Genetic history of Cambridgeshire before and after the Black Death.

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

Were there royal herds? Understanding herd management and mobility using isotopic characterizations of cattle tooth enamel from Early Dynastic Ur.

During the third millennium BC, Mesopotamia (the land between the Tigris and Euphrates Rivers, in modern Iraq-Syria), was dominated by the world's earliest cities and states, which were ruled by powerful elites. Ur, in present-day southern Iraq, was one of the largest and most important of these cities, and irrigation-based agriculture and large herds of domesticated animals were the twin mainstays of the economy and diet. Texts suggest that the societies of the Mesopotamian city-states were extremely hierarchical and underpinned by institutionalised and heavily-managed farming systems. Prevailing narratives suggest that the animal management strategies within these farming systems in the third millennium BC were homogenous. There have been few systematic science-based studies of human and animal diets, mobility, or other forms of human-animal interaction in Mesopotamia, but such approaches can inform understanding of past economies, including animal management, social hierarchies, diet and migration. Oxygen, carbon and strontium isotopic analysis of animal tooth enamel from both royal and private/non-royal burial contexts at Early Dynastic Ur (2900-2350 BC) indicate that a variety of herd management strategies and habitats were exploited. These data also suggest that there is no correlation between animal-management practices and the cattle found in royal or private/non-royal burial contexts. The results demonstrate considerable divergence between agro-pastoral models promoted by the state and the realities of day-to-day management practices. The data from Ur suggest that the animals exploited different plant and water sources, and that animals reared in similar ways ended up in different depositional contexts.

Isotope data from amino acids indicate Darwin's ground sloth was not an herbivore.

Fossil sloths are regarded as obligate herbivores for reasons including peculiarities of their craniodental morphology and that all living sloths feed exclusively on plants. We challenge this view based on isotopic analyses of nitrogen of specific amino acids, which show that Darwin's ground sloth Mylodon darwinii was an opportunistic omnivore. This direct evidence of omnivory in an ancient sloth requires reevaluation of the ecological structure of South American Cenozoic mammalian communities, as sloths represented a major component of these ecosystems across the past 34 Myr. Furthermore, by analyzing modern mammals with known diets, we provide a basis for reliable interpretation of nitrogen isotopes of amino acids of fossils. We argue that a widely used equation to determine trophic position is unnecessary, and that the relative isotopic values of the amino acids glutamate and phenylalanine alone permit reliable reconstructions of trophic positions of extant and extinct mammals.

Lipid residues in pottery from the Indus Civilisation in northwest India.

This paper presents novel insights into the archaeology of food in ancient South Asia by using lipid residue analysis to investigate what kinds of foodstuffs were used in ceramic vessels by populations of the Indus Civilisation in northwest India. It examines how vessels were used in urban and rural Indus settlements during the Mature Harappan period (c.2600/2500-1900 BC), the relationship between vessels and the products within them, and identifies whether changes in vessel use occurred from the Mature Harappan to Late Harappan periods, particularly during climatic instability after 4.2 ka BP (c.2100 BC). Despite low lipid concentrations, which highlight challenges with conducting residue analysis in arid, seasonally-wet and alkaline environments, 71% of the vessels yielded appreciable quantities of lipid. Lipid profiles revealed the use of animal fats in vessels, and contradictory to faunal evidence, a dominance of non-ruminant fats, with limited evidence of dairy processing. The absence of local modern reference fats makes this dataset challenging to interpret, and it is possible that plant products or mixtures of plant and animal products have led to ambiguous fatty acid-specific isotopic values. At the same time, it appears that urban and rural populations processed similar types of products in vessels, with limited evidence for change in vessel use from the urban to the post-urban period. This study is a systematic investigation into pot lipid residues from multiple sites, demonstrating the potential of the method for examining ancient Indus foodways and the need for the development of further research in ancient organic residues in South Asia.

Carbon and nitrogen isotopic variability in foxtail millet (Setaria italica) with watering regime.

