Population genomics of Bronze Age Eurasia.

The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

Which isotopes should we choose? Entropy-based feature ranking enables evaluation of the information content of stable isotopes in archaeofaunal material.

RATIONALE: Methods for multi-isotope analyses are gaining in importance in anthropological, archaeological, and ecological studies. However, when material is limited (i.e., archaeological remains), it is obligatory to decide a priori which isotopic system(s) could be omitted without losing information. METHODS: We introduce a method that enables feature ranking of isotopic systems on the basis of distance-based entropy. The feature ranking method is evaluated using Gaussian Mixture Model (GMM) clustering as well as a cluster validation index ("trace index"). RESULTS: Combinations of features resulting in high entropy values are less important than those resulting in low entropy values structuring the dataset into more distinct clusters. Therefore, this method allows us to rank isotopic systems. The isotope ranking depends on the analyzed dataset, for example, consisting of terrestrial mammals or fish. The feature ranking results were verified by cluster analysis. CONCLUSIONS: Entropy-based feature ranking can be used to a priori select the isotopic systems that should be analyzed. Consequently, we strongly suggest that this method should be applied if only limited material is available.

Multi-isotope provenancing of archaeological skeletons including cremations in a reference area of the European Alps.

RATIONALE: Due to the spatial heterogeneity of stable isotope ratios of single elements measured in attempts to georeference bioarchaeological finds, multi-isotope fingerprints are frequently employed under the assumption that similar isotopic signatures are indicative of similar shared environments by the individuals studied. The extraction of the spatial information from multi-isotope datasets, however, is challenging. METHODS: Gaussian mixture clustering of six- to seven-dimensional isotopic fingerprints measured in archaeological animal and human bones was performed. Uncremated animal bones served for an isotopic mapping of a specific reference area of eminent archaeological importance, namely the Inn-Eisack-Adige passage across the European Alps. The fingerprints consist of 87 Sr/86 Sr, 208 Pb/204 Pb, 207 Pb/204 Pb, 206 Pb/204 Pb, 208 Pb/207 Pb, and 206 Pb/207 Pb ratios, and δ18 Ophosphate values in uncremated bone apatite, while the thermally unstable δ18 O values of human cremations from this region were discarded. RESULTS: The bone finds were successfully decontaminated. Animal and human isotope clusters not only reflect individual similarities in the multi-isotopic fingerprints, but also permit a spatial allocation of the finds. This holds also for cremated finds where the δ18 Ophosphate value is no longer informative. To our knowledge, for the first time Pb stable isotopes have been systematically studied in cremated skeletal remains and proved significant in a region that was sought after for its ore deposits in prehistory. CONCLUSIONS: Gaussian mixture clustering is a promising method for the interpretation of multi-isotopic fingerprints aiming at detecting and quantifying migration and trade.

Using Gaussian Mixture Model clustering for multi-isotope analysis of archaeological fish bones for palaeobiodiversity studies.

RATIONALE: Modern methods in mass spectrometry permit fast accumulation of a huge amount of data. The analysis of multi-isotope data sets of archaeological remains is of increasing importance for the study of palaeobiodiversity. However, common bivariate isotopic data analysis fails to detect certain patterns in a multi-dimensional data set. This problem can be solved by cluster analysis. METHODS: Gaussian Mixture Model (GMM) clustering was applied to a multi-isotope data set including 184 individual mass spectrometric measurements (δ(13) Ccollagen , δ(15) Ncollagen , δ(13) Ccarbonate , and δ(18) Ocarbonate values) of archaeological fish bones (n = 46) from the Viking Haithabu and medieval Schleswig sites in northern Germany. The number of components was first restricted to the expected number of three (freshwater, brackish, and marine environment). Subsequently, classification was conducted with respect to an optimal Bayesian Information Criterion (BIC). RESULTS: Restriction of the number of components to three clusters leads to the expected clustering results according to the gross ecological niches (freshwater, brackish, marine). The isotopic data of fish bone were, however, optimally clustered into four clearly separated, reasonable groups, namely a freshwater, a brackish, and two marine groups. The two marine clusters differ in their oxygen isotope ratios, indicating different water temperature and therefore probably imported fish. Restriction of the number of clusters resulted in better training and test results. CONCLUSIONS: The GMM clustering method is applicable to complex multi-dimensional stable isotope data sets established by isotope ratio mass spectrometry (IRMS). This exemplary application resulted in an identification of habitat preferences and non-local individuals. Depending on the scientific question to be solved, restriction of the cluster size could lead to a better reproducibility; however, with loss of dissolution. Copyright © 2016 John Wiley & Sons, Ltd.

