Extensive pedigrees reveal the social organization of a Neolithic community.

Social anthropology and ethnographic studies have described kinship systems and networks of contact and exchange in extant populations1-4. However, for prehistoric societies, these systems can be studied only indirectly from biological and cultural remains. Stable isotope data, sex and age at death can provide insights into the demographic structure of a burial community and identify local versus non-local childhood signatures, archaeogenetic data can reconstruct the biological relationships between individuals, which enables the reconstruction of pedigrees, and combined evidence informs on kinship practices and residence patterns in prehistoric societies. Here we report ancient DNA, strontium isotope and contextual data from more than 100 individuals from the site Gurgy 'les Noisats' (France), dated to the western European Neolithic around 4850-4500 BC. We find that this burial community was genetically connected by two main pedigrees, spanning seven generations, that were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups. The microdemographic structure of individuals linked and unlinked to the pedigrees reveals additional information about the social structure, living conditions and site occupation. The absence of half-siblings and the high number of adult full siblings suggest that there were stable health conditions and a supportive social network, facilitating high fertility and low mortality5. Age-structure differences and strontium isotope results by generation indicate that the site was used for just a few decades, providing new insights into shifting sedentary farming practices during the European Neolithic.

Tracing the genetic legacy in the French Caribbean islands: A study of mitochondrial and Y-chromosome lineages in the Guadeloupe archipelago.

OBJECTIVES: The history of the Caribbean region is marked by numerous and various successive migration waves that resulted in a global blending of African, European, and Amerindian lineages. As the origin and genetic composition of the current population of French Caribbean islands has not been studied to date, we used both mitochondrial DNA and Y-chromosome markers to complete the characterization of the dynamics of admixture in the Guadeloupe archipelago. MATERIALS AND METHODS: We sequenced the mitochondrial hypervariable regions and genotyped mitochondrial and Y-chromosomal single nucleotide polymorphisms (SNPs) of 198 individuals from five localities of the Guadeloupe archipelago. RESULTS: The maternal haplogroups revealed a blend of 85% African lineages (mainly traced to Western, West-Central, and South-Eastern Africa), 12.5% Eurasian lineages, and 0.5% Amerindian lineages. We highlighted disequilibria between European paternal contribution (44%) and European maternal contribution (7%), pointing out an important sexual asymmetry. Finally, the estimated Native American component was strikingly low and supported the near-extinction of native lineages in the region. DISCUSSION: We confirmed that all historically known migratory events indeed left a visible genetic imprint in the contemporary Caribbean populations. The data gathered clearly demonstrated the significant impact of the transatlantic slave trade on the Guadeloupean population's constitution. Altogether, the data in our study confirm that in the Caribbean region, human population variation is correlated with colonial and postcolonial policies and unique island histories.

Ancient DNA reveals temporal population structure within the South-Central Andes area.

OBJECTIVES: The main aim of this work was to contribute to the knowledge of pre-Hispanic genetic variation and population structure among the South-central Andes Area by studying individuals from Quebrada de Humahuaca, North-western (NW) Argentina. MATERIALS AND METHODS: We analyzed 15 autosomal STRs in 19 individuals from several archaeological sites in Quebrada de Humahuaca, belonging to the Regional Developments Period (900-1430 AD). Compiling autosomal, mitochondrial, and Y-chromosome data, we evaluated population structure and differentiation among eight South-central Andean groups from the current territories of NW Argentina and Peru. RESULTS: Autosomal data revealed a structuring of the analyzed populations into two clusters which seemed to represent different temporalities in the Andean pre-Hispanic history: pre-Inca and Inca. All pre-Inca samples fell into the same cluster despite being from the two different territories of NW Argentina and Peru. Also, they were systematically differentiated from the Peruvian Inca group. These results were mostly confirmed by mitochondrial and Y-chromosome analyses. We mainly found a clearly different haplotype composition between clusters. DISCUSSION: Population structure in South America has been mostly studied on current native groups, mainly showing a west-to-east differentiation between the Andean and lowland regions. Here we demonstrated that genetic population differentiation preceded the European contact and might have been more complex than thought, being found within the South-central Andes Area. Moreover, divergence among temporally different populations might be reflecting socio-political changes occurred in the evermore complex pre-Hispanic Andean societies.

Multi-scale ancient DNA analyses confirm the western origin of Michelsberg farmers and document probable practices of human sacrifice.

