Ancient DNA from the first European farmers in 7500-year-old Neolithic sites

The ancestry of modern Europeans is a subject of debate among geneticists, archaeologists, and anthropologists. A crucial question is the extent to which Europeans are descended from the first European farmers in the Neolithic Age 7500 years ago or from Paleolithic hunter-gatherers who were present in Europe since 40,000 years ago. 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. Our finding lends weight to a proposed Paleolithic ancestry for modern Europeans.     

Comment on "Widespread RNA and DNA sequence differences in the human transcriptome"

Li et al. (Research Articles, 1 July 2011, p. 53; published online 19 May 2011) reported large numbers of differences between DNA and messenger RNA in human cells, indicating unprecedented levels of RNA editing, and including sequence changes not produced by any of the known RNA editing mechanisms. However, common sources of systematic errors in high-throughput sequencing technology, which were not properly accounted for in this study, explain most of the claimed differences.     

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Klein et al. (Reports, 7 December 2007, p. 1642) used individuals with a polymorphism adjacent to the dopamine receptor 2 gene as naturally occurring models for reduced brain dopamine receptor density in a probabilistic learning task. We raise the concern that this polymorphism resides in the gene for the kinase ANKK1, where it causes a nonconservative amino acid exchange.     

Comment on "Reconstructing past climate from noisy data"

von Storch et al. (Reports, 22 October 2004, p. 679) criticized the ability of the "hockey stick" climate field reconstruction method to yield realistic estimates of past variation in Northern Hemisphere temperature. However, their conclusion was based on incorrect implementation of the reconstruction procedure. Calibration was performed using detrended data, thus artificially removing a large fraction of the physical response to radiative forcing.     

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Turner et al. (Reports, 20 October 2006, p. 449) measured sedimentation from Hurricanes Katrina and Rita in coastal Louisiana and inferred that storm deposition overwhelms direct Mississippi River sediment input. However, their annualized hurricane deposition rate is overestimated, whereas riverine deposition is underestimated by at least an order of magnitude. Their numbers do not provide a credible basis for decisions about coastal restoration.     

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Tilman et al. (Reports, 8 December 2006, p. 1598) argued that low-input high-diversity grasslands can provide a substantial proportion of global energy needs. We contend that their conclusions are not substantiated by their experimental protocol. The authors understated the management inputs required to establish prairies, extrapolated globally from site-specific results, and presented potentially misleading energy accounting.     

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Comment on "Detecting awareness in the vegetative state"

Owen et al. (Brevia, 8 September 2006, p. 1402) claimed that a patient's brain activity revealed that she was consciously responding to commands despite being in a vegetative state. However, several alternative explanations were not eliminated. Specifically, the activity could reflect unconscious reactions to the last word in the command, not conscious decisions to respond. A refined experimental design could clarify these issues.     

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Schmitz and Motani (Reports, 6 May 2011, p. 705) claimed to definitively reconstruct activity patterns of Mesozoic archosaurs using the anatomy of the orbit and scleral ring. However, we find serious flaws in the data, methods, and interpretations of this study. Accordingly, it is not yet possible to reconstruct the activity patterns of most fossil archosaurs with a high degree of confidence.     

Comment on "Early domesticated fig in the Jordan Valley"

Kislev et al. (Reports, 2 June 2006, p. 1372) described Neolithic parthenocarpic fig fruits and proposed that they derive from trees propagated only by cuttings and thus represent the first domesticated plant of the Neolithic Revolution. Because parthenocarpic fig trees naturally produce both seeded and seedless fruits and are capable of spontaneous reproduction, we argue that the finds do not necessarily indicate cultivation, nor horticulture predating grain crops.     

Comment on "Whole-genome shotgun sequencing of mitochondria from ancient hair shafts"

Gilbert et al. (Reports, 28 September 2007, p. 1927) reported that "hair shafts surpass comparably stored bone as an aDNA source [...] in regard to preservation and concentration of mtDNA." When experimental parameters are carefully controlled for, including adequate sampling, quantitative polymerase chain reaction analysis, and modeling the decay of DNA, the general importance of this claim is not supported.     

Comment on "Reconstructing the origin of Andaman islanders"

On the basis of mitochondrial DNA sequence analyses, Thangaraj et al. (Brevia, 13 May 2005, p. 996) proposed that Andaman islanders descended from the first humans to migrate out of Africa. We identified mitochondrial DNA from two northeast Indian Rajbanshi individuals that shares three specific mutations with the M31a lineage observed in the Great Andamanese, which suggests that the predecessor of haplogroup M31 originated on the Indian subcontinent.