Was molar incisor hypomineralisation (MIH) present in archaeological case series?

OBJECTIVE: With respect to the unknown aetiology of molar incisor hypomineralisation (MIH), it is unclear whether this phenomenon was overlooked in the last century as a result of a high number of caries in children or if this developmental disorder was not present until then. Therefore, this study determined the presence of MIH in historical dentitions and teeth. MATERIALS AND METHODS: Dental remains from late medieval (n = 191, twelfth-sixteenth century, Regensburg, Germany), post-medieval (n = 33, sixteenth-eighteenth century, Passau, Germany) and modern age archaeological skeletal series (n = 99, nineteenth-twentieth century, Altdorf, Germany) were examined for MIH. In addition, linear enamel hypoplasia (LEH), diffuse opacities, hypoplasia and Turner's teeth were documented. RESULTS: MIH-related demarcated opacities or enamel breakdowns were found in only 15 (0.4 %) of the 3891 examined permanent teeth. Ten cases (3.1 %) from a total of 323 dentitions were classified as having MIH. In contrast, 98 individuals (30.3 %) showed LEH. Other enamel disorders were recorded in 64 individuals (19.8 %). CONCLUSION: With respect to the low number of affected dentitions and teeth, MIH most likely did not exist or was at least rarely present in the investigated archaeological case series. CLINICAL RELEVANCE: This study supports the hypothesis that MIH may be linked to contemporary living conditions or other health-related factors.

Yersinia pestis DNA from skeletal remains from the 6(th) century AD reveals insights into Justinianic Plague.

Yersinia pestis, the etiologic agent of the disease plague, has been implicated in three historical pandemics. These include the third pandemic of the 19(th) and 20(th) centuries, during which plague was spread around the world, and the second pandemic of the 14(th)-17(th) centuries, which included the infamous epidemic known as the Black Death. Previous studies have confirmed that Y. pestis caused these two more recent pandemics. However, a highly spirited debate still continues as to whether Y. pestis caused the so-called Justinianic Plague of the 6(th)-8(th) centuries AD. By analyzing ancient DNA in two independent ancient DNA laboratories, we confirmed unambiguously the presence of Y. pestis DNA in human skeletal remains from an Early Medieval cemetery. In addition, we narrowed the phylogenetic position of the responsible strain down to major branch 0 on the Y. pestis phylogeny, specifically between nodes N03 and N05. Our findings confirm that Y. pestis was responsible for the Justinianic Plague, which should end the controversy regarding the etiology of this pandemic. The first genotype of a Y. pestis strain that caused the Late Antique plague provides important information about the history of the plague bacillus and suggests that the first pandemic also originated in Asia, similar to the other two plague pandemics.

Community differentiation and kinship among Europe's first farmers.

Community differentiation is a fundamental topic of the social sciences, and its prehistoric origins in Europe are typically assumed to lie among the complex, densely populated societies that developed millennia after their Neolithic predecessors. Here we present the earliest, statistically significant evidence for such differentiation among the first farmers of Neolithic Europe. By using strontium isotopic data from more than 300 early Neolithic human skeletons, we find significantly less variance in geographic signatures among males than we find among females, and less variance among burials with ground stone adzes than burials without such adzes. From this, in context with other available evidence, we infer differential land use in early Neolithic central Europe within a patrilocal kinship system.