In Europe, the Middle Neolithic is characterized by an important diversification of cultures. In northeastern France, the appearance of the Michelsberg culture has been correlated with major cultural changes and interpreted as the result of the settlement of new groups originating from the Paris Basin. This cultural transition has been accompanied by the expansion of particular funerary practices involving inhumations within circular pits and individuals in "non-conventional" positions (deposited in the pits without any particular treatment). If the status of such individuals has been highly debated, the sacrifice hypothesis has been retained for the site of Gougenheim (Alsace). At the regional level, the analysis of the Gougenheim mitochondrial gene pool (SNPs and HVR-I sequence analyses) permitted us to highlight a major genetic break associated with the emergence of the Michelsberg in the region. This genetic discontinuity appeared to be linked to new affinities with farmers from the Paris Basin, correlated to a noticeable hunter-gatherer legacy. All of the evidence gathered supports (i) the occidental origin of the Michelsberg groups and (ii) the potential implication of this migration in the progression of the hunter-gatherer legacy from the Paris Basin to Alsace / Western Germany at the beginning of the Late Neolithic. At the local level, we noted some differences in the maternal gene pool of individuals in "conventional" vs. "non-conventional" positions. The relative genetic isolation of these sub-groups nicely echoes both their social distinction and the hypothesis of sacrifices retained for the site. Our investigation demonstrates that a multi-scale aDNA study of ancient communities offers a unique opportunity to disentangle the complex relationships between cultural and biological evolution.

Investigating mitochondrial DNA relationships in Neolithic Western Europe through serial coalescent simulations.

Recent ancient DNA studies on European Neolithic human populations have provided persuasive evidence of a major migration of farmers originating from the Aegean, accompanied by sporadic hunter-gatherer admixture into early Neolithic populations, but increasing toward the Late Neolithic. In this context, ancient mitochondrial DNA data collected from the Neolithic necropolis of Gurgy (Paris Basin, France), the largest mitochondrial DNA sample obtained from a single archeological site for the Early/Middle Neolithic period, indicate little differentiation from farmers associated to both the Danubian and Mediterranean Neolithic migration routes, as well as from Western European hunter-gatherers. To test whether this pattern of differentiation could arise in a single unstructured population by genetic drift alone, we used serial coalescent simulations. We explore female effective population size parameter combinations at the time of the colonization of Europe 45000 years ago and the most recent of the Neolithic samples analyzed in this study 5900 years ago, and identify conditions under which population panmixia between hunter-gatherers/Early-Middle Neolithic farmers and Gurgy cannot be rejected. In relation to other studies on the current debate of the origins of Europeans, these results suggest increasing hunter-gatherer admixture into farmers' group migrating farther west in Europe.

Ancient mitochondrial DNA from the middle neolithic necropolis of Obernai extends the genetic influence of the LBK to west of the Rhine.

OBJECTIVES: The arrival of Neolithic farmers in Europe was the source of major cultural and genetic transitions. Neolithic settlers brought a new set of maternal lineages (mitochondrial DNA), recently well-characterized on the continental road, from the Balkans to West Germany (Rhine River). In the present study, the first mitochondrial DNA data from groups associated with this continental expansion wave located west of the Rhine River has been provided and their genetic affinities with contemporary groups have been discussed. MATERIAL AND METHODS: The mitochondrial DNA analysis of 27 human remains originating from Obernai (5,000-4,400 cal. BC), a necropolis located in French Alsace Region and attributed to Grossgartach, Planig-Friedberg, and Roessen cultures was conducted. RESULTS AND DISCUSSION: Among the 27 individuals studied, 15 HVR-I sequences and 17 mitochondrial haplogroups could be determined. The analysis of the Obernai gene pool clearly confirmed the genetic homogeneity of Linearbandkeramik (LBK) groups on both sides of the Rhine River. Notably, one N1a sequence found in Obernai is shared with LBK farmers from Central Europe, including one individual from the Flomborn site located approximately 200 km north-east of Obernai. On the whole, data gathered so far showed major genetic influence of the Danubian wave from Transdanubia to Atlantic French Coast, going by Alsace Region. However, the genetic influence of descendants from the Mediterranean Neolithic expansion and the significant hunter-gatherer admixture detected further west in the Paris Basin were not perceived in the Obernai necropolis. CONCLUSIONS: Genetic homogeneity and continuity within LBK groups can be proposed on both sides of the Rhine River for the middle Neolithic groups. Nevertheless, mitochondrial data gathered so far for Neolithic groups from the entire extant French Territory clearly point out the complexity and the variability of Neolithic communities interactions that is worthy of further investigation.

