Genome Analysis Traces Regional Dispersal of Rice in Taiwan and Southeast Asia

Abstract

The dispersal of rice (Oryza sativa) following domestication influenced massive social and cultural changes across South, East, and Southeast Asia. The history of dispersal across islands of Southeast 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 through Taiwan and the northern Philippines using whole-genome re-sequencing 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 3500 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 Southeast Asia respectively. We find that the temperate japonica component of these indigenous Taiwan populations diverged from northeast Asia subpopulations at about 2600 BP, while gene flow from the northern Philippines occurred before ∼1300 years 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.

Amis Pacilo and Yami Cipoho are not the same as the Pacific breadfruit starch crop—Target enrichment phylogenomics of a long-misidentified Artocarpus species sheds light on the northward Austronesian migration from the Philippines to Taiwan

“…100 km south of Taiwan and Lanyu [11,14] across the Bashi Channel (Fig 1). The conjecture that Yami represents a northward Austronesian migration from the Philippines to Taiwan is also consistent with the idea that Neolithic Taiwan was part of the integral maritime trade networks around the South China Sea [15][16][17]. Surprisingly, however, archaeological and genetic studies both suggest that Yami are closer to Formosan indigenous peoples than the Ivatan [18,19].…”

Origin and Demographic History of Philippine Pigs Inferred from Mitochondrial DNA

“…Although various literature indicated that the Neolithic expansion was associated with the movements of domestic animals ( Diamond and Bellwood, 2003 ; Piper, 2017 ), a recent study suggest that this was unlikely for chickens as it favored the translocation route from MSEA via Sundaland, and subsequently followed by the southward diffusion from the Philippines into the Pacific islands ( Godinez et al, 2021 ). Moreover, contrary to the prediction of the out-of-Taiwan theory, there is recent evidence of gene flow of indigenous rice from Northern Luzon to Taiwan that occurred ∼1,300 years ago ( Alam et al, 2021 ) favoring the hypothesis of south to north expansion. Thus, this finding may stimulate scientific interest in the complexity of the introduction and dispersal of domestic pigs, particularly the Lanyu pig into the Philippines.…”

“…These patterns of genetic variation may also reflect the multifaceted history of rich trade and barter between travelers and coastal communities, including river movements in coastal settlements in the Philippines in prehistoric and protohistoric times ( Fox, 1967 ). For example, the extent of trade networks around the South China Sea and the Austronesian trade sphere, which included MSEA, Indonesia, the Philippines, Taiwan and southern China, and India to the west ( Hung et al, 2007 ; Alam et al, 2021 ) is very complex, which could likely be linked to the enormous movements of domestic animals and other material cultures. This could include domestic pigs, where episodic admixture of pig lineages from different geographic regions may have occurred, as indicated by the mtDNA signatures of present-day Philippine pig populations.…”

Episodes of Diversification and Isolation in Island Southeast Asian and Near Oceanian Male Lineages

“…S3 , Supplementary Material online). Many of these expansions and population movements that occurred after ∼4 kya were likely triggered by the introduction of agriculture from Austronesian-speaking cultural communities ( Deng et al 2020 ; Alam et al 2021 ), perhaps coupled in some places with the growing influence of local Papuan agricultural practices that had commenced as early as ∼10 kya ( Denham and Haberle 2008 ).…”