Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague.

The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague's formative years in terms of its early evolution and ecology.

Reconstructing the historical expansion of industrial swine production from Landsat imagery.

In the USA, historical data on the period over which industrial swine farms have operated are usually only available at the county scale and released every 5 years via the USDA Census of Agriculture, leaving the history of the swine industry and its potential legacy effects on the environment poorly understood. We developed a changepoint-based workflow that recreates the construction timelines of swine farms, specifically by identifying the construction years of swine manure lagoons from historical Landsat 5 imagery for the period of 1984 to 2012. The study focused on the Coastal Plain of North Carolina, a major pork-producing state in the USA. The algorithm successfully predicted the year of swine waste lagoon construction (+ /- 1 year) with an accuracy of approximately 94% when applied to the study area. By estimating the year of construction of 3405 swine waste lagoons in NC, we increased the resolution of available information on the expansion of swine production from the county scale to spatially-explicit locations. We further analyzed how the locations of swine waste lagoons changed in proximity to water resources over time, and found a significant increase in swine waste lagoon distances to the nearest water feature across the period of record.

Pastoral subsistence and mounted fighting in the Eastern Tianshan Mountain region: New insights from the Shirenzigou worked bone assemblage.

Situated at a geographic crossroads, the eastern Tianshan Mountain region in northwest China is crucial to understanding various economic, social, and cultural developments on the Eurasian Steppes. One promising way to gain a better knowledge of ancient subsistence economy, craft production, and social change in the eastern Tianshan Mountain region is to study the artifact assemblages from archaeological contexts. Here, we present an analysis of 488 worked animal bones from the large site of Shirenzigou (ca. 1300-1 BCE), to date the largest assemblage of this kind uncovered in the eastern Tianshan Mountain region. We classified these worked bones into six categories, including "ritual objects", "ornaments", "tools", "worked astragali", "warfare and mobility", and "indeterminate". The identification of animal species and skeletal elements indicates that worked bones from Shirenzigou are characterized by a predominance of caprine products, particularly worked astragali, which is consistent with the large proportion of caprine fragments found in animal remains associated with food consumption. This demonstrates the contribution of caprine pastoralism to bone working activities at Shirenzigou. The making of most worked bones does not appear to have required advanced or specialized skills. Considering the absence of dedicated bone working space, alongside the variability in raw material selection and in dimensions of certain types of artifacts, we infer that worked bone production at Shirenzigou was not standardized. In terms of raw material selection and mode of production, Shirenzigou differed from their settled, farming counterparts in the Yellow River valley of northern China. In addition, along with the evidence for violence and horseback riding, the increasing use of bone artifacts associated with warfare and mobility during the late occupation phase of Shirenzigou reflects growing social instability and implies the likely emergence of single mounted horsemen, equipped with light armors, in the region during the late first millennium BCE. Our results provide new insights into animal resource exploitation and changing lifeways of early pastoral societies in the eastern Tianshan Mountain region, expanding our knowledge of the economic, social, and political milieu of late Bronze Age and early Iron Age eastern Eurasia.

Cattle management in an Iron Age/Roman settlement in the Netherlands: Archaeozoological and stable isotope analysis.

Cattle were the predominant domestic animal in the Iron Age and Roman Netherlands, yet their management is still incompletely understood. Some aspects of cattle management, such as birth season and the provision of fodder, have received little or no attention so far. This paper is the first to investigate these aspects for the Iron Age and Roman Netherlands, through a case study of the site of Houten-Castellum. The rural settlement of Houten-Castellum was inhabited from the Middle Iron Age to the Middle Roman period, allowing a comparison between the Iron Age and Roman period. Excavations at this site have yielded a large, well-preserved animal bone assemblage. This paper investigates cattle husbandry by using an integrated approach, combining a multi-isotope analysis (oxygen, carbon and strontium) with archaeozoological and archaeobotanical results from Houten-Castellum and comparing the results with archaeobotanical evidence for fodder and evidence for dairy use for the Iron Age and Roman Netherlands in general. While our data set is small and results must therefore be interpreted cautiously, there is convincing evidence for an extended birth season in the Middle Iron Age, as well as the use of fodder.

Stable isotopes reveal intensive pig husbandry practices in the middle Yellow River region by the Yangshao period (7000-5000 BP).

