Ancient DNA Research Articles

CARE-ing for Indigenous nonhuman genomic data - rethinking our approach.

Earlier this year, an international group of scientists published a paper in ScienceAdvances on the draft genome of the little bush moa (Anomalopteryx didiformis), one of about nine species of extinct flightless birds endemic to Aotearoa (New Zealand). The genome was sequenced from the ancient DNA of a "poorly provenanced" fossil bone acquired by the Royal Ontario Museum. It held important clues about the moa's evolutionary history and aspects of its biology.

High levels of consanguinity in a child from Paquimé, Chihuahua, Mexico.

This study reports results from the ancient DNA analysis of a unique child burial at Paquimé, northern Chihuahua, Mexico. Located between Mesoamerican and Ancestral Puebloan groups, Paquimé (also known as Casas Grandes) was a vibrant multicultural centre during the 13th-14th centuries AD. Archaeologists have long debated Paquimé's social organization. Our analysis of Burial 23-8 has revealed that this child, placed under the centre post of an important room, had parents who were close genetic relatives. We argue that this child's consanguinity and special depositional context resulted from an elite family's practice of aggrandizing social status.

Ancient DNA sheds light on the funerary practices of late Neolithic collective burial in southern France.

The Aven de la Boucle (Corconne, Gard, southern France) is a karst shaft used as a collective burial between 3600 and 2800 cal BCE. The site encompasses the skeletal remains of approximately 75 individuals comprising a large majority of adult individuals, represented by scattered and commingled remains. To date, few studies have explored the potential of ancient DNA to tackle the documentation of Neolithic collective burials, and the funerary selection rules within such structures remain largely debated. In this study, we combine genomic analysis of 37 individuals with archaeo-anthropological data and Bayesian modelling of radiocarbon dates. Through this multidisciplinary approach, we aim to characterize the identity of the deceased and their relationships, as well as untangle the genetic diversity and funerary dynamics of this community. Genomic results identify 76% of male Neolithic individuals, suggesting a marked sex-biased selection. Available data emphasize the importance of biological relatedness and a male-mediated transmission of social status, as the affiliation to a specific male-lineage appears as a preponderant selection factor. The genomic results argue in favour of 'continuous' deposits between 3600 and 2800 BCE, carried out by the same community, despite cultural changes reflected by the ceramic material.

Unveiling Bishop Teodomiro of Iria Flavia? An attempt to identify the discoverer of St James's tomb through osteological and biomolecular analyses (Santiago de Compostela, Galicia, Spain)

After St James the Apostle, Bishop Teodomiro of Iria-Flavia is the most important figure associated with the pilgrimage to Santiago de Compostela. He supposedly discovered the apostolic tomb after a divine revelation between AD 820 and 830 yet, until the discovery, in 1955, of a tombstone inscribed with his name, his very existence was a matter of some debate. Here, the authors employ a multi-stranded analytical approach, combining osteoarchaeology, radiocarbon dating, stable isotope and ancient DNA analyses to demonstrate that human bones associated with the tombstone, in all likelihood, represent the earthly remains of Bishop Teodomiro.

Population structure of Dugong dugon across the Indo-Pacific revealed by historical mitogenomes.

Sirenia, an iconic marine taxon with a tropical and subtropical worldwide distribution, face an uncertain future. All species are designated 'Vulnerable' to extinction by the IUCN. Nonetheless, a comprehensive understanding of geographic structuring across the global range is lacking, impeding our ability to highlight particularly vulnerable populations for conservation priority. Here, we use ancient DNA to investigate dugong (Dugong dugon) population structure, analysing 56 mitogenomes from specimens comprising the known historical range. Our results reveal geographically structured and distinct monophyletic clades characterized by contrasting evolutionary histories. We observe deep-rooted and divergent lineages in the East (Indo-Pacific) and obtain new evidence for the relatively recent dispersal of dugongs into the western Indian Ocean. All populations are significantly differentiated from each other with western populations having approximately 10-fold lower levels of genetic variation than eastern Indo-Pacific populations. Additionally, we find a significant temporal loss of genetic diversity in western Indian Ocean dugongs since the mid-twentieth century, as well as a decline in population size beginning approximately 1000 years ago. Our results add to the growing body of evidence that dugong populations are becoming ever more susceptible to ongoing human action and global climate change.

