(Last Update Nov 10)
I first became aware of this research in an ISBA4 abstract, and now it seems that a full article has been published in PLoS Biology.
Today, a fascinating new paper has appeared which completes the picture by studying for the first time both mtDNA and Y-chromosomes from a Central European Linearbandkeramik site, Derenburg Meerenstieg II in Germany.
From the paper:
We successfully typed 17 individuals for mtDNA, which together with a previous study  provided data for 22 individuals from the Derenburg graveyard (71% of all samples collected for genetic analysis; Tables 1 and S1), and significantly extended the genetic dataset of the LBK (n = 42), to our knowledge the largest Neolithic database available.
Table 1 has a summary of the new data.
Two individuals belonged to Y-chromosome paragroup F*(xG,H,I,J,K), and one to haplogroup G2a3.
From the paper:
The multiplexed single base extension (SBE) approach with its shortened flanking regions around targeted SNPs significantly increases the chance of successful Y-chromosomal amplifications, which have remained problematic for aDNA studies, as have nuclear loci in general, because of the much lower cellular copy number compared to mitochondrial loci. The multiplexed SBE approach promises to open the way to studying the paternal history of past populations, which is of paramount importance in determining how the social organization of prehistoric societies impacted the population dynamics of the past.
The mtDNA data is more plentiful, and the authors write:
Out of 25 different haplotypes present in 42 LBK samples, 11 are found at high frequency in nearly all present-day populations under study, a further ten have limited geographic distribution, and the remaining four haplotypes are unique to Neolithic LBK populations (Table S4).
This suggests to me that there has not been massive extinction (due to selection or any other factor) of the Neolithic gene pool, as only four unique haplotypes to LBK individuals were found. Moreover, even these could potentially still exist, although they might not have been sampled yet.
From the paper:
The 11 widespread haplotypes are mainly basal (i.e., constituting a basal node within the corresponding hg) for Western Eurasian mitochondrial hgs H, HV, V, K, T, and W. While these haplotypes are relatively uninformative for identifying genetic affiliations to extant populations, this finding is consistent within an ancient population (5,500–4,900 cal B.C., i.e., prior to recent population expansions), in which basal haplotypes might be expected to be more frequent than derived haplotypes (e.g., end tips of branches within hgs).
From the paper:
The next ten LBK haplotypes were unequally spread among present-day populations and for this reason potentially contain information about geographical affinities. We found nine modern-day population pools in which the percentage of these haplotypes is significantly higher than in other population pools (p>0.01, two-tailed z test; Figure 1; Table S4): (a) North and Central English, (b) Croatians and Slovenians, (c) Czechs and Slovaks, (d) Hungarians and Romanians, (e) Turkish, Kurds, and Armenians, (f) Iraqis, Syrians, Palestinians, and Cypriotes, (g) Caucasus (Ossetians and Georgians), (h) Southern Russians, and (i) Iranians. Three of these pools (b–d) originate near the proposed geographic center of the earliest LBK in Central Europe and presumably represent a genetic legacy from the Neolithic. However, the other matching population pools are from Near East regions (except [a] and [h]), which is consistent with this area representing the origin of the European Neolithic, an idea that is further supported by Iranians sharing the highest number of informative haplotypes with the LBK (7.2%; Table S4). The remaining pool (a) from North and Central England shares an elevated frequency of mtDNA T2 haplotypes with the LBK, but otherwise appears inconsistent with the proposed origin of the Neolithic in the Near East. It has been shown that certain alleles (here hgs) can accumulate in frequency while surfing on the wave of expansion, eventually resulting in higher frequencies relative to the proposed origin ,. Several of the other population pools also show a low but nonsignificant level of matches, which may relate to pre-Neolithic distributions or subsequent demographic movements (Figure 1).As I have noted before, frequency is an uncertain guide to where a lineage has originated, as Neolithic founders may have left more descendants in freshly colonized regions than in their homelands. Nonetheless, with the exception of the English, the "high match" populations are all within the broad trajectory of Neolithic populations from the Fertile Crescent to Central Europe.
