The Neolithic transition in west Eurasia occurred in two main steps: the gradual development of sedentism and plant cultivation in the Near East and the subsequent spread of Neolithic cultures into ...the Aegean and across Europe after 7000 cal BCE. Here, we use published ancient genomes to investigate gene flow events in west Eurasia during the Neolithic transition. We confirm that the Early Neolithic central Anatolians in the ninth millennium BCE were probably descendants of local hunter–gatherers, rather than immigrants from the Levant or Iran. We further study the emergence of post-7000 cal BCE north Aegean Neolithic communities. Although Aegean farmers have frequently been assumed to be colonists originating from either central Anatolia or from the Levant, our findings raise alternative possibilities: north Aegean Neolithic populations may have been the product of multiple westward migrations, including south Anatolian emigrants, or they may have been descendants of local Aegean Mesolithic groups who adopted farming. These scenarios are consistent with the diversity of material cultures among Aegean Neolithic communities and the inheritance of local forager know-how. The demographic and cultural dynamics behind the earliest spread of Neolithic culture in the Aegean could therefore be distinct from the subsequent Neolithization of mainland Europe.
Çatalhöyük is one of the most widely recognized and extensively researched Neolithic settlements. The site has been used to discuss a wide range of aspects associated with the spread of the Neolithic ...lifestyle and the social organization of Neolithic societies. Here, we address both topics using newly generated mitochondrial genomes, obtained by direct sequencing and capture-based enrichment of genomic libraries, for a group of individuals buried under a cluster of neighboring houses from the classical layer of the site's occupation. Our data suggests a lack of maternal kinship between individuals interred under the floors of Çatalhöyük buildings. The findings could potentially be explained either by a high variability of maternal lineages within a larger kin group, or alternatively, an intentional selection of individuals for burial based on factors other than biological kinship. Our population analyses shows that Neolithic Central Anatolian groups, including Çatalhöyük, share the closest affinity with the population from the Marmara Region and are, in contrast, set further apart from the Levantine populations. Our findings support the hypothesis about the emergence and the direction of spread of the Neolithic within Anatolian Peninsula and beyond, emphasizing a significant role of Central Anatolia in this process.
In 2021, we published the results of genomic analyses carried out on the famous bishop of Lund, Peder Winstrup, and the mummified remains of a 5–6-month-old fetus discovered in the same burial. We ...concluded that the two individuals were second-degree relatives and explored the genealogy of Peder Winstrup to further understand the possible relation between them. Through this analysis, we found that the boy was most probably Winstrup’s grandson and that the two were equally likely related either through Winstrup’s son, Peder, or his daughter, Anna Maria von Böhnen. To further resolve the specific kinship relation, we generated more genomic data from both Winstrup and the boy and implemented more recently published analytical tools in detailed Y chromosome- and X chromosome-based kinship analyses to distinguish between the competing hypotheses regarding maternal and paternal relatedness. We found that the individuals’ Y chromosome lineages belonged to different sub-lineages and that the X-chromosomal kinship coefficient calculated between the two individuals were elevated, suggesting a grandparent–grandchild relation through a female, i.e., Anna Maria von Böhnen. Finally, we also performed metagenomic analyses, which did not identify any pathogens that could be unambiguously associated with the fatalities.
Ancient DNA (aDNA) obtained from human remains is typically fragmented and present in relatively low amounts. Here we investigate a set of optimal methods for producing aDNA data by comparing ...silica-based DNA extraction and aDNA library preparation protocols. We also test the efficiency of whole-genome enrichment (WGC) on ancient human samples by modifying a number of parameter combinations. We find that the Dabney extraction protocol performs significantly better than alternatives. We further observed a positive trend with the BEST library protocol indicating lower clonality. Notably, our results suggest that WGC is effective at retrieving endogenous DNA, particularly from poorly-preserved human samples, by increasing human endogenous proportions by 5x. Thus, aDNA studies will be most likely to benefit from our results.
We studied a set of methods used to generate ancient genome data from archaeological human samples from different sites and periods, and with varying levels of preservation. In these experiments we compared two sample preparation techniques, two silica-based DNA extraction protocols, and two aDNA library preparation protocols. Finally, we explored the efficiency of whole-genome capture (WGC) on aDNA libraries with different characteristics by comparing a set of protocol modifications.
The archaeological documentation of the development of sedentary farming societies in Anatolia is not yet mirrored by a genetic understanding of the human populations involved, in contrast to the ...spread of farming in Europe 1–3. Sedentary farming communities emerged in parts of the Fertile Crescent during the tenth millennium and early ninth millennium calibrated (cal) BC and had appeared in central Anatolia by 8300 cal BC 4. Farming spread into west Anatolia by the early seventh millennium cal BC and quasi-synchronously into Europe, although the timing and process of this movement remain unclear. Using genome sequence data that we generated from nine central Anatolian Neolithic individuals, we studied the transition period from early Aceramic (Pre-Pottery) to the later Pottery Neolithic, when farming expanded west of the Fertile Crescent. We find that genetic diversity in the earliest farmers was conspicuously low, on a par with European foraging groups. With the advent of the Pottery Neolithic, genetic variation within societies reached levels later found in early European farmers. Our results confirm that the earliest Neolithic central Anatolians belonged to the same gene pool as the first Neolithic migrants spreading into Europe. Further, genetic affinities between later Anatolian farmers and fourth to third millennium BC Chalcolithic south Europeans suggest an additional wave of Anatolian migrants, after the initial Neolithic spread but before the Yamnaya-related migrations. We propose that the earliest farming societies demographically resembled foragers and that only after regional gene flow and rising heterogeneity did the farming population expansions into Europe occur.
