Author Correction: 137 ancient human genomes from across the Eurasian steppes.

with In this Article, Angela M. Taravella and Melissa A. Wilson Sayres have been added to the author list (associated with: School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University, Tempe, AZ, USA). The author list and Author Information section have been corrected online.

137 ancient human genomes from across the Eurasian steppes.

For thousands of years the Eurasian steppes have been a centre of human migrations and cultural change. Here we sequence the genomes of 137 ancient humans (about 1× average coverage), covering a period of 4,000 years, to understand the population history of the Eurasian steppes after the Bronze Age migrations. We find that the genetics of the Scythian groups that dominated the Eurasian steppes throughout the Iron Age were highly structured, with diverse origins comprising Late Bronze Age herders, European farmers and southern Siberian hunter-gatherers. Later, Scythians admixed with the eastern steppe nomads who formed the Xiongnu confederations, and moved westward in about the second or third century BC, forming the Hun traditions in the fourth-fifth century AD, and carrying with them plague that was basal to the Justinian plague. These nomads were further admixed with East Asian groups during several short-term khanates in the Medieval period. These historical events transformed the Eurasian steppes from being inhabited by Indo-European speakers of largely West Eurasian ancestry to the mostly Turkic-speaking groups of the present day, who are primarily of East Asian ancestry.

Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans.

Human parvovirus B19 (B19V) is a ubiquitous human pathogen associated with a number of conditions, such as fifth disease in children and arthritis and arthralgias in adults. B19V is thought to evolve exceptionally rapidly among DNA viruses, with substitution rates previously estimated to be closer to those typical of RNA viruses. On the basis of genetic sequences up to ∼70 years of age, the most recent common ancestor of all B19V has been dated to the early 1800s, and it has been suggested that genotype 1, the most common B19V genotype, only started circulating in the 1960s. Here we present 10 genomes (63.9-99.7% genome coverage) of B19V from dental and skeletal remains of individuals who lived in Eurasia and Greenland from ∼0.5 to ∼6.9 thousand years ago (kya). In a phylogenetic analysis, five of the ancient B19V sequences fall within or basal to the modern genotype 1, and five fall basal to genotype 2, showing a long-term association of B19V with humans. The most recent common ancestor of all B19V is placed ∼12.6 kya, and we find a substitution rate that is an order of magnitude lower than inferred previously. Further, we are able to date the recombination event between genotypes 1 and 3 that formed genotype 2 to ∼5.0-6.8 kya. This study emphasizes the importance of ancient viral sequences for our understanding of virus evolution and phylogenetics.

"Mind the gap"-Assessing methods for aligning age determination and growth rate in multi-molar sequences of dietary isotopic data.

OBJECTIVES: Creating multi-tooth sequences of micro-sampled stable isotope (SI) analytical data can help track 20+ years of individual dietary history. Inferences about individual and population level behavioral patterns require cross-calibration of the timing of dietary changes recorded by each tooth. Dentin sections from contemporaneous tissues (eg, in M1 and M2) reflect dietary signature for the time of growth. Contemporary sections should produce similar values, allowing alignment of temporally overlapping portions of teeth into multi-tooth sequences. Published methods for determining the ages of incremental sections do not provide guidance for adjustment when poor alignment between individual tooth sequences is encountered. The primary objective is to address this problem; examine cause(s), assess the effects of the standard growth-model on available age-assessment techniques, and provide a viable solution. METHODS: Investigating difficulty in aligning a 3-molar sequence at Shamanka II, an Early Neolithic (7000-5700 BP) Kitoi hunter-gatherer cemetery in Cis-Baikal, Siberia, we employed 10 age assessment models and 13 variants of 2 published growth rate methods on 3 individuals of different age and sex. RESULTS: At Shamanka II, dentin initiation and/or growth rates were different from the mostly European, reference populations used to create published age-estimation/growth rate models. Initiation ages for M2 and M3 were delayed. Root formation rates were on the rapid end of known development parameters. CONCLUSIONS: Age-assessment methods customized to dentin initiation ages and growth parameters of Siberian populations produced a hybrid growth rate model for dentin section ages and improved alignment for multi-tooth SI sequences over published models.

Skeletal growth in early and late Neolithic foragers from the Cis-Baikal region of Eastern Siberia.

