Forager-farmer transition at the crossroads of East and Southeast Asia 4900 years ago.

The southward expansion of East Asian farmers profoundly influenced the social evolution of Southeast Asia by introducing cereal agriculture. However, the timing and routes of cereal expansion in key regions are unclear due to limited empirical evidence. Here we report macrofossil, microfossil, multiple isotopic (C/N/Sr/O) and paleoproteomic data directly from radiocarbon-dated human samples, which were unearthed from a site in Xingyi in central Yunnan and which date between 7000 and 3300 a BP. Dietary isotopes reveal the earliest arrival of millet ca. 4900 a BP, and greater reliance on plant and animal agriculture was indicated between 3800 and 3300 a BP. The dietary differences between hunter-gatherer and agricultural groups are also evident in the metabolic and immune system proteins analysed from their skeletal remains. The results of paleoproteomic analysis indicate that humans had divergent biological adaptations, with and without farming. The combined application of isotopes, archaeobotanical data and proteomics provides a new approach to documenting dietary and health changes across major subsistence transitions.

Plant domestication and agricultural ecologies.

Plant life defines the environments to which animals adapt and provides the basis of food webs. This was equally true for hunter-gatherer economies of ancestral humans, yet through the domestication of plants and the creation of agricultural ecologies based around them, human societies transformed vegetation and transported plant taxa into new geographical regions. These human-plant interactions ultimately co-evolved, increasing human population densities, technologies of farming, and the diversification of landraces and crop complexes. Research in archaeology on preserved plant remains (archaeobotany) and on the genomes of crops, including ancient genomes, has transformed our scientific understanding of the complex relationships between humans and plants that are entailed by domestication. Key realizations of recent research include the recognition that: the co-evolution of domesticates and cultures was protracted, the adaptations of plant populations were unintended results of human economies rather than intentional breeding, domestication took place in dozens of world regions involving different crops and cultures, and convergent evolution can be recognized among cropping types - such as among seed crops, tuber crops, and fruit trees. Seven general domestication pathways can be defined for plants. Lessons for the present-day include: the importance of diversity in the past; genetic diversity within species has the potential to erode over time, but also to be rescued through processes of integration; similarly, diversification within agricultural ecosystems has undergone processes of decline, including marginalised, lost and 'forgotten' crops, as well as processes of renewal resulting from trade and human mobility that brought varied crops and varieties together.

The biocultural origins and dispersal of domestic chickens.

Though chickens are the most numerous and ubiquitous domestic bird, their origins, the circumstances of their initial association with people, and the routes along which they dispersed across the world remain controversial. In order to establish a robust spatial and temporal framework for their origins and dispersal, we assessed archaeological occurrences and the domestic status of chickens from ∼600 sites in 89 countries by combining zoogeographic, morphological, osteometric, stratigraphic, contextual, iconographic, and textual data. Our results suggest that the first unambiguous domestic chicken bones are found at Neolithic Ban Non Wat in central Thailand dated to ∼1650 to 1250 BCE, and that chickens were not domesticated in the Indian Subcontinent. Chickens did not arrive in Central China, South Asia, or Mesopotamia until the late second millennium BCE, and in Ethiopia and Mediterranean Europe by ∼800 BCE. To investigate the circumstances of their initial domestication, we correlated the temporal spread of rice and millet cultivation with the first appearance of chickens within the range of red junglefowl species. Our results suggest that agricultural practices focused on the production and storage of cereal staples served to draw arboreal red junglefowl into the human niche. Thus, the arrival of rice agriculture may have first facilitated the initiation of the chicken domestication process, and then, following their integration within human communities, allowed for their dispersal across the globe.

A stepwise route to domesticate rice by controlling seed shattering and panicle shape.

