The evolution of rice: molecular vignettes on its origins and spread

The domesticated species Oryza sativa or Asian rice evolved starting approximately 9,000 years ago and from its centers of origin in China and India has subsequently spread throughout the Old World (and in historical times in the New World as well). This species is one of the key domesticated crop plants in the world and has emerged as a model for studying the origins and spread of domesticated taxa as well as in investigating the genetic basis for plant variation under domestication. Archaeological data has been critical in dissecting the origins and spread of rice throughout Asia, but molecular information has also provided a complementary approach to examining the evolutionary dynamics of this species. The evolutionary history of a species can leave its footprints within its genome. Moreover, genetic studies allow us to study the history of traits that do not leave an archaeological record—for example, grain stickiness or flowering time—which can provide insights into how crop species are adopted by different cultures. In this review, several molecular studies into the origin and spread of Asian rice are discussed and we explore the advances these genetic studies offer in our understanding of the evolution of domesticated species. We also explore how archaeological data can provide critical insights that can help refine genetic models of the origin and spread of domesticated species.     

Micro-CT-assisted determination of the shattering and non-shattering phenotypes of charred rice spikelet bases from archaeological sites: a new methodological approach

The selection of a non-shattering phenotype is a pivotal change in the process of rice domestication. However, current research is heavily restricted by the preservation conditions of macro-plant remains in early and middle Neolithic sites, as very limited well-preserved rice spikelet bases could be retrieved. We present a non-destructive method based on micro-computed tomographic (CT) scanning, which could provide detailed visualization of the internal structures of charred spikelet bases and efficiently discriminate the shattering and non-shattering phenotypes of rice spikelet bases according to the abundance of fusiform echinate phytoliths. It could be widely applied in different contexts, especially those poorly preserved specimens and tempers in pottery sherds, greatly improving our knowledge of rice domestication.     

关于中国稻作起源证据的讨论与商榷

本文是对傅稻镰等人最近的文章批评中国栽培水稻起源研究缺乏证据、提出长江下游水稻栽培开始于公元前4000年这一观点一文的回应。我们首先考察中国从野生稻采集到水稻栽培过程研究的相关文献．进而从水稻形态学和考古学的角度对早期水稻遗存加以研究。讨论集中在以下三个方面：长江流域最早水稻栽培的时间：长江下游和淮河流域初期栽培水稻的遗存;考古遗存所见水稻粒形态大小变化的意义。我们也考察了傅文用来区分野生水稻和栽培水稻的几个标准：考古纪录中所见的未成熟稻遗存、水稻粒的增大和水稻粒的形态。根据已经发表的资料和我们对水稻的研究,我们认为到全新世早期（距今9000年前后）,南北中国的新石器时代居民就可能已经收获野生稻并开始水稻栽培了。     

The cultivation of perennial rice,an early phase in Southeast Asian agriculture?

Domesticated rice, Oryza sativa L., though a perennial, is nowadays usually cultivated as an annual. This has led a number of commentators to misinterpret the historical record. The older view that rice was domesticated around the Bay of Bengal and in parts of mainland Southeast Asia has been replaced by competing views of earliest domestication in that region and in the Yangzi valley. Botanical considerations point clearly to the retention of perennial characteristics while archaeological and historical evidences point to cultivation with more than a single harvest from an initial planting – the practice of ratooning. Evidence is reviewed briefly for China and more extensively for Southeast Asia. Modern field evidence is used to support the notion that ratooning was probably more widespread in the past and that this practice may represent an early phase in the history of rice agriculture in Southeast Asia as it does in China.     