Pre-Hispanic Mortuary Practices in Quebrada de Humahuaca (North-Western Argentina): Genetic Relatedness among Individuals Buried in the Same Grave.

Almost all pre-Hispanic societies from Quebrada de Humahuaca (north-western Argentina) buried their defuncts in domestic areas, demonstrating the importance of death and its daily presence among the living. Presumably, the collective graves contained related individuals, a hypothesis that can be tested through the study of ancient DNA. This study analyzes autosomal and uniparental genetic markers in individuals from two archaeological sites in Quebrada de Humahuaca occupied during the Late Formative (1450-1050 BP) and Regional Developments I (1050-700 BP) periods. Mitochondrial and Y-chromosome haplotypes were compared in order to establish possible maternal and paternal relatedness. Genotypes for 15 autosomal STRs were used to calculate pairwise relatedness coefficients and pedigree probabilities. High kinship levels among individuals buried in the same graves were found in both sites. Although only two particular cases were analyzed, these results represent an important contribution to the study of mortuary practices in the region by means of ancient DNA.

Early Medieval Muslim Graves in France: First Archaeological, Anthropological and Palaeogenomic Evidence.

The rapid Arab-Islamic conquest during the early Middle Ages led to major political and cultural changes in the Mediterranean world. Although the early medieval Muslim presence in the Iberian Peninsula is now well documented, based in the evaluation of archeological and historical sources, the Muslim expansion in the area north of the Pyrenees has only been documented so far through textual sources or rare archaeological data. Our study provides the first archaeo-anthropological testimony of the Muslim establishment in South of France through the multidisciplinary analysis of three graves excavated at Nimes. First, we argue in favor of burials that followed Islamic rites and then note the presence of a community practicing Muslim traditions in Nimes. Second, the radiometric dates obtained from all three human skeletons (between the 7th and the 9th centuries AD) echo historical sources documenting an early Muslim presence in southern Gaul (i.e., the first half of 8th century AD). Finally, palaeogenomic analyses conducted on the human remains provide arguments in favor of a North African ancestry of the three individuals, at least considering the paternal lineages. Given all of these data, we propose that the skeletons from the Nimes burials belonged to Berbers integrated into the Umayyad army during the Arab expansion in North Africa. Our discovery not only discusses the first anthropological and genetic data concerning the Muslim occupation of the Visigothic territory of Septimania but also highlights the complexity of the relationship between the two communities during this period.

When the waves of European Neolithization met: first paleogenetic evidence from early farmers in the southern Paris Basin.

An intense debate concerning the nature and mode of Neolithic transition in Europe has long received much attention. Recent publications of paleogenetic analyses focusing on ancient European farmers from Central Europe or the Iberian Peninsula have greatly contributed to this debate, providing arguments in favor of major migrations accompanying European Neolithization and highlighting noticeable genetic differentiation between farmers associated with two archaeologically defined migration routes: the Danube valley and the Mediterranean Sea. The aim of the present study was to fill a gap with the first paleogenetic data of Neolithic settlers from a region (France) where the two great currents came into both direct and indirect contact with each other. To this end, we analyzed the Gurgy 'Les Noisats' group, an Early/Middle Neolithic necropolis in the southern part of the Paris Basin. Interestingly, the archaeological record from this region highlighted a clear cultural influence from the Danubian cultural sphere but also notes exchanges with the Mediterranean cultural area. To unravel the processes implied in these cultural exchanges, we analyzed 102 individuals and obtained the largest Neolithic mitochondrial gene pool so far (39 HVS-I mitochondrial sequences and haplogroups for 55 individuals) from a single archaeological site from the Early/Middle Neolithic period. Pairwise FST values, haplogroup frequencies and shared informative haplotypes were calculated and compared with ancient and modern European and Near Eastern populations. These descriptive analyses provided patterns resulting from different evolutionary scenarios; however, the archaeological data available for the region suggest that the Gurgy group was formed through equivalent genetic contributions of farmer descendants from the Danubian and Mediterranean Neolithization waves. However, these results, that would constitute the most ancient genetic evidence of admixture between farmers from both Central and Mediterranean migration routes in the European Neolithization debate, are subject to confirmation through appropriate model-based approaches.

Genetic diversity of a late prehispanic group of the Quebrada de Humahuaca, northwestern Argentina.