With respect to the Y-chromosomal evidence:
The Y chromosome hgs obtained from the three Derenburg early Neolithic individuals are generally concordant with the mtDNA data (Table 1). Interestingly, we do not find the most common Y chromosome hgs in modern Europe (e.g., R1b, R1a, I, and E1b1), which parallels the low frequency of the very common modern European mtDNA hg H (now at 20%–50% across Western Eurasia) in the Neolithic samples. Also, while both Neolithic Y chromosome hgs G2a3 and F* are rather rare in modern-day Europe, they have slightly higher frequencies in populations of the Near East, and the highest frequency of hg G2a is seen in the Caucasus today . The few published ancient Y chromosome results from Central Europe come from late Neolithic sites and were exclusively hg R1a . While speculative, we suggest this supports the idea that R1a may have spread with late Neolithic cultures from the east .Hopefully more Y-chromosome results from different Neolithic sites will turn up more derived haplogroups. Haplogroup G has been implicated as a Neolithic lineage as early as Semino et al. (2010), but clearly this is just the beginning of the reconstruction of Neolithic Y-DNA gene pools, and hopefully Y-DNA can be extracted from Mesolithic samples of similar age.
PCA (on the left) shows the outlier status of the Neolithic samples with respect to extant populations. Either natural selection, or later demographic events have led to a quite different gene pool today than what existed in central Europe thousands of years ago.
From the paper:
To better understand which particular hgs made the Neolithic populations appear either Near Eastern or (West) European, we compared average hg frequencies of the total LBK (LBK42) and Derenburg (DEB22) datasets to two geographically pooled meta-population sets from Europe and the Near East (Tables 2 and S6; 41 and 14 populations, respectively). PC correlates and component loadings (Figure 2) showed a pattern similar to average hg frequencies (Table 2) in both large meta-population sets, with the LBK dataset grouping with Europeans because of a lack of mitochondrial African hgs (L and M1) and preHV, and elevated frequencies of hg V. In contrast, low frequencies of hg H and higher frequencies for HV, J, and U3 promoted Near Eastern resemblances. Removal of individuals with shared haplotypes within the Derenburg dataset (yielding dataset LBK34) did not noticeably decrease the elevated frequencies of J and especially HV in the Neolithic data.
Most importantly, PC correlates of the second component showed that elevated or high frequencies of hgs T, N1a, K, and W were unique to LBK populations, making them appear different from both Europe and Near East. The considerable within-hg diversity of all four of these hgs (especially T and N1a; Table 1) suggests that this observation is unlikely to be an artifact of random genetic drift leading to elevated frequencies in small, isolated populations.
The pooled European and Near Eastern meta-populations are necessarily overgeneralizations, and there are likely to be subsets of Near Eastern populations that are more similar to the Neolithic population. Interestingly, both the PCA and the MDS plots identified Georgians, Ossetians, and Armenians as candidate populations (Figures 2 and S1).
The authors also mapped genetic distances between all 42 Neolithic mtDNA samples (left) and only the Derenburg site (right), with "greener" signifying smaller distance. They write:
In agreement with the PCA and MDS analyses, populations from the area bounding modern-day Turkey, Armenia, Iraq, and Iran demonstrated a clear genetic similarity with the LBK population (Figure 3A). This relationship was even stronger in a second map generated with just the Neolithic Derenburg individuals (Figure 3B). Interestingly, the map of the combined LBK data also suggested a possible geographic route for the dispersal of Neolithic lineages into Central Europe: genetic distances gradually increase from eastern Anatolia westward across the Balkans, and then northwards into Central Europe. The area with lower genetic distances follows the course of the rivers Danube and Dniester, and this natural corridor has been widely accepted as the most likely inland route towards the Carpathian basin as well as the fertile Loess plains further northwest.
How ancient DNA is rewriting theories based on modern populations:
aDNA data offers a powerful new means to test evolutionary models and assumptions. The European lineage with the oldest coalescent age, U5, has indeed been found to prevail in the indigenous hunter–gatherers ,. However, mtDNA hgs J2a1a and T1, which because of their younger coalescence ages have been suggested to be Neolithic immigrant lineages ,, are so far absent from the samples of early farmers in Central Europe. Similarly, older coalescence ages were used to support hgs K, T2, H, and V as “postglacial/Mesolithic lineages,” and yet these have been revealed to be common only in Neolithic samples. The recent use of whole mitochondrial genomes and the refinement of mutation rate estimates have resulted in a general reduction in coalescence ages , which would lead to an improved fit with the aDNA data.
