Ancient DNA provides insights into 4,000 years of resource economy across Greenland.

The success and failure of past cultures across the Arctic was tightly coupled to the ability of past peoples to exploit the full range of resources available to them. There is substantial evidence for the hunting of birds, caribou and seals in prehistoric Greenland. However, the extent to which these communities relied on fish and cetaceans is understudied because of taphonomic processes that affect how these taxa are presented in the archaeological record. To address this, we analyse DNA from bulk bone samples from 12 archaeological middens across Greenland covering the Palaeo-Inuit, Norse and Neo-Inuit culture. We identify an assemblage of 42 species, including nine fish species and five whale species, of which the bowhead whale (Balaena mysticetus) was the most commonly detected. Furthermore, we identify a new haplotype in caribou (Rangifer tarandus), suggesting the presence of a distinct lineage of (now extinct) dwarfed caribou in Greenland 3,000 years ago.

Million-year-old DNA sheds light on the genomic history of mammoths.

Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.

Bile acids and oxo-metabolites as markers of human faecal input in the ancient Pompeii ruins.

Small organic molecules, lipids, proteins, and DNA fragments can remain stable over centuries. Powerful and sensitive chemical analysis can therefore be used to characterize ancient remains for classical archaeological studies. This bio-ecological dimension of archaeology can contribute knowledge about several aspects of ancient life, including social organization, daily habits, nutrition, and food storage. Faecal remains (i.e. coprolites) are particularly interesting in this regard, with scientists seeking to identify new faecal markers. Here, we report the analysis of faecal samples from modern-day humans and faecal samples from a discharge pit on the site of the ruins of ancient Pompeii. We propose that bile acids and their gut microbiota oxo-metabolites are the most specific steroid markers for detecting faecal inputs. This is due to their extreme chemical stability and their exclusive occurrence in vertebrate faeces, compared to other ubiquitous sterols and steroids.

Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA.

Working with mitochondrial DNA from highly degraded samples is challenging. We present a whole mitogenome Illumina-based sequencing method suitable for highly degraded samples. The method makes use of double-stranded library preparation with hybridization-based target enrichment. The aim of the study was to implement a new user-friendly method for analysing many ancient DNA samples at low cost. The method combines the Swift 2S™ Turbo library preparation kit and xGen® panel for mitogenome enrichment. Swift allows to use low input of aDNA and own adapters and primers, handles inhibitors well, and has only two purification steps. xGen is straightforward to use and is able to leverage already pooled libraries. Given the ancient DNA is more challenging to work with, the protocol was developed with several improvements, especially multiplying DNA input in case of low concentration DNA extractions followed by AMPure® beads size selection and real-time pre-capture PCR monitoring in order to avoid cycle-optimization step. Nine out of eleven analysed samples successfully retrieved mitogenomes. Hence, our method provides an effective analysis of whole mtDNA, and has proven to be fast, cost-effective, straightforward, with utilisation in population-wide research of burial sites.

Kinship and social organization in Copper Age Europe. A cross-disciplinary analysis of archaeology, DNA, isotopes, and anthropology from two Bell Beaker cemeteries.

We present a high-resolution cross-disciplinary analysis of kinship structure and social institutions in two Late Copper Age Bell Beaker culture cemeteries of South Germany containing 24 and 18 burials, of which 34 provided genetic information. By combining archaeological, anthropological, genetic and isotopic evidence we are able to document the internal kinship and residency structure of the cemeteries and the socially organizing principles of these local communities. The buried individuals represent four to six generations of two family groups, one nuclear family at the Alburg cemetery, and one seemingly more extended at Irlbach. While likely monogamous, they practiced exogamy, as six out of eight non-locals are women. Maternal genetic diversity is high with 23 different mitochondrial haplotypes from 34 individuals, whereas all males belong to one single Y-chromosome haplogroup without any detectable contribution from Y-chromosomes typical of the farmers who had been the sole inhabitants of the region hundreds of years before. This provides evidence for the society being patrilocal, perhaps as a way of protecting property among the male line, while in-marriage from many different places secured social and political networks and prevented inbreeding. We also find evidence that the communities practiced selection for which of their children (aged 0-14 years) received a proper burial, as buried juveniles were in all but one case boys, suggesting the priority of young males in the cemeteries. This is plausibly linked to the exchange of foster children as part of an expansionist kinship system which is well attested from later Indo-European-speaking cultural groups.

Increased rate of close-kin unions in the central Andes in the half millennium before European contact.

