It is interesting that one out of three mtDNA haplotypes is not observed in modern dogs, just as all seven Paleolithic ones are not so observed. This, together with the apparently dramatic change in frequency of clade C since the Neolithic, is perfectly consistent with selection I hypothesized about earlier, which in the case of dogs may have been human-induced.
Journal of Archaeological Science doi:10.1016/j.jas.2008.10.011
Ancient DNA supports lineage replacement in European dog gene pool: insight into Neolithic South-East France
M.F. Deguilloux et al.
We report palaeogenetic analysis of domesticated dog (Canis familiaris) remains excavated from three archaeological sites from South-East France and dating from Middle Neolithic. Ancient DNA analysis was attempted on teeth and bone samples taken from 11 dogs. Three 266-base-pair fragments of the mitochondrial genome hypervariable region I (HVR-I) could be retrieved and revealed two haplotypes belonging to HVR-I lineage C. These three sequences were compared to the sequences of Swedish and Italian Neolithic dogs and permitted to confirm that clade C was largely represented all over Western Europe during this period. One haplotype defined in Neolithic French dog was observed for the first time in Canis mtDNA, underlining the loss of mitochondrial diversity in Europe since the Neolithic. Finally, these results point out mitochondrial lineage replacement in Europe, since lineage C represents only 5% of extant European dogs. Altogether, these results support the proposition that palaeogenetic studies are essential for the reconstruction of the past demographic history and the domestication process of dogs.