It is well-known that pigs (Sus scrofa) were domesticated very early in Neolithic China, but far less is known about the processes by which pig husbandry intensified so that pork became the most important animal protein for humans are less clear. Here, we explore pig feeding practices using the carbon and nitrogen isotope composition of bone collagen, focusing on developments in pig husbandry during the Yangshao period (7000-5000 BP) in the middle Yellow River region of China, and at the site of Xipo (5800-5000 BP) in particular. The results show that the diets of domestic pigs at Xipo were dominated by millet foods. Comparisons with other Yangshao sites in the region show a trend of increasing millet foddering for pigs throughout the Yangshao period. These results, and comparisons of the isotopic data for pigs against those for humans from the Xipo cemetery (5300-5000 BP), suggest that pigs were closely managed by humans. The evidence points to an intensification of Neolithic pig husbandry in the middle Yellow River region from this period.

Bones geometric morphometrics illustrate 10th millennium cal. BP domestication of autochthonous Cypriot wild boar (Sus scrofa circeus nov. ssp).

Epipaleolithic hunter-gatherers from the Near East introduced wild boars (Sus scrofa) to Cyprus, with the Early Pre-Pottery Neolithic (PPN) settlers hunting the wild descendants of these boars. However, the geographic origin of the Cypriot boar and how they were integrated into the earliest forms of pig husbandry remain unsolved. Here, we present data on 11,000 to 9000 cal. BP Sus scrofa from the PPN sites of Klimonas and Shillourokambos. We compared them to contemporaneous populations from the Near East and to Neolithic and modern populations in Corsica, exploring their origin and evolution using biosystematic signals from molar teeth and heel bones (calcanei), using 2D and 3D geometric morphometrics. We found that the Cypriot PPN lineage of Sus scrofa originates from the Northern Levant. Yet, their phenotypic idiosyncrasy suggest that they evolved into an insular sub-species that we named Sus scrofa circeus, referring to Circe, the metamorphosis goddess that changed Ulysses companions into pigs. The phenotypic homogeneity among PPNA Klimonas wild boars and managed populations of PPNB Shillourokambos suggests that local domestication has been undertaken on the endemic S. s. circeus, strengthening the idea that Cyprus was integrated into the core region of animal domestication.

Seasonal calving in European Prehistoric cattle and its impacts on milk availability and cheese-making.

Present-day domestic cattle are reproductively active throughout the year, which is a major asset for dairy production. Large wild ungulates, in contrast, are seasonal breeders, as were the last historic representatives of the aurochs, the wild ancestors of cattle. Aseasonal reproduction in cattle is a consequence of domestication and herding, but exactly when this capacity developed in domestic cattle is still unknown and the extent to which early farming communities controlled the seasonality of reproduction is debated. Seasonal or aseasonal calving would have shaped the socio-economic practices of ancient farming societies differently, structuring the agropastoral calendar and determining milk availability where dairying is attested. In this study, we reconstruct the calving pattern through the analysis of stable oxygen isotope ratios of cattle tooth enamel from 18 sites across Europe, dating from the 6th mill. cal BC (Early Neolithic) in the Balkans to the 4th mill. cal BC (Middle Neolithic) in Western Europe. Seasonal calving prevailed in Europe between the 6th and 4th millennia cal BC. These results suggest that cattle agropastoral systems in Neolithic Europe were strongly constrained by environmental factors, in particular forage resources. The ensuing fluctuations in milk availability would account for cheese-making, transforming a seasonal milk supply into a storable product.

Evidence for early dispersal of domestic sheep into Central Asia.

The development and dispersal of agropastoralism transformed the cultural and ecological landscapes of the Old World, but little is known about when or how this process first impacted Central Asia. Here, we present archaeological and biomolecular evidence from Obishir V in southern Kyrgyzstan, establishing the presence of domesticated sheep by ca. 6,000 BCE. Zooarchaeological and collagen peptide mass fingerprinting show exploitation of Ovis and Capra, while cementum analysis of intact teeth implicates possible pastoral slaughter during the fall season. Most significantly, ancient DNA reveals these directly dated specimens as the domestic O. aries, within the genetic diversity of domesticated sheep lineages. Together, these results provide the earliest evidence for the use of livestock in the mountains of the Ferghana Valley, predating previous evidence by 3,000 years and suggesting that domestic animal economies reached the mountains of interior Central Asia far earlier than previously recognized.

Investigating Neolithic caprine husbandry in the Central Pyrenees: Insights from a multi-proxy study at Els Trocs cave (Bisaurri, Spain).

