Ancient DNA Studies Research Articles

Leveraging ancient DNA to uncover signals of natural selection in Europe lost due to admixture or drift.

Large ancient DNA (aDNA) studies offer the chance to examine genomic changes over time, providing direct insights into human evolution. While recent studies have used time-stratified aDNA for selection scans, most focus on single-locus methods. We conducted a multi-locus genotype scan on 708 samples spanning 7000 years of European history. We show that the G12 statistic, originally designed for unphased diploid data, can effectively detect selection in aDNA processed to create 'pseudo-haplotypes'. In simulations and at known positive control loci (e.g., lactase persistence), G12 outperforms the allele frequency-based selection statistic, SweepFinder2, previously used on aDNA. Applying our approach, we identified 14 candidate regions of selection across four time periods, with half the signals detectable only in the earliest period. Our findings suggest that selective events in European prehistory, including from the onset of animal domestication, have been obscured by neutral processes like genetic drift and demographic shifts such as admixture.

Interpreting the demic diffusion of early farming in Europe with a three-population model

In 1971, Ammerman and Cavalli-Sforza demonstrated that reaction-diffusion equations could be usefully applied to the archaeological question of the spread of early farming in Europe. Their basic premise was demic diffusion, i.e., the iterative short-range colonization of virgin land by the descendants of the original Near Eastern farmers. This hypothesis has been vindicated by ancient DNA studies, which show limited acculturation of the autochthonous hunter-gatherers, who when converted to farming were apparently assimilated into preexisting farming communities. In this brief report, I describe a reaction-diffusion model incorporating various interactions among the Near Eastern farmers, converted farmers, and hunter-gatherers. Predictions, derived in terms of the model parameters, are examined vis-à-vis the ancient DNA and archaeological evidence. Of particular interest is the theoretical requirement that the hunter-gatherers behaved more competitively toward the converted farmers than the Near Eastern (specifically Anatolian) famers. Based on “Ammerman AJ, Cavalli-Sforza LL. Measuring the rate of spread of early farming in Europe. Man 1971; 6: 674-688.”

Testing times: disentangling admixture histories in recent and complex demographies using ancient DNA.

Our knowledge of human evolutionary history has been greatly advanced by paleogenomics. Since the 2020s, the study of ancient DNA has increasingly focused on reconstructing the recent past. However, the accuracy of paleogenomic methods in resolving questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation remains an open question. We evaluated the performance and behavior of two commonly used methods, qpAdm and the f3-statistic, on admixture inference under a diversity of demographic models and data conditions. We performed two complementary simulation approaches-firstly exploring a wide demographic parameter space under four simple demographic models of varying complexities and configurations using branch-length data from two chromosomes-and secondly, we analyzed a model of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudohaploidization. We observe that population differentiation is the primary factor driving qpAdm performance. Notably, while complex gene flow histories influence which models are classified as plausible, they do not reduce overall performance. Under conditions reflective of the historical period, qpAdm most frequently identifies the true model as plausible among a small candidate set of closely related populations. To increase the utility for resolving fine-scaled hypotheses, we provide a heuristic for further distinguishing between candidate models that incorporates qpAdm model P-values and f3-statistics. Finally, we demonstrate a significant performance increase for qpAdm using whole-genome branch-length f2-statistics, highlighting the potential for improved demographic inference that could be achieved with future advancements in f-statistic estimations.

Ancient genomic analysis of a Chinese hereditary elite from the Northern and Southern Dynasties

China's Northern and Southern Dynasties period (3rd–6th centuries AD) marked a significant era of ethnic integration in northern China. However, previous ancient DNA studies have primarily focused on northern ethnic groups, with limited research on the genetic formation of the hereditary elite family, especially considering their abundant archaeological record and clear material identity. In this study, we obtained the ancient genome of a hereditary elite family, Gao Bin (高宾, 503 AD–572 AD), at 0.6473-fold coverage with 475,132 single-nucleotide polymorphisms (SNPs) on the 1240k panel. His mitochondrial haplogroup belonged to Z4 and Y-haplogroup to O1a1a2b-F2444∗. The genetic profile of Gao Bin was most similar to that of the northern Han Chinese. He could be modeled as deriving all his ancestry from Late Neolithic to Iron Age Yellow River farmers without influence from Northeast Asia, Korea, or the Mongolian Plateau. Our study sheds light on the genetic formation of hereditary elite families in the context of the Southern and Northern Dynasties ethnic integration.