RATIONALE: Carbonised plant remains are analysed for reconstruction of past climates and agricultural regimes. Several recent studies have used C4 plants to address related questions, and correlations between modern C4 plant δ13 C values and rainfall have been found. The millets were important food crops in prehistoric Eurasia, yet little is known about causes of isotopic variation within millet species. Previous research has shown there to be significant isotopic variation between millet accessions. Here we compare isotope ratios from plants grown under different watering regimes. This allows for a consideration of whether or not Setaria italica is a good proxy for environmental reconstruction. METHODS: We compare stable isotope ratios of Setaria italica plants grown in a controlled environment chamber with different watering regimes. We compare the carbon isotope ratios of leaves and grains, and the nitrogen isotope ratios of grains, from 12 accessions of Setaria italica. RESULTS: We find significant isotopic variability between watering regimes. Carbon isotope ratios are positively correlated with water availability, and on average vary by 1.9‰ and 1.7‰ for leaves and grains, respectively. Grain nitrogen isotope ratios also vary with watering regime; however, the highest isotope ratios are found with the 130-mL watering regime. CONCLUSIONS: The carbon isotope ratios of Setaria italica are strongly correlated with water availability. However, the correlation is the opposite to that seen in studies of C3 plants. The difference in isotopic ratio due to watering regime is comparable with that seen between different accessions; thus distinguishing between changing varieties of Setaria italica and changing climate is problematic. In terms of grain nitrogen isotope ratios, the highest δ15 N values were not associated with the lowest watering regime. Again, δ15 N variation is comparable with that which would be expected from an aridity effect or a manuring effect, and thus distinguishing between these factors is probably problematic.

Carbon and nitrogen isotopic signatures of hair, nail, and breath from tropical African human populations.

RATIONALE: Stable isotopic analyses are increasingly used to study the diets of past and present human populations. Yet, the carbon and nitrogen isotopic data of modern human diets collected so far are biased towards Europe and North America. Here, we address this gap by reporting on the dietary isotopic signatures of six tropical African communities: El Molo, Turkana (Kerio), Luhya (Webuye), Luhya (Port Victoria), and Luo (Port Victoria) from Kenya, and Baka from Cameroon; representing four subsistence strategies: fishing, pastoralism, agriculturalism, and hunter-gatherer. METHODS: We used an elemental analyser coupled in continuous-flow mode to an isotope ratio mass spectrometer to measure the carbon and nitrogen isotopic ratios of hair (n = 134) and nail (n = 80) and the carbon isotopic ratios of breath (n = 184) from these communities, as well as the carbon and nitrogen isotopic ratios of some food samples from the Kenyan communities. RESULTS: We expand on the known range of δ13 C values in human hair through the hunter-gatherer Baka, with a diet based on C3 plants, and through the agriculturalist Luhya (Webuye), with a diet based on C4 plants. In addition, we found that the consumption of fish from East African lakes is difficult to detect isotopically due to the combined effects of high nitrogen isotopic ratios of plants and the low nitrogen isotopic ratios of fish. Finally, we found that some of the communities studied are markedly changing their diets through increasing sedentism and urbanisation. CONCLUSIONS: Our findings contribute substantially to the understanding of the environmental, demographic, and economic dynamics that affect the dietary landscape of different tropical populations of Africa. These results highlight the importance of studying a broader sample of human populations and their diet, with a focus on their precise context - from both isotopic and more general anthropological perspectives.

East Anglian early Neolithic monument burial linked to contemporary Megaliths.