Sheep remains constitute the main archaeozoological evidence for the presence of Early Neolithic human groups in the highlands of the Southern Pyrenees but understanding the role of herding activities in the Neolithisation process of this mountain ecosystem calls for the analysis of large and well-dated faunal assemblages. Cova de Els Trocs (Bisaurri, Huesca, Spain), a cave located at 1564 m a.s.l on the southern slopes of the Central Pyrenees, is an excellent case study since it was seasonally occupied throughout the Neolithic (ca. 5312-2913 cal. BC) and more than 4000 caprine remains were recovered inside. The multi-proxy analytical approach here presented has allowed us to offer new data elaborating on vertical mobility practices and herd management dynamics as has not been attempted up until now within Neolithic high-mountain sites in the Iberian Peninsula. For the first time, δ18O and δ13C stable isotope analyses offer direct evidence on both the regular practice of altitudinal movements of sheep flocks and the extended breeding season of sheep. Autumn births are recorded from the second half of the fifth millennium cal. BC onwards. Age-at-death distributions illustrate the progressive decline in caprine perinatal mortality together with the rising survival rate of individuals older than six months of age and the larger frequency of adults. This trend alongside the 'off-season' lambing signal at the implementation of husbandry techniques over time, probably aiming to increase the size of the flocks and their productivity. Palaeoparasitological analyses of sediment samples document also the growing reliance on herding activities of the human groups visiting the Els Trocs cave throughout the Neolithic sequence. In sum, our work provides substantial arguments to conclude that the advanced herding management skills of the Early Neolithic communities arriving in Iberia facilitated the anthropisation process of the subalpine areas of the Central Pyrenees.

New evidence on the earliest domesticated animals and possible small-scale husbandry in Atlantic NW Europe.

The distribution of the first domesticated animals and crops along the coastal area of Atlantic NW Europe, which triggered the transition from a hunter-gatherer-fisher to a farmer-herder economy, has been debated for many decades among archaeologists. While some advocate a gradual transition in which indigenous hunter-gatherers from the very beginning of the 5th millennium cal BC progressively adopted Neolithic commodities, others are more in favor of a rapid transition near the end of the 5th millennium caused by a further northwest migration of farmers-herders colonizing the lowlands. Here, radiocarbon dated bones from sheep/goat and possibly also cattle are presented which provide the first hard evidence of an early introduction of domesticated animals within a hunter-gatherer context in NW Belgium, situated ca. 80 km north of the agro-pastoral frontier. Based on their isotope signal it is suggested that these first domesticates were probably not merely obtained through exchange with contemporaneous farmers but were kept locally, providing evidence of small-scale local stockbreeding in the lowlands maybe as early as ca. 4800/4600 cal BC. If confirmed by future in-depth isotope analyses, the latter testifies of intense contact and transmission of knowledge in this early contact period, which is also visible in the material culture, such as the lithic and pottery technology. It also implies direct and prolonged involvement of farmer-herders, either through visiting specialists or intermarriage, which follows recent genetic evidence demonstrating much more hunter-gatherer ancestry in early farmer's genes in western Europe compared to central and SE Europe.

The earliest domestic cat on the Silk Road.

We present the earliest evidence for domestic cat (Felis catus L., 1758) from Kazakhstan, found as a well preserved skeleton with extensive osteological pathologies dating to 775-940 cal CE from the early medieval city of Dzhankent, Kazakhstan. This urban settlement was located on the intersection of the northern Silk Road route which linked the cities of Khorezm in the south to the trading settlements in the Volga region to the north and was known in the tenth century CE as the capital of the nomad Oghuz. The presence of this domestic cat, presented here as an osteobiography using a combination of zooarchaeological, genetic, and isotopic data, provides proxy evidence for a fundamental shift in the nature of human-animal relationships within a previously pastoral region. This illustrates the broader social, cultural, and economic changes occurring within the context of rapid urbanisation during the early medieval period along the Silk Road.

A southern African archaeological database of organic containers and materials, 800 cal BC to cal AD 1500: Possible implications for the transition from foraging to livestock-keeping.

Although evidence of organic materials has consistently been reported in the archaeology of southern Africa little attention has been given to how this evidence, so slight in comparison to pottery and lithics, might be used to understand the transition from foraging to livestock-keeping in southern African Archaeology. We have compiled a geo-referenced, radiocarbon database of these organic, material culture remains, with particular reference to containers made of ostrich eggshell, wood, gourd, tortoise shell, twine, and leather over a 2300-year period to capture the periods before and after the appearance of livestock. We have mapped the organic materials for the period 800 cal BC to cal AD 1500 and explored the subsistence base of those who used them. This distribution is compared to that of pottery and livestock remains-conventionally the two archaeological markers of pastoralists. The paper interrogates what this might add to the vexed question of how the practice of livestock-keeping and pottery-making spread into and through the region (the hunter-herder debate). Our analysis suggests that ostrich eggshell containers can be used as a proxy for hunter-gatherers. By comparing areas of bead manufacture with those that have evidence only of bead use, we show the areas to which items may have travelled, along already established hunter-gatherer exchange networks. Our results suggest that hunter-gatherers widely and quickly adopted pottery across southern Africa in a process of cultural diffusion and local innovation, and that this was possibly the main mechanism for the dispersal of livestock at 2100 years ago.

Latitudinal gradient in dairy production with the introduction of farming in Atlantic Europe.

The introduction of farming had far-reaching impacts on health, social structure and demography. Although the spread of domesticated plants and animals has been extensively tracked, it is unclear how these nascent economies developed within different environmental and cultural settings. Using molecular and isotopic analysis of lipids from pottery, here we investigate the foods prepared by the earliest farming communities of the European Atlantic seaboard. Surprisingly, we find an absence of aquatic foods, including in ceramics from coastal sites, except in the Western Baltic where this tradition continued from indigenous ceramic using hunter-gatherer-fishers. The frequency of dairy products in pottery increased as farming was progressively introduced along a northerly latitudinal gradient. This finding implies that early farming communities needed time to adapt their economic practices before expanding into more northerly areas. Latitudinal differences in the scale of dairy production might also have influenced the evolution of adult lactase persistence across Europe.

There and back again: A zooarchaeological perspective on Early and Middle Bronze Age urbanism in the southern Levant.

Multiple arguments for or against the presence of 'urban' settlements in the Early Bronze Age of the southern Levant have identified the need to compare these settlements against their rural hinterlands through multiple lines of evidence. This meta-analysis of zooarchaeological data from the region compares and identifies patterns of animal production, provisioning and consumption between the supposed "urban" and rural sites of the southern Levant from the Early Bronze (EB) against the (more widely recognised urban) Middle Bronze (MB) Ages. It also identifies distinct and regionally specific patterns in animal production and consumption that can be detected between urban and rural sites of the southern Levant. The taxonomic and age profiles from EB Ia and Ib sites do not demonstrate any urban versus rural differentiation patterning, even though fortifications appear in the EB Ib. Beginning in the EB II and clearly visible in the EB III, there is differentiation between rural and urban sites in the taxonomic and age proportions. Differentiation is repeated in the MB II. The clear differentiation between "urban" and rural zooarchaeological assemblages from the EB II-III and MB suggest that rural sites are provisioning the larger fortified settlements. This pattern indicates that these sites are indeed urban in nature, and these societies are organized at the state-level. From the EB II onwards, there is a clear bias in the large centres towards the consumption of cattle and of subadult sheep and goats with a corresponding bias in smaller rural sites towards the consumption of adult sheep and goats and a reduced presence of cattle. After the emergence of this differential pattern, it disappears with the decline in social complexity at the end of the Early Bronze Age, only to come 'back again' with the re-emergence of urban settlement systems in the Middle Bronze Age.

Camelid husbandry in the Atacama Desert? A stable isotope study of camelid bone collagen and textiles from the Lluta and Camarones Valleys, northern Chile.

Management of camelids in the coastal valleys of the Andes has generated much debate in recent years. Zooarchaeological and isotopic studies have demonstrated that in the coastal valleys of northern and southern Peru there were locally maintained camelid herds. Because of the hyperarid conditions of the northern coast of Chile, this region has been assumed to be unsuitable for the raising of camelids. In this study we report stable carbon and nitrogen isotopic compositions of camelid bone collagen and textiles made from camelid fiber from Late Intermediate Period (LIP) and Late Horizon (LH) occupations in northern Chilean river valleys. The camelid bone collagen isotopic compositions are consistent with these animals originating in the highlands, although there is a significant difference in the camelids dating to the LIP and LH, possibly because of changes made to distribution and exchange networks by the Inca in the LH. There were no differences between the isotopic compositions of the camelid fibers sampled from textiles in the LIP and LH, suggesting that either the production of camelid fiber was unchanged by the Inca or the changes that were made do not present visible isotopic evidence. Several camelid fiber samples from both the LIP and LH present very high δ13C and δ15N values, comparable to human hair samples from one site (Huancarane) in the Camarones Valley. These data suggest that people in the northern valleys of Chile may have kept small numbers of animals specifically for fiber production. Overall, however, the vast majority of the textile samples have isotopic compositions that are consistent with an origin in the highlands. These data suggest that the hyperarid coastal river valleys of northern Chile did not support substantial camelid herds as has been interpreted for northern Peru.

