Major leaps forward in understanding rice both in genetics and archaeology have taken place in the past decade or so-with the publication of full draft genomes for indica and japonica rice, on the one hand, and with the spread of systematic flotation and increased recovery of archaeological spikelet bases and other rice remains on early sites in China, India and Southeast Asia. This paper will sketch a framework that coherently integrates the evidence from these burgeoning fields. This framework implies a reticulate framework in the phylogeny of early cultivated rice, with multiple starts of cultivation (two is perhaps not enough) but with the key consolidations of adaptations that must have been spread through hybridisation and therefore long-distance cultural contacts.Archaeobotanical evidence allows us to document the gradual evolutionary process of domestication through rice spikelet bases and grain size change. Separate trends in grain size change can be identified in India and China. The earliest centre of rice domestication was in the Yangtze basin of China, but a largely separate trajectory into rice cultivation can be traced in the Ganges plains of India. Intriguingly, contact-induced hybridisation is indicated for the early development of indica in northern India, ca. 2000 BC. An updated synthesis of the interwoven patterns of the spread of various rice varieties throughout Asia and to Madagascar can be suggested in which rice reached most of its historical range of important cultivation by the Iron Age. The distribution of wild rice and genetic diversity in domesticated ricesRice is a highly diversified crop, being grown from the equator to over 40°N, from sea-level ca. 2,700 m in parts of the Himalayas and in a wide ecological range of cultivation systems. Although there is much less ecological variation found within its wild progenitor complex (Oryza rufipogon and Oryza nivara), these are nonetheless distributed over a wide geographical range and a spectrum of ecological niches from permanent to seasonal wetlands. As the origins of cultivation must have developed in places where hunter-gatherers were utilising wild populations, the distribution of the wild progenitor, in the past when cultivation began, is a key element in identifying the origins of rice. There are three lines of approach to inferring this without archaeological evidence, including (1) the Electronic supplementary material The online version of this article (

We review the origins and dispersal of rice in Asia based on a data base of 443 archaeobotanical reports. Evidence is considered in terms of quality, and especially whether there are data indicating the mode of cultivation, in flooded ('paddy' or 'wet') or non-flooded ('dry') fields. At present it appears that early rice cultivation in the Yangtze region and southern China was based on wet, paddy-field systems from early on, before 4000 bc, whereas early rice in northern India and Thailand was predominantly dry rice at 2000 bc, with a transition to flooded rice documented for India at c. 1000 bc. On the basis of these data we have developed a GIS spatial model of the spread of rice and the growth of land area under paddy rice. This is then compared with a review of the spread of ungulate livestock (cattle, water buffalo, sheep, goat) throughout the Old World. After the initial dispersal through Europe and around the Mediterranean (7000-4000 bc), the major period of livestock expansion is after 3000 bc, into the Sub-Saharan savannas, through monsoonal India and into central China. Further expansion, to southern Africa and Southeast Asia dates mostly after 1000 bc. Based on these two data sets we provide a quantitative model of the land area under irrigated rice, and its likely methane output, through the mid to late Holocene, for comparison to a more preliminary estimate of the expansion of methane-producing livestock. Both data sets are congruent with an anthropogenic source of later Holocene methane after 3000 bc, although it may be that increase in methane input from livestock was most significant in the 3000-1000 bc period, whereas rice paddies become an increasingly significant source especially after 2000 bc.

No abstract

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’.

We have compiled an extensive database of archaeological evidence for rice across Asia, including 400 sites from mainland East Asia, Southeast Asia and South Asia. This dataset is used to compare several models for the geographical origins of rice cultivation and infer the most likely region(s) for its origins and subsequent outward diffusion. The approach is based on regression modelling wherein goodness of fit is obtained from power law quantile regressions of the archaeologically inferred age versus a least-cost distance from the putative origin(s). The Fast Marching method is used to estimate the least-cost distances based on simple geographical features. The origin region that best fits the archaeobotanical data is also compared to other hypothetical geographical origins derived from the literature, including from genetics, archaeology and historical linguistics. The model that best fits all available archaeological evidence is a dual origin model with two centres for the cultivation and dispersal of rice focused on the Middle Yangtze and the Lower Yangtze valleys.

No abstract

28Rice (Oryza sativa) is one of the world's most important food crops. We reconstruct 29

The history of human settlement in Southeast Asia has been complex and involved several distinct dispersal events. Here, we report the analyses of 1825 individuals from Southeast Asia including new genome-wide genotype data for 146 individuals from three Mainland Southeast Asian (Burmese, Malay and Vietnamese) and four Island Southeast Asian (Dusun, Filipino, Kankanaey and Murut) populations. While confirming the presence of previously recognised major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesian expansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers. Given the extensive presence of trade goods, cultural and linguistic evidence of Indian influence in Southeast Asia starting from 2.5 kya, we also detect traces of a South Asian signature in different populations in the region dating to the last couple of thousand years.