Skeletal growth is explored between Early Neolithic (EN) (8000 to 6800 BP) and Late Neolithic (LN) (6000 to 5200 BP) foragers from the Cis-Baikal region of Eastern Siberia. Previous studies suggest that increased systemic stress and smaller adult body size characterize the EN compared to LN. On this basis, greater evidence for stunting and wasting is expected in the EN compared to LN. Skeletal growth parameters assessed here include femoral and tibial lengths, estimated stature and body mass, femoral midshaft cortical thickness, total bone thickness, and medullary width. Forward selection was used to fit polynomial lines to each skeletal growth parameter relative to dental age in the pooled samples, and standardized residuals were compared between groups using t tests. Standardized residuals of body mass and femoral length were significantly lower in the EN compared to LN sample, particularly from late infancy through early adolescence. However, no significant differences in the standardized residuals for cortical thickness, medullary width, total bone thickness, tibial length, or stature were found between the groups. Age ranges for stunting in femoral length and wasting in body mass are consistent with environmental perturbations experienced at the cessation of breast feeding and general resource insecurity in the EN compared to LN sample. Differences in relative femoral but not tibial length may be associated with age-specific variation in growth-acceleration for the distal and proximal limb segments. Similarity in cortical bone growth between the two samples may reflect the combined influences of systemic and mechanical factors on this parameter.

Bone quality in prehistoric, Cis-Baikal forager femora: a micro-CT analysis of cortical canal microstructure.

Bone quality, a contributor to bone strength, is determined by structural and mechanical properties, which may be analyzed by gross and/or microscopic methods. Variables that contribute to bone quality, such as porosity, can provide insight into the health and lifestyles of people in prehistory. This study tests the ability of microcomputed tomography (µCT) to capture and characterize cortical canal systems in archaeological bone. Seven variables and 71 femora are analyzed to explore bone dynamics in prehistoric foragers from Lake Baikal, Siberia. The results indicate that canal number and canal separation differ significantly (P < 0.05) between age-at-death categories, but only for the pooled and male samples. When merged into a new variable by means of principal components analysis, canal diameter and canal surface to canal volume are also able to discriminate amongst age-at-death categories, as well as between the sexes. However, the overall lack of significant differences between the sexes and amongst age-at-death categories indicates that Baikal forager bone quality (i.e., canal architecture) did not change drastically throughout the lifespan. Interestingly, principal component one identified an untested variable that contributes to canal microstructure variability, and a sexual division of labor may promote divergent trends in canal degree of anisotropy between the sexes. Overall, µCT provides an alternate method for exploring bone quality in archaeological remains, complementing existing methods such as thin-sectioning and gross morphological analyses.

The evolution of dog diet and foraging: Insights from archaeological canids in Siberia.

Research on the evolution of dog foraging and diet has largely focused on scavenging during their initial domestication and genetic adaptations to starch-rich food environments following the advent of agriculture. The Siberian archaeological record evidences other critical shifts in dog foraging and diet that likely characterize Holocene dogs globally. By the Middle Holocene, body size reconstruction for Siberia dogs indicates that most were far smaller than Pleistocene wolves. This contributed to dogs' tendencies to scavenge, feed on small prey, and reduce social foraging. Stable carbon and nitrogen isotope analysis of Siberian dogs reveals that their diets were more diverse than those of Pleistocene wolves. This included habitual consumption of marine and freshwater foods by the Middle Holocene and reliance on C4 foods by the Late Holocene. Feeding on such foods and anthropogenic waste increased dogs' exposure to microbes, affected their gut microbiomes, and shaped long-term dog population history.

Infant and child diet in Neolithic hunter-fisher-gatherers from Cis-Baikal, Siberia: intra-long bone stable nitrogen and carbon isotope ratios.

Analysis of stable nitrogen and carbon isotopes (δ(15) N and δ(13) C) from subadults and adults allows for assessment of age-related dietary changes, including breastfeeding and weaning, and adoption of an adult diet. In one of the first studies of hunter-fisher-gatherer subadults from Eurasia, three Neolithic (8,800-5,200 calBP) mortuary sites from southwestern Siberia are analyzed to evaluate hypothesized differences in weaning age between Early versus Late Neolithic groups. An intra-individual sampling methodology is used to compare bone formed at different ages. Collagen samples (n = 143) from three different growth areas of long bones-the proximal metaphysis, diaphysis, and distal metaphysis-were obtained from 49 subadults aged birth to 10 years. In infants (birth to 3 years, n = 23) contrasting the δ(15) N values of the metaphysis, which contains newer bone, to the δ(15) N values of the diaphysis, which contains older bone, permits a more precise determination of breastfeeding-weaning status. In Early and Late Neolithic groups breast milk was the major protein source until the age of 2-3 years. However, there are differences in the age of weaning completion and duration: Early Neolithic groups weaned their infants at a later age and over a shorter amount of time. Differences may have affected infant morbidity and mortality, and female fecundity and inter-birth intervals. Stable isotope values in older subadults (4-10 years, n = 26) do not differ from adults suggesting the absence of age-based food allocation.

Activity-induced dental modification in holocene siberian hunter-fisher-gatherers.