Mitogenomic diversity in Sacred Ibis Mummies sheds light on early Egyptian practices.

The ancient catacombs of Egypt harbor millions of well-preserved mummified Sacred Ibis (Threskiornis aethiopicus) dating from ~600BC. Although it is known that a very large number of these 'votive' mummies were sacrificed to the Egyptian God Thoth, how the ancient Egyptians obtained millions of these birds for mummification remains unresolved. Ancient Egyptian textual evidences suggest they may have been raised in dedicated large-scale farms. To investigate the most likely method used by the priests to secure birds for mummification, we report the first study of complete mitochondrial genomes of 14 Sacred Ibis mummies interred ~2500 years ago. We analysed and compared the mitogenomic diversity among Sacred Ibis mummies to that found in modern Sacred Ibis populations from throughout Africa. The ancient birds show a high level of genetic variation comparable to that identified in modern African populations, contrary to the suggestion in ancient hieroglyphics (or ancient writings) of centralized industrial scale farming of sacrificial birds. This suggests a sustained short-term taming of the wild migratory Sacred Ibis for the ritual yearly demand.

Genetics without genes? The centrality of genetic markers in livestock genetics and genomics.

In this paper, rather than focusing on genes as an organising concept around which historical considerations of theory and practice in genetics are elucidated, we place genetic markers at the heart of our analysis. This reflects their central role in the subject of our account, livestock genetics concerning the domesticated pig, Sus scrofa. We define a genetic marker as a (usually material) element existing in different forms in the genome, that can be identified and mapped using a variety (and often combination) of quantitative, classical and molecular genetic techniques. The conjugation of pig genome researchers around the common object of the marker from the early-1990s allowed the distinctive theories and approaches of quantitative and molecular genetics concerning the size and distribution of gene effects to align (but never fully integrate) in projects to populate genome maps. Critical to this was the nature of markers as ontologically inert, internally heterogeneous and relational. Though genes as an organising and categorising principle remained important, the particular concatenation of limitations, opportunities, and intended research goals of the pig genetics community, meant that a progressively stronger focus on the identification and mapping of markers rather than genes per se became a hallmark of the community. We therefore detail a different way of doing genetics to more gene-centred accounts. By doing so, we reveal the presence of practices, concepts and communities that would otherwise be hidden.

Historical trends in Hawaiian game harvest and hunter participation in Hawai'i from 1946-2008.

At present, 21 game species have been successfully established in Hawai'i for the purpose of recreational and subsistence hunting. However, it is unknown how these management efforts have affected hunting and recreation trends in Hawai'i and how the patterns may parallel national data. Consequently, managers and biologists in Hawai'i have little reliable harvest and hunting participation information on which to base current and future management goals. This study provides the first ever analysis of public hunting data in the state of Hawai'i, and is one of only a handful nationally to investigate long-term hunting dynamics in the United States. Our goal was to understand historical hunting trends in the state of Hawai'i in order to provide baseline information to assist in current and future management efforts. Based upon this goal, our objectives were to investigate the influence that time, location, and species have had on both game harvest and hunter participation from 1946 to 2008 across the inhabited islands of Hawai'i. We used 62 years of data from Pittman-Robertson reports to evaluate temporal trends in game harvest and hunter participation for all species, individual species, and taxonomic groups (mammals and birds) at both state and island levels. Since 1946, trends in game harvest and hunter participation in Hawai'i have varied widely by island and species, suggesting that game management may be most effective when approached at the island or species level. Across the state the overall harvest has declined, with only a handful of species being harvested in greater numbers over time on several islands. However, our findings do highlight inconsistencies and potential biases in harvest collection data that are critical for science-based management. In particular, because every game species in Hawai'i has been introduced, there is a critical need to improve harvest data collection and couple it with monitoring data in order to provide management and policy recommendations and develop better conservation planning guidelines.