Intraskeletal isotopic compositions (δ(13) C, δ(15) N) of bone collagen: nonpathological and pathological variation.

Paleodiet research traditionally interprets differences in collagen isotopic compositions (δ(13) C, δ(15) N) as indicators of dietary distinction even though physiological processes likely play some role in creating variation. This research investigates the degree to which bone collagen δ(13) C and δ(15) N values normally vary within the skeleton and examines the influence of several diseases common to ancient populations on these isotopic compositions. The samples derive from two medieval German cemeteries and one Swiss reference collection and include examples of metabolic disease (rickets/osteomalacia), degenerative joint disease (osteoarthritis), trauma (fracture), infection (osteomyelitis), and inflammation (periostitis). A separate subset of visibly nonpathological skeletal elements from the German collections established normal intraindividual variation. For each disease type, tests compared bone lesion samples to those near and distant to the lesions sites. Results show that normal (nonpathological) skeletons exhibit limited intraskeletal variation in carbon- and nitrogen-isotope ratios, suggesting that sampling of distinct elements is appropriate for paleodiet studies. In contrast, individuals with osteomyelitis, healed fractures, and osteoarthritis exhibit significant intraskeletal differences in isotope values, depending on whether one is comparing lesions to near or to distant sites. Skeletons with periostitis result in significant intraskeletal differences in nitrogen isotope values only, while those with rickets/osteomalacia do not exhibit significant intraskeletal differences. Based on these results, we suggest that paleodiet researchers avoid sampling collagen at or close to lesion sites because the isotope values may be reflecting both altered metabolic processes and differences in diet relative to others in the population.

Reconstructing palaeodiet from the skeleton with stable isotopes - on the interpretation of multi-dimensional datasets.

The analysis of stable isotopes in archaeological human and animal skeletal finds is a routine method in the field of archaeometry. Multi-dimensional datasets are this way easily generated what, however, demands new interpretive approaches. Cluster analyses are capable of detecting multi-dimensional similarities among the isotopic signatures and are thus superior over traditional uni- and bivariate evaluations. This study aims to demonstrate the potential of Gaussian Mixture Model (GMM) clustering for palaeodiet reconstruction. We reevaluate previously published isotopic datasets obtained on early medieval skeletal finds from Upper Bavaria (Germany), also including some individuals from "special burials", e.g., from separated burial sites or circular enclosures. This manageable and easy-to-understand dataset contains four-dimensional isotope signatures (δ13Ccollagen, δ15N, δ13Ccarbonate, δ18Ocarbonate) of 27 individuals. We illustrate the iterative process of cluster analysis and the additional benefit of its outcome for the interpretation of the data. This includes the recognition of noisy isotope data and of those isotope systems that are essential. In our example, three isotope systems were required for a correct palaeodiet reconstruction. While δ13Ccollagen and δ15N values are commonly used for palaeodiet reconstructions, δ13Ccarbonate values, including additional information on dietary carbohydrates and fats, are required for a meaningful cluster separation and, thus, the interpretation of the individuals' diet. No general correlation between dietary quality and grave goods was detectable.

Diet and mobility in Early Medieval Bavaria: a study of carbon and nitrogen stable isotopes.

This study investigates patterns of mobility in Early Medieval Bavaria through a combined study of diet and associated burial practice. Carbon and nitrogen isotope ratios were analyzed in human bone samples from the Late Roman cemetery of Klettham and from the Early Medieval cemeteries of Altenerding and Straubing-Bajuwarenstrasse. For dietary comparison, samples of faunal bone from one Late Roman and three Early Medieval settlement sites were also analyzed. The results indicate that the average diet was in keeping with a landlocked environment and fairly limited availability of freshwater or marine resources. The diet appears not to have changed significantly from the Late Roman to the Early Medieval period. However, in the population of Altenerding, there were significant differences in the diet of men and women, supporting a hypothesis of greater mobility among women. Furthermore, the isotopic evidence from dietary outliers is supported by "foreign" grave goods and practices, such as artificial skull modification. These results reveal the potential of carbon and nitrogen isotope analysis for questions regarding migration and mobility.