This palaeogenetic study focused on the analysis of a late prehispanic Argentinean group from the Humahuaca valley, with the main aim of reconstructing its (micro)evolutionary history. The Humahuaca valley, a natural passageway from the eastern plains to the highlands, was the living environment of Andean societies whose cultural but especially biological diversity is still poorly understood. We analyzed the DNA extracted from 39 individuals who populated this upper valley during the Regional Development period (RDP) (between the 11th and 15th centuries CE), to determine their maternal and paternal genetic ancestry. Some mitochondrial and Y-chromosomal haplotypes specific to the Andean region are consistent with an origin in the highlands of Central Andes. On the other hand, a significant genetic affinity with contemporary admixed communities of the Chaco area was detected. Expectedly, recent demographic events, such as the expansion of the Inca Empire or the European colonization, have changed the original mitochondrial gene pool of the ancient Humahuaca Valley community. Finally, we identified a particular geographical organization of the prehispanic populations of Northwestern Argentina. Our results suggest that the communities of the region were divided between two different spheres of interaction, which is consistent with assumptions made by means of craniometric traits.

Ancient DNA: A window to the past of Europe.

OBJECTIVES: The history of European populations is characterised by numerous migrations or demographic events that are likely to have had major impacts on the European gene pool patterns. This paper will focus on how ancient DNA (aDNA) data contribute to our understanding of past population dynamics in Europe. METHODS: Technological challenges of the palaeogenetic approach will be discussed. With these limitations in mind, it will be shown that the acquisition of aDNA now permits a glimpse of how human genetic diversity has changed, spatially and temporally, in Europe, from the Palaeolithic through to the present day. RESULTS: Although early modern human DNA sequences come only from rare exceptionally well-preserved specimens, genetic samples of a reasonable size are becoming available for the Mesolithic and the Neolithic periods, permitting a discussion of regional variation in the inferred mode of the spread of farming. Palaeogenetic data collected for ancient and more recent periods regularly demonstrate genetic discontinuity between past and present populations. CONCLUSIONS: The results indicate that only large diachronic aDNA datasets from throughout Europe will permit researchers to reliably identify all demographic and evolutionary events that shaped the modern European gene pool.

Application of the iPLEX™ Gold SNP genotyping method for the analysis of Amerindian ancient DNA samples: benefits for ancient population studies.

Important developments in the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique have generated new perspectives regarding SNP genotyping, which are particularly promising for ancient population-based studies. The main aim of the present study was to investigate the application of a MALDI-TOF MS-based SNP genotyping technique, called iPLEX(®) Gold, to analyze Amerindian ancient DNA samples. The first objective was to test the sensitivity of the method, which is recommended for DNA quantities between 10 and 5 ng, for ancient biological samples containing DNA molecules that were degraded and present in minute quantities. The second objective was to detail the advantages of this technique for studies on ancient populations. Two multiplexes were designed, allowing the major Amerindian mitochondrial and Y haplogroups to be determined simultaneously. This analysis has never been described before. Results demonstrated the reliability and accuracy of the method; data were obtained for both mitochondrial and nuclear DNA using picogram (pg) quantities of nucleic acid. This technique has the advantages of both MS and minisequencing techniques; thus, it should be included in the protocols for future ancient DNA studies.

Paleogenetical study of pre-Columbian samples from Pampa Grande (Salta, Argentina).

Ancient DNA recovered from 21 individuals excavated from burial sites in the Pampa Grande (PG) region (Salta province) of North-Western Argentina (NWA) was analyzed using various genetic markers (mitochondrial DNA, autosomal STRs, and Y chromosomal STRs). The results were compared to ancient and modern DNA from various populations in the Andean and North Argentinean regions, with the aim of establishing their relationships with PG. The mitochondrial haplogroup frequencies described (11% A, 47% B, and 42% D) presented values comparable to those found for the ancient Andean populations from Peru and San Pedro de Atacama. On the other hand, mitochondrial and Y chromosomal haplotypes were specific to PG, as they did not match any other of the South American populations studied. The described genetic diversity indicates homogeneity in the genetic structure of the ancient Andean populations, which was probably facilitated by the intense exchange network in the Andean zone, in particular among Tiwanaku, San Pedro de Atacama, and NWA. The discovery of haplotypes unique to PG could be due to a loss of genetic diversity caused by recent events affecting the autochthonous populations (establishment of the Inca Empire in the region, colonization by the Europeans).