Historical and archaeogenomic identification of high-status Englishmen at Jamestown, Virginia

The authors report on ancient DNA data from two human skeletons buried within the chancel of the 1608–1616 church at the North American colonial settlement of Jamestown, Virginia. Available archaeological, osteological and documentary evidence suggest that these individuals are Sir Ferdinando Wenman and Captain William West, kinsmen of the colony's first Governor, Thomas West, Third Baron De La Warr. Genomic analyses of the skeletons identify unexpected maternal relatedness as both carried the mitochondrial haplogroup H10e. In this unusual case, aDNA prompted further historical research that led to the discovery of illegitimacy in the West family, an aspect of identity omitted, likely intentionally, from genealogical records.

Is cross-species horizontal gene transfer responsible for gallbladder carcinogenesis

BackgroundCross-species horizontal gene transfer (HGT) involves the transfer of genetic material between different species of organisms. In recent years, mounting evidence has emerged that cross-species HGT does take place and may play a role in the development and progression of diseases.MethodsTranscriptomic data obtained from patients with gallbladder cancer (GBC) was assessed for the differential expression of antisense RNAs (asRNAs). The Basic Local Alignment Search Tool (BLAST) was used for cross-species analysis with viral, bacterial, fungal, and ancient human genomes to elucidate the evolutionary cross species origins of these differential asRNAs. Functional enrichment analysis and text mining were conducted and a network of asRNAs targeting mRNAs was constructed to understand the function of differential asRNAs better.ResultsA total of 17 differentially expressed antisense RNAs (asRNAs) were identified in gallbladder cancer tissue compared to that of normal gallbladder. BLAST analysis of 15 of these asRNAs (AFAP1-AS1, HMGA2-AS1, MNX1-AS1, SLC2A1-AS1, BBOX1-AS1, ELFN1-AS1, TRPM2-AS, DNAH17-AS1, DCST1-AS1, VPS9D1-AS1, MIR1-1HG-AS1, HAND2-AS1, PGM5P4-AS1, PGM5P3-AS1, and MAGI2-AS) showed varying degree of similarities with bacterial and viral genomes, except for UNC5B-AS1 and SOX21-AS1, which were conserved during evolution. Two of these 15 asRNAs, (VPS9D1-AS1 and SLC2A1-AS1) exhibited a high degree of similarity with viral genomes (Chikungunya virus, Human immunodeficiency virus 1, Stealth virus 1, and Zika virus) and bacterial genomes including (Staphylococcus sp., Bradyrhizobium sp., Pasteurella multocida sp., and, Klebsiella pneumoniae sp.), indicating potential HGT during evolution.ConclusionThe results provide novel evidence supporting the hypothesis that differentially expressed asRNAs in GBC exhibit varying sequence similarity with bacterial, viral, and ancient human genomes, indicating a potential shared evolutionary origin. These non-coding genes are enriched with methylation and were found to be associated with cancer-related pathways, including the P53 and PI3K-AKT signaling pathways, suggesting their possible involvement in tumor development.

Bayesian Inference Under the Multispecies Coalescent with Ancient DNA Sequences.

