Dataset Information

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.

SUBMITTER: Alam O

PROVIDER: S-EPMC8557449 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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

Alam Ornob O Gutaker Rafal M RM Wu Cheng-Chieh CC Hicks Karen A KA Bocinsky Kyle K Castillo Cristina Cobo CC Acabado Stephen S Fuller Dorian D d'Alpoim Guedes Jade A JA Hsing Yue-Ie YI Purugganan Michael D MD

Molecular biology and evolution 20211001 11

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 archae ...[more]

PMID: 34240169

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Project description:BackgroundMuch of the data resolution of the haploid non-recombining Y chromosome (NRY) haplogroup O in East Asia are still rudimentary and could be an explanatory factor for current debates on the settlement history of Island Southeast Asia (ISEA). Here, 81 slowly evolving markers (mostly SNPs) and 17 Y-chromosomal short tandem repeats were used to achieve higher level molecular resolution. Our aim is to investigate if the distribution of NRY DNA variation in Taiwan and ISEA is consistent with a single pre-Neolithic expansion scenario from Southeast China to all ISEA, or if it better fits an expansion model from Taiwan (the OOT model), or whether a more complex history of settlement and dispersals throughout ISEA should be envisioned.ResultsWe examined DNA samples from 1658 individuals from Vietnam, Thailand, Fujian, Taiwan (Han, plain tribes and 14 indigenous groups), the Philippines and Indonesia. While haplogroups O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 follow a decreasing cline from Taiwan towards Western Indonesia, O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 decline northward from Western Indonesia towards Taiwan. Compared to the Taiwan plain tribe minority groups the Taiwanese Austronesian speaking groups show little genetic paternal contribution from Han. They are also characterized by low Y-chromosome diversity, thus testifying for fast drift in these populations. However, in contrast to data provided from other regions of the genome, Y-chromosome gene diversity in Taiwan mountain tribes significantly increases from North to South.ConclusionThe geographic distribution and the diversity accumulated in the O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 haplogroups on one hand, and in the O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 haplogroups on the other, support a pincer model of dispersals and gene flow from the mainland to the islands which likely started during the late upper Paleolithic, 18,000 to 15,000 years ago. The branches of the pincer contributed separately to the paternal gene pool of the Philippines and conjointly to the gene pools of Madagascar and the Solomon Islands. The North to South increase in diversity found for Taiwanese Austronesian speaking groups contrasts with observations based on mitochondrial DNA, thus hinting to a differentiated demographic history of men and women in these populations.

Project description:BackgroundThe role played by regional organisations in climate change adaptation and health is growing in Southeast Asia, with the Asian Development Bank and the Asia-Pacific Regional Forum on Health and Environment both supporting health and adaptation initiatives. There is, however, a lack of empirical research on the value that regional organisations add to national health-related adaptation. This qualitative research compares regional project and governance-based models of adaptation and health support in Southeast Asia, providing an analysis of strengths and weaknesses of each, as well as possibilities for improvement.MethodsAn existing adaptation assessment framework was modified for this research, and used as a guide to gather and analyse data from academic and grey literature, policy documents and interviews in order to qualitatively assess two organisations and their different models of adaptation and health support.ResultsThis research found differing strengths in the approaches to climate change and health used by the Asian Development Bank and by the Asia-Pacific Regional Forum on Health and Environment. The regional forum has vision, high levels of perceived legitimacy, and access to 'in-house' expertise in public health and climate change. Conversely, the Asian Development Bank has strengths in project management and access to significant financial resources to support work in climate change and health.ConclusionWhen regional organisations, such as the Asian Development Bank and the Asia-Pacific Regional Forum on Health and Environment, have membership and mandate overlaps, their work will likely benefit from well designed, institutionalised and incentivised coordination mechanisms. Coordination can reduce redundancies as well as the administrative workload on partner government agencies. In the case-study examined, the Asian Development Bank's project management expertise complements the vision and high levels of perceived legitimacy of the Asia-Pacific Regional Forum on Health and Environment, thus a coordinated approach could deliver improved adaptation and health outcomes.

Dataset Information

Genome analysis traces regional dispersal of rice in Taiwan and Southeast Asia.

Publications

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

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