Sea spray correction in δ13Ccarbonate, δ18Ocarbonate, δ18Ophosphate, and δ34Scollagen values of coastal humans - A methodological approach.

The so-called sea spray effect influences animals and humans living in coastal regions. As a consequence, δ13Ccarbonate, δ18Ocarbonate, δ18Ophosphate, and δ34Scollagen isotope values of affected individuals are more positive than otherwise expected. However, the effect is hidden in the case of humans who actually might have consumed marine food what would (partly) explain their isotopic signature. In order to correct for the sea spray effect in humans the dietary proportions were calculated based on the δ13Ccollagen and δ15Ncollagen isotope values using stable isotope mixing models. Four different programs (SISUS, simmr, IsotopeR, MixSIAR) were applied which resulted in quite different calculated diets. Each individual human can be corrected for the sea spray effect using the calculated proportion of terrestrial food (e.g. domesticated mammals, plants) and the approximated sea spray effect for each isotopic system. The differences in the calculated food proportions detected for the different mixing model programs, however, lead to differences in the correction procedure. We suggest using the dietary proportions as obtained by probabilistic SISUS rather than those of the Bayesian programs (simmr, IsotopeR, MixSIAR). The correction against the sea spray effect using the dietary proportions calculated by SISUS was supported by Gaussian Mixture Model (GMM) clustering which also enables the identification of probably non-local individuals in the dataset.

Provenance analysis of cremated skeletal remains by stable isotopes.

Cremated human remains are a rather neglected research substrate in physical anthropology; its investigation is still mainly restricted to the osteological level. The application of archaeometric methods to cremations is limited because the organic skeletal components are fully combusted at high temperatures. Stable isotope ratios of heavy elements such as strontium and lead, however, are thermally stable and permit research targeting questions of mobility, migration, and trade. In many cremations, neither dental remains nor the petrous bone are preserved. In such case, no skeletal element that retains the isotopic signature of childhood is available and compact bone has to be chosen instead. This raises interpretive problems, since due to its slow remodeling rate, compact bone integrates the element uptake over many years prior to death. This can generate a mixed isotope ratio in migrants. Such mixed ratios are no longer compatible with the place of origin, and not yet with the place of recovery. Provenance analysis with a single isotope ratio (mostly 87Sr/86Sr) therefore has its limits. A combination of strontium and lead stable isotopes in cremations generates a multi-dimensional isotopic fingerprint that is however more difficult to interpret. Data mining methods that permit a similarity search are a promising approach. In this paper, possibilities and limitations of stable isotope analysis of cremated finds are discussed together with the substrate-specific methodological and interpretive problems. The research potential is demonstrated by use of selected examples.

Modelling strontium isotopes in past biospheres - Assessment of bioavailable 87Sr/86Sr ratios in local archaeological vertebrates based on environmental signatures.

87Sr/86Sr isotopic ratios in skeletal remains of archaeological vertebrates are used for provenance analysis since long. However, the definition of the past bioavailable isotopic ratio at the site of recovery is not known beforehand and geological maps can provide no more than gross expectations. Therefore, the assessment of the "local Sr isotopic signature" is still of crucial importance. In this study, we present a tool for the prediction of such local isotopic signatures by creating a concentration weighted mixing model that links lithospheric, biospheric, and atmospheric strontium per site. The major strontium sources and their input into an animal's body were assessed by choosing elemental strontium and its isotopic signature in groundwater, soil, vegetation, and precipitation as components for the mixing model, augmented by literature values. The model was applied to 24 sites located in the alpine transect of the Inn-Eisack-Adige-Brenner passage across the European Alps, a passage used since the Mesolithic. Predicted local bioavailable 87Sr/86Sr ratios were compared with measured values from locally excavated archaeozoological bone samples from three taxa of large and mainly residential vertebrates (cattle, pig, red deer) to verify the models' accuracy. With regard to the fact that the environmental samples predict the past local bioavailable 87Sr/86Sr at a specific site while the vertebrates had different and species-specific home ranges, thereby integrating strontium from a region of primarily unknown size, the model is capable of assigning reasonable expectation values. For 11 sites, up to 100% of the vertebrate isotopic signatures were correctly predicted. Mismatches at the remaining sites are explainable by special environmental factors, and also the fact that some import of animals can never be excluded beforehand. Suggestions for site-specific adjustments of the model are made.