Analyzing ancient DNA of the central Andes, Ringbauer and colleagues identify a markedly elevated rate of unions of closely related parents after ca. 1000 CE. This change of mating preferences sheds new light on a unique system of social organization based on ancestry ("ayllu") whereby within-group unions were preferred to facilitate sharing of resources.

Estimation of Natural Selection and Allele Age from Time Series Allele Frequency Data Using a Novel Likelihood-Based Approach.

Temporally spaced genetic data allow for more accurate inference of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel likelihood-based method for jointly estimating selection coefficient and allele age from time series data of allele frequencies. Our approach is based on a hidden Markov model where the underlying process is a Wright-Fisher diffusion conditioned to survive until the time of the most recent sample. This formulation circumvents the assumption required in existing methods that the allele is created by mutation at a certain low frequency. We calculate the likelihood by numerically solving the resulting Kolmogorov backward equation backward in time while reweighting the solution with the emission probabilities of the observation at each sampling time point. This procedure reduces the two-dimensional numerical search for the maximum of the likelihood surface, for both the selection coefficient and the allele age, to a one-dimensional search over the selection coefficient only. We illustrate through extensive simulations that our method can produce accurate estimates of the selection coefficient and the allele age under both constant and nonconstant demographic histories. We apply our approach to reanalyze ancient DNA data associated with horse base coat colors. We find that ignoring demographic histories or grouping raw samples can significantly bias the inference results.

Detecting and Quantifying Natural Selection at Two Linked Loci from Time Series Data of Allele Frequencies with Forward-in-Time Simulations.

Recent advances in DNA sequencing techniques have made it possible to monitor genomes in great detail over time. This improvement provides an opportunity for us to study natural selection based on time serial samples of genomes while accounting for genetic recombination effect and local linkage information. Such time series genomic data allow for more accurate estimation of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel Bayesian statistical framework for inferring natural selection at a pair of linked loci by capitalising on the temporal aspect of DNA data with the additional flexibility of modeling the sampled chromosomes that contain unknown alleles. Our approach is built on a hidden Markov model where the underlying process is a two-locus Wright-Fisher diffusion with selection, which enables us to explicitly model genetic recombination and local linkage. The posterior probability distribution for selection coefficients is computed by applying the particle marginal Metropolis-Hastings algorithm, which allows us to efficiently calculate the likelihood. We evaluate the performance of our Bayesian inference procedure through extensive simulations, showing that our approach can deliver accurate estimates of selection coefficients, and the addition of genetic recombination and local linkage brings about significant improvement in the inference of natural selection. We also illustrate the utility of our method on real data with an application to ancient DNA data associated with white spotting patterns in horses.

Integration of ancient DNA with transdisciplinary dataset finds strong support for Inca resettlement in the south Peruvian coast.

Ancient DNA (aDNA) analysis provides a powerful means of investigating human migration, social organization, and a plethora of other crucial questions about humanity's past. Recently, specialists have suggested that the ideal research design involving aDNA would include multiple independent lines of evidence. In this paper, we adopt a transdisciplinary approach integrating aDNA with archaeological, biogeochemical, and historical data to investigate six individuals found in two cemeteries that date to the Late Horizon (1400 to 1532 CE) and Colonial (1532 to 1825 CE) periods in the Chincha Valley of southern Peru. Genomic analyses indicate that these individuals are genetically most similar to ancient and present-day populations from the north Peruvian coast located several hundred kilometers away. These genomic data are consistent with 16th century written records as well as ceramic, textile, and isotopic data. These results provide some of the strongest evidence yet of state-sponsored resettlement in the pre-Colonial Andes. This study highlights the power of transdisciplinary research designs when using aDNA data and sets a methodological standard for investigating ancient mobility in complex societies.

New insights on Neolithic food and mobility patterns in Mediterranean coastal populations.