In the fourth millennium BCE a cultural phenomenon of monumental burial structures spread along the Atlantic façade. Megalithic burials have been targeted for aDNA analyses, but a gap remains in East Anglia, where Neolithic structures were generally earthen or timber. An early Neolithic (3762-3648 cal. BCE) burial monument at the site of Trumpington Meadows, Cambridgeshire, UK, contained the partially articulated remains of at least three individuals. To determine whether this monument fits a pattern present in megalithic burials regarding sex bias, kinship, diet and relationship to modern populations, teeth and ribs were analysed for DNA and carbon and nitrogen isotopic values, respectively. Whole ancient genomes were sequenced from two individuals to a mean genomic coverage of 1.6 and 1.2X and genotypes imputed. Results show that they were brothers from a small population genetically and isotopically similar to previously published British Neolithic individuals, with a level of genome-wide homozygosity consistent with a small island population sourced from continental Europe, but bearing no signs of recent inbreeding. The first Neolithic whole genomes from a monumental burial in East Anglia confirm that this region was connected with the larger pattern of Neolithic megaliths in the British Isles and the Atlantic façade.

Osteobiography: The History of the Body as Real Bottom-Line History.

What is osteobiography good for? The last generation of archaeologists fought to overcome the traditional assumption that archaeology is merely ancillary to history, a substitute to be used when written sources are defective; it is now widely acknowledged that material histories and textual histories tell equally valid and complementary stories about the past. Yet the traditional assumption hangs on implicitly in biography: osteobiography is used to fill the gaps in the textual record rather than as a primary source in its own right. In this article we compare the textual biographies and material biographies of two thirteenth-century townsfolk from medieval England-Robert Curteis, attested in legal records, and "Feature 958," excavated archaeologically and studied osteobiographically. As the former shows, textual biographies of ordinary people mostly reveal a few traces of financial or legal transactions. Interpreting these traces, in fact, implicitly presumes a history of the body. Osteobiography reveals a different kind of history, the history of the body as a locus of appearance and social identity, work, health and experience. For all but a few textually rich individuals, osteobiography provides a fuller and more human biography. Moreover, textual visibility is deeply biased by class and gender; osteobiography offers particular promise for Marxist and feminist understandings of the past.

Ancient human parallel lineages within North America contributed to a coastal expansion.

Little is known regarding the first people to enter the Americas and their genetic legacy. Genomic analysis of the oldest human remains from the Americas showed a direct relationship between a Clovis-related ancestral population and all modern Central and South Americans as well as a deep split separating them from North Americans in Canada. We present 91 ancient human genomes from California and Southwestern Ontario and demonstrate the existence of two distinct ancestries in North America, which possibly split south of the ice sheets. A contribution from both of these ancestral populations is found in all modern Central and South Americans. The proportions of these two ancestries in ancient and modern populations are consistent with a coastal dispersal and multiple admixture events.

Investigation of a Medieval Pilgrim Burial Excavated from the Leprosarium of St Mary Magdalen Winchester, UK.

We have examined the remains of a Pilgrim burial from St Mary Magdalen, Winchester. The individual was a young adult male, aged around 18-25 years at the time of death. Radiocarbon dating showed the remains dated to the late 11th-early 12th centuries, a time when pilgrimages were at their height in Europe. Several lines of evidence in connection with the burial suggested this was an individual of some means and prestige. Although buried within the leprosarium cemetery, the skeleton showed only minimal skeletal evidence for leprosy, which was confined to the bones of the feet and legs. Nonetheless, molecular testing of several skeletal elements, including uninvolved bones all showed robust evidence of DNA from Mycobacterium leprae, consistent with the lepromatous or multibacillary form of the disease. We infer that in life, this individual almost certainly suffered with multiple soft tissue lesions. Genotyping of the M.leprae strain showed this belonged to the 2F lineage, today associated with cases from South-Central and Western Asia. During osteological examination it was noted that the cranium and facial features displayed atypical morphology for northern European populations. Subsequently, geochemical isotopic analyses carried out on tooth enamel indicated that this individual was indeed not local to the Winchester region, although it was not possible to be more specific about their geographic origin.

Fecal carbon and nitrogen isotopic analysis as an indicator of diet in Kanyawara chimpanzees, Kibale National Park, Uganda.