Ancient DNA (aDNA) is increasingly being used to investigate questions such as the phylogenetic relationships and divergence times of extant and extinct species. If aDNA samples are sufficiently old, expected branch lengths (in units of nucleotide substitutions) are reduced relative to contemporary samples. This can be accounted for by incorporating sample ages into phylogenetic analyses. Existing methods that use tip (sample) dates infer gene trees rather than species trees, which can lead to incorrect or biased inferences of the species tree. Methods using a multispecies coalescent (MSC) model overcome these issues. We developed an MSC model with tip dates and implemented it in the program bpp. The method performed well for a range of biologically realistic scenarios, estimating calibrated divergence times and mutation rates precisely. Simulations suggest that estimation precision can be best improved by prioritizing sampling of many loci and more ancient samples. Incorrectly treating ancient samples as contemporary in analyzing simulated data, mimicking a common practice of empirical analyses, led to large systematic biases in model parameters, including divergence times. Two genomic datasets of mammoths and elephants were analyzed, demonstrating the method's empirical utility.

Fast and Accurate Estimation of Selection Coefficients and Allele Histories from Ancient and Modern DNA.

We here present CLUES2, a full-likelihood method to infer natural selection from sequence data that is an extension of the method CLUES. We make several substantial improvements to the CLUES method that greatly increases both its applicability and its speed. We add the ability to use ancestral recombination graphs on ancient data as emissions to the underlying hidden Markov model, which enables CLUES2 to use both temporal and linkage information to make estimates of selection coefficients. We also fully implement the ability to estimate distinct selection coefficients in different epochs, which allows for the analysis of changes in selective pressures through time, as well as selection with dominance. In addition, we greatly increase the computational efficiency of CLUES2 over CLUES using several approximations to the forward-backward algorithms and develop a new way to reconstruct historic allele frequencies by integrating over the uncertainty in the estimation of the selection coefficients. We illustrate the accuracy of CLUES2 through extensive simulations and validate the importance sampling framework for integrating over the uncertainty in the inference of gene trees. We also show that CLUES2 is well-calibrated by showing that under the null hypothesis, the distribution of log-likelihood ratios follows a χ2 distribution with the appropriate degrees of freedom. We run CLUES2 on a set of recently published ancient human data from Western Eurasia and test for evidence of changing selection coefficients through time. We find significant evidence of changing selective pressures in several genes correlated with the introduction of agriculture to Europe and the ensuing dietary and demographic shifts of that time. In particular, our analysis supports previous hypotheses of strong selection on lactase persistence during periods of ancient famines and attenuated selection in more modern periods.

Long shared haplotypes identify the Southern Urals as a primary source for the 10th century Hungarians.

During the Hungarian Conquest in the 10th century CE, the early medieval Magyars, a group of mounted warriors from Eastern Europe, settled in the Carpathian Basin. They likely introduced the Hungarian language to this new settlement area, during an event documented by both written sources and archaeological evidence. Previous archaeogenetic research identified the newcomers as migrants from the Eurasian steppe. However, genome-wide ancient DNA from putative source populations has not been available to test alternative theories of their precise source. We generated genome-wide ancient DNA data for 131 individuals from candidate archaeological contexts in the Circum-Uralic region in present-day Russia. Our results tightly link the Magyars to people of the Early Medieval Karayakupovo archaeological horizon on both the European and Asian sides of the southern Urals. Our analyes show that ancestors of the people of the Karayakupovo archaeological horizon were established in the Southern Urals by the Iron Age and that their descendants persisted locally in the Volga-Kama region until at least the 14th century.

FIB-SEM Study of Archaeological Human Petrous Bones: 3D Structures and Diagenesis

The petrous bone generally preserves ancient DNA better than other fossil bones. One reason for this is that the inner layer of the petrous bone of pigs and humans contains about three times as many osteocytes as other bones, and hence more DNA. A FIB-SEM study of modern pig petrous bones showed that the 3D structure of the thin inner layer is typical of woven bone that forms in the fetus, whereas the thicker outer layer has a lamellar structure. The lamellar structure is common in mammalian bones. Here we study human petrous bones that are about 2500 years old, obtained from three Phoenician sites in Sicily, Italy. A detailed FIB-SEM study of two of these bones, one well preserved and the other poorly preserved, shows that the 3D bone type structure of the human petrous inner layer is woven bone, and the outer layer is lamellar bone. These are the same bone type structures found in pig petrous bones. Furthermore, by comparing nine differently preserved petrous bones from the same archaeological region and age, we show that their collagen contents vary widely, implying that organic material can be significantly altered during diagenesis. The mineral crystals are better preserved and hence less crystalline in the inner layers compared to the outer layers. We therefore infer that the best-preserved DNA in fossil petrous bones should be found in the thin inner layers immediately adjacent to the otic cavity where much more DNA is initially present and the mineral phase tends to be better preserved.

