When I was at high school, mumblety-mumble years ago, the accepted wisdom was that modern humans and Neandertals were sub-species in the same genus: Homo sapiens sapiens and H. sapiens neandertalensis. That changed, to the view that they were probably separate species, with analyses of new fossil finds. More recently, molecular biology techniques have enabled researchers to compare sapiens & Neandertal genomes. The latest study in this area has reconstructed the Neandertal mitochondrial genome, adding even more support to the idea that these really are two separate species.
A large research team (Green et al., 2008) obtained mtDNA fragments from a 38,000 year-old Neandertal bone. They used a technique called high-throughput sequencing to sequence these fragments & use them to reconstruct the individual's complete mtDNA sequence. Ancient DNA sequences tend to be short (in this study they ranged from 30 base pairs to 289bp long, & so scientists have a fair bit of difficulty in reconstructing the complete sequence. Green & his colleagues used a method that aligned each mtDNA sequence with a human (sapiens) reference mtDNA sequence. They also allowed for the possibility of contamination with modern DNA, something which turned out to be very rare, and concluded that [the] assembled mtDNA sequence, therefore, represents a reliable reconstruction of the mtDNA that this Neandertal individual carried when alive.
The next step was to compare the Neandertal sequence with data from other primates, looking at sequence differences between: modern humans; humans & the Neandertal mtDNA; and modern humans & chimpanzees. The result: the Neandertal material fell outside the range of modern sapiens. And a phylogeny constructed using the mtDNA data from humans (N = 54), chimpanzees & bonobos, and the Neandertal also excluded the Neandertal from the modern human sample.
The data also allowed for an estimation of the likely date of divergence between H. neandertalensis & H. sapiens - around 660,000 years ago, which fits with earlier estimates. (The authors comment, though, that this assumption wasbased on an estimated divergence date between humans and chimps of 6-8 million years ago - a change in this date would mean the human-Neandertal date would also need to be reviewed.) And the team concluded that the most recent common ancestor of human and Neandertal mtDNA lived more than two or three times as long ago as the most recent common ancestor of extant human mtDNAs.
R.E. Green, A-S. Malaspinas, J. Krause, A.W. Briggs, P.L.F. Johnson, C. Uhler, M. Meyer, J.M Good, T. Maricic, U. Stenzel, K. Prufer, M. Siebauer, H.A. Burbano, M. Ronan, J.M. Rothberg, M. Egholm, P. Rudan, D. Brajkovic, Z. Kucan, I. Gusic, M. Wikstrom, L. Laakkonen, J. Kelso, M. Slatkin, & S. Paabo (2008). A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134: 416-426