Bioarchaeology of Bronze and Iron Age skeletal finds from a microregion in Central Mongolia.

This paper gives a state of the art report of an ongoing interdisciplinary project on bioarchaeological research on cemeteries in the Upper Orkhon valley, Central Mongolia, in particular at the Maikhan Tolgoi site. The archaeological focus is on the investigation of the development, use and transformation of a ritual landscape in the course of the Bronze and Iron Age. The contribution of physical anthropology is an osteological and archaeometric analysis of the human inhumations with regard to life-style and subsistence economy. A specific topic relates to the emergence of the first mounted nomads in the region. Macro- and microscopical inspection of the skeletons excavated to date reveal that males, females and children had been buried at this exceptional cemetery, and that many of the adults died at a conspicuously advanced age. Palaeodiet was reconstructed by stable carbon and nitrogen isotopes in bone collagen, followed by an isotopic sourcing. We show that freshwater fish was consumed on a regular basis, and that the demands of protein and carbohydrate were largely covered by secondary animal products. First analysis of stable strontium and oxygen isotopes in bone apatite suggests a considerable catchment area of the burial site.

Evidence for sea spray effect on oxygen stable isotopes in bone phosphate - Approximation and correction using Gaussian Mixture Model clustering.

Palaeobiodiversity research based on stable isotope analysis in coastal environments can be severely hampered by the so-called "sea spray" effect. This effect shifts the isotopic signal of terrestrial individuals towards too marine values. It is commonly agreed upon that sea spray influences sulphur stable isotopes. However, we were able to approximate a remarkable sea spray effect also in carbon and oxygen stable isotopes of bone carbonate previously. In the present study we could approximate a minimum sea spray effect of about 13.9% even present in oxygen isotope values of bone phosphate, which was validated by Gaussian Mixture Model (GMM) clustering. This approximated value is by some magnitudes smaller than the minimum sea spray effect approximated for both δ13Ccarb and δ18Ocarb, and quite close to the sea spray detected for δ34Scoll in a previous study. It may therefore be interpreted as purer minimum sea spray signal compared to the approximation in bone carbonate. Furthermore, detection of sea spray in δ18Ophos can serve as additional validation of the effect present in bone carbonate, which is more prone to diagenetic alteration compared to bone phosphate. Moreover, the presence of the sea spray effect in both δ18Ocarb and δ18Ophos demonstrates that sea spray can be taken up by terrestrial mammals not only via food (δ18Ocarb) but also via drinking water (δ18Ophos). Finally, this study once more confirmed that calculation of δ18Ophos from δ18Ocarb values using a fixed oxygen isotope spacing (Δδ18O) can be highly misleading, especially in coastal environments affected by sea spray.

Basics in paleodemography: a comparison of age indicators applied to the early medieval skeletal sample of Lauchheim.

Recent advances in the methods of skeletal age estimation have rekindled interest in their applicability to paleodemography. The current study contributes to the discussion by applying several long established as well as recently developed or refined aging methods to a subsample of 121 adult skeletons from the early medieval cemetery of Lauchheim. The skeletal remains were analyzed by 13 independent observers using a variety of aging techniques (complex method and other multimethod approaches, Transition Analysis, cranial suture closure, auricular surface method, osteon density method, tooth root translucency measurement, and tooth cementum annulation counting). The age ranges and mean age estimations were compared and results indicate that all methods showed smaller age ranges for the younger individuals, but broader age ranges for the older age groups.

Genotyping Yersinia pestis in Historical Plague: Evidence for Long-Term Persistence of Y. pestis in Europe from the 14th to the 17th Century.