Population genomics of Central Asian peoples unveil ancient Trans-Eurasian genetic admixture and cultural exchanges

Central Asia, a crucible of prehistoric and historical Trans-Eurasian interactions, has been pivotal in shaping cultural exchanges, population dynamics, and genetic admixture. Recent insights from ancient DNA studies have shed light on the extensive population turnover within this region, encompassing a spectrum of groups from Paleolithic hunter-gatherers to Holocene herders and the nomadic pastoralist empires of historical times. The genomic analysis of ancient pathogens across the Eurasian steppe has further deepened our understanding of pathogen origins, clonal expansions, and the intricate processes of host-pathogen coevolution in relation to varying pathogen exposures and their spread. We consolidate the latest findings pertaining to the ancient human and pathogen genomes of Central Asia, elucidating their profound influence on the genomic tapestry of contemporary Central Asians. A notable gap in the current genomic databases for Central Asia is underscored, particularly within the scope of genomics-driven precision medicine. We stress the urgent need for the development of extensive, region-specific genomic resources that hold promise for revealing the genetic blueprints underlying human traits and diseases, refining polygenic scoring models for predictive medicine, and bolstering genomic research endeavors across Central Asia.

Ancient DNA study of Cervus canadensis unearthed from the Royal Sacrificial Site of the Northern Wei Dynasty in Inner Mongolia Autonomous Region, China

The practice of animal sacrifice was widespread in ancient societies, and the study of sacrificial animals holds significant importance. In this study, three samples excavated from the Royal Sacrificial Site of the Northern Wei Dynasty in Inner Mongolia Autonomous Region, China were initially identified as Cervinae subfamily animal based on their morphology. Through alignment analysis and principal component analysis, these samples were identified as belonging to the species Cervus canadensis. Meanwhile, through phylogenetic analyses and genetic distance calculations, it was determined that all three samples were of the Cervus canadensis alashanicus subspecies, proving the utility of ancient DNA technology in accurate subspecies identification. The analysis of the mitochondrial D-loop region revealed that the ancient Cervus canadensis alashanicus dated to 3800 BP and 5100 BP differed significantly from the modern ones in opposition to 1500 BP samples which were similar to them. The low genetic diversity of modern Cervus canadensis alashanicus was formed at least 1500 years ago and have lasted till today. In addition, as suggested by historical documents and archaeological studies, it is evident that the reverence for deer within the Tuoba Xianbei population had become a significant element of their culture and belief system. The identification of Cervus canadensis species in this study serves as evidence of the Northern Wei Emperor’s utilization of totem animals as sacrificial offerings to heaven.

How the Sima de los Huesos was won.

Although the first discovery of a human fossil in the Sima de los Huesos took place in 1976, systematic excavations did not begin there until 1984. Since then, this site has been continuously excavated in month-long camps. The site is dated by different radiometric techniques to between 430,000 and 300,000 years ago. Until the 2023 campaign, just over 7000 human fossils have been recovered, constituting the largest collection of fossils prior to Homo sapiens ever discovered. The fossils correspond to a minimum of 29 individuals of both sexes and different ages at death, from preadolescents to a specimen of advanced age. Comparative anatomy and ancient DNA studies both suggest that this is a population closely related to Homo neanderthalensis. The great variety and extraordinary quality of the fossils recovered have allowed us to carry out a series of investigations that have greatly increased our knowledge about the evolution of Homo in the Middle Pleistocene. Among the most important discoveries, it has been possible to establish body size and proportions, the confirmation that the origin of the accumulation of human fossils was of an anthropic nature, that those past humans took care of disabled individuals and who were capable of having an oral language almost as complex and efficient as that of our own species.

Evaluation of a New DNA Extraction Method on Challenging Bone Samples Recovered from a WWII Mass Grave.