Asian rice (Oryza sativa L.) is consumed by more than half of the world's population. Despite its global importance, the process of early rice domestication remains unclear. During domestication, wild rice (Oryza rufipogon Griff.) acquired non-seed-shattering behavior, allowing humans to increase grain yield. Previous studies argued that a reduction in seed shattering triggered by the sh4 mutation led to increased yield during rice domestication, but our experiments using wild introgression lines show that the domesticated sh4 allele alone is insufficient for shattering loss in O. rufipogon. The interruption of abscission layer formation requires both sh4 and qSH3 mutations, demonstrating that the selection of shattering loss in wild rice was not as simple as previously suggested. Here we identified a causal single-nucleotide polymorphism at qSH3 within the seed-shattering gene OsSh1, which is conserved in indica and japonica subspecies but absent in the circum-aus group of rice. Through harvest experiments, we further demonstrated that seed shattering alone did not significantly impact yield; rather, yield increases were observed with closed panicle formation controlled by SPR3 and further augmented by nonshattering, conferred by integration of sh4 and qSH3 alleles. Complementary manipulation of panicle shape and seed shattering results in a mechanically stable panicle structure. We propose a stepwise route for the earliest phase of rice domestication, wherein selection of visible SPR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3, which together led to the loss of shattering.

A novel cost framework reveals evidence for competitive selection in the evolution of complex traits during plant domestication.

Most models of selection incorporate some notion of environmental degradation where the majority of the population becomes less fit concerning a character resulting in pressure to adapt. Such models have been variously associated with an adaptation cost, the substitution load. Conversely, adaptative mutations that represent an improvement in fitness in the absence of environmental change have generally been assumed to be associated with negligible cost. However, such adaptations could represent a competitive advantage that diminishes resource availability for others and so induces a cost. This type of adaptation in the form of seedling competition has been suggested as a mechanism for increases in seed sizes during domestication, a trait associated with the standard stabilizing selection model. We present a novel cost framework for competitive selection that demonstrates significant differences in behaviour to environmental-based selection in intensity, intensity over time and directly contrasts with the expectations of the standard model. Grain metrics of nine archaeological crops fit a mixed model in which episodes of competitive selection often emerge from shifting optimum episodes of stabilizing selection, highlighting the potential prevalence of the mechanism outlined here and providing fundamental insight into the factors driving domestication.

Emerging evidence of plant domestication as a landscape-level process.

The evidence from ancient crops over the past decade challenges some of our most basic assumptions about the process of domestication. The emergence of crops has been viewed as a technologically progressive process in which single or multiple localized populations adapt to human environments in response to cultivation. By contrast, new genetic and archaeological evidence reveals a slow process that involved large populations over wide areas with unexpectedly sustained cultural connections in deep time. We review evidence that calls for a new landscape framework of crop origins. Evolutionary processes operate across vast distances of landscape and time, and the origins of domesticates are complex. The domestication bottleneck is a redundant concept and the progressive nature of domestication is in doubt.

Transition From Wild to Domesticated Pearl Millet (Pennisetum glaucum) Revealed in Ceramic Temper at Three Middle Holocene Sites in Northern Mali.

Imprints of domesticated pearl millet (Pennisetum glaucum (L.) R. Br.) spikelets, observed as temper in ceramics dating to the third millennium BC, provide the earliest evidence for the cultivation and domestication process of this crop in northern Mali. Additional sherds from the same region dating to the fifth and fourth millennium BC were examined and found to have pearl millet chaff with wild morphologies. In addition to studying sherds by stereomicroscopy and subjecting surface casts to scanning electron microscopy (SEM), we also deployed X-ray microcomputed tomography (microCT) on eleven sherds. This significantly augmented the total dataset of archaeological pearl millet chaff remains from which to document the use of the wild pearl millet as ceramic temper and the evolution of its morphology over time. Grain sizes were also estimated from spikelets preserved in the ceramics. Altogether, we are now able to chart the evolution of domesticated pearl millet in western Africa using three characteristics: the evolution of nonshattering stalked involucres; the appearance of multiple spikelet involucres, usually paired spikelets; and the increase in grain size. By the fourth millennium BC, average grain breadth had increased by 28%, although spikelet features otherwise resemble the wild type. In the third millennium BC, the average width of seeds is 38% greater than that of wild seeds, while other qualitative features of domestication are indicated by the presence of paired spikelets and the appearance of nondehiscent, stalked involucres. Nonshattering spikelets had probably become fixed by around 2000 BC, while increases in average grain size continued into the second millennium BC. These data now provide a robust sequence for the morphological evolution of domesticated pearl millet, the first indigenous crop domesticated in western Africa. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10437-021-09428-8.