Ancient DNA (aDNA) recovered from plague victims of the second plague pandemic (14th to 17th century), excavated from two different burial sites in Germany, and spanning a time period of more than 300 years, was characterized using single nucleotide polymorphism (SNP) analysis. Of 30 tested skeletons 8 were positive for Yersinia pestis-specific nucleic acid, as determined by qPCR targeting the pla gene. In one individual (MP-19-II), the pla copy number in DNA extracted from tooth pulp was as high as 700 gene copies/µl, indicating severe generalized infection. All positive individuals were identical in all 16 SNP positions, separating phylogenetic branches within nodes N07_N10 (14 SNPs), N07_N08 (SNP s19) and N06_N07 (s545), and were highly similar to previously investigated plague victims from other European countries. Thus, beside the assumed continuous reintroduction of Y. pestis from central Asia in multiple waves during the second pandemic, long-term persistence of Y. pestis in Europe in a yet unknown reservoir host has also to be considered.

Application of isotopic mixing models for palaeodietary and paleoecological studies.

The application of mixing models for the sourcing of dietary end members, which mix into consumer collagen delta13C and delta15N isotopic ratios, has clear benefits for understanding human palaeodiet and human and vertebrate palaeoecology. This is because traditional visual or conventional statistical interpretations of bivariate plots may be erroneous or misleading. In terms of their biological meaning, measured isotopic ratios are proxies, therefore, an in-depth reflection on their intended purpose is requisite prior to analysis. A detailed reconstruction of individual palaeodiet is impossible, but an assessment of changes in the importance of gross dietary end members should provide valuable clues to ancient subsistence economies. Mixing models require the establishment of isotopic data for a considerable amount of bioarchaeological finds associated with human skeletons. However, when discussed within the archaeological context, they provide feasible and plausible solutions. Moreover, mixing models offer the opportunity to hypothesize "missing end members", the traces of which do not show up in the archaeological record at all.

Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis.

BACKGROUND: Yersinia pestis has caused at least three human plague pandemics. The second (Black Death, 14-17th centuries) and third (19-20th centuries) have been genetically characterised, but there is only a limited understanding of the first pandemic, the Plague of Justinian (6-8th centuries). To address this gap, we sequenced and analysed draft genomes of Y pestis obtained from two individuals who died in the first pandemic. METHODS: Teeth were removed from two individuals (known as A120 and A76) from the early medieval Aschheim-Bajuwarenring cemetery (Aschheim, Bavaria, Germany). We isolated DNA from the teeth using a modified phenol-chloroform method. We screened DNA extracts for the presence of the Y pestis-specific pla gene on the pPCP1 plasmid using primers and standards from an established assay, enriched the DNA, and then sequenced it. We reconstructed draft genomes of the infectious Y pestis strains, compared them with a database of genomes from 131 Y pestis strains from the second and third pandemics, and constructed a maximum likelihood phylogenetic tree. FINDINGS: Radiocarbon dating of both individuals (A120 to 533 AD [plus or minus 98 years]; A76 to 504 AD [plus or minus 61 years]) places them in the timeframe of the first pandemic. Our phylogeny contains a novel branch (100% bootstrap at all relevant nodes) leading to the two Justinian samples. This branch has no known contemporary representatives, and thus is either extinct or unsampled in wild rodent reservoirs. The Justinian branch is interleaved between two extant groups, 0.ANT1 and 0.ANT2, and is distant from strains associated with the second and third pandemics. INTERPRETATION: We conclude that the Y pestis lineages that caused the Plague of Justinian and the Black Death 800 years later were independent emergences from rodents into human beings. These results show that rodent species worldwide represent important reservoirs for the repeated emergence of diverse lineages of Y pestis into human populations. FUNDING: McMaster University, Northern Arizona University, Social Sciences and Humanities Research Council of Canada, Canada Research Chairs Program, US Department of Homeland Security, US National Institutes of Health, Australian National Health and Medical Research Council.