Bones and teeth represent a common finding in ancient DNA studies and in forensic casework, even after a long burial. Genetic typing is the gold standard for the personal identification of skeletal remains, but there are two main factors involved in the successful DNA typing of such samples: (1) the set-up of an efficient DNA extraction method; (2) the identification of the most suitable skeletal element for the downstream genetic analyses. In this paper, a protocol based on the processing of 0.5 g of bone powder decalcified using Na2EDTA proved to be suitable for a semi-automated DNA extraction workflow using the Maxwell® FSC DNA IQ™ Casework Kit (Promega, Madison, WI, USA). The performance of this method in terms of DNA recovery and quality was compared with a full demineralisation extraction protocol based on Qiagen technology and kits. No statistically significant differences were scored according to the DNA recovery and DNA degradation index (p-values ≥ 0.176; r ≥ 0.907). This new DNA extraction protocol was applied to 88 bone samples (41 femurs, 19 petrous bones, 12 metacarpals and 16 molars) allegedly belonging to 27 World War II Italian soldiers found in a mass grave on the isle of Cres (Croatia). The results of the qPCR performed by the Quantifiler Human DNA Quantification kit showed values above the lowest Limit of Quantification (lLOQ; 23 pg/µL) for all petrous bones, whereas other bone types showed, in most cases, lower amounts of DNA. Replicate STR-CE analyses showed successful typing (that is, >12 markers) in all tests on the petrous bones, followed by the metacarpals (83.3%), femurs (52.2%) and teeth (20.0%). Full profiles (22/22 autosomal markers) were achieved mainly in the petrous bones (84.2%), followed by the metacarpals (41.7%). Stochastic amplification artefacts such as drop-outs or drop-ins occurred with a frequency of 1.9% in the petrous bones, whereas they were higher when the DNA recovered from other bone elements was amplified (up to 13.9% in the femurs). Overall, the results of this study confirm that petrous bone outperforms other bone elements in terms of the quantity and quality of the recovered DNA; for this reason, if available, it should always be preferred for genetic testing. In addition, our results highlight the need for accurate planning of the DVI operation, which should be carried out by a multi-disciplinary team, and the tricky issue of identifying other suitable skeletal elements for genetic testing. Overall, the results presented in this paper support the need to adopt preanalytical strategies positively related to the successful genetic testing of aged skeletal remains in order to reduce costs and the time of analysis.

Ancient DNA study of canid remains excavated from the Houtaomuga archaeological site, Northeast China

Ancient DNA study of canid remains excavated from the Houtaomuga archaeological site, Northeast China

Holme I (Seahenge) and Holme II: ritual responses to climate change in Early Bronze Age Britain

Holme I and II were contemporary, adjacent Early Bronze Age (EBA) oak-timber enclosures exposed intertidally at Holme-next-the-sea, Norfolk, England, in 1998. Holme I enclosed a central upturned tree-stump, its function and intent unknown. Holme II is thought a mortuary structure. Both are proposed here best explained as independent ritual responses to reverse a period of severe climate deterioration recorded before 2049 BC when their timbers were felled. Holme I is thought erected on the summer-solstice, when the cuckoo traditionally stopped singing, departing to the ‘Otherworld’. It replicated the cuckoo’s supposed overwintering quarters: a tree-hole or the ‘bowers of the Otherworld’ represented by the tree-stump, remembered in folklore as ‘penning-the-cuckoo’ where a cuckoo is confined to keep singing and maintain summer. The cuckoo symbolised male-fertility being associated with several Indo-European goddesses of fertility that deified Venus - one previously identified in EBA Britain. Some mortal consorts of these goddesses appear to have been ritually sacrificed at Samhain. Holme II may be an enclosure for the body of one such ‘sacral king’. These hypotheses are considered, using abductive reasoning, as ‘inferences to the best explanations’ from the available evidence. They are supported with environmental data, astronomic and biological evidence, regional folklore, toponymy, and an ethnographic analogy with indigenous Late Iron Age practices that indirect evidence indicates were undertaken in EBA Britain. Cultural and religious continuity is supported by textual sources, the material record and ancient DNA (aDNA) studies.

Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA

Low-coverage imputation is becoming ever more present in ancient DNA (aDNA) studies. Imputation pipelines commonly used for present-day genomes have been shown to yield accurate results when applied to ancient genomes. However, post-mortem damage (PMD), in the form of C-to-T substitutions at the reads termini, and contamination with DNA from closely related species can potentially affect imputation performance in aDNA. In this study, we evaluated imputation performance (i) when using a genotype caller designed for aDNA, ATLAS, compared to bcftools, and (ii) when contamination is present. We evaluated imputation performance with principal component analyses and by calculating imputation error rates. With a particular focus on differently imputed sites, we found that using ATLAS prior to imputation substantially improved imputed genotypes for a very damaged ancient genome (42% PMD). Trimming the ends of the sequencing reads led to similar improvements in imputation accuracy. For the remaining genomes, ATLAS brought limited gains. Finally, to examine the effect of contamination on imputation, we added various amounts of reads from two present-day genomes to a previously downsampled high-coverage ancient genome. We observed that imputation accuracy drastically decreased for contamination rates above 5%. In conclusion, we recommend (i) accounting for PMD by either trimming sequencing reads or using a genotype caller such as ATLAS before imputing highly damaged genomes and (ii) only imputing genomes containing up to 5% of contamination.

Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria

The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modeled as a mixture of sources from ancient Anatolia, Levant, and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5 to 6 kya onward, around the time agriculture appeared in the region. Our study characterizes the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of studies of ancient DNA in the region.

Ancient genomes and the evolutionary path of modern humans

Growing evidence from archaic and early modern human genomes brings new insights to the emergence of modern humans. We recount recent information collected from ancient DNA studies that inform us about the evolutionary pathway to modern humanity. These findings point to both individual- and population-level advantages underlying modern human expansion.

Why kinship still needs anthropologists in the 21st century

With the rise of ancient DNA studies in prehistoric archaeology, terms such as matriliny and patriliny are commonly used in scholarly literature. From a sociocultural anthropological perspective, however, the two terms are not as simple and unproblematic as is widely accepted among archaeogeneticists. Matriliny and patriliny are umbrella terms for societies with a wide range of political and kinship practices, with or without a state. Moreover, archaeogenetic literature has assumed specific associations with matrilineal and patrilineal descent that are not supported by sociocultural anthropology. To properly understand the diversity of human sociopolitical forms in both the deep and recent past, archaeology – in its broadest sense, including archaeogenetics – must avoid essentializing prehistoric communities without exploring the empirical nuances that are well documented ethnographically. Finally, the article calls for more engagement in debates on kinship and sociopolitical organization in prehistory from sociocultural anthropological perspectives.

Genetic history of Cambridgeshire before and after the Black Death.

The extent of the devastation of the Black Death pandemic (1346-1353) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at the local scale. Here, we report 275 ancient genomes, including 109 with coverage >0.1×, from later medieval and postmedieval Cambridgeshire of individuals buried before and after the Black Death. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. While we detect long-term shifts in local genetic ancestry in Cambridgeshire, we find no evidence of major changes in genetic ancestry nor higher differentiation of immune loci between cohorts living before and after the Black Death.

Working Ethically with Ancient DNA from Composites in the United States

AbstractThis article discusses ethical frameworks for planning and implementing composite research in the United States. Composites, defined here as archaeological materials with multiple genetic sources, include materials such as sediment, coprolites, birch pitch, and dental calculus. Although composites are increasingly used in genetic research, the ethical considerations of their use in ancient DNA studies have not been widely discussed. Here, we consider how composites’ compositions, contexts, and potential to act as proxies can affect research plans and offer an overview of the primary ethical concerns of ancient DNA research. It is our view that ethical principles established for analyses of Ancestral remains and related materials can be used to inform research plans when working with composite evidence. This work also provides a guide to archaeologists unfamiliar with genetics analyses in planning research when using composite evidence from the United States with a focus on collaboration, having a clear research plan, and using lab methods that provide the desired data with minimal destruction. Following the principles discussed in this article and others allows for engaging in composite research while creating and maintaining positive relationships with stakeholders.

Chronology and paleoclimatic context of hominin occupations in the Fenhe River Basin of northern China during the middle to Late Pleistocene

The relationship between climate change and hominin evolution over the Pleistocene in East Asia is still poorly understood, in particular due to the limited number of archaeological finds and fossils with reliable chronologies. Paleolithic sites preserved in loess-paleosol sequences in eastern Chinese Loess Plateau provide prospective evidence for understanding hominin evolution and dispersion across the Middle to Late Pleistocene in northern China. The Fenhe River Basin has been known as a key area for paleolithic sites and fossil hominins. Here, quartz Optically stimulated luminescence (OSL) and K-feldspar post-infrared infrared stimulated luminescence (pIRIR) dating was employed on 61 samples from 13 paleolithic sites in the Fenhe River Basin. The reliability of the ages are checked by analysis of luminescence characteristics and comparison between quartz OSL and K-feldspar pIRIR ages. Paleoclimatic records were established using alternating loess-paleosol sequences, and multi-proxy indices of grain size, magnetic susceptibility, CaCO3 and color from the dated sites. These results provide the reliable chronology for hominin presence in the Fenhe River Basin spanning the past three glacial-interglacial cycles. Our results show that this region experienced predominantly dusty, dry and cold conditions during glacials and comparatively moist and warm interglacial conditions, that are sensitive to variations in East Asian Summer and Winter Monsoon (EASM and EAWM respectively) intensities over glacial-interglacial timescales. The Fenhe River Basin is a key geographic refuge for hominins during glacial-interglacial climatic changes in northern China. It was occupied over glacial and interglacial periods spanning at least the last 370 ky, and the evidence for hominin presence is especially clear from ∼250 to 60 ka and since ∼35 ka. The frequency of hominin activity, as indicated by the number of archaeological sites and density of stone artifacts, increased during warm and humid periods of MIS 7 and MIS 5, in contrast to the cold, windy, and dry period of MIS 6. Site numbers increased in MIS 3 and the Last Glacial Maximum, in association with microblade technology. The dating results indicate that hominins with ‘modern’ features may have occurred in the Fenhe River Basin ∼140 ka ago, however, the exact timing of modern human occupation in the region needs a more combined approach consisting of morphological, ancient DNA and geochronological studies.

