Ancient Individuals Research Articles

A new investigative strategy to diagnose \u03b2-thalassemia syndrome in past human populations

The study of thalassaemia syndromes in archeological human remains is of growing interest in the field of paleopathology. However, a definitive diagnosis of the disease in skeletonized individuals remains difficult. Several non-specific bone lesions have been suggested as the most likely evidence of β-thalassaemia syndrome. In particular, skull lesions have been considered by several scholars as the most indicative of this hematopoietic disorder, while other authors have identified postcranial lesions as the best evidence of β-thalassemia. In this study, we reviewed the main features that have been identified in β-thalassaemia patients thanks to an extensive bibliographic research of clinical cases, radiological and microscopic analyses. Our aim was to discern between those skeletal lesions that can be considered “indicative/diagnostic” and those that are “indicative/non-diagnostic” of β-thalassaemia syndrome. With this knowledge, we developed a new evaluation form (Eva-BeTa) and tested it on previously published archeological cases. Based on our results, we believe that Eva-BeTa can be a valid diagnostic tool for the identification of ancient individuals potentially affected by β-thalassemia for further genetic confirmation.

A genetic history of the pre-contact Caribbean.

Humans settled the Caribbean ~6,000 years ago, with ceramic use and intensified agriculture marking a shift from the Archaic to the Ceramic Age ~2,500 years ago1–3. We report genome-wide data from 174 individuals from The Bahamas, Hispaniola, Puerto Rico, Curaçao, and Venezuela co-analyzed with published data. Archaic Age Caribbean people derive from a deeply divergent population closest to Central and northern South Americans; contrary to previous work4, we find no support for ancestry contributed by a population related to North Americans. Archaic lineages were >98% replaced by a genetically homogeneous ceramic-using population related to Arawak-speakers from northeast South America who moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools reflecting small effective population sizes which we estimate to be a minimum of Ne=500–1500 and a maximum of Ne=1530–8150 on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the analyzed individuals lived. Census sizes are unlikely to be more than ten-fold larger than effective population sizes, so previous estimates of hundreds of thousands of people are too large5–6. Confirming a small, interconnected Ceramic Age population7, we detect 19 pairs of cross-island cousins, close relatives ~75 kilometers apart in Hispaniola, and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically-differentiated groups from the mainland but instead reflected interactions within an interconnected Caribbean world1,8.

Post-last glacial maximum expansion of Y-chromosome haplogroup C2a-L1373 in northern Asia and its implications for the origin of Native Americans.

Subbranches of Y-chromosome haplogroup C2a-L1373 are founding paternal lineages in northern Asia and Native American populations. Our objective was to investigate C2a-L1373 differentiation in northern Asia and its implications for Native American origins. Sequences of rare subbranches (n = 43) and ancient individuals (n = 37) of C2a-L1373 (including P39 and MPB373), were used to construct phylogenetic trees with age estimation by BEAST software. C2a-L1373 expanded rapidly approximately 17.7,000-14.3,000 years ago (kya) after the last glacial maximum (LGM), generating numerous sublineages which became founding paternal lineages of modern northern Asian and Native American populations (C2a-P39 and C2a-MPB373). The divergence pattern supports possible initiation of differentiation in low latitude regions of northern Asia and northward diffusion after the LGM. There is a substantial gap between the divergence times of C2a-MPB373 (approximately 22.4 or 17.7 kya) and C2a-P39 (approximately 14.3 kya), indicating two possible migration waves. We discussed the decreasing time interval of "Beringian standstill" (2.5 ky or smaller) and its reduced significance. We also discussed the multiple possibilities for the peopling of the Americas: the "Long-term Beringian standstill model," the "Short-term Beringian standstill model," and the "Multiple waves of migration model." Our results support the argument from ancient DNA analyses that the direct ancestor group of Native Americans is an admixture of "Ancient Northern Siberians" and Paleolithic communities from the Amur region, which appeared during the post-LGM era, rather than ancient populations in greater Beringia, or an adjacent region, before the LGM.

