Mitochondrial phylogeography is a useful tool for the study of wild populations. But applying phylogeography to domestic species is more complicated....
A classic example of the use of mitochondrial DNA (mtDNA) diversity to infer the history of domestication refers to dogs (Canis familiaris). Four to six mitochondrial haplogroups (Hg) have been described in genetic studies of modern dogs, indicating recurrent domestication or backcrosses between domestic dogs and wild wolves (Canis lupus). Three of the major Hgs are distributed throughout the world, whereas one (D) is restricted to Europe, especially in breeds originating in Scandinavia. Similar patterns of fragmented genetic diversity have been used to argue for local domestication in other species. Such scenario could apply to dogs as they appear as early as 9000 years ago in Scandinavia, and as dogs and wolf remains have been found on the same sites (Malmström et al. 2008:4).
So, they sampled ancient DNA from Neolithic and medieval dog skeletons, to look for the D haplogroup, which would provide evidence that these ancient dogs had a unique and separate origin from other domesticated dogs elsewhere in the world.
Except, it wasn't there.
Our results indicate that Hg frequencies have been altered in Scandinavian dogs since their first arrival. Interestingly, while Hg C is overrepresented in our ancient material, there is a complete lack of the Scandinavian group D in our ancient dataset. Hg D is the one that could support a Scandinavian origin whereas Hg C is suggested to be of Asian origin. Thus, we find no obvious evidence for prehistoric canid domestication in Scandinavia. An external origin of Scandinavian dogs is supported by morphologic data, as even the oldest remains of dogs in Scandinavia were of smaller size than those of prehistoric and extant wolves. While canid domestication may have occurred in other parts of Europe, Scandinavian dogs were likely imported and had experienced a long period of morphological change under human control before they reached the Scandinavian peninsula (Malmström et al. 2008:7).
Fair enough -- the mitochondrial gene pool of Scandinavian dogs has rapidly changed under human influence during the last few thousand years. No word on where the D haplogroup that characterizes today's Scandinavian dogs has come from; whether introgression from local wolves or dogs elsewhere in Europe.
Why does this remind me of human evolution? Well, consider this 2005 paper by Wolfgang Haak and colleagues:
Here we present an analysis of ancient DNA from early European farmers. We successfully extracted and sequenced intact stretches of maternally inherited mitochondrial DNA (mtDNA) from 24 out of 57 Neolithic skeletons from various locations in Germany, Austria, and Hungary. We found that 25% of the Neolithic farmers had one characteristic mtDNA type and that this type formerly was widespread among Neolithic farmers in Central Europe. Europeans today have a 150-times lower frequency (0.2%) of this mtDNA type, revealing that these first Neolithic farmers did not have a strong genetic influence on modern European female lineages.
I discussed this paper when it came out, noting that one explanation for the results is selection, either in favor of the N1a type in Neolithic farmers or against it later. The change in frequency in post-Neolithic Europeans is clearly not consistent with drift. On the basis of other genetic loci, migration from other populations cannot explain the catastrophic decline in frequency of the N1a type, which the ancient DNA data show was widespread across central Europe. So, there would appear to have been local selection against N1a.
The Scandinavian dogs are showing the inverse pattern -- a now-common mtDNA type was formerly not present at a measurable frequency, at least in the available sample of ancient dogs. With dogs, of course, there is every reason to expect selection imposed by humans. The only question is whether the selection was directly on the mtDNA itself, or whether the mtDNA has been carried along fortuitously with other selected genes. The extreme inbreeding under recent intensive breeding would allow either scenario -- unlike in humans, where no extreme inbreeding occurred.
I want to point out the parallels and differences clearly, because I'm writing this week about effective population sizes and inbreeding. There are many geneticists who hold out the possibility of extreme degrees of inbreeding in post-Neolithic humans. Genetic, archaeological and historic data -- not to mention common sense -- weigh against this possibility. However, many prefer to maintain a strict view that natural selection occurs rarely, if ever.
Malmström H, Vilà C, Gilbert MTP, Storå J, Willerslev E, Holmlund G, Gotherstrom A. 2008. Barking up the wrong tree: Modern northern European dogs fail to explain their origin. BMC Evol Biol 8:71. doi:10.1186/1471-2148-8-71
Haak W, Forster P, Bramanti B, Matsumura S, Brandt G, Tänzer M, Villems R, Renfrew C, Gronenborn D, Alt KW, Burger J. 2005. Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science 310:1016-1018. doi:10.1126/science.1118725