Laura Morelli; Daniela Contu; Federico Santoni; Michael B. Whalen; Paolo Francalacci; Francesco Cucca

“ We have also assessed other Y-chromosome haplogroups proposed to be markers of the Neolithic diffusion of farmers and compared their intra-lineage variation—defined by short tandem repeats (STRs) —in Anatolia and in Sardinia, the only Western population where these lineages are present at appreciable frequencies and where there is substantial archaeological and genetic evidence of pre-Neolithic human occupation. ”

“ They also illustrate the risk of a reductionist model focusing only on one individual haplogroup without considering more realistic population dynamics; groups of individuals - not just specific lineages - move from one population to another in the presence of a real gene flow, and the mechanisms of diffusion of cultural knowledge may have also differed over time and geographic area. ”

“ The data indicate that Sardinia does not contain a subset of the variability present in Anatolia and that the shared variability between these populations is best explained by an earlier, pre-Neolithic dispersal of haplogroups from a common ancestral gene pool. Overall, these results are consistent with the cultural diffusion and do not support the demic model of agriculture diffusion. ”

“ Abstract Two alternative models have been proposed to explain the spread of agriculture in Europe during the Neolithic period. The demic diffusion model postulates the spreading of farmers from the Middle East along a Southeast to Northeast axis. ”

“ Conversely, the cultural diffusion model assumes transmission of agricultural techniques without substantial movements of people. Support for the demic model derives largely from the observation of frequency gradients among some genetic variants, in particular haplogroups defined by single nucleotide polymorphisms (SNPs) in the Y-chromosome. A recent network analysis of the R-M269 Y chromosome lineage has purportedly corroborated Neolithic expansion from Anatolia, the site of diffusion of agriculture. ”

“ The size effect of any genetic flow, if observed, could be further assessed by simulating data under different models and comparing simulated data summaries with the observed data. This more complex analysis would serve to reconstruct the separate contributions of complex migratory waves, and to take into account parameters, such as the initial effective population size, the degree of admixture with local population, the effect of gene flow with neighboring population over time as well as of convergent evolution at STR loci. ”

“ These reconstructed population histories depend on models for mutation and the expected genealogical structure and prior distributions for parameters of interest. By summarizing the population histories we can see the sorts of population history and ranges of parameters that are consistent with the data in the present. At equilibrium, the set of most likely population histories (represented as trees) is obtained by sampling from the posterior probability distribution of all possible trees, given the observed data and the assumed underlying genetic and demographic model. ”

“ Hence, also this set of analyses clearly indicates that, at least in Sardinia, the genetic contribution of the Neolithic settlers was negligible, despite the presence of Y-chromosome lineages that have been considered specific markers of such diffusion. Indeed, all together the various sets of data suggest that the clines of frequencies observed in Europe for some other markers predate the introduction of agriculture and that the E, G and J clades also came to Sardinia by a pre-Neolithic pathway. It could be argued that this latter set of analyses are valid for Sardinia ”

“ Furthermore, even the genetic landscape of the South-Eastern populations that acquired the Neolithic technology radiating from Anatolia, seemed to be shaped by autochthonous demographic expansions not related to the spread of people from Anatolia [7] . Overall, these observations indicate that the presence/absence of a single STR marker in the network can critically affect analyses, interpretation of the data and conclusions as does the use of different STR mutation rates. ”

“ However, while this model is plausible in a limited area and over a limited period of time (for instance this is observed in areas of central Africa where hunter-gatherers still live near farmers) it is difficult to envision a simplified multigenerational scenario where only male farmers repeatedly migrate and spread their genes across Europe over several thousand years. ”

“ The inferred BATWING values are conservative, since we used a generation time of 25 years and the more robust and reliable mode-based estimates instead of the more commonly-used mean and median measures that tend to provide much older values for all the parameters assessed with BATWING [13] , [37] , [38] . ”

“ Table 3 "Percentage of representative lineages in the Sardinian and Anatolian samples and percentage of shared haplotypes with the compared population. (10.1371/journal.pone.0010419.t003) "thumbAnatolian population data are from [14] . Individually, R-M269 represents the most informative lineage for which previous studies have reached conflicting conclusions. Therefore, to have a more definitive picture we constructed a network of R-M269 considering not only Anatolia and Sardinia but also the Balkan, Georgian, Iberian and North-Western European populations (figure 2A) . ”