Archaeogenetics: Tracing ancient migrations from the Yellow River

Migration from the Yellow River homeland of Sino-Tibetan languages and people has impacted humans inEast Asia for more than 6,000 years. A new study of ancient DNA from southwest China reveals an important component of this migration history.

Genomic insights into the complex demographic history and inbreeding phenomena during Zhou Dynasty on the Central Plains of China.

In the Central Plains of China during the Zhou Dynasty (1046-256 BCE), the social hierarchy gradually solidified, accompanied by frequent wars and the phenomena of multicultural and multi-ethnic integration. These social phenomena collectively influenced the population's genetic structure at that time. However, our understanding of the genetic history of this period remains largely unknown owing to limited ancient DNA studies. In this study, we successfully obtained 11 ancient genomes from the Guanzhuang site during the Zhou Dynasty on the central plain of China. Our findings revealed remarkable genetic continuity with the Neolithic populations of the Yellow River Basin and emphasized genetic diversity through the analysis of uniparental genetic markers. Population structure analysis further confirmed the genetic similarity between the Guanzhuang population and ancient populations of the Yellow River Basin and indicated genetic exchanges with ancient populations from surrounding regions. Intriguingly, signs of inbreeding within the Guanzhuang community cast doubt on the stringent enforcement of the contemporary marital regulations against consanguineous marriages within the same surname or clan. These revelations significantly enhance our insight into the complex interplay of ancient demography and societal organization, concurrently presenting a genetic perspective to view the complex evolution of Chinese civilization's multiethnic.

Edible flora in pre-Columbian Caribbean coprolites: Expected and unexpected data.

Coprolites, or mummified feces, are valuable sources of information on ancient cultures as they contain ancient DNA (aDNA). In this study, we analyzed ancient plant DNA isolated from coprolites belonging to two pre-Columbian cultures (Huecoid and Saladoid) from Vieques, Puerto Rico, using shotgun metagenomic sequencing to reconstruct diet and lifestyles. We also analyzed DNA sequences of putative phytopathogenic fungi, likely ingested during food consumption, to further support dietary habits. Our findings show that pre-Columbian Caribbean cultures had a diverse diet consisting of maize (Zea mays), sweet potato (Ipomoea batatas), chili peppers (Capsicum annuum), peanuts (Arachis spp.), papaya (Carica papaya), tomato (Solanum lycopersicum) and, very surprisingly cotton (Gossypium barbadense) and tobacco (Nicotiana sylvestris). Modelling of putative phytopathogenic fungi and plant interactions confirmed the potential consumption of these plants as well as edible fungi, particularly Ustilago spp., which suggest the consumption of maize and huitlacoche. These findings suggest that a variety of dietary, medicinal, and hallucinogenic plants likely played an important role in ancient human subsistence and societal customs. We compared our results with coprolites found in Mexico and the United States, as well as present-day faeces from Mexico, Peru, and the United States. The results suggest that the diet of pre-Columbian cultures resembled that of present-day hunter-gatherers, while agriculturalists exhibited a transitional state in dietary lifestyles between the pre-Columbian cultures and larger scale farmers and United States individuals. Our study highlights differences in dietary patterns related to human lifestyles and provides insight into the flora present in the pre-Columbian Caribbean area. Importantly, data from ancient fecal specimens demonstrate the importance of ancient DNA studies to better understand pre-Columbian populations.