•Pre-pottery farmers had low genetic diversity, akin to Mesolithic hunter-gatherers•Genetic diversity levels are higher in the subsequent Pottery Neolithic•Central Anatolian farmers belonged to the same gene pool as early European farmers•Copper Age genetic affinities suggest a second wave of Anatolian gene flow
Kılınç et al. study ancient genomes from the earliest farmers of central Anatolia, one of the first areas where farming appears outside the Fertile Crescent. Genetic diversity increases as the Neolithic develops, indicating rising mobility. Similarities between Anatolian and European farmers suggest two gene flow events from Anatolia into Europe.
The impact of human mobility on the northern European urban populations during the Viking and Early Middle Ages and its repercussions in Scandinavia itself are still largely unexplored. Our study of ...the demographics in the final phase of the Viking era is the first comprehensive multidisciplinary investigation that includes genetics, isotopes, archaeology, and osteology on a larger scale. This early Christian dataset is particularly important as the earlier common pagan burial tradition during the Iron Age was cremation, hindering large-scale DNA analyses. We present genome-wide sequence data from 23 individuals from the 10th to 12th century Swedish town of Sigtuna. The data revealed high genetic diversity among the early urban residents. The observed variation exceeds the genetic diversity in distinct modern-day and Iron Age groups of central and northern Europe. Strontium isotope data suggest mixed local and non-local origin of the townspeople. Our results uncover the social system underlying the urbanization process of the Viking World of which mobility was an intricate part and was comparable between males and females. The inhabitants of Sigtuna were heterogeneous in their genetic affinities, probably reflecting both close and distant connections through an established network, confirming that early urbanization processes in northern Europe were driven by migration.
•A case study reveals mobility between population clusters within the Viking world•Archaeology, osteology, genetics, and isotopes highlight nuanced migration patterns•Local, regional, and long-distance immigrants are identified in the town of Sigtuna•We report 23 new ancient human genomes from the 10th to the 12th century CE Sweden
Krzewińska et al. report genetic and isotopic data from 23 Viking Age individuals from Sweden. By complementing archaeological and osteological data with paleogenetic and isotope data, a high level of mobility within the early medieval world can be detected, revealing the cosmopolitan nature of the late Viking towns.
There is growing interest in uncovering genetic kinship patterns in past societies using low‐coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, ...NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first‐degree related pairs can be accurately classified even with 1 K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third‐degree relatives from unrelated pairs or second‐degree relatives was also possible with high accuracy (F1 > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first‐cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra‐low‐coverage genomes.
Objectives
North Mesopotamia has witnessed dramatic social change during the Holocene, but the impact of these events on its demographic history is poorly understood. Here, we study this question by ...analysing genetic data from the recently excavated Late Iron Age settlement of Çemialo Sırtı in Batman, southeast Turkey. Archaeological and radiocarbon evidence indicate that the site was inhabited during the second and first millennia BCE. Çemialo Sırtı reveals nomadic items of the Early Iron Age, as well as items associated with the Late Achaemenid and subsequent Hellenistic Periods. We compare Çemialo Sırtı mitochondrial DNA profiles with earlier and later populations from west Eurasia to describe genetic continuity patterns in the region.
Materials and methods
A total of 16 Çemialo Sırtı individuals' remains were studied. PCR and Sanger sequencing were used to obtain mitochondrial DNA HVRI‐HVRII sequences. We studied haplotype diversity and pairwise genetic distances using FST, comparing the Çemialo Sırtı population with ancient and modern‐day populations from west Eurasia. Coalescent simulations were carried out to test continuity for specific population comparisons.
Results
Mitochondrial DNA (mtDNA) haplotypes from 12 Çemialo Sırtı individuals reveal high haplotype diversity in this population, conspicuously higher than early Holocene west Eurasian populations, which supports the notion of increasing population admixture in west Eurasia through the Holocene. In its mtDNA composition, Çemialo Sırtı shows highest affinity to Neolithic north Syria and Neolithic Anatolia among ancient populations studied, and to modern‐day southwest Asian populations. Based on population genetic simulations we cannot reject continuity between Neolithic and Iron Age, or between Iron Age and present‐day populations of the region.
Discussion
Despite the region's complex sociopolitical history and indication for increased genetic diversity over time, we find no evidence for sharp shifts in north Mesopotamian maternal genetic composition within the last 10,000 years.
The Neolithic transition in west Eurasia occurred in two main steps: the gradual development of sedentism and plant cultivation in the Near East and the subsequent spread of Neolithic cultures into ...the Aegean and across Europe after 7000 cal BCE. Here, we use published ancient genomes to investigate gene flow events in west Eurasia during the Neolithic transition. We confirm that the Early Neolithic central Anatolians in the ninth millennium BCE were probably descendants of local hunter–gatherers, rather than immigrants from the Levant or Iran. We further study the emergence of post-7000 cal BCE north Aegean Neolithic communities. Although Aegean farmers have frequently been assumed to be colonists originating from either central Anatolia or from the Levant, our findings raise alternative possibilities: north Aegean Neolithic populations may have been the product of multiple westward migrations, including south Anatolian emigrants, or they may have been descendants of local Aegean Mesolithic groups who adopted farming. These scenarios are consistent with the diversity of material cultures among Aegean Neolithic communities and the inheritance of local forager know-how. The demographic and cultural dynamics behind the earliest spread of Neolithic culture in the Aegean could therefore be distinct from the subsequent Neolithization of mainland Europe.
Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic ...diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c.13,790 BP and c.1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (N
) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.
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