Ancient DNA gives new insights into a Norman Neolithic monumental cemetery dedicated to male elites

READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics

The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy. For sufficient amounts of data, it can classify up to third-degree relatedness and differentiate between the two types of first-degree relatedness, full siblings and parent-offspring. READv2 enables user-friendly, efficient, and nuanced analysis of biological relatedness, facilitating a deeper understanding of past social structures.

Using Runs of Homozygosity and Machine Learning to Disentangle Sources of Inbreeding and Infer Self-Fertilization Rates

Runs of homozygosity (ROHs) are indicative of elevated homozygosity and inbreeding due to mating of closely related individuals. Self-fertilization can be a major source of inbreeding which elevates genome-wide homozygosity and thus should also create long ROHs. While ROHs are frequently used to understand inbreeding in the context of conservation and selective breeding, as well as for consanguinity of populations and their demographic history, it remains unclear how ROH characteristics are altered by selfing and if this confounds expected signatures of inbreeding due to demographic change. Using simulations, we study the impact of the mode of reproduction and demographic history on ROHs. We apply random forests to identify unique characteristics of ROHs, indicative of different sources of inbreeding. We pinpoint distinct features of ROHs that can be used to better characterize the type of inbreeding the population was subjected to and to predict outcrossing rates and complex demographic histories. Using additional simulations and four empirical datasets, two from highly selfing species and two from mixed-maters, we predict the selfing rate and validate our estimations. We find that self-fertilization rates are successfully identified even with complex demography. Population genetic summary statistics improve algorithm accuracy particularly in the presence of additional inbreeding, e.g. from population bottlenecks. Our findings highlight the importance of ROHs in disentangling confounding factors related to various sources of inbreeding and demonstrate situations where such sources cannot be differentiated. Additionally, our random forest models provide a novel tool to the community for inferring selfing rates using genomic data.

Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders

The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother-daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation.

Patrilineal segmentary systems provide a peaceful explanation for the post-Neolithic Y-chromosome bottleneck

Studies have found a pronounced decline in male effective population sizes worldwide around 3000-5000 years ago. This bottleneck was not observed for female effective population sizes, which continued to increase over time. Until now, this remarkable genetic pattern was interpreted as the result of an ancient structuring of human populations into patrilineal groups (gathering closely related males) violently competing with each other. In this scenario, violence is responsible for the repeated extinctions of patrilineal groups, leading to a significant reduction in male effective population size. Here, we propose an alternative hypothesis by modelling a segmentary patrilineal system based on anthropological literature. We show that variance in reproductive success between patrilineal groups, combined with lineal fission (i.e., the splitting of a group into two new groups of patrilineally related individuals), can lead to a substantial reduction in the male effective population size without resorting to the violence hypothesis. Thus, a peaceful explanation involving ancient changes in social structures, linked to global changes in subsistence systems, may be sufficient to explain the reported decline in Y-chromosome diversity.

Female biased adult sex ratio in the Bronze Age cemetery of Shahr-i Sokhta (Iran) as an indicator of long distance trade and matrilocality

OBJECTIVES

This paper starts from the unusual observation of the overrepresentation of females among adults in the cemetery of Bronze Age Shahr-i Sokhta (Seistan, Iran) and explores the post marital residence pattern. By integrating taphonomical (skeletal preservation), anthropological (sex ratio [SR], sexual dimorphism, stress indicators, age at death), archeological (long distance trade indicators, habitation floor area, social role of women), and ancient DNA (heterozygosity levels in X chromosomes) data we test the hypothesis of post marital matrilocality in the site.

METHODS

We computed the SR (pelvis-based sex determination) in a random unpublished adult sample from the cemetery of Shahr-i Sokhta and in two samples previously published by other authors. We used comparative data on SR from: a large Supra Regional multi-chronological sample of sites, n = 47, with 8808 adult sexed individuals, from Southern Europe, Egypt, Middle East, Southern Russia; a Regional Bronze Age sample of sites (n = 10) from Bactria Margiana and Indus Valley with 1324 adult sexed individuals. We estimated the heterozygosity levels in X chromosomes compared with the rest of the autosomes on the assumption that in a matrilocal society females should show lower variability than men.

RESULTS

Adult SR in a sample (n = 549) from Shahr-i Sokhta is 70.5, the overrepresentation of females is shared with Regional Bronze Age sites from Bactria Margiana (SR = 72.09) and Indus Valley (SR = 67.54). On the contrary, in a larger Supra Regional multi-chronological sample of sites, mean SR ranges between 112.7 (Bronze Age) and 163.1 (Middle Ages). Taphonomical and anthropological indicators do not explain the overrepresentation of female skeletons. Archeological indicators suggest a high social status of women and that the society was devoted to long range trade activities. heterozygosity levels in X chromosomes are in agreement with a matrilocal society.

CONCLUSIONS

Indicators suggest that Bronze Age Shahr-ì Sokhta was a matrilocal society and that long distance trade was an important economic factor producing an overrepresentation of adult female skeletons in the cemetery.

The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes

More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.

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.

Kinship practices in the early state El Argar society from Bronze Age Iberia

The Early Bronze Age in Europe is characterized by social and genetic transformations, starting in the early 3rd millennium BCE. New settlement and funerary structures, artifacts and techniques indicate times of change with increasing economic asymmetries and political hierarchization. Technological advances in metallurgy also played an important role, facilitating trade and exchange networks, which became tangible in higher levels of mobility and connectedness. Archeogenetic studies have revealed a substantial transformation of the genetic ancestry around this time, ultimately linked to the expansion of steppe- and forest steppe pastoralists from Eastern Europe. Evidence for emerging infectious diseases such as Yersinia pestis adds further complexity to these tumultuous and transformative times. The El Argar complex in southern Iberia marks the genetic turnover in southwestern Europe ~ 2200 BCE that accompanies profound changes in the socio-economic structure of the region. To answer the question of who was buried in the emblematic double burials of the El Argar site La Almoloya, we integrated results from biological relatedness analyses and archaeological funerary contexts and refined radiocarbon-based chronologies from 68 individuals. We find that the El Argar society was virilocally and patrilineally organized and practiced reciprocal female exogamy, supported by pedigrees that extend up to five generations along the paternal line. Synchronously dated adult males and females from double tombs were found to be unrelated mating partners, whereby the incoming females reflect socio-political alliances among El Argar groups. In three cases these unions had common offspring, while paternal half-siblings also indicate serial monogamy or polygyny.