A Dynamic 6,000-Year Genetic History of Eurasia’s Eastern Steppe

SummaryThe Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region’s population history. Here, we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe.

Three Phases of Ancient Migration Shaped the Ancestry of Human Populations in Vanuatu

The archipelago of Vanuatu has been at the crossroads of human population movements in the Pacific for the past three millennia. To help address several open questions regarding the history of these movements, we generated genome-wide data for 11 ancient individuals from the island of Efate dating from its earliest settlement to the recent past, including five associated with the Chief Roi Mata's Domain World Heritage Area, and analyzed them in conjunction with 34 published ancient individuals from Vanuatu and elsewhere in Oceania, as well as present-day populations. Our results outline three distinct periods of population transformations. First, the four earliest individuals, from the Lapita-period site of Teouma, are concordant with eight previously described Lapita-associated individuals from Vanuatu and Tonga in having almost all of their ancestry from a "First Remote Oceanian" source related to East and Southeast Asians. Second, both the Papuan ancestry predominating in Vanuatu for the past 2,500 years and the smaller component of Papuan ancestry found in Polynesians can be modeled as deriving from a single source most likely originating in New Britain, suggesting that the movement of people carrying this ancestry to Remote Oceania closely followed that of the First Remote Oceanians in time and space. Third, the Chief Roi Mata's Domain individuals descend from a mixture of Vanuatu- and Polynesian-derived ancestry and are related to Polynesian-influenced communities today in central, but not southern, Vanuatu, demonstrating Polynesian genetic input in multiple groups with independent histories.

Distribution of maternal lineages in hunter-gatherer societies of the southern coast of Tierra del Fuego, Argentina.

The aim of this work is to explore the maternal genetic diversity of hunter-gatherers of the southern Tierra del Fuego, specifically the north coast of Beagle Channel, the Península Mitre, and Isla de los Estados through ancient mitochondrial DNA analysis. The hypervariable regions 1 and 2 of the mitochondrial genome of five individuals from the north coast of Beagle Channel, six individuals from Península Mitre, and one individual from Isla de los Estados were analyzed. Through diversity statistics, Analysis of Molecular Variance (AMOVA), and Median Joining networks analyses, maternal relationships in the region were evaluated and phylogenetic similarities between ancient and contemporary populations of Tierra del Fuego were determined. The mitochondrial DNA lineages from the ancient individuals analyzed reveals the presence of subclades C1b and D1g. Pattern of decreasing genetic diversity toward the South is observed. The AMOVAs performed found no statistically significant differences between individuals of the north coast of Beagle Channel and Península Mitre-Isla de los Estados, and modern Yámana populations. Median joining network of haplotypes of clades C1 and D1g, show the same results. Ethnohistoric and ethnographic records of Península Mitre show that this region was occupied during the 19th century by Haush or Manekenk populations, although their biological, cultural, and subsistence characterization is unclear. We explore their maternal lineages and encounter low levels of genetic diversity and the absence of population differentiation with modern Yámana groups. We suggest that Península Mitre-Isla de los Estado was part of the same hunting and gathering populations as those of the Beagle Channel.

Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography

Archaeological research documents major technological shifts among people who have lived in the southern tip of South America (South Patagonia) during the last thirteen millennia, including the development of marine-based economies and changes in tools and raw materials. It has been proposed that movements of people spreading culture and technology propelled some of these shifts, but these hypotheses have not been tested with ancient DNA. Here we report genome-wide data from 20 ancient individuals, and co-analyze it with previously reported data. We reveal that immigration does not explain the appearance of marine adaptations in South Patagonia. We describe partial genetic continuity since ~6600 BP and two later gene flows correlated with technological changes: one between 4700–2000 BP that affected primarily marine-based groups, and a later one impacting all <2000 BP groups. From ~2200–1200 BP, mixture among neighbors resulted in a cline correlated to geographic ordering along the coast.

