I doubt the estimates are wrong. They're not even based on haplogroup frequencies, so Barac's criticism is moot. They were derived using a method that Chikhi et al. argue convincingly is vastly more accurate:
Similarly, Semino et al. (16) have used their results from the non-recombining Y-chromosome region (NRY) to argue that the genetic contribution of Neolithic people may have been as low as 22%. This figure represents the proportion in Europe of the four haplotypes (Eu4, -9, -10, and -11), which were singled out because they show a distinct gradient from the epicenter of the agricultural revolution in the Levant. Although this gradient may well have been established during the Neolithic transition, it is not clear that the proportion of these haplotypes should provide an estimate of admixture proportions. Indeed, admixture is a demographic process, and, as such, it affects the entire genome.
...
One basic reason for the discrepancy between our and Semino et al.'s interpretation is that they used only a subset of information from selected haplotypes. Such an approach could make inefficient use of the data, or introduce bias. Conversely, the likelihood calculations on which our method is based can take advantage of all of the information present in the allelic distributions, without preselection of any allele. ... A particular innovation of our approach is that it estimates the trend in the Neolithic contribution directly, rather than evaluating it indirectly from the clines in allele frequencies.
And even greater accuracy is achieved by factoring in genetic drift:
The method takes into account, and quantifies, the effect of genetic drift since the time of admixture in each population. This innovation in the method is important because the populations are expected to have expanded after acquiring agriculture and, consequently, to have experienced a reduction in genetic drift. Because the archaeological data suggest that the timing of this transition varied from place to place in Europe, the method should be able to pick up a signature of this sequence in the genetic data.
As a result, the data correlates better with archeological records:
One of the most striking results was obtained for the Sardinian sample (Fig. 1). Semino et al.'s ordination of the haplotype frequencies showed the Sardinian sample clustering with Greek and Albanian samples, far removed from the Basque samples. That result appeared at odds with archaeological data that suggest a limited Neolithic immigration in Sardinia (e.g., ref. 32). Conversely, in Fig. 1a, Sardinia appears as an outlier with a significantly high proportion of Palaeolithic genes. This result suggests that the Y-chromosome differentiation observed between Basques and Sardinians today is due to drift from common Palaeolithic ancestors, with little input of genes from the Near East, rather than to a greater Neolithic immigration in Sardinia. This result shows the importance in separating drift from admixture in the analysis of ancient demographic events.
And it also supports Cavalli-Sforza's original demic diffusion model:
This finding leads us to reject a predominantly cultural transmission of agriculture. Instead, we argue that the demic diffusion model introduced by Ammerman and Cavalli-Sforza [Ammerman, A. J. & Cavalli-Sforza, L. L. (1984) The Neolithic Transition and the Genetics of Populations in Europe (Princeton Univ. Press, Princeton)] captures the major features of this dramatic episode in European prehistory.
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Europe-wide gradients of allele frequencies have repeatedly been described since the early work of Ammerman and Cavalli-Sforza (1, 5, 12, 13, 28). They were originally interpreted as a consequence of the admixture between low density local hunter-gatherers and the large numbers of new-coming farmers from the Near East.
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Our assessment of the demographic impact of the Neolithic expansion into Europe is largely independent from, but appears consistent with, archaeological evidence, simulations, and classical studies of allele frequencies. Despite some reports of its demise, the original model proposed by Ammerman and Cavalli-Sforza is more alive than ever.
Finally, the study's results have been duplicated analyzing nuclear DNA:
Clines of nuclear DNA markers suggest a largely Neolithic ancestry of the European gene pool
Comparisons between archaeological findings and allele frequencies at protein loci suggest that most genes of current Europeans descend from populations that have been expanding in Europe in the last 10,000 years, in the Neolithic period. Recent mitochondrial data have been interpreted as indicating a much older, Paleolithic ancestry. In a spatial autocorrelation study at seven hypervariable loci in Europe (four microsatellites, two larger, tandem-repeat loci, and a sequence polymorphism) broad clinal patterns of DNA variation were recognized. The observed clines closely match those described at the protein level, in agreement with a possible Near Eastern origin for the ancestral population. Separation times between populations were estimated on the basis of a stepwise mutation model. Even assuming low mutation rates and long generation times, we found no evidence for population splits older than 10,000 years, with the predictable exception of Saami (Lapps). The simplest interpretation of these results is that the current nuclear gene pool largely reflects the westward and northward expansion of a Neolithic group. This conclusion is now supported by purely genetic evidence on the levels and patterns of microsatellite diversity, rather than by correlations of biological and nonbiological data. We argue that many mitochondrial lineages whose origin has been traced back to the Paleolithic period probably reached Europe at a later time.
http://www.pubmedcentral.nih.gov/art...rtype=abstract
Neolithic Gene Frequencies in Europeans
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Originally Posted by Medhammer
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