Des empreintes d'épillets de mil domestiqué (Pennisetum glaucum (L.) R. Br.) observées dans des céramiques datées du 3e millénaire av. J.-C. provenant du nord du Mali constituent les plus anciens témoins de la mise en culture et de la domestication de cette céréale. Des tessons supplémentaires issus de la même région se rapportant aux 5e et 4e millénaires av. J.-C. ont été examinés et ont révélé des empreintes de balle de mil de morphologies sauvages. En plus de l'observation de leurs surfaces par stéréo-microscopie, et de l'observation des moulages d'empreintes au microscope à balayage, onze d'entre eux ont fait l'objet des micro-tomographies aux rayons X (microCT). Ces examens enrichissent considérablement l'ensemble des données archéologiques concernant l'utilisation du mil sauvage comme dégraissant végétal et son évolution morphologique à travers le temps. La taille des grains a aussi été estimée à partir des épillets conservés dans la céramique. En tenant compte des données enregistrées lors d'études antérieures, nous pouvons désormais retracer l'évolution du mil domestiqué en Afrique de l'Ouest à travers trois caractéristiques : l'évolution des involucres pédonculés à égrenage non-spontané; l'apparition d'involucres multiples par épillets, des épillets appariés le plus souvent; l'augmentation de la taille des grains au vu de leur largeur. Déjà au 4e millénaire avant J.-C., la largeur moyenne des grains a augmenté de 28% bien que les caractéristiques de l'épillet ressemblent au type sauvage. Au 3e millénaire avant J.-C., elle est 38% supérieure à celle du morphotype sauvage, tandis que des caractéristiques qualitatives de la domestication sont avérées par la présence d'épillets appariés et par celle d'involucres pédonculés à égrenage non-spontané. La non-déhiscence des épillets est un caractéristique de la domesticité qui s'est probablement fixé vers 2000 avant J.-C., tandis que l'augmentation de la taille moyenne des grains s'est poursuivie tout au long du 2e millénaire av. J.-C. Ces données fournissent désormais une séquence robuste concernant l'évolution morphologique du mil, la première céréale indigène domestiquée en Afrique de l'Ouest.

The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae).

Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using newly generated RNA-seq data for a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions.

People have shaped most of terrestrial nature for at least 12,000 years.

Archaeological and paleoecological evidence shows that by 10,000 BCE, all human societies employed varying degrees of ecologically transformative land use practices, including burning, hunting, species propagation, domestication, cultivation, and others that have left long-term legacies across the terrestrial biosphere. Yet, a lingering paradigm among natural scientists, conservationists, and policymakers is that human transformation of terrestrial nature is mostly recent and inherently destructive. Here, we use the most up-to-date, spatially explicit global reconstruction of historical human populations and land use to show that this paradigm is likely wrong. Even 12,000 y ago, nearly three quarters of Earth's land was inhabited and therefore shaped by human societies, including more than 95% of temperate and 90% of tropical woodlands. Lands now characterized as "natural," "intact," and "wild" generally exhibit long histories of use, as do protected areas and Indigenous lands, and current global patterns of vertebrate species richness and key biodiversity areas are more strongly associated with past patterns of land use than with present ones in regional landscapes now characterized as natural. The current biodiversity crisis can seldom be explained by the loss of uninhabited wildlands, resulting instead from the appropriation, colonization, and intensifying use of the biodiverse cultural landscapes long shaped and sustained by prior societies. Recognizing this deep cultural connection with biodiversity will therefore be essential to resolve the crisis.