A 47,000 year archaeological and palaeoenvironmental record from Juukan 2 rockshelter on the western Hamersley Plateau of the Pilbara region, Western Australia

Archaeological and palaeoenvironmental investigations at Juukan 2 rockshelter have yielded new information on the ancient Aboriginal occupation of the Pilbara uplands in northwest Australia. Using multiple lines of evidence, including lithic, faunal, pollen, ancient DNA, radiocarbon dating, optically stimulated luminescence, and Bayesian chronological modelling, we show that Aboriginal people occupied the western Hamersley Plateau as early as 47,000 years ago (47 ka). Late Pleistocene populations utilised a diverse range of tool technologies, including bone points, grindstones, and flaked stone artefacts. Palaeoclimatic conditions at Juukan 2 rockshelter varied greatly over the past 47 ka, with repeated site visits by people, including during the peak hyper-arid phase of the Last Glacial Maximum (LGM) c. 21 ± 2 ka. Ancient starch analyses of the ground stone artefacts show the processing of Ipomoea (Bush Potato) from around 42 ka to the present day. Pronounced increases in the discard of stone artefacts and bone in the last 3500 years are interpreted to be the result of increased frequency of site use. A braided hair fragment dated to this period has demonstrated genetic links between the earlier rockshelter occupants and contemporary Puutu Kunti Kurrama and Pinikura peoples, who have maintained strong cultural connections to the area.

Genetic affinity of cave burial and Hmong-Mien populations in Guangxi inferred from ancient genomes

Genetic affinity of cave burial and Hmong-Mien populations in Guangxi inferred from ancient genomes

Sedimentary ancient DNA sequences reveal marine ecosystem shifts and indicator taxa for glacial-interglacial sea ice conditions

Sedimentary ancient DNA (sedaDNA) analysis is a promising new approach for reconstructing the impact of past climate and environmental changes on marine paleobiodiversity. By recovering, amplifying, and sequencing taxonomically informative sedaDNA fragments preserved in sediments, it is possible to assess the response of a broad range of eukaryote taxa, including non-fossilizing lineages, to past climate change. Here we present a unique marine derived sedaDNA metabarcoding record, spanning the penultimate glacial-interglacial transition across Marine Isotope Stages 6 to 5d (>135–107 ka) from an Eirik Drift core-site in the Labrador Sea. We identified a range of marine groups including dinoflagellates, diatoms, coccolithophores, chlorophytes, and copepods. There were representatives of primary/secondary producers, grazers, and parasites, which may represent remnants of complex ecosystems and ancient food webs. There were significant biodiversity shifts following the penultimate deglaciation and changing sea ice conditions throughout the Last Interglacial. These shifts reflected the striking increase in community richness during periods of seasonal sea ice and reduction under extensive perennial sea ice cover and open ocean. We identify two potential sedaDNA indicator taxa sequences associated with past seasonal sea ice which are most likely pico-eukaryote representatives of Micromonas and Pyramimonas, both green algae with known sea ice associations in modern ecosystems. Our work demonstrates the importance of high resolution marine sedaDNA metabarcoding for unravelling climate-ecosystem linkages and strengthens the potential of sedaDNA signals for past sea ice reconstructions through indicator sequences.

