A tale of two rice varieties: Modelling the prehistoric dispersals of japonica and proto-indica rices

Abstract

We model the prehistoric dispersals of two rice varieties, japonica and proto-indica, across Asia using empirical evidence drawn from an archaeobotanical dataset of 400 sites from mainland East, Southeast and South Asia. The approach is based on regression modelling wherein goodness of fit is obtained from log-log quantile regressions of the archaeologically inferred age versus a least-cost distance from the origin(s) of dispersal. The Fast Marching method is used to estimate the least-cost distances based on simple geographical features. We explicitly test three hypotheses for the arrival of japonica rice to India where, it has been proposed, it hybridized with the indigenous proto-indica, subsequently spreading again throughout India. Model selection, based on information criteria, highlights the role of the Inner Asia Mountain Corridor in introducing japonica rice into northeast India, followed closely by a 'mixed route' model, where japonica was also almost simultaneously introduced via Assam, Bangladesh and Myanmar. Finally, we estimate the impact of future archaeological work on model selection, further strengthening the importance of the Inner Asia Mountain Corridor.

Genomic history and ecology of the geographic spread of rice

“…Archaeological evidence [6][7][8] indicates that cultivation of japonica rice began ~9,000 years before present (yBP) in the lower Yangtze Valley, while proto-indica rice cultivation started >5,000 yBP in the lower Ganges valley 9 . Archaeological 10 and most population genetic analyses [11][12][13] suggest that important domestication alleles have a single origin in japonica rice in East Asia.…”

Genomic history and ecology of the geographic spread of rice

“…Archaeological evidence ( 4–6 ) indicates that cultivation of japonica rice began ∼9,000 years before present (yBP) in the lower Yangtze Valley, while proto-indica rice cultivation started >5,000 yBP in the lower Ganges valley ( 7 ). Archaeological ( 8 ) and most population genetic analyses ( 9–11 ) suggest that important domestication alleles have a single origin in japonica rice in East Asia.…”

“…Archaeological data shows the general directionality of rice dispersal ( 7, 13 ); the details of dispersal routes, times, and the environmental forces that shaped dispersal patterns, however, remain unknown. Here, we undertake population genomic analyses to examine environmental factors associated with the geographic distribution of rice diversity, and reconstruct the ancient dispersal of rice in Asia.…”

Dry, rainfed or irrigated? Reevaluating the role and development of rice agriculture in Iron Age-Early Historic South India using archaeobotanical approaches

“…There is a period of approximately 1000 years in which the transition from using proto- indica rice (the early rice variety indigenous to India) to supplement subsistence in the Ganges Basin to the use of rice as a primary cultivated domestic crop across the Indo-Gangetic Basin occurred, c.2500 BC (Silva et al 2018). There is a hiatus, however, before rice cultivation is taken up in drier parts of India: the Deccan and South India (Fig.…”

“…1 a Locations and time periods of archaeological sites in South India with published archaeobotanical data recorded in Stevens et al (2016). b Map showing the spread of rice across South Asia based on Fast-March modelling, from Silva et al (2018). Sites in black have macrobotanical remains of domesticated-type rice spikelet bases; sites in red are those studied in this article…”