UPDATE (Oct 20):
The paper makes a significant contribution to the phylogeny of N1a by full sequencing of mtDNAs belonging to individuals from different populations, ascribing the Neolithic sequences to several identified clades. That part of the paper is solid and interesting.
My main problems with the paper are threefold:
1. The paper attempts to infer the origin of mtDNA founders using TMRCA estimates. But, as I have pointed out, TMRCAs of clades tell us nothing about where the common ancestors lived. The TMRCA of Latin American R1b, for example, predates the arrival of Western Europeans into the Americas by thousands of years.
2. The paper attempts to infer the origin of mtDNA founders using modern populations. Given the clear evidence for discontinuity between the Mesolithic and Neolithic and present in Central Europe, due to either demography or selection, I find it a very questionable proposition. If N1a turns up in dated human remains associated with a Mesolithic culture of Europe prior to the arrival of the Neolithic economy, then the hypothesis that it is a forager lineage is unsubstantiated.
3. Finally, the paper uses the frequency of identified subclades to infer the location of the founders. In addition to the above 2 criticisms, I must point out that this puts the cart before the horse. In a uniform landscape, we do expect present-day frequency to be related to the place of origin of a mutation. But, we are not dealing with such a landscape. In particular, we are dealing with an expanding population exploiting new territory. As an analogy, the few people who made the crossing into the Americas left a few relatives in the Old World, and produced a plethora of new ones (descendants) in the New World. They did so by exploiting their new environment.
An additional objection, is, of course, that the idea of Mesolithic N1a in Europe requires a virtual partition of pre-Neolithic European populations, to account for its non-existence among north/central Mesolithic North/Central Europeans. That is hard to swallow, unless by "Mesolithic" one means "very shortly before the Neolithic", which would make it possible for a lineage to establish itself in e.g., the Balkans shortly prior to the onset of the Neolithic, and begin expanding shortly thereafter. However, I don't see how an argument could be made for such a scenario, and, of course, I doubt that genetic dating methods in modern populations have enough precision to allow one to distinguish between late Mesolithic and early Neolithic intrusions.
BMC Evolutionary Biology 2010, 10:304doi:10.1186/1471-2148-10-304
Mitochondrial haplogroup N1a phylogeography, with implication to the origin of European farmers
Malliya GOUNDER Palanichamy et al.
Tracing the genetic origin of central European farmer N1a lineages can provide a unique opportunity to assess the patterns of the farming technology spread into central Europe in the human prehistory. Here, we have chosen twelve N1a samples from modern populations which are most similar with the farmer N1a types and performed the complete mitochondrial DNA genome sequencing analysis. To assess the genetic and phylogeographic relationship, we performed a detailed survey of modern published N1a types from Eurasian and African populations.
The geographic origin and expansion of farmer lineages related N1a subclades have been deduced from combined analysis of 19 complete sequences with 166 N1a haplotypes. The phylogeographic analysis revealed that the central European farmer lineages have originated from different sources: from eastern Europe, local central Europe, and from the Near East via southern Europe.
The results obtained emphasize that the arrival of central European farmer lineages did not occur via a single demic diffusion event from the Near East at the onset of the Neolithic spread of agriculture into Europe. Indeed these results indicate that the Neolithic transition process was more complex in central Europe and possibly the farmer N1a lineages were a result of a 'leapfrog' colonization process.