A genetic history of China

Human Evolution The history of human movements into and within China has been difficult to determine solely from archaeological investigations or genetic studies of contemporary peoples. Yang et al. sequenced DNA from 26 individuals from 9500 to 300 years ago from locations within China. Analyses of these individuals, along with previously sequenced ancient individuals and present-day genomes representing global populations, show a split between ancient humans in northern and southern China. Neolithic northern Chinese individuals are closest to modern-day East Asians, whereas ancient individuals from southern China are most closely related to modern-day Southeast Asians and show an affinity to modern-day Austronesian populations. These results indicate that there was a southward movement and admixture of peoples during the Neolithic that gave rise to modern-day populations in East Asia. Science this issue p. [282][1] [1]: /lookup/doi/10.1126/science.aba0909

A novel method of male sex identification of human ancient skeletal remains.

Sex identification of ancient individuals is important to understand aspects of the culture, demographic structure, religious practices, disease association, and the history of the ancient civilizations. Sex identification is performed using anthropometric measurements and molecular genetics techniques, including quantification of the X and Y chromosomes. These approaches are not always reliable in subadult, or fragmented, incomplete skeletons or when the DNA is highly degraded. Most of the methods include the identification of the male and female sexes, but the absence of a specific marker for the males does not mean that the sample obtained was from a female. This study aims (1) to identify new male-specific regions that allow male identification; (2) to contrast the effectiveness of these markers against AMELX/AMELY and anthropometric measurement procedures; and (3) to test the efficacy of these markers in archaeological samples. For the first two aims, we used known sex samples, and for the third aim, we used samples from different archaeological sites. A novel molecular technique to identify male-specific regions by amplification of TTTY7, TSPY3, TTTY2, and TTTY22 genes of the human Y chromosome was developed. The results showed amplification of the specific DNA regions of Y chromosome in male individuals, with no amplification being observed in any of the female samples, confirming their specificity for male individuals. This approach complements the current procedures, such as the AMELX/AMELY test and anthropometric principle.

A 2,000\u2013year-old specimen with intraerythrocytic Bartonella quintana

Photogrammetry and cascading microscopy investigations of dental pulp specimens collected from 2,000-year-old individuals buried in a Roman necropolis in Besançon, France, revealed unprecedented preserved tissular and cellular morphology. Photogrammetry yielded 3-D images of the smallest archaeological human remains ever recovered. Optical microscopy examinations after standard haematoxylin-phloxine-saffron staining and anti-glycophorin A immunohistochemistry exposed dental pulp cells, in addition erythrocytes were visualised by electron microscopy, which indicated the ancient dental pulp trapped a blood drop. Fluorescence in situ hybridisation applied on red blood cells revealed the louse-borne pathogen Bartonella quintana, a finding confirmed by polymerase chain reaction assays. Through paleohistology and paleocytology, we demonstrate that the ancient dental pulp preserved intact blood cells at the time of the individual’s death, offering an unprecedented opportunity to engage in direct and indirect tests to diagnose pathogens in ancient buried individuals.

Ancient genomes from present-day France unveil 7,000 years of its demographic history

Genomic studies conducted on ancient individuals across Europe have revealed how migrations have contributed to its present genetic landscape, but the territory of present-day France has yet to be connected to the broader European picture. We generated a large dataset comprising the complete mitochondrial genomes, Y-chromosome markers, and genotypes of a number of nuclear loci of interest of 243 individuals sampled across present-day France over a period spanning 7,000 y, complemented with a partially overlapping dataset of 58 low-coverage genomes. This panel provides a high-resolution transect of the dynamics of maternal and paternal lineages in France as well as of autosomal genotypes. Parental lineages and genomic data both revealed demographic patterns in France for the Neolithic and Bronze Age transitions consistent with neighboring regions, first with a migration wave of Anatolian farmers followed by varying degrees of admixture with autochthonous hunter-gatherers, and then substantial gene flow from individuals deriving part of their ancestry from the Pontic steppe at the onset of the Bronze Age. Our data have also highlighted the persistence of Magdalenian-associated ancestry in hunter-gatherer populations outside of Spain and thus provide arguments for an expansion of these populations at the end of the Paleolithic Period more northerly than what has been described so far. Finally, no major demographic changes were detected during the transition between the Bronze and Iron Ages.

