two distant specimens to share a sequence unless the effective size of the European population were very small. I would say this speculation is rather far from the data, considering that only a very short length of sequence is available, and that the known Neandertals vary at only one nucleotide in this short length.
The second interpretation concerns the time period over which the known Neandertal diversity accumulated. The authors seem to be concerned with the hypothesis that Neandertal genetic variation may have been greatly limited by the glacial maximum that occurred around 130,000 years ago. They estimate the dates at which mutations happened among the known Neandertal sequences, under several different assumptions about which changes were important or should be neglected. The most relevant, excluding the probable artifacts of the Feldhofer 1 sequence but including the long sequences available to date, estimates 162,000 ± 41,700 years for the most recent common ancestor and 92,000 ± 25,000 years for the mutation at site 16,258 shared by the El Sidrón sequence and the Feldhofer 1 and Vindija sequences. I don't thing there's really any story here, although if these dates are accurate, they show that the Neandertal mtDNA substantially postdates the origins of most Neandertal features in the Middle Pleistocene European sample. In this context, the interesting question is what factors led Neandertal variation to be comparably limited compared to human variation.
Lalueza-Fox C et al. 2005. Neandertal evolutionary genetics: mitochondrial DNA data from the Iberian peninsula. Mol Biol Evol Advance Access.