OBJECTIVES: The shorter-term overview from feces provides scope to investigate dietary fluctuations. We assess the correlation of stable isotopic fecal values with recorded seasonal diet of 10 adult chimpanzees (P. t. schweinfurthii) of the Kanyawara community (Kibale National Park, Uganda) and whether fecal nitrogen levels (%N) indicate a change in crude protein intake. MATERIALS AND METHODS: We recorded food eaten by each ape and collected both concurrent fecal samples (N = 115) and plant foods eaten by this community (N = 64). We compared fecal δ13 C and δ15 N values (also %N) with: (a) plant values; (b) feeding data; and (c) food-items found macroscopically in the fecal samples. Interspecies and intraspecies differences in plant and fecal isotope values (and %N) as well as seasonality in diet were determined using parametric and nonparametric tests. RESULTS: No difference in plant δ13 C and δ15 N values was found at intraspecies or interspecies level. Fecal isotope values reflected a diet of C3 plants from evergreen forest vegetation. Seasonal differences in δ13 C and δ15 N corresponded with aspects of feeding and fecal macroscopic data, but only at community level. A change in crude protein intake was not indicated from %N content. DISCUSSION: This study further validates the use of staple isotope analyses of primate feces to provide a dietary overview, revealing seasonal differences at community level; however, conclusive results may be limited for individuals when using short sampling periods. Further study of variables that influence fecal %N content is also suggested to interpret crude protein intake.

Red deer bone and antler collagen are not isotopically equivalent in carbon and nitrogen.

RATIONALE: Bone and antler collagen δ(13) C and δ(15) N values are often assumed to be equivalent when measured in palaeodietary, palaeoclimate and palaeocological studies. Although compositionally similar, bone grows slowly and is remodelled whereas antler growth is rapid and remodelling does not occur. These different patterns of growth could result in isotopic difference within antler and between the two tissue types. Here we test whether red deer (Cervus elaphus) bone and antler δ(13) C and δ(15) N values are equivalent, and whether intra-antler isotopic values are uniform. METHODS: Bone and antler were isotopically analysed from six stags that lived in a temperate maritime climate on the Isle of Rum, Scotland. Multiple antlers from different years were sampled per individual, together with a single bone sample per individual. Up to 12 samples were taken along the length of each antler (total of 25 antlers, 259 samples) so that a chronological record of the isotopic composition during antler growth could be obtained. Collagen was extracted and its δ(13) C and δ(15) N values were measured by continuous-flow isotope ratio mass spectrometry. RESULTS: Intra-antler collagen isotope signatures vary, and show that not all antlers from an individual or a growth year are equivalent in carbon and nitrogen isotopic ratios. δ(15) N values typically increase with distance along antler length, but no overall trend is observed in δ(13) C values. An isotopic offset is visible between bone and antler, with bone δ(13) C and δ(15) N values being higher in most cases. CONCLUSIONS: Bone and antler collagen δ(13) C and δ(15) N values are not isotopically equivalent and are therefore not directly comparable in palaeodietary, palaeoclimate and palaeocological studies. Bone and antler collagen isotopic differences probably relate to differential metabolic processes during the formation of the two tissues. Intra- and inter-antler isotopic variations probably reflect the isotopic composition of an individual's diet rather than physiological parameters, and may have the potential to provide high-resolution individual-specific information in modern and ancient cervid populations. Copyright © 2016 John Wiley & Sons, Ltd.

Intraspecific carbon and nitrogen isotopic variability in foxtail millet (Setaria italica).