Ancient DNA indicates human population shifts and admixture in northern and southern China.

Human genetic history in East Asia is poorly understood. To clarify population relationships, we obtained genome-wide data from 26 ancient individuals from northern and southern East Asia spanning 9500 to 300 years ago. Genetic differentiation in this region was higher in the past than the present, which reflects a major episode of admixture involving northern East Asian ancestry spreading across southern East Asia after the Neolithic, thereby transforming the genetic ancestry of southern China. Mainland southern East Asian and Taiwan Strait island samples from the Neolithic show clear connections with modern and ancient individuals with Austronesian-related ancestry, which supports an origin in southern China for proto-Austronesians. Connections among Neolithic coastal groups from Siberia and Japan to Vietnam indicate that migration and gene flow played an important role in the prehistory of coastal Asia.

Assessing DNA Sequence Alignment Methods for Characterizing Ancient Genomes and Methylomes

Applying high-throughput DNA sequencing technologies to the ancient DNA molecules preserved in subfossil material can provide genetic information from past individuals, populations and communities at the genomic scale. The combination of dedicated statistical techniques and specific molecular tools aimed at reducing the impact of post-mortem DNA damage can also help recover epigenetic data from ancient individuals. However, the capacity of different sequence aligners to identify ultrashort and deaminated ancient DNA templates, and their impact on the characterization of ancient methylomes, remain overlooked. In this study, we use both simulated and real ancient DNA sequence data to benchmark the performance of the read alignment tools most commonly used in ancient DNA research. We identify a read alignment strategy making use of the Bowtie2 aligner that substantially reduce computational times but shows increased sensitivity relative to previous recommendations based on the BWA aligner. This strategy significantly improves the genome coverage especially when DNA templates are shorter than 90bp, as is typically the case for ancient DNA. It also impacts on ancient DNA methylation estimates as it maximizes coverage improvement within CpG dinucleotide contexts, which hold the vast majority of DNA methylation marks in mammals. Our work contributes to improve the accuracy of DNA methylation maps and to maximize the amount of recoverable genetic information from archaeological and subfossil material. As the molecular complexity of ancient DNA libraries is generally limited, the mapping strategy recommended here is essential to both limit sequencing costs and sample destruction.

Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus

Here, we report genome-wide data analyses from 110 ancient Near Eastern individuals spanning the Late Neolithic to Late Bronze Age, a period characterized by intense interregional interactions for the Near East. We find that 6th millennium BCE populations of North/Central Anatolia and the Southern Caucasus shared mixed ancestry on a genetic cline that formed during the Neolithic between Western Anatolia and regions in today's Southern Caucasus/Zagros. During the Late Chalcolithic and/or the Early Bronze Age, more than half of the Northern Levantine gene pool was replaced, while in the rest of Anatolia and the Southern Caucasus, we document genetic continuity with only transient gene flow. Additionally, we reveal a genetically distinct individual within the Late Bronze Age Northern Levant. Overall, our study uncovers multiple scales of population dynamics through time, from extensive admixture during the Neolithic period to long-distance mobility within the globalized societies of the Late Bronze Age. VIDEO ABSTRACT.