稻作农业起源研究中的植物考古学

早期稻作农业是植物考古学的一个研究热点。本文首先厘清了农业、栽培和驯化等稻作农业发展中的常用术语。进而对区分野生稻与驯化稻,即反映“半驯化”特征的几个指标包括基盘、谷粒尺寸和植硅石分别展开讨论。文章结合我们对现代野生稻和栽培稻的测量数据以及田螺山的工作,引用了国内外诸多考古实例和最新的分子学证据,证据表明上述几个指标在某些程度上多少可以作为性状来判断驯化稻是否已经出现,但是随着农业景观概念的提出,耕地杂草群落作为农田系统研究的证据．为稻作农业出现和发展研究展开了新视野。     

Archaeogenetic study of prehistoric rice remains from Thailand and India: evidence of early <Emphasis Type="Italic">japonica</Emphasis> in South and Southeast Asia

We report a successful extraction and sequencing of ancient DNA from carbonized rice grains (Oryza sativa) from six archaeological sites, including two from India and four from Thailand, ranging in age from ca. 2500 to 1500 BP. In total, 221 archaeological grains were processed by PCR amplification and primary-targeted fragments were sequenced for comparison with modern sequences generated from 112 modern rice populations, including crop and wild varieties. Our results include the genetic sequences from both the chloroplast and the nuclear genomes, based on four markers from the chloroplast and six from the nuclear genome. These markers allow differentiation of indica rice from japonica rice, the two major subspecies of Asian rice (O. sativa) considered to have separate geographical origins. One nuclear marker differentiates tropical and temperate forms of subspecies japonica. Other markers relate to phenotypic variation selected for under domestication, such as non-shattering, grain stickiness (waxy starch) and pericarp colour. Recovery and identification of sequences from nuclear markers was generally poor, whereas recovery of chloroplast sequences was successful, with at least one of four markers recovered in 61 % of archaeological grains. This allowed for successful differentiation of indica or japonica subspecies variety, with japonica identified in all the Thai material and a mixture of indica and japonica chloroplasts in the two Indian assemblages. Rice subspecies was also assessed through conventional archaeobotanical methods relying on grain metrics, based on measurements from 13 modern populations and 499 archaeological grains. Grain metrics also suggest a predominance of japonica-type grains in the Southeast Asian sites and a mixture of japonica and indica in the Indian sites with indica in the minority. The similar results of grain metrics and ancient DNA (aDNA) affirm that grain measurements have some degree of reliability in rice subspecies identification. The study also highlights the great potential of ancient DNA recovery from archaeological rice. The data generated in the present study adds support to the model of rice evolution that includes hybridization between japonica and proto-indica.     

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.

     

Agricultural Origins and Frontiers in South Asia: A Working Synthesis

The accumulation of recent data from archaeobotany, archaeozoology and Neolithic excavations from across South Asia warrants a new overview of early agriculture in the subcontinent. This paper attempts a synthesis of these data while recommending further systematic work and methodological developments. The evidence for origins and dispersals of important crops and livestock from Southwest Asia into South Asia is reviewed. In addition evidence for indigenous plant and animal domestication in India is presented. Evidence for probable indigenous agricultural developments in Gujarat, the Middle Ganges, Eastern India, and Southern India are reviewed. An attempt is made to highlight regions of important frontiers of interaction between early farmers and hunter-gatherers. The current evidence suggests that the Neolithic trajectories in different parts of South Asia differ from each other. Indigenous centers of plant domestication in India also differ from the often discussed trajectory of Southwest Asia, while suggesting some similarities with agricultural origins in Africa and Eastern North America as well as secondary agricultural developments on the peripheries of Eurasia. An erratum to this article can be found at     

On the Origins and Dissemination of Domesticated Sorghum and Pearl Millet across Africa and into India: a View from the Butana Group of the Far Eastern Sahel

Four decades have passed since Harlan and Stemler (1976) proposed the eastern Sahelian zone as the most likely center of Sorghum bicolor domestication. Recently, new data on seed impressions on Butana Group pottery, from the fourth millennium BC in the southern Atbai region of the far eastern Sahelian Belt in Africa, show evidence for cultivation activities of sorghum displaying some domestication traits. Pennisetum glaucum may have been undergoing domestication shortly thereafter in the western Sahel, as finds of fully domesticated pearl millet are present in southeastern Mali by the second half of the third millennium BC, and present in eastern Sudan by the early second millennium BC. The dispersal of the latter to India took less than 1000 years according to present data. Here, we review the middle Holocene Sudanese archaeological data for the first time, to situate the origins and spread of these two native summer rainfall cereals in what is proposed to be their eastern Sahelian Sudan gateway to the Red Sea and the Indian Ocean trade.     