RATIONALE: Isotopic palaeodietary studies generally focus on bone collagen from human and/or animal remains. While plant remains are rarely analysed, it is known that plant isotope values can vary as a result of numerous factors, including soil conditions, the environment and type of plant. The millets were important food crops in prehistoric Eurasia, yet little is known about the isotopic differences within millet species. METHODS: Here we compare the stable isotope ratios within and between Setaria italica plants grown in a controlled environment chamber. Using homogenised samples, we compare carbon isotope ratios of leaves and grains, and nitrogen isotope ratios of grains, from 29 accessions of Setaria italica. RESULTS: We find significant isotopic variability within single leaves and panicles, and between leaves and panicles within the same plant, which must be considered when undertaking plant isotope studies. We find that the leaves and grains from the different accessions have a ca 2‰ range in δ(13) C values, while the nitrogen isotope values in the grains have a ca 6‰ range. We also find an average offset of 0.9‰ between leaves and grains in their δ(13) C values. CONCLUSIONS: The variation found is large enough to have archaeological implications and within- and between-plant isotope variability should be considered in isotope studies. The range in δ(15) N values is particularly significant as it is larger than the typical values quoted for a trophic level enrichment, and as such may lead to erroneous interpretations of the amount of animal protein in human or animal diets. It is therefore necessary to account for the variability in plant stable isotope values during palaeodietary reconstructions. Copyright © 2016 John Wiley & Sons, Ltd.

Late Pleistocene/Early Holocene Migratory Behavior of Ungulates Using Isotopic Analysis of Tooth Enamel and Its Effects on Forager Mobility.

Zooarchaeological and paleoecological investigations have traditionally been unable to reconstruct the ethology of herd animals, which likely had a significant influence on the mobility and subsistence strategies of prehistoric humans. In this paper, we reconstruct the migratory behavior of red deer (Cervus elaphus) and caprids at the Pleistocene-Holocene transition in the northeastern Adriatic region using stable oxygen isotope analysis of tooth enamel. The data show a significant change in δ18O values from the Pleistocene into the Holocene, as well as isotopic variation between taxa, the case study sites, and through time. We then discuss the implications of seasonal faunal availability as determining factors in human mobility patterns.

On the Use of Biomineral Oxygen Isotope Data to Identify Human Migrants in the Archaeological Record: Intra-Sample Variation, Statistical Methods and Geographical Considerations.

Oxygen isotope analysis of archaeological skeletal remains is an increasingly popular tool to study past human migrations. It is based on the assumption that human body chemistry preserves the δ18O of precipitation in such a way as to be a useful technique for identifying migrants and, potentially, their homelands. In this study, the first such global survey, we draw on published human tooth enamel and bone bioapatite data to explore the validity of using oxygen isotope analyses to identify migrants in the archaeological record. We use human δ18O results to show that there are large variations in human oxygen isotope values within a population sample. This may relate to physiological factors influencing the preservation of the primary isotope signal, or due to human activities (such as brewing, boiling, stewing, differential access to water sources and so on) causing variation in ingested water and food isotope values. We compare the number of outliers identified using various statistical methods. We determine that the most appropriate method for identifying migrants is dependent on the data but is likely to be the IQR or median absolute deviation from the median under most archaeological circumstances. Finally, through a spatial assessment of the dataset, we show that the degree of overlap in human isotope values from different locations across Europe is such that identifying individuals' homelands on the basis of oxygen isotope analysis alone is not possible for the regions analysed to date. Oxygen isotope analysis is a valid method for identifying first-generation migrants from an archaeological site when used appropriately, however it is difficult to identify migrants using statistical methods for a sample size of less than c. 25 individuals. In the absence of local previous analyses, each sample should be treated as an individual dataset and statistical techniques can be used to identify migrants, but in most cases pinpointing a specific homeland should not be attempted.

The globalization of naval provisioning: ancient DNA and stable isotope analyses of stored cod from the wreck of the Mary Rose, AD 1545.

A comparison of ancient DNA (single-nucleotide polymorphisms) and carbon and nitrogen stable isotope evidence suggests that stored cod provisions recovered from the wreck of the Tudor warship Mary Rose, which sank in the Solent, southern England, in 1545, had been caught in northern and transatlantic waters such as the northern North Sea and the fishing grounds of Iceland and Newfoundland. This discovery, underpinned by control data from archaeological samples of cod bones from potential source regions, illuminates the role of naval provisioning in the early development of extensive sea fisheries, with their long-term economic and ecological impacts.