Monsoon forced evolution of savanna and the spread of agro-pastoralism in peninsular India.

An unresolved issue in the vegetation ecology of the Indian subcontinent is whether its savannas, characterized by relatively open formations of deciduous trees in C4-grass dominated understories, are natural or anthropogenic. Historically, these ecosystems have widely been regarded as anthropogenic-derived, degraded descendants of deciduous forests. Despite recent work showing that modern savannas in the subcontinent fall within established bioclimatic envelopes of extant savannas elsewhere, the debate persists, at least in part because the regions where savannas occur also have a long history of human presence and habitat modification. Here we show for the first time, using multiple proxies for vegetation, climate and disturbances from high-resolution, well-dated lake sediments from Lonar Crater in peninsular India, that neither anthropogenic impact nor fire regime shifts, but monsoon weakening during the past ~ 6.0 kyr cal. BP, drove the expansion of savanna at the expense of forests in peninsular India. Our results provide unambiguous evidence for a climate-induced origin and spread of the modern savannas of peninsular India at around the mid-Holocene. We further propose that this savannization preceded and drove the introduction of agriculture and development of sedentism in this region, rather than vice-versa as has often been assumed.

Agricultural diversification in West Africa: an archaeobotanical study of the site of Sadia (Dogon Country, Mali).

While narratives of the spread of agriculture are central to interpretation of African history, hard evidence of past crops and cultivation practices are still few. This research aims at filling this gap and better understanding the evolution of agriculture and foodways in West Africa. It reports evidence from systematic flotation samples taken at the settlement mounds of Sadia (Mali), dating from 4 phases (phase 0=before first-third century AD; phase 1=mid eighth-tenth c. AD; phase 2=tenth-eleventh c. AD; phase 3=twelfth-late thirteenth c. AD). Flotation of 2200 l of soil provided plant macro-remains from 146 archaeological samples. As on most West African sites, the most dominant plant is pearl millet (Pennisetum glaucum). But from the tenth century AD, sorghum (Sorghum bicolor) and African rice (Oryza glaberrima) appear in small quantities, and fonio (Digitaria exilis) and barnyard millet/hungry rice (Echinochloa sp.), sometimes considered weeds rather than staple crops, are found in large quantities. Some samples also show remains of tree fruits from savannah parklands, such as baobab (Adansonia digitata), marula (Sclerocarya birrea), jujube (Ziziphus sp.), shea butter (Vittelaria paradoxa) and African grapes (Lannea microcarpa). Fonio and Echinochloa sp. cultivation appears here to be a later addition that helped to diversify agriculture and buffer against failures that might affect the monoculture of pearl millet. This diversification at the end of the 1st millennium AD matches with other evidence found in West Africa.

Two-season agriculture and irrigated rice during the Dian: radiocarbon dates and archaeobotanical remains from Dayingzhuang, Yunnan, Southwest China.

Historical sources describe irrigation and intensive agriculture being practiced in lowland Yunnan from at least the first century AD, but so far archaeobotanical remains allowing investigation of this issue have been scarce. Here, we present new archaeobotanical evidence, including macro-botanical and phytoliths results, from the Dian settlement site of Dayingzhuang, with direct AMS radiocarbon dates on two wheat grains falling between 750 and 390 BC. We compare these results with contemporary Dian sites and analyse the agricultural systems in Central Yunnan between the eight and fourth centuries BC. We propose that agriculture was intensified toward the end of the Dian through both multiple cropping seasons and increased evidence for irrigated rice fields. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12520-020-01268-y.

Genomic history and ecology of the geographic spread of rice.