Influence of grinding on the preservation of starch grains from rice

China is a major centre for rice domestication, where starch grain analysis has been widely applied to archaeological grinding tools to gain information about plant use by ancient Chinese societies. However, few rice starch grains have been identified to date. To understand this apparent scarcity of starch grains from rice, dry- and wet-grinding experiments with stone tools were carried out on four types of cereals: rice (Oryza sativa L.), foxtail millet (Setaria italica), Job's tears (Coix lacryma-jobi L.) and barley (Hordeum vulgare L.). The results reveal that dry-grinding produces significant damage to starches to the point where they may be undetected in archaeological samples, while wet-grinding causes only slight morphological changes to the starch grains. Moreover, rice starch grains have the most substantial alterations from dry-grinding, possibly impeding their identification. These findings provide a possible means to explain the relative scarcity of rice starch grains recovered from archaeological grinding tools, which it is suggested was caused by the use of the dry-grinding technique. Therefore, it is suggested that rice starch grains have been likely underrepresented in the archaeological record, and previous interpretations of starch analyses need to be reconsidered.     

New data and new issues for the study of origin of rice agriculture in China

China was one of the major centers for the origin of agriculture in the world. The origins of agriculture in China, especially the origin of rice agriculture, made a significant contribution not only to the occurrence of Chinese civilization but also to the development of world history. Recently, the study on the origin of rice agriculture has attracted the attention of the academic community due to the dramatic development of archaeobotanical research in China. In recent years, the flotation technique has widely implemented in archaeological excavations in China. As the result, a tremendous amount of plant remains have been recovered from archaeological sites, including those much related to the study of early rice agriculture. The new data provide direct archaeological evidence for, and raise some new issues about, the origin of rice agriculture in China. For example, the rice remains from the Shangshan site, dated to ca. 10,000 cal. B.P., suggest the beginning of rice cultivation regardless of whether that rice was domesticated or not. The quantitative analysis of plant remains recovered by floatation from the Jiahu site, dated to ca. 8,000 cal. B.P., revealed that the subsistence of the Jiahu people mainly relied on fishing/hunting/gathering, while the products of rice cultivation and animal husbandry were only a supplement to their diet. The ongoing excavation, with floatation and water-sieving, at the Tianluoshan site, dated to 6,000 to 7,000 cal. B.P., suggests that rice farming, though important, was only part of a broader subsistence pattern of the Hemudu Culture, and rice domestication culminated after 6,500 B.P and the beginning of rice domestication remain unclear.     

Current issues in Chinese Neolithic archaeology

Every year archaeologists in China discover numerous rich sites demonstrating significant regional variability in Neolithic cultures, primarily from about 6500 B.C. to 1900 B.C. This paper discusses a topic not covered in detail in current or forthcoming publications, the origins and development of agricultural systems. Recent fieldwork in both northern and southern China suggests that initial steps toward settled agricultural villages began circa 11,000 B.P. I review evidence for the cultivation of millet, rice, and other plants as well as animal husbandry in different regions of China. There are several later Neolithic sites in northern China with evidence for rice cultivation. I suggest how future research projects can investigate regional variation and change over time in subsistence and settlement during the Neolithic Period.     