Economic Diversification Supported the Growth of Mongolia\u2019s Nomadic Empires

Populations in Mongolia from the late second millennium B.C.E. through the Mongol Empire are traditionally assumed, by archaeologists and historians, to have maintained a highly specialized horse-facilitated form of mobile pastoralism. Until recently, a dearth of direct evidence for prehistoric human diet and subsistence economies in Mongolia has rendered systematic testing of this view impossible. Here, we present stable carbon and nitrogen isotope measurements of human bone collagen, and stable carbon isotope analysis of human enamel bioapatite, from 137 well-dated ancient Mongolian individuals spanning the period c. 4400 B.C.E. to 1300 C.E. Our results demonstrate an increase in consumption of C4 plants beginning at c. 800 B.C.E., almost certainly indicative of millet consumption, an interpretation supported by archaeological evidence. The escalating scale of millet consumption on the eastern Eurasian steppe over time, and an expansion of isotopic niche widths, indicate that historic Mongolian empires were supported by a diversification of economic strategies rather than uniform, specialized pastoralism.

Predicting Personality of Ancient People based on Transfer Learning

Abstract It is important to identify the personality of ancient people, which may help us understand more about culture change. The traditional method, self-report, is difficult to conduct research on ancient Chinese historical individuals. With the development of artificial intelligence, Transfer Learning provides a new way to identify the personality of ancient people. In this paper, we proposed Unsupervised Entropy Regression Domain Adaptation(UERDA) and Semi-supervised Entropy Regression Domain Adaptation (SERDA) based on Transfer Learning. We used the micro-blog data on Sina Weibo and autobiography data of ancient Chinese individuals for distribution adaptation, to train the personality prediction model and predicted the big-five personality traits of ancient individuals. For joint distribution adaptation, UERDA uses information entropy to realize unsupervised domain adaptation based on the regression task. SERDA is a semi-supervised method based on UERDA to improve the accuracy of the Transfer Learning model in the regression task. Compared with traditional algorithm PCA, RMSE of UERDA has decreased by 2.23 on average, and RMSE of SERDA has decreased by 3.16 on average. The experimental results showed that Transfer Learning achieved good performance in terms of the prediction of the big five personality traits of ancient people, which provides a new way for research on ancient people and culture change.

Diet analysis reveals pre-historic meals among the Loma San Gabriel at La Cueva de Los Muertos Chiquitos, Rio Zape, Mexico (600–800 CE)

Coprolites have been a source of study for archeologists due to several reasons: they not only provide information on the life and nutritional habits of ancient individuals but also on their health. In this paper, we processed 10 coprolites collected at La Cueva de Los Muertos Chiquitos (600–800 CE), Rio Zape, Mexico, with acetolysis solution for pollen analysis. The number of pollen grains/gram of each coprolite sample was quantified along with the macroscopic remains of these samples. The main food item ingested by the population was maize, followed by Agave. Squash blossoms were also part of their food source determined by the presence of pollen grains. In macroremains, we identified rodent bones, plant seeds, and Agave fibers. The macroscopic analysis of the samples fits with the analysis of smaller remains, giving an idea of the meal represented by each coprolite analyzed. We relate these results to previous microbiome studies of coprolite samples from the same archeological site and provide a discussion on the relevancy of studying macro- and microremains that can be applied to microbiome interpretation analysis.

Exposure to geogenic lithium in ancient Andeans: Unraveling lithium in mummy hair using LA-ICP-MS

The ancient Andeans, who lived along the coastal region of the arid Atacama Desert in present day Chile had access to scarce freshwater via a few small rivers originating from the Andean Altiplano. Due to volcanic-derived lithium minerals and their solubility in water, the surface water in the Atacama Desert region is rich with lithium (Li); often many orders of magnitude higher than that of other rivers in the world. The goal of this study was to examine whether ancient Andean mummy individuals (n = 145) from four burial areas in northern Chile (Azapa, Camarones, Lluta and Morro) were exposed to geogenic lithium by conducting laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) on a single strand of hair per individual. The resulting concentrations for Li in mummy hair [Site, Median, Range (μg/g), n: Azapa, 0.38, 0.04–2.91 μg/g, n = 98; Morro, 0.33, 0.03–0.65 μg/g, n = 14; Camarones, 0.61, 0.07–12.8 μg/g, n = 31; Lluta, 2.9, 2.7–3.1 μg/g, n = 2] had the following order: Lluta > Camarones > Azapa > Morro. Hair-Li concentration of the Andean mummies were nearly 20 times elevated when compared to concentrations of Li in the hair of contemporary populations in other regions. Exposure to Li as revealed in hair appears to be depend in part on where ancient Andeans were buried, and generally correlates well with dissolved Li in associated rivers.