Rice (Oryza sativa) is one of the world's most important food crops, and is comprised largely of japonica and indica subspecies. Here, we reconstruct the history of rice dispersal in Asia using whole-genome sequences of more than 1,400 landraces, coupled with geographic, environmental, archaeobotanical and paleoclimate data. Originating around 9,000 yr ago in the Yangtze Valley, rice diversified into temperate and tropical japonica rice during a global cooling event about 4,200 yr ago. Soon after, tropical japonica rice reached Southeast Asia, where it rapidly diversified, starting about 2,500 yr BP. The history of indica rice dispersal appears more complicated, moving into China around 2,000 yr BP. We also identify extrinsic factors that influence genome diversity, with temperature being a leading abiotic factor. Reconstructing the dispersal history of rice and its climatic correlates may help identify genetic adaptations associated with the spread of a key domesticated species.

Agricultural systems in Bangladesh: the first archaeobotanical results from Early Historic Wari-Bateshwar and Early Medieval Vikrampura.

The present paper reports the first systematic archaeobotanical evidence from Bangladesh together with direct AMS radiocarbon dates on crop remains. Macro-botanical remains were collected by flotation from two sites, Wari-Bateshwar (WB), an Early Historic archaeological site, dating mainly between 400 and 100 BC, with a later seventh century AD temple complex, and Raghurampura Vikrampura (RV), a Buddhist Monastery (vihara) located within the Vikrampura city site complex and dating to the eleventh and sixteenth centuries AD. Despite being a tropical country, with high rainfall and intensive soil processes, our work demonstrates that conventional archaeobotany, the collection of macro-remains through flotation, has much potential towards putting together a history of crops and agricultural systems in Bangladesh. The archaeobotanical assemblage collected from both sites indicates the predominance of rice agriculture, which would have been practiced in summer. Spikelet bases are of domesticated type rice, while grain metrics suggest the majority of rice was probably subspecies japonica. The presence of some wetland weeds suggests at least some of the rice was grown in wet (flooded) systems, but much of it may have been rainfed as inferred from the Southeast Asian weed Acmella paniculata. Other crops include winter cereals, barley and possible oat, and small numbers of summer millets (Pennisetum glaucum, Sorghum bicolor, Setaria italica), a wide diversity of summer and winter pulses (14 spp.), cotton, sesame and mustard seed. Pulse crops included many known from India. Thus, while most crops indicate diffusion of crops from India eastwards, the absence of indica rice could also indicate some diffusion from Southeast Asia. The later site RV also produced evidence of the rice bean (Vigna umbellata), a domesticate of mainland Southeast Asia. These data provide the first empirical evidence for reconstructing past agriculture in Bangladesh and for the role of connections to both India and mainland Southeast Asia in the development of crop diversity in the Ganges delta region.

Assessing the occurrence and status of wheat in late Neolithic central China: the importance of direct AMS radiocarbon dates from Xiazhai.

The introduction of wheat into central China is thought to have been one of the significant contributions of interactions between China and Central Asia which began in the 3rd millennium bc. However, only a limited number of Neolithic wheat grains have been found in central China and even fewer have been directly radiocarbon dated, making the date when wheat was adopted in the region and its role in subsistence farming uncertain. Based on systematic archaeobotanical data and direct dating of wheat remains from the Xiazhai site in central China, as well as a critical review of all reported discoveries of Neolithic and Bronze Age wheat from this region, we conclude that many wheat finds are intrusive in Neolithic contexts. We argue that the role of wheat in the subsistence of the late Neolithic and early Bronze Age of central China was minimal, and that wheat only began to increase in its subsistence role in the later Bronze Age during the Zhou dynasty after ca. 1000 bc.

The domestication syndrome in vegetatively propagated field crops.