The use of teeth as tools provides clues to past subsistence patterns and cultural practices. Five Holocene period hunter-fisher-gatherer mortuary sites from the south-western region of Lake Baikal, Siberia, Russian Federation, are observed for activity-induced dental modification (AIDM) to further characterize their adaptive regimes. Grooves on the occlusal surfaces of teeth are observed in 25 out of 123 individuals (20.3%) and were most likely produced during the processing of fibers from plants and animals, for making items such as nets and cordage. Regional variation in the frequency of individuals with occlusal grooves is found in riverine versus lakeshore sites. This variation suggests that production of material culture items differed, perhaps in relation to different fishing practices. There is also variation in the distribution of grooves by sex: grooves are found predominately in females, except at the Late Neolithic-Bronze Age river site of Ust'-Ida I where grooves are found exclusively in males. Occlusal grooves were cast using polyvinylsiloxane and maxillary canine impressions were examined by scanning electron microscopy (SEM) to determine striation patterns. Variation in striae orientation suggests that a variety of activities, and/or different manufacturing techniques, were involved in groove production. Overall, the variability in occlusal groove frequency, sex and regional distribution, and microscopic striae patterns, points to the multiplicity of activities and ways in which people used their mouths and teeth in cultural activities.

Origins and genetic legacy of prehistoric dogs.

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry.

An innovative method to visualise mastoiditis using a hand-held X-ray system.

OBJECTIVE: We explore the utility of using a hand-held X-ray system to diagnose mastoiditis in archaeological populations. MATERIALS: A sample (n = 56) of hunter-fisher-gatherers from the Early Neolithic (8,000-7,000/6,800 cal. BP) Cis-Baikal cemetery of Shamanka II (Russia) were examined. METHODS: Images were taken medio-laterally, approximately 90° to a sensor temporarily affixed to the lateral surface of the mastoid process. Digital radiographs were analysed for signs of mastoiditis occurring pre- and/or post-puberty. RESULTS: Two thirds of individuals (39/56) exhibited evidence of mastoiditis. Chronic mastoiditis and chronic sinusitis co-occurred in 61.5% (24/39) of observable individuals. CONCLUSIONS: This method was found to be an effective, convenient, and versatile non-destructive alternative to sectioning and traditional radiographic imaging. SIGNIFICANCE: This is the first project to adapt a hand-held X-ray system for imaging and diagnosis of mastoiditis and this approach encourages future analyses of this infection. LIMITATIONS: The cost of the imaging system is limiting and there are few comparative images taken in the same plane. SUGGESTIONS FOR FURTHER RESEARCH: Further research should create a larger catalogue of comparative radiographs and assess the diagnostic potential of imaging the mastoid process to rather than imaging the entire pneumatized portion of the temporal bone.

The first horse herders and the impact of early Bronze Age steppe expansions into Asia.

The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyzed 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after, but not at the time of, Yamnaya culture. We find no evidence of steppe ancestry in Bronze Age Anatolia from when Indo-European languages are attested there. Thus, in contrast to Europe, Early Bronze Age Yamnaya-related migrations had limited direct genetic impact in Asia.

Paleopathological description and diagnosis of metastatic carcinoma in an Early Bronze Age (4588+34 Cal. BP) forager from the Cis-Baikal region of Eastern Siberia.

Extensive osteolytic and osteoblastic lesions were observed on the skeletal remains of an adult male excavated from an Early Bronze Age cemetery dated to 4556+32 years BP, located in the Cis-Baikal region of Siberia (Russian Federation). Lytic lesions ranged in size from several mm to over 60 mm in diameter and had irregular, moth-eaten borders. Many of these lesions destroyed trabecular bone, though a hollowed shell of cortical bone often remained observable. Radiographic analysis revealed numerous lytic lesions within trabecular bone that had not yet affected the cortex. Blastic lesions were identified as spiculated lines, bands, or nodules of mostly immature (woven) bone formed at irregular intervals. Anatomical elements with the greatest involvement included those of the axial skeleton (skull, vertebrae, sacrum, ribs, and sternum) as well as proximal appendicular elements (ossa coxae, proximal femora, clavicles, scapulae, and proximal humeri). Osteocoalescence of destructive foci was observed on the ilium and frontal bone, with the largest lesion found on the right ilium. Differential diagnoses include metastatic carcinoma, mycotic infections, tuberculosis, Langerhan's cell histiocytosis, and multiple myeloma. Based on lesion appearance and distribution, age and sex of the individual, as well as pathogen endemism, the most likely diagnostic option for this set of lesions is metastatic carcinoma. The age and sex of this individual and appearance of the lesions may reflect carcinoma of the lung or, possibly, prostate. This represents one of the earliest cases of metastatic carcinoma worldwide and the oldest case documented thus far from Northeast Asia.