OBJECTIVES: The aims of this research are to explore the diet, mobility, social organization, and environmental exploitation patterns of early Mediterranean farmers, particularly the role of marine and plant resources in these foodways. In addition, this work strives to document possible gendered patterns of behavior linked to the neolithization of this ecologically rich area. To achieve this, a set of multiproxy analyses (isotopic analyses, dental calculus, microremains analysis, ancient DNA) were performed on an exceptional deposit (n = 61) of human remains from the Les Bréguières site (France), dating to the transition of the sixth to the fifth millennium BCE. MATERIALS AND METHODS: The samples used in this study were excavated from the Les Bréguières site (Mougins, Alpes-Maritimes, France), located along the southeastern Mediterranean coastline of France. Stable isotope analyses (C, N) on bone collagen (17 coxal bones, 35 craniofacial elements) were performed as a means to infer protein intake during tissue development. Sulfur isotope ratios were used as indicators of geographical and environmental points of origin. The study of ancient dental calculus helped document the consumption of plants. Strontium isotope analysis on tooth enamel (n = 56) was conducted to infer human provenance and territorial mobility. Finally, ancient DNA analysis was performed to study maternal versus paternal diversity within this Neolithic group (n = 30). RESULTS: Stable isotope ratios for human bones range from -20.3 to -18.1‰ for C, from 8.9 to 11.1‰ for N and from 6.4 to 15‰ for S. Domestic animal data range from -22.0 to -20.2‰ for C, from 4.1 to 6.9‰ for N, and from 10.2 to 12.5‰ for S. Human enamel 87 Sr/86 Sr range from 0.7081 to 0.7102, slightly wider than the animal range (between 0.7087 and 0.7096). Starch and phytolith microremains were recovered as well as other types of remains (e.g., hairs, diatoms, fungal spores). Starch grains include Triticeae type and phytolith includes dicotyledons and monocot types as panicoid grasses. Mitochondrial DNA characterized eight different maternal lineages: H1, H3, HV (5.26%), J (10.53%), J1, K, T (5.2%), and U5 (10.53%) but no sample yielded reproducible Y chromosome SNPs, preventing paternal lineage characterization. DISCUSSION: Carbon and nitrogen stable isotope ratios indicate a consumption of protein by humans mainly focused on terrestrial animals and possible exploitation of marine resources for one male and one undetermined adult. Sulfur stable isotope ratios allowed distinguishing groups with different geographical origins, including two females possibly more exposed to the sea spray effect. While strontium isotope data do not indicate different origins for the individuals, mitochondrial lineage diversity from petrous bone DNA suggests the burial includes genetically differentiated groups or a group practicing patrilocality. Moreover, the diversity of plant microremains recorded in dental calculus provide the first evidence that the groups of Les Bréguières consumed a wide breadth of plant foods (as cereals and wild taxa) that required access to diverse environments. This transdisciplinary research paves the way for new perspectives and highlights the relevance for novel research of contexts (whether recently discovered or in museum collections) excavated near shorelines, due to the richness of the biodiversity and the wide range of edible resources available.

A dynastic elite in monumental Neolithic society.

The nature and distribution of political power in Europe during the Neolithic era remains poorly understood1. During this period, many societies began to invest heavily in building monuments, which suggests an increase in social organization. The scale and sophistication of megalithic architecture along the Atlantic seaboard, culminating in the great passage tomb complexes, is particularly impressive2. Although co-operative ideology has often been emphasised as a driver of megalith construction1, the human expenditure required to erect the largest monuments has led some researchers to emphasize hierarchy3-of which the most extreme case is a small elite marshalling the labour of the masses. Here we present evidence that a social stratum of this type was established during the Neolithic period in Ireland. We sampled 44 whole genomes, among which we identify the adult son of a first-degree incestuous union from remains that were discovered within the most elaborate recess of the Newgrange passage tomb. Socially sanctioned matings of this nature are very rare, and are documented almost exclusively among politico-religious elites4-specifically within polygynous and patrilineal royal families that are headed by god-kings5,6. We identify relatives of this individual within two other major complexes of passage tombs 150 km to the west of Newgrange, as well as dietary differences and fine-scale haplotypic structure (which is unprecedented in resolution for a prehistoric population) between passage tomb samples and the larger dataset, which together imply hierarchy. This elite emerged against a backdrop of rapid maritime colonization that displaced a unique Mesolithic isolate population, although we also detected rare Irish hunter-gatherer introgression within the Neolithic population.

Beyond broad strokes: sociocultural insights from the study of ancient genomes.

In the field of human history, ancient DNA has provided answers to long-standing debates about major movements of people and has begun to inform on other important facets of the human experience. The field is now moving from mostly large-scale supraregional studies to a more local perspective, shedding light on socioeconomic processes, inheritance rules, marriage practices and technological diffusion. In this Review, we summarize recent studies showcasing these types of insights, focusing on methods used to infer sociocultural aspects of human behaviour. This approach often involves working across disciplines - such as anthropology, archaeology, linguistics and genetics - that have until recently evolved in separation. Multidisciplinary dialogue is important for an integrated reconstruction of human history, which can yield extraordinary insights about past societies, reproductive behaviours and even lifestyle habits that would not be possible to obtain otherwise.

Ancestral Population Genomics with Jocx, a Coalescent Hidden Markov Model.