The archaeobotany of Indian pulses: identification,processing and evidence for cultivation

Abstract

Pulses are a significant component of traditional subsistence in South Asia. Reliable identification criteria for identifying these from archaeological seed remains are reviewed. The botanical evidence relating to the wild progenitors and their distribution, especially of Indian natives (Macrotyloma uniflorum, Vigna radiata, Vigna mungo) is summarised, including new evidence from primary botanical research. The problem of seed size increase in pulses is reviewed through a focused study on Vigna spp., in which it is shown that seed enlargement is delayed by 1–2,000 years after initial cultivation. The taphonomy of archaeological pulses is considered in the context of crop-processing of pulses, in which an important distinction can be drawn between free-threshing and pod-threshing types. The total archaeobotanical record for pulses in South Asia (India and Pakistan) is summarised and key regional differences are highlighted.     

Wild and domesticated forms of rice (Oryza sp.) in early agriculture at Qingpu, lower Yangtze, China: evidence from phytoliths

Rice cultivation in parts of the Yangtze valley, eastern China, is thought to date to at least the early Holocene. Using phytolith analysis, sediments from an exposed profile at Qingpu in the lower Yangtze were examined in detail in order to contribute to the growing body of information relating to the history of rice agriculture in the Yangtze delta area. The presence of phytoliths from domesticated rice, Oryza sativa, indicates that rice agriculture was well developed at Qingpu by ca. 2350 BP and may have increased in intensity from ca. 2100 BP. Rice cultivation at Qingpu was comparatively late in relation to other areas in the Yangtze valley, possibly due to the seasonal intrusion of saline waters, while the cultivation of wild rice remained a prominent feature of food production in the area to at least as late as ca. 1800 BP. Results presented here support the existence of a period of overlap, during which both wild and domesticated forms of rice were cultivated, rather than a linear transition from wild to domesticated rice cultivation and the possible influence of environmental factors over farming in an area subjected to frequent flooding.     

A review of archaeology in mainland Southeast Asia

This article outlines recent advances in establishing and understanding the prehistoric sequence in mainland Southeast Asia. Research has been unevenly distributed, varying from virtually none in Cambodia to a marked intensity in Hong Kong and the adjoining mainland. A new pattern is becoming apparent, due in no small part to the new findings in southern China. It is argued that despite its long history of occupation, beginning withHomo erectus almost a million years ago, tropical Southeast Asia was occupied by scattered inland groups and larger, possibly sedentary coastal foragers until exposed to intrusive agricultural societies during the third millennium BC. These communities, which originated ultimately in the Yangzi Valley, brought with them rice cultivation and were responsible for the wide distribution of Austroasiatic languages. The three divisions of this language superfamily are now distributed from eastern India to southern China. Following a relatively brief Neolithic period, small and autonomous communities, particularly in Lingnan and Bac Bo (Guangdong and Guangxi provinces of China and the area of the Red River Delta), were exposed to exchange contact with the Shang state of the Chinese Central Plains, and this brought exotic jades and bronzes. Within this context, a local bronze industry was established between 1500 and 1000 BC over much of Southeast Asia, but without any obvious social developments until the middle of the first millennium BC, when several major changes occurred. These incorporated iron smelting and forging and exposure in the southern parts of the region to Indian mercantile contact and along the northern margins to the expanding Chinese empire. Adaptations varied regionally, from the establishment of warrior chiefdoms to counter the Chinese to the construction of water control systems in the arid heart of Southeast Asia to alleviate environmental unpredictability. It is within these regional changes that we can identify trends toward the establishment of states, some of which persisted in an unbroken lineage to the present.     

Archaeobotanical remains from the mid-first millennium AD site of Kaerdong in western Tibet

In this study, we present the preliminary result of archaeobotanical investigation at Kaerdong in western Tibet. The result shows that agropastoralism with combined strategies of foraging, hunting and fishing was in practice at the location between approximately 455 and 700 cal. AD. Our results also show that herding animals grazed at meadows above 4300 m above sea level (masl), and dung was used as fuel. The presence of a rice grain together with spikelet bases indicates that rice was a component of food resources possibly as a result of a trade and exchange system. In addition, tatary buckwheat grains were also recovered at the site.     