A multi‐method approach to dating the burial and skeleton of Kiacatoo Man, New South Wales, Australia

ABSTRACTKiacatoo Man, a large, rugged Aboriginal adult buried in the Lachlan riverine plains of southeastern Australia, was discovered in 2011. Laser‐ablation uranium series analysis on bone yielded a minimum age for the burial of 27.4 ± 0.4 ka (2σ). Single‐grain, optically stimulated luminescence ages on quartz sediment in which the grave had been dug gave a weighted mean age of 26.4 ± 1.5 ka (1σ). Luminescence samples from the grave infill and from sediment beneath the grave exhibit overdispersed dose distributions consistent with bioturbation or other disturbance, which has obscured the burial signal. The overlap between the minimum (U‐series) and maximum (luminescence) ages places the burial between 27.0 and 29.4 ka (2σ). Luminescence ages obtained from the channel belt of between 28 ± 2 and 25 ± 3 ka indicate that fluvial sedimentation was occurring before the Last Glacial Maximum, which is consistent with the broader geomorphic setting. Together, these results are internally and regionally consistent, and indicate that Kiacatoo Man was one of the more ancient individuals so far identified in Australia. His remains are important to our understanding of patterns of biological variation and other processes that have shaped people in the Murray‐Darling Basin through time. Copyright © 2019 John Wiley &amp; Sons, Ltd.

Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese.

Modern East Asians derived from the admixture of aborigines and incoming farmers expanding from Yellow and Yangtze River Basins. Distinct genetic differentiation and subsequent admixture between Northeast Asians and Southeast Asians subsequently evidenced by the mitochondrial DNA, Y-chromosomal variations, and autosomal SNPs. Recently, population geneticists have paid more attention to the genetic polymorphisms and background of southern-Han Chinese and southern native populations. The genetic legacy of northern-Han remains uncharacterized. Thus, we performed this comprehensive population genetic analyses of modern and ancient genetic variations aiming to yield new insight into the formation of modern Han, and the genetic ancestry and phylogenetic relationship of the northern-Han Chinese population. We first genotyped 25 forensic associated markers in 3,089 northern-Han Chinese individuals using the new-generation of the Huaxia Platinum System. And then we performed the first meta-analysis focused on the genetic affinity between Asian Neolithic∼Iron Age ancients and modern northern-Han Chinese by combining mitochondrial variations in 417 ancient individuals from 13 different archeological sites and 812 modern individuals, as well as Y-chromosomal variations in 114 ancient individuals from 12 Neolithic∼Iron Age sites and 2,810 modern subjects. We finally genotyped 643,897 genome-wide nucleotide polymorphisms (SNPs) in 20 Shanxi Han individuals and combined with 1,927 modern humans and 40 Eurasian ancient genomes to explore the genetic structure and admixture of northern-Han Chinese. We addressed genetic legacy, population structure and phylogenetic relationship of northern-Han Chinese via various analyses. Our population genetic results from five different reference datasets indicated that Shanxi Han shares a closer phylogenetic relationship with northern-neighbors and southern ethnically close groups than with Uyghur and Tibetan. Genome-wide variations revealed that modern northern-Han derived their ancestry from Yakut-related population (25.2%) and She-related population (74.8%). Summarily, the genetic mixing that led to the emergence of a Han Chinese ethnicity occurred at a very early period, probably in Neolithic times, and this mixing involved an ancient Tibeto-Burman population and a local pre-Sinitic population, which may have been linguistically Altaic.