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.
Abstract
The dispersal of rice (Oryza sativa) following domestication influenced massive social and cultural changes across South, East, and Southeast (SE) Asia. The history of dispersal across ...islands of SE Asia, and the role of Taiwan and the Austronesian expansion in this process remain largely unresolved. Here, we reconstructed the routes of dispersal of O. sativa ssp. japonica rice to Taiwan and the northern Philippines using whole-genome resequencing of indigenous rice landraces coupled with archaeological and paleoclimate data. Our results indicate that japonica rice found in the northern Philippines diverged from Indonesian landraces as early as 3,500 years before present (BP). In contrast, rice cultivated by the indigenous peoples of the Taiwanese mountains has complex origins. It comprises two distinct populations, each best explained as a result of admixture between temperate japonica that presumably came from northeast Asia, and tropical japonica from the northern Philippines and mainland SE Asia, respectively. We find that the temperate japonica component of these indigenous Taiwan populations diverged from northeast Asia subpopulations at about 2,600 BP, whereas gene flow from the northern Philippines had begun before ∼1,300 BP. This coincides with a period of intensified trade established across the South China Sea. Finally, we find evidence for positive selection acting on distinct genomic regions in different rice subpopulations, indicating local adaptation associated with the spread of japonica rice.
We examine the Holocene loess record in the Heye Catchment on the margins of the Tibetan Plateau (TP) and China Loess Plateau (CLP) to determine: the region to which the Heye Catchment climate is ...more similar; temporal change in wind strength; and modification of the loess record by mass wasting and human activity. Luminescence and radiocarbon dating demonstrate loess deposited in two periods: >11–8.6 ka and <5.1 ka. The 8.6–5.1 ka depositional hiatus, which coincides with the Mid-Holocene Climatic Optimum, is more similar to the loess deposition cessation in the TP than to the loess deposition deceleration in the CLP. Grain-size analysis suggests the Heye loess is a mixture of at least three different grain-size distributions and that it may derive from multiple sources. A greater proportion of coarse sediments in the older loess may indicate stronger winds compared with the more recent depositional period. Gravel incorporated into younger loess most likely comes from bedrock exposed in slump scarps. Human occupation of the catchment, for which the earliest evidence is 3.4 ka, postdates the onset of slumping; thus the slumps may have created a livable environment for humans.
In prehistoric coastal and western-central Thailand, rice was the dominant cultivar. In eastern-central Thailand, however, the first known farmers cultivated millet. Using one of the largest ...collections of archaeobotanical material in Southeast Asia, this article examines how cropping systems were adapted as domesticates were introduced into eastern-central Thailand. The authors argue that millet reached the region first, to be progressively replaced by rice, possibly due to climatic pressures. But despite the increasing importance of rice, dryland, rain-fed cultivation persisted throughout ancient central Thailand, a result that contributes to refining understanding of the development of farming in Southeast Asia.
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