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Liu D, Ko AMS, Stoneking M. The genomic diversity of Taiwanese Austronesian groups: Implications for the "Into- and Out-of-Taiwan" models. PNAS NEXUS 2023; 2:pgad122. [PMID: 37200801 PMCID: PMC10187666 DOI: 10.1093/pnasnexus/pgad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/20/2023]
Abstract
The origin and dispersal of the Austronesian language family, one of the largest and most widespread in the world, have long attracted the attention of linguists, archaeologists, and geneticists. Even though there is a growing consensus that Taiwan is the source of the spread of Austronesian languages, little is known about the migration patterns of the early Austronesians who settled in and left Taiwan, i.e. the "Into-Taiwan" and "out-of-Taiwan" events. In particular, the genetic diversity and structure within Taiwan and how this relates to the into-/out-of-Taiwan events are largely unexplored, primarily because most genomic studies have largely utilized data from just two of the 16 recognized Highland Austronesian groups in Taiwan. In this study, we generated the largest genome-wide data set of Taiwanese Austronesians to date, including six Highland groups and one Lowland group from across the island and two Taiwanese Han groups. We identified fine-scale genomic structure in Taiwan, inferred the ancestry profile of the ancestors of Austronesians, and found that the southern Taiwanese Austronesians show excess genetic affinities with the Austronesians outside of Taiwan. Our findings thus shed new light on the Into- and Out-of-Taiwan dispersals.
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Affiliation(s)
- Dang Liu
- To whom correspondence should be addressed: ;
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Izawa T. Reloading DNA History in Rice Domestication. PLANT & CELL PHYSIOLOGY 2022; 63:1529-1539. [PMID: 35656860 PMCID: PMC9680854 DOI: 10.1093/pcp/pcac073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/14/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Although crop domestication is a prehistoric event, DNA (or genome) sequences of modern cultivars and the accession lines of wild relatives contain information regarding the history of crop domestication and the breeding process. Accordingly, with plentiful genomic data, many new findings have been obtained concerning the crop domestication process, for which various (some controversial) interpretations exist. Since approximately 20 years ago, dozens of quantitative trait genes (QTGs) related to the domestication process have been cloned from several crops including rice, a global staple food. However, the determination of how and when these QTGs were involved in rice domestication requires a precise understanding of the DNA code. In addition to the identification of domestication-related QTGs, large-scale rice genome analysis based on short-read Illumina data (but with shallow depth) including more than 1,000 rice cultivars and hundreds of wild rice (or Oryza rufipogon) lines, along with extensive genome analysis including more than 3,000 cultivars with sufficient Illumina data, has been reported. From these data, the genome-wide changes during rice domestication have been explained. However, these genome-wide changes were not interpreted based on QTG changes for domestication-related traits during rice domestication. In addition, a substantial gap remains between the archeological hypothesis based on ancient relics and findings from DNA variations among current cultivars. Thus, this review reconsiders the present status of rice domestication research from a biologist's perspective.
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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. PLoS One 2022; 17:e0272680. [PMID: 36178903 PMCID: PMC9524695 DOI: 10.1371/journal.pone.0272680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/10/2022] [Indexed: 11/23/2022] Open
Abstract
‘Breadfruit’ is a common tree species in Taiwan. In the indigenous Austronesian Amis culture of eastern Taiwan, ‘breadfruit’ is known as Pacilo, and its fruits are consumed as food. On Lanyu (Botel Tobago) where the indigenous Yami people live, ‘breadfruit’ is called Cipoho and used for constructing houses and plank-boats. Elsewhere in Taiwan, ‘breadfruit’ is also a common ornamental tree. As an essential component of traditional Yami culture, Cipoho has long been assumed to have been transported from the Batanes Island of the Philippines to Lanyu. As such, it represents a commensal species that potentially can be used to test the hypothesis of the northward Austronesian migration ‘into’ Taiwan. However, recent phylogenomic studies using target enrichment show that Taiwanese ‘breadfruit’ might not be the same as the Pacific breadfruit (Artocarpus altilis), which was domesticated in Oceania and widely cultivated throughout the tropics. To resolve persistent misidentification of this culturally and economically important tree species of Taiwan, we sampled 36 trees of Taiwanese Artocarpus and used the Moraceae probe set to enrich 529 nuclear genes. Along with 28 archived Artocarpus sequence datasets (representing a dozen taxa from all subgenera), phylogenomic analyses showed that all Taiwanese ‘breadfruit’ samples, together with a cultivated ornamental tree from Hawaii, form a fully supported clade within the A. treculianus complex, which is composed only of endemic Philippine species. Morphologically, the Taiwanese ‘breadfruit’ matches the characters of A. treculianus. Within the Taiwanese samples of A. treculianus, Amis samples form a fully supported clade derived from within the paraphyletic grade composed of Yami samples, suggesting a Lanyu origin. Results of our target enrichment phylogenomics are consistent with the scenario that Cipoho was transported northward from the Philippines to Lanyu by Yami ancestors, though the possibility that A. treculianus is native to Lanyu cannot be ruled out completely.
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Deng Z, Kuo SC, Carson MT, Hung HC. Early Austronesians Cultivated Rice and Millet Together: Tracing Taiwan's First Neolithic Crops. FRONTIERS IN PLANT SCIENCE 2022; 13:962073. [PMID: 35937368 PMCID: PMC9355678 DOI: 10.3389/fpls.2022.962073] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 06/20/2022] [Indexed: 05/29/2023]
Abstract
This study presents the first directly dated physical evidence of crop remains from the Early Neolithic archaeological layers in Taiwan. Systematic sampling and analysis of macro-plant remains suggested that Neolithic farmers at the Zhiwuyuan (Botanical Garden) site in Taipei, northern Taiwan, had cultivated rice and foxtail millet together at least 4,500 years ago. A more comprehensive review of all related radiocarbon dates suggests that agriculture emerged in Taiