Repeated plague infections across six generations of Neolithic Farmers.

In the period between 5,300 and 4,900 calibrated years before present (cal. BP), populations across large parts of Europe underwent a period of demographic decline1,2. However, the cause of this so-called Neolithic decline is still debated. Some argue for an agricultural crisis resulting in the decline3, others for the spread of an early form of plague4. Here we use population-scale ancient genomics to infer ancestry, social structure and pathogen infection in 108 Scandinavian Neolithic individuals from eight megalithic graves and a stone cist. We find that the Neolithic plague was widespread, detected in at least 17% of the sampled population and across large geographical distances. We demonstrate that the disease spread within the Neolithic community in three distinct infection events within a period of around 120 years. Variant graph-based pan-genomics shows that the Neolithic plague genomes retained ancestral genomic variation present in Yersinia pseudotuberculosis, including virulence factors associated with disease outcomes. In addition, we reconstruct four multigeneration pedigrees, the largest of which consists of 38 individuals spanning six generations, showing a patrilineal social organization. Lastly, we document direct genomic evidence for Neolithic female exogamy in a woman buried in a different megalithic tomb than her brothers. Taken together, our findings provide a detailed reconstruction of plague spread within a large patrilineal kinship group and identify multiple plague infections in a population dated to the beginning of the Neolithic decline.

Gentlemen, husbandmen, and industrious wives: The role of gender in imagining Indian agriculture.

The Agricultural and Horticultural Society of India (AHSI), founded in 1820, remains the most important producer of English-language knowledge regarding the cultivation of plants in colonial India. Members included missionaries, colonial officials, tea and indigo planters, merchants and bankers, as well as the Bengali bhadralok elites of Calcutta and some Indian princes. The writings it produced were highly gendered. Often they focus on how "improving" the political economy and agricultural productivity would create masculine identities, such as gentlemen landowners and industrious peasant husbandman. Yet I also argue that women's agricultural work was fundamental in imagining this path towards "improvement." Using descriptions of Indian farming and labor practices from the Society's meeting minutes and published transactions, as well as additional writings by its members and missionary founders, I show how many European members of the Society viewed women working outside of domestic pursuits as a sign of Indian inferiority. At the same time, many argued for the benefits of women's work, which they viewed as fundamental in making Indian households more productive. Women and their labor were a lynchpin in creating the idea of the effeminate Indian man as well as the solution for improving him. It was this intersection of race with gender which helped to define agriculture as a discipline much closer to practical knowledge than abstract science. While some European women were able to participate in the Society's production of scientific knowledge because of agriculture's practical nature, Indian knowledge (whether from men or women) tended to be openly dismissed as tradition or habit rather than truly practical. The overlap of gender with race consequently helped to create a hierarchy between practical knowledge and tradition.

100 ancient genomes show repeated population turnovers in Neolithic Denmark.

Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1-4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5-7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.

The selection landscape and genetic legacy of ancient Eurasians.

The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer's disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.

Early contact between late farming and pastoralist societies in southeastern Europe.

Archaeogenetic studies have described two main genetic turnover events in prehistoric western Eurasia: one associated with the spread of farming and a sedentary lifestyle starting around 7000-6000 BC (refs. 1-3) and a second with the expansion of pastoralist groups from the Eurasian steppes starting around 3300 BC (refs. 4,5). The period between these events saw new economies emerging on the basis of key innovations, including metallurgy, wheel and wagon and horse domestication6-9. However, what happened between the demise of the Copper Age settlements around 4250 BC and the expansion of pastoralists remains poorly understood. To address this question, we analysed genome-wide data from 135 ancient individuals from the contact zone between southeastern Europe and the northwestern Black Sea region spanning this critical time period. While we observe genetic continuity between Neolithic and Copper Age groups from major sites in the same region, from around 4500 BC on, groups from the northwestern Black Sea region carried varying amounts of mixed ancestries derived from Copper Age groups and those from the forest/steppe zones, indicating genetic and cultural contact over a period of around 1,000 years earlier than anticipated. We propose that the transfer of critical innovations between farmers and transitional foragers/herders from different ecogeographic zones during this early contact was integral to the formation, rise and expansion of pastoralist groups around 3300 BC.

Northwest African Neolithic initiated by migrants from Iberia and Levant.

In northwestern Africa, lifestyle transitioned from foraging to food production around 7,400 years ago but what sparked that change remains unclear. Archaeological data support conflicting views: (1) that migrant European Neolithic farmers brought the new way of life to North Africa1-3 or (2) that local hunter-gatherers adopted technological innovations4,5. The latter view is also supported by archaeogenetic data6. Here we fill key chronological and archaeogenetic gaps for the Maghreb, from Epipalaeolithic to Middle Neolithic, by sequencing the genomes of nine individuals (to between 45.8- and 0.2-fold genome coverage). Notably, we trace 8,000 years of population continuity and isolation from the Upper Palaeolithic, via the Epipaleolithic, to some Maghrebi Neolithic farming groups. However, remains from the earliest Neolithic contexts showed mostly European Neolithic ancestry. We suggest that farming was introduced by European migrants and was then rapidly adopted by local groups. During the Middle Neolithic a new ancestry from the Levant appears in the Maghreb, coinciding with the arrival of pastoralism in the region, and all three ancestries blend together during the Late Neolithic. Our results show ancestry shifts in the Neolithization of northwestern Africa that probably mirrored a heterogeneous economic and cultural landscape, in a more multifaceted process than observed in other regions.

Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia.

We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.

An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers.

Human culture, biology, and health were shaped dramatically by the onset of agriculture ∼12,000 y B.P. This shift is hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a decline in physiological health as inferred from skeletal remains. Here, we consider osteological and ancient DNA data from the same prehistoric individuals to study human stature variation as a proxy for health across a transition to agriculture. Specifically, we compared "predicted" genetic contributions to height from paleogenomic data and "achieved" adult osteological height estimated from long bone measurements for 167 individuals across Europe spanning the Upper Paleolithic to Iron Age (∼38,000 to 2,400 B.P.). We found that individuals from the Neolithic were shorter than expected (given their individual polygenic height scores) by an average of −3.82 cm relative to individuals from the Upper Paleolithic and Mesolithic (P = 0.040) and −2.21 cm shorter relative to post-Neolithic individuals (P = 0.068), with osteological vs. expected stature steadily increasing across the Copper (+1.95 cm relative to the Neolithic), Bronze (+2.70 cm), and Iron (+3.27 cm) Ages. These results were attenuated when we additionally accounted for genome-wide genetic ancestry variation: for example, with Neolithic individuals −2.82 cm shorter than expected on average relative to pre-Neolithic individuals (P = 0.120). We also incorporated observations of paleopathological indicators of nonspecific stress that can persist from childhood to adulthood in skeletal remains into our model. Overall, our work highlights the potential of integrating disparate datasets to explore proxies of health in prehistory.

Wild cereal grain consumption among Early Holocene foragers of the Balkans predates the arrival of agriculture.

Forager focus on wild cereal plants has been documented in the core zone of domestication in southwestern Asia, while evidence for forager use of wild grass grains remains sporadic elsewhere. In this paper, we present starch grain and phytolith analyses of dental calculus from 60 Mesolithic and Early Neolithic individuals from five sites in the Danube Gorges of the central Balkans. This zone was inhabited by likely complex Holocene foragers for several millennia before the appearance of the first farmers ~6200 cal BC. We also analyzed forager ground stone tools (GSTs) for evidence of plant processing. Our results based on the study of dental calculus show that certain species of Poaceae (species of the genus Aegilops) were used since the Early Mesolithic, while GSTs exhibit traces of a developed grass grain processing technology. The adoption of domesticated plants in this region after ~6500 cal BC might have been eased by the existing familiarity with wild cereals.

Before humans invented agriculture and the first farmers appeared in southwestern Asia, other ancient foragers (also known as hunter-gatherers) in southeastern Europe had already developed a taste for consuming wild plants. There is evidence to suggest that these foragers were intensely gathering wild cereal grains before the arrival of agriculture. However, until now, the only place outside southwestern Asia this has been shown to have occurred is in Greece, and is dated around 20,000 years ago. In the past, researchers proposed that forager societies in the Balkans also consumed wild cereals before transitioning to agriculture. But this has been difficult to prove because plant foods are less likely to preserve than animal bones and teeth, making them harder to detect in prehistoric contexts. To overcome this, Cristiani et al. studied teeth from 60 individuals found in archaeological sites between Serbia and Romania, which are attributed to the Mesolithic and Early Neolithic periods. Food particles extracted from crusty deposits on the teeth (called the dental calculus) were found to contain structures typically found in plants. In addition, Cristiani et al. discovered similar plant food residues on ground stone tools which also contained traces of wear associated with the processing of wild cereals. These findings suggest that foragers in the central Balkans were already consuming certain species of wild cereal grains 11,500 years ago, before agriculture arrived in Europe. It is possible that sharing knowledge about plant resources may have helped introduce domesticated plant species in to this region as early as 6500 BC. This work challenges the deep-rooted idea that the diet of hunter-gatherers during the Palaeolithic and Mesolithic periods primarily consisted of animal proteins. In addition, it highlights the active role the eating habits of foragers might have played in introducing certain domesticated plant species that have become primary staples of our diet today.

Potential interactions between Mesolithic hunter-gatherers and Neolithic farmers in the Western Mediterranean: The geochronological data revisited.

In the Western Mediterranean, the Neolithic mainly developed and expanded during the sixth millennium BCE. In these early phases, it generally spread through the displacement of human groups, sometimes over long distances, as shown, for example, by the Impressa sites documented on the northern shores. These groups then settled new territories which they gradually appropriated and exploited. The question of their potential interaction with groups of Late Mesolithic hunter-gatherers living in the area prior to their arrival is therefore crucial. Were their encounters based on conflict and resistance or, on the contrary, on exchange and reciprocity? Many hypotheses have been put forward on this matter and many papers written. Before we can consider these potential interactions however, we must first ascertain that these different human groups really did meet-an implicit assumption in all these studies, which is, in reality, much less certain than one might think. The population density of the Late Mesolithic groups varied greatly throughout the Mediterranean, and it is possible that some areas were relatively devoid of human presence. Before any Neolithization scenarios can be considered, we must therefore first determine exactly which human groups were present in a given territory at a given time. The precise mapping of sites and the chronological modeling of their occupation enriches our understanding of the Neolithization process by allowing high-resolution regional models to be developed, which alone can determine the timing of potential interactions between Mesolithic and Neolithic groups. Various international research programs have recently produced several hundred new radiocarbon dates, based on selected samples from controlled contexts. The geochronological modelling of these data at the scale of the Western Mediterranean shows contrasting situations, probably related to different social and environmental processes. These results suggest that we should consider a varied range of Neolithization mechanisms, rather than uniform or even binary models.

The Major Source of Antioxidants Intake From Typical Diet Among Rural Farmers in North-eastern Japan in the 1990s.

BACKGROUND: Previous Japanese studies have led to the erroneous conclusion of antioxidant capacity (AOC) intakes of the overall Japanese diet due to limitations in the number and types of food measured, especially in rice and seafood intake. The aims of the study were to construct an AOC database of foods representative of the typical Japanese diet and to clarify the high contributors to AOC intake from the overall diet of the Japanese population. METHODS: Commonly consumed foods were estimated using 3-day dietary records (DRs) over the four seasons among 55 men and 58 women in Japan. To generate an AOC database suitable for the typical Japanese diet, hydrophilic (H-)/lipophilic (L-) oxygen radical absorbance capacity (ORAC) values of foods in each food group were measured via validated methods using the food intake rankings. Subsequently, we estimated the AOC intake and the AOC characteristics of a typical Japanese diet. RESULTS: Of 989 food items consumed by the participants, 189 food items were measured, which covered 78.8% of the total food intake. The most commonly consumed types of antioxidant-containing food were tea, soybean products, coffee, and rice according to H-ORAC, and soybean products, fish and shellfish, vegetables, and algae according to L-ORAC. CONCLUSIONS: The characteristics of high AOC intake in rice and seafood more appropriately reflected the Japanese-style diet. Further studies are expected to clarify the association between food-derived AOC and its role in preventing or ameliorating lifestyle-related diseases.