Advances in East Polynesian zooarchaeology: Special Issue introduction, review (2016–2024), and assessment

ABSTRACTThis article both introduces our Special Issue on “Zooarchaeology and Human Ecodynamics in East Polynesia” and reviews recent research from East Polynesia at large. The seven articles and discussion essay derive from a symposium at the 14th International Council for Archaeozoology (ICAZ) conference in Cairns, Australia (2023). To contextualize these contributions, we review recent studies (2016–2024) from the region relating to human–animal relationships, including morphological, ancient DNA, and stable isotope research. Seven areas or themes emerge from our review, representing substantive, analytical and technical domains. These include (1) geographic coverage; (2) methodological issues; (3) assessments of anthropogenic impacts; (4) studies of domestic and commensal taxa; (5) animals in social, ritual and symbolic roles; (6) engagement with historical records and traditional ecological knowledges (TEK); and (7) emerging technologies. We conclude with a brief summary of recent achievements and propose future directions for zooarchaeological studies in East Polynesia and the wider Pacific.

Ancient genomes provide insights into the genetic history in the historical era of southwest China

Ancient genomes provide insights into the genetic history in the historical era of southwest China

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 mitochondrial genome reveals matrilineal genetic inheritance of Chinese goats

As one of the most important domestic animals in ancient China, the origin, diffusion and matrilineal inheritance of goats have been important issues of archaeological research. In this study, we successfully extracted mitochondrial whole genome sequences from 77 samples of goat remains excavated from 16 sites in China, which date back from the Late Neolithic (4300-3800 BP) to the Ming Dynasty (600-400 BP). The results of ancient DNA analysis indicated that the Chinese goat matrilineages began to expand 7000-6000 years ago. The discovery of sub-lineages A2 and B2 suggests that they may have evolved or derived in China. The expansion of lineage A and the decline in the number of lineage B provide important evidence for the eastward migration of humans from the western part of the Eurasian continent. Furthermore, this study confirms that ancient Chinese goats had contributed genetically to the modern goats of China, and that the Chinese goats are genetically related to goats in South and Southeast Asia. Mitochondrial genome analysis of ancient Chinese goats not only provides an important resource for future analyses and research, but also offers new perspectives for the origin and diffusion of domestic goats.

Improving data archiving practices in ancient genomics

Ancient DNA is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is appropriately archived, its long-term value will not be fully realised. I surveyed publicly archived data from 42 recent ancient genomics studies. Half of the studies archived incomplete datasets, preventing accurate replication and representing a loss of data of potential future use. No studies met all criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: (1) archive all sequencing reads, not just those that aligned to a reference genome, (2) archive read alignments too, but as secondary analysis files, (3) provide correct experiment metadata on samples, libraries and sequencing runs, (4) provide informative sample metadata, (5) archive data from low-coverage and negative experiments, and (6) document archiving choices in papers, and peer review these. Given the reliance on destructive sampling of finite material, ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data.

Repeated plague infections across six generations of Neolithic Farmers

In the period between 5,300 and 4,900 calibrated years before present (cal. bp), populations across large parts of Europe underwent a period of demographic decline1,2. However, the cause of this so-called Neolithic decline is still debated. Some argue for an agricultural crisis resulting in the decline3, others for the spread of an early form of plague4. Here we use population-scale ancient genomics to infer ancestry, social structure and pathogen infection in 108 Scandinavian Neolithic individuals from eight megalithic graves and a stone cist. We find that the Neolithic plague was widespread, detected in at least 17% of the sampled population and across large geographical distances. We demonstrate that the disease spread within the Neolithic community in three distinct infection events within a period of around 120 years. Variant graph-based pan-genomics shows that the Neolithic plague genomes retained ancestral genomic variation present in Yersinia pseudotuberculosis, including virulence factors associated with disease outcomes. In addition, we reconstruct four multigeneration pedigrees, the largest of which consists of 38 individuals spanning six generations, showing a patrilineal social organization. Lastly, we document direct genomic evidence for Neolithic female exogamy in a woman buried in a different megalithic tomb than her brothers. Taken together, our findings provide a detailed reconstruction of plague spread within a large patrilineal kinship group and identify multiple plague infections in a population dated to the beginning of the Neolithic decline.