Coalescence theory lets us probe the past demographics of present-day genetic samples and much information about the past can be gleaned from variation in rates of coalescence event as we trace genetic lineages back in time. Fewer and fewer lineages will remain, however, so there is a limit to how far back we can explore. Without recombination, we would not be able to explore ancient speciation events because of this-any meaningful species concept would require that individuals of one species are closer related than they are to individuals of another species, once speciation is complete. Recombination, however, opens a window to the deeper past. By scanning along a genomic alignment, we get a sequential variant of the coalescence process as it looked at the time of the speciation. This pattern of coalescence times is fixed at speciation time and does not erode with time; although accumulated mutations and genomic rearrangements will eventually hide the signal, it enables us to glance at events in the past that would not be observable without recombination. So-called coalescence hidden Markov models allow us to exploit this, and in this chapter, we present the tool Jocx that uses a framework of these models to infer demographic parameters in ancient speciation events.

Kinship-based social inequality in Bronze Age Europe.

Revealing and understanding the mechanisms behind social inequality in prehistoric societies is a major challenge. By combining genome-wide data, isotopic evidence, and anthropological and archaeological data, we have gone beyond the dominating supraregional approaches in archaeogenetics to shed light on the complexity of social status, inheritance rules, and mobility during the Bronze Age. We applied a deep microregional approach and analyzed genome-wide data of 104 human individuals deriving from farmstead-related cemeteries from the Late Neolithic to the Middle Bronze Age in southern Germany. Our results reveal individual households, lasting several generations, that consisted of a high-status core family and unrelated low-status individuals; a social organization accompanied by patrilocality and female exogamy; and the stability of this system over 700 years.

Ancient DNA and bioarchaeological perspectives on European and African diversity and relationships on the colonial Delaware frontier.

OBJECTIVES: Ancient DNA (aDNA) and standard osteological analyses applied to 11 skeletons at a late 17th to early 18th century farmstead site in Delaware to investigate the biological and social factors of settlement and slavery in colonial America. MATERIALS AND METHODS: Osteological analysis and mitochondrial DNA (mtDNA) sequencing were conducted for all individuals and the resulting data contextualized with archaeological and documentary evidence. RESULTS: Individuals of European and African descent were spatially separated in this colonial cemetery. The skeletal remains exhibited differences in osteological features and maternal genetic ancestry. A specific mtDNA haplotype appeared in a subset of the European-descended individuals suggesting they were maternally related. Individuals of African descent were not maternally related, and instead showed a diversity of haplotypes affiliated with present-day Western, Central, and Eastern regions of Africa. DISCUSSION: Along with the bioarchaeological and documentary evidence, the aDNA findings contribute to our understanding of life on the colonial Delaware frontier. Evidence of maternal relatedness among European-descended individuals at the site demonstrates kin-based settlements in 17th century Delaware and provides preliminary identifications of individuals. The maternal genetic diversity of the individuals with African descent aligns with the routes of the trans-Atlantic slave trade but broadens our understanding of the ancestries of persons involved in it. Burial positioning, osteological pathology, and lack of maternal kinship among individuals of African descent provide tangible evidence for the emergence of racialized labor and society in Delaware during the late 17th century.

Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples.

Both the total amount and the distribution of heterozygous sites within individual genomes are informative about the genetic diversity of the population they belong to. Detecting true heterozygous sites in ancient genomes is complicated by the generally limited coverage achieved and the presence of post-mortem damage inflating sequencing errors. Additionally, large runs of homozygosity found in the genomes of particularly inbred individuals and of domestic animals can skew estimates of genome-wide heterozygosity rates. Current computational tools aimed at estimating runs of homozygosity and genome-wide heterozygosity levels are generally sensitive to such limitations. Here, we introduce ROHan, a probabilistic method which substantially improves the estimate of heterozygosity rates both genome-wide and for genomic local windows. It combines a local Bayesian model and a Hidden Markov Model at the genome-wide level and can work both on modern and ancient samples. We show that our algorithm outperforms currently available methods for predicting heterozygosity rates for ancient samples. Specifically, ROHan can delineate large runs of homozygosity (at megabase scales) and produce a reliable confidence interval for the genome-wide rate of heterozygosity outside of such regions from modern genomes with a depth of coverage as low as 5-6× and down to 7-8× for ancient samples showing moderate DNA damage. We apply ROHan to a series of modern and ancient genomes previously published and revise available estimates of heterozygosity for humans, chimpanzees and horses.

Ancient Mitochondrial Genomes Reveal the Absence of Maternal Kinship in the Burials of Çatalhöyük People and Their Genetic Affinities.

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.