Morphometric Analysis of Sus Remains from Neolithic Sites in the Wei River Valley,China, with Implications for Domestication

Size variation of Sus remains within and between sites is examined for the Neolithic sites in the Wei River valley in China. The coefficient of variation [V] for pig measurements at the sites of Wayaogou, Quanhucun and Jiangzhai was calculated, and we observed patterns that show evidence of two populations of different‐size pigs, supporting the likelihood that both wild and domestic pigs were present. Also, size reduction of pigs can be traced within the Neolithic‐early Bronze Age archaeo‐faunal sequence of the Wei River valley. This size reduction was accompanied by an increase of coefficients of variation through the Neolithic. Both of these trends were probably the consequences of pig domestication, and the morphometric differences probably provide evidence for the different stages of pig domestication in this region. Copyright © 2013 John Wiley & Sons, Ltd.     

Wild or domesticated: DNA analysis of ancient water buffalo remains from north China

Recent zooarchaeological studies on water buffalo (Bubalus sp.) remains from China and south Asia question the traditional view that water buffalo were first domesticated in Neolithic China over 7000 years ago. The results from several recent population genetic studies of modern domesticated buffalo (Bubalus bubalis) are not consistent with each other, placing the original center of buffalo's domestication in south Asia, southeast Asia, or China. This paper reports a study using an ancient DNA approach to analyze water buffalo remains from Neolithic sites in north China to investigate their affinities with modern domesticated water buffalo, and to shed light on the origin of modern domesticated water buffalo in China.A 169 bp fragment of D-loop mitochondrial DNA was successfully amplified and verified for 13 of 24 bone samples obtained from seven archaeological sites along the Wei River valley in Shaanxi Province, China. The bone samples which yielded positive DNA can be dated to 8000–3600 cal. BP. The phylogenetic analysis of the obtained DNA sequences along with modern water buffalo sequences indicated that the ancient water buffalos were not the direct ancestor of modern domesticated water buffalo. However, the phylogenetic analysis, along with BLAST searches of these ancient DNA sequences, did demonstrate their relatedness to water buffalo more so than to any other bovid species, confirming the existence of indigenous wild (but now extinct) water buffalo species (B. mephistopheles) in ancient China.The DNA analysis of these ancient remains failed to establish direct links between modern domesticated water buffalo (B. bubalis) and indigenous water buffalo (B. mephistopheles) from ancient China. If further DNA studies of more ancient remains from other regions of China confirm the observation of solely indigenous water buffalo species in ancient China, it would suggest modern water buffalo might not have been first domesticated in China.     

江苏泗洪韩井遗址水稻驯化的植硅体证据及相关问题

韩井遗址顺山集文化一期由洼地和水沟组成的水稻田,很可能是目前发现的最早与人类驯化水稻相关的遗迹,植硅体分析也在一定程度上对这一论断给予支持。从顺山集文化一期到二期,韩井遗址均以水稻双峰型植硅体居多,而且其百分比和浓度(均值)均呈现增多的态势;水稻扇型和横排哑铃型植硅体表现出相反的规律。与同时期顺山集遗址相比,韩井遗址的水稻扇型植硅体尺寸偏小。水稻扇型植硅体鱼鳞状纹饰个数和水稻双峰型植硅体形态测量用于水稻驯化程度的判定上,表现出非协同性。陶胎中掺入破碎稻壳是韩井遗址水稻栽培与驯化实践的又一反映。     

东南亚地区农业起源研究综论

自20世纪50年代始,东南亚地区的农业起源探索历程至今已半个多世纪。大量考古发现表明,东南亚早期农业的性质是依赖于根系作物的驯化和块茎作物的栽培,该地区早期农业的特点与树木栽培的实践紧密相连,但农业起源的时间尺度仍未很好地建立。基于东南亚地区植物遗存和农业性质的特殊性,多种研究方法得以运用,也相继提出了许多不同的理念。东南亚地区农业起源的研究对中国华南地区早期农业的探索具有很好的启示作用。