BACKGROUND: Vegetatively propagated crops are globally significant in terms of current agricultural production, as well as for understanding the long-term history of early agriculture and plant domestication. Today, significant field crops include sugarcane (Saccharum officinarum), potato (Solanum tuberosum), manioc (Manihot esculenta), bananas and plantains (Musa cvs), sweet potato (Ipomoea batatas), yams (Dioscorea spp.) and taro (Colocasia esculenta). In comparison with sexually reproduced crops, especially cereals and legumes, the domestication syndrome in vegetatively propagated field crops is poorly defined. AIMS AND SCOPE: Here, a range of phenotypic traits potentially comprising a syndrome associated with early domestication of vegetatively propagated field crops is proposed, including: mode of reproduction, yield of edible portion, ease of harvesting, defensive adaptations, timing of production and plant architecture. The archaeobotanical visibility of these syndrome traits is considered with a view to the reconstruction of the geographical and historical pathways of domestication for vegetatively propagated field crops in the past. CONCLUSIONS: Although convergent phenotypic traits are identified, none of them are ubiquitous and some are divergent. In contrast to cereals and legumes, several traits seem to represent varying degrees of plastic response to growth environment and practices of cultivation, as opposed to solely morphogenetic 'fixation'.

New findings on the significance of Jebel Moya in the eastern Sahel.

This paper presents new excavation data and new radiometric dates for Jebel Moya, south-central Sudan. These data suggest revisions to previous chronological understandings of the site. New excavations, initiated in 2017, show a longer, more continuous occupation of the site than has been previously recognised. Archaeozoological and archaeobotanical analyses provide evidence for domesticated taxa. Archaeobotanical evidence is dominated by domesticated sorghum (Sorghum bicolor), radiocarbon dated to c. 2550-2210 BC. Faunal remains include cattle and goat/sheep. A late third-millennium BC date on the human skeleton excavated in the 2017 season also shows that mortuary activity began early in the site's history, contemporary with domesticated faunal and botanical remains. These initial results indicate the long-term association of the site with pastoralism and agriculture and with environmental change. Jebel Moya's continued potential to serve as a chronological and cultural reference point for future studies in south-central Sudan and the eastern Sahel is reinforced.

A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history.

Tetraploid emmer wheat (Triticum turgidum ssp. dicoccon) is a progenitor of the world's most widely grown crop, hexaploid bread wheat (Triticum aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals to be domesticated in the old world; it was cultivated from around 9700 BC in the Levant1,2 and subsequently in south-western Asia, northern Africa and Europe with the spread of Neolithic agriculture3,4. Here, we report a whole-genome sequence from a museum specimen of Egyptian emmer wheat chaff, 14C dated to the New Kingdom, 1130-1000 BC. Its genome shares haplotypes with modern domesticated emmer at loci that are associated with shattering, seed size and germination, as well as within other putative domestication loci, suggesting that these traits share a common origin before the introduction of emmer to Egypt. Its genome is otherwise unusual, carrying haplotypes that are absent from modern emmer. Genetic similarity with modern Arabian and Indian emmer landraces connects ancient Egyptian emmer with early south-eastern dispersals, whereas inferred gene flow with wild emmer from the Southern Levant signals a later connection. Our results show the importance of museum collections as sources of genetic data to uncover the history and diversity of ancient cereals.

Sedentism and plant cultivation in northeast China emerged during affluent conditions.

The reasons and processes that led hunter-gatherers to transition into a sedentary and agricultural way of life are a fundamental unresolved question of human history. Here we present results of excavations of two single-occupation early Neolithic sites (dated to 7.9 and 7.4 ka) and two high-resolution archaeological surveys in northeast China, which capture the earliest stages of sedentism and millet cultivation in the second oldest center of domestication in the Old World. The transition to sedentism coincided with a significant transition to wetter conditions in north China, at 8.1-7.9 ka. We suggest that these wetter conditions were an empirical precondition that facilitated the complex transitional process to sedentism and eventually millet domestication in north China. Interestingly, sedentism and plant domestication followed different trajectories. The sedentary way of life and cultural norms evolved rapidly, within a few hundred years, we find complex sedentary villages inhabiting the landscape. However, the process of plant domestication, progressed slowly over several millennia. Our earliest evidence for the beginning of the domestication process appear in the context of an already complex sedentary village (late Xinglongwa culture), a half millennia after the onset of cultivation, and even in this phase domesticated plants and animals were rare, suggesting that the transition to domesticated (sensu stricto) plants in affluent areas might have not played a substantial role in the transition to sedentary societies.