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SummaryArchaeological research shows that the dispersal of the Neolithic took a more complex turn when reaching western Europe, painting a contrasted picture of interactions between autochthonous hunter-gatherers (HGs) and incoming farmers. In order to clarify the mode, the intensity, and the regional variability of biological exchanges implied in these processes, we report new palaeogenomic data from Occitanie, a key region in Southern France. Genomic data from 28 individuals originating from six sites spanning from c. 5,500 to c. 2,500 BCE allow us to characterize regional patterns of ancestries throughout the Neolithic period. Results highlight major differences between the Mediterranean and Continental Neolithic expansion routes regarding both migration and interaction processes. High proportions of HG ancestry in both Early and Late Neolithic groups in Southern France support multiple pulses of inter-group gene flow throughout time and space and confirm the need for regional studies to address the complexity of the processes involved.

Summary There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today’s genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000–500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. Video Abstract, Graphical Abstract, Highlights • Ancient DNA transect reveals north-south substructure of Andean highlands by 5,800 BP • After 5,800 BP, gene flow mixed highland people with their neighbors • After 2,000 BP, striking genetic continuity through rise and fall of major cultures, Genome-wide data from 89 ancient humans illuminates the changes to the genetic landscape in the Central Andes over 9,000 years, revealing large-scale gene flow and cosmopolitan societies in the Tiwanaku and Inca polities.

How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [1, 2]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [3-5]; and (2) multiple dispersal, i.e., additional earlier population expansions that may have contributed to the genetic diversity of some present-day humans outside of Africa [6-9]. Many variants of these models focus largely on Asia and Australasia, neglecting human dispersal into Europe, thus explaining only a subset of the entire colonization process outside of Africa [3-5, 8, 9]. The genetic diversity of the first modern humans who spread into Europe during the Late Pleistocene and the impact of subsequent climatic events on their demography are largely unknown. Here we analyze 55 complete human mitochondrial genomes (mtDNAs) of hunter-gatherers spanning ∼35,000 years of European prehistory. We unexpectedly find mtDNA lineage M in individuals prior to the Last Glacial Maximum (LGM). This lineage is absent in contemporary Europeans, although it is found at high frequency in modern Asians, Australasians, and Native Americans. Dating the most recent common ancestor of each of the modern non-African mtDNA clades reveals their single, late, and rapid dispersal less than 55,000 years ago. Demographic modeling not only indicates an LGM genetic bottleneck, but also provides surprising evidence of a major population turnover in Europe around 14,500 years ago during the Late Glacial, a period of climatic instability at the end of the Pleistocene.

The recovery of genetic material from preserved hard skeletal remains is an essential part of ancient DNA, archaeological and forensic research. However, there is little understanding about the relative concentrations of DNA within different tissues, the impact of sampling methods on extracted DNA, or the role of environmentally-determined degradation rates on DNA survival in specimens. We examine these issues by characterizing the mitochondrial DNA (mtDNA) content of different hard and soft tissues in 42 ancient human and bovid specimens at a range of fragment lengths (77–235 bp) using real-time PCR. Remarkably, the standard drill speeds used to sample skeletal material ( c . 1000 RPM) were found to decrease mtDNA yields up to 30 times (by 3.1 × 10 5 mtDNA copies on average) compared to pulverization in a bone mill. This dramatic negative impact appears to relate to heat damage, and disappeared at very low drill speeds (e.g. 100 RPM). Consequently, many ancient DNA and forensic studies may have obtained false negative results, especially from important specimens which are commonly sampled with drills to minimize signs of damage. The mtDNA content of tooth cementum was found to be five times higher than the commonly used dentine (141 bp, p = 0.01), making the cementum-rich root tip the best sample for ancient human material. Lastly, mtDNA was found to display a consistent pattern of exponential fragmentation across many depositional environments, with different rates for geographic areas and tissue types, improving the ability to predict and understand DNA survival in preserved specimens.