The authors speak about demic diffusion being the best match for their data:
Therefore at a large scale, a demic diffusion model of genetic input from the Near East into Central Europe is the best match for our observations. It is notable that recent anthropological research has come to similar conclusions ,. On a regional scale, “leap-frog” or “individual pioneer” colonization models, where early farmers initially target the economically favorable Loess plains in Central Europe ,, would explain both the relative speed of the LBK expansion and the clear genetic Near Eastern connections still seen in these pioneer settlements, although the resolving power of the genetic data is currently unable to test the subtleties of these models.
Demic diffusion, at least as it was proposed initially, implies interaction between expanding farmers and local foragers, with gene pools becoming increasingly "forager" the further one goes from the source of the Neolithic. But, this is not really what we observe in the data, and there is no real evidence of forager DNA in Central European Neolithic (1/42 U5a). Whatever the terminology, it appears that genetics is adding extra firepower to the diffusionist camp of archaeological debates, and contradicting the suppositions of the acculturationists.
UPDATE I (Nov 10):
What is most disappointing about the study is that apparently the SNPs defining the Y-clade IJ were not typed in the samples. So, the two F* samples are certainly not I or J, but they could very well already be IJ. Haplogroup IJ largely tracks the path of the farmers from the Near East to the Balkans and Central Europe, and hopefully a re-examination of the Derenburg remains can be made to include the IJ-defining markers.
It is also fascinating that the presence of 33.3% haplogroup G2 in the German Neolithic is matched by a presence of 33.3% haplogroup G2 in 7th c. Bavarian knights, and maybe even the latest French royalty. The Y-DNA landscape of Europe is still largely empty in space and time, and it will be exciting to see it filled out over the next years.
Certainly, the new Haak et al. study has achieved what Haak et al. (2005), and pretty much every ancient DNA study since has achieved: to surprise us.
UPDATE II (November 10):
It is extremely important to note that the authors have not disproved that the F* Y-chromosomes belonged to derived clades (e.g., haplogroup I or haplogroup J) of the phylogeny. For example, haplogroup I is defined by 7 polymorphisms according to ISOGG.
Today only chromosomes that possess all 7 of them seem to be extant, but these polymorphisms occurred in an unknown order in the line of descent leading to modern I men.
The authors typed only M170, one of these 7 polymorphisms, but it could very well be the case that the F* samples were derived for one or more of the remaining 6 ones, and were thus either ancestors or "cousins" of extant European haplogroup-I bearing men.
It is imperative for internal tree markers to be tested in the F* bearing chromosomes to determine their status.
PLoS Biol 8(11): e1000536. doi:10.1371/journal.pbio.1000536
Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities
Wolfgang Haak et al.
In Europe, the Neolithic transition (8,000–4,000 B.C.) from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic (40,000 B.C.). However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. To date, inferences about the genetic make up of past populations have mostly been drawn from studies of modern-day Eurasian populations, but increasingly ancient DNA studies offer a direct view of the genetic past. We genetically characterized a population of the earliest farming culture in Central Europe, the Linear Pottery Culture (LBK; 5,500–4,900 calibrated B.C.) and used comprehensive phylogeographic and population genetic analyses to locate its origins within the broader Eurasian region, and to trace potential dispersal routes into Europe. We cloned and sequenced the mitochondrial hypervariable segment I and designed two powerful SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data from 21 individuals from a complete LBK graveyard at Derenburg Meerenstieg II in Germany. These results considerably extend the available genetic dataset for the LBK (n = 42) and permit the first detailed genetic analysis of the earliest Neolithic culture in Central Europe (5,500–4,900 calibrated B.C.). We characterized the Neolithic mitochondrial DNA sequence diversity and geographical affinities of the early farmers using a large database of extant Western Eurasian populations (n = 23,394) and a wide range of population genetic analyses including shared haplotype analyses, principal component analyses, multidimensional scaling, geographic mapping of genetic distances, and Bayesian Serial Simcoal analyses. The results reveal that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting a major genetic input from this area during the advent of farming in Europe. However, the LBK population also showed unique genetic features including a clearly distinct distribution of mitochondrial haplogroup frequencies, confirming that major demographic events continued to take place in Europe after the early Neolithic.