Using Maize δ15N values to assess soil fertility in fifteenth- and sixteenth-century ad Iroquoian agricultural fields.

Native Americans developed agronomic practices throughout the Western Hemisphere adapted to regional climate, edaphic conditions, and the extent of dependence on agriculture for subsistence. These included the mounding or "corn hill" system in northeastern North America. Iroquoian language speakers of present-day New York, USA, and Ontario and Québec, Canada were among those who used this system. While well-known, there has been little archaeological documentation of the system. As a result, there is scant archaeological evidence on how Iroquoian farmers maintained soil fertility in their often-extensive agricultural fields. Using δ15N values obtained on fifteenth- and sixteenth-century AD maize kernels from archaeological sites in New York and Ontario, adjusted to take into account changes that result from charring as determined through experiments, we demonstrate that Iroquoian farmers were successful at maintaining nitrogen in their agricultural fields. These results add to our archaeological knowledge of Iroquoian agronomic practices. Our results also indicate the potential value of obtaining δ15N values on archaeological maize in the investigation of Native American agronomic practices.

"¡Viva La Clinica!": The United Farm Workers' Fight for Medical Care.

Farm work is among the most dangerous and unhealthy occupations in the United States, but efforts to address farm workers' health needs have been sporadic and inadequate. In the 1960s and 1970s, the United Farm Workers of America (UFW) famously organized workers in California's grape and lettuce fields and won national and international recognition through its boycott tactics. The UFW also opened several medical clinics, staffed by volunteer nurses and physicians, and created the Robert F. Kennedy Medical Plan, a medical insurance program, for its members. Both efforts were initially successful, but foundered in the face of many obstacles, including the reluctance of the UFW leadership to organize undocumented farm workers. However, the UFW's medical work laid the foundation for continuing efforts on behalf of farm workers' and undocumented people's right to health care.

Mapping the cattle industry in Brazil's most dynamic cattle-ranching state: Slaughterhouses in Mato Grosso, 1967-2016.

The state of Mato Grosso is Brazil's agribusiness powerhouse with a cattle herd of 30.2 million head in 2017. With land use patterns heavily influenced by beef production, which requires substantial land inputs, the state is a key target for environmental conservation. Yet the spatial and temporal dynamics of slaughterhouses in Mato Grosso remain largely unknown due to data limitations. Here, we provide a novel method to map slaughterhouse expansion and contraction. We analyzed the opening and closing of 133 plants between 1967 and 2016 in Mato Grosso and estimated the geographic locations and slaughter volumes. This was achieved by triangulating across multiple data sources including a registry of 21 million companies, government records of three million slaughter transactions (Portuguese acronym GTA), and high resolution satellite imagery. Our study is the first to include longitudinal information and both inspected (for food quality) and uninspected slaughterhouses. The results show that 72 plants operated in 2016 through 52 holding companies. By measuring geographic distances between active plants and pasture areas, we documented a 29% increase in the density of plants during 2000-2016, showing an expansion of the cattle slaughter infrastructure. We identified three periods of expansion: 1967-1995, with 15.1% of the plant openings; 1996-2003, with 24.6%; and 2004-2016, with 60.3%. While closings likely occurred throughout the period studied, no data were available prior to 2002. We estimated a minimum value for the volume of uninspected slaughter as 2-3% for 2013-2016. We conclude by discussing potential applications of the data, a deidentified version of which is made available through an online repository. The method developed here can be replicated for the whole country, which would increase our understanding of the dynamics of cattle slaughter and their impact on land use.

Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia.

Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. Here, we report the first genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity (~80-90%) between the hunter-gatherers and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.

Amino acid 15 N analysis reveals change in the importance of freshwater resources between the hunter-gatherer and farmer in the Neolithic upper Tigris.

OBJECTIVE: The inhabitants of several sites in the Upper Tigris Valley, such as Hakemi Use, domesticated animals and cereals during the Pottery Neolithic period, while the inhabitants in this valley were hunter-gatherers in the Pre-Pottery Neolithic period, consuming freshwater and terrestrial food resources. However, there is considerable uncertainty surrounding whether or not changes in dietary food composition accompanied the shift in food production away from foraging. In order to reveal the impact of the development of agriculture on the human diet over the Pre-Pottery and Pottery Neolithic periods in this region, we analyzed the isotopic compositions of amino acids from the farmers at the Hakemi Use Pottery Neolithic site, and compared them with those from the Pre-Pottery hunter-gatherers in the close region. MATERIALS AND METHODS: Herein, we report the nitrogen isotopic compositions of amino acids, as well as both carbon and nitrogen isotopic compositions of bulk collagen, from human and faunal remains collected from Hakemi Use. RESULTS: Whereas freshwater resources were consumed by hunter-gatherers in this region during the Pre-Pottery period, the δ15 N values of glutamic acid (δ15 NGlu ) and phenylalanine (δ15 NPhe ) suggest that freshwater food resources were rarely consumed by inhabitants following the development of agriculture. DISCUSSION: Despite living in similar settings by the Tigris as its inhabitants during the Pre-Pottery period, the farmers of the Pottery Neolithic period depended less on freshwater resources for their diets relative to the hunter-gatherers of the Pre-Pottery Neolithic period.

'One tooth one child': evaluating the effects of diet and fertility on the oral health of women from archaeological sites in South America.

Women from ancient societies have shown a higher prevalence of dental caries in comparison with men. Recent research has shown that the relationship between increased oestrogen production during pregnancy and decreased salivary flow is a possible cause for the higher levels of caries in women, which is in contrast to the traditional view of sexual division of labour resulting in unequal access to cariogenic food. In order to test these two hypotheses, individuals exhumed from 12 South American archaeological sites were examined for markers of oral health (caries, ante mortem tooth loss, deep caries, and enamel hypoplasia) and compared in terms of fertility (Crude Birth Rate) and subsistence systems. Our results suggest that diet and other cultural practices remain the most important factors affecting oral health and that the effects of hormones can be masked by them. Such findings add to the discussion regarding the availability of micronutrients in such societies affecting caries experience in pregnant women, because of their special nutritional requirements.

Spreading Waves in a Farmers and Hunter-Gatherers Model of the Neolithic Transition in Europe.

The Neolithic transition began the spread of early agriculture throughout Europe through interactions between farmers and hunter-gatherers about 10,000 years ago. Archeological evidence produced by radiocarbon dating indicates that the expanding velocity of farming is roughly constant all over Europe. Theoretical understanding of such evidence has been performed from mathematical modeling viewpoint. However, the expanding velocity determined by existing modeling approaches is faster than the observed velocity. For understanding this difference, we propose a three-component reaction-diffusion system which consists of two different types of farmers (sedentary and migratory) and hunter-gatherers from the viewpoint of the influence of farming technology. Our purpose is to study the relation between the expanding velocity of farmers and the farming technology parameter (say, [Formula: see text]). In this paper, we mainly focus on the one-dimensional traveling wave solution with minimal velocity and show that the minimal velocity decreases, as [Formula: see text] increases. This can be compatible with the observed velocity when farming technology is developed. Our results suggest that the reason for the slowdown of the Neolithic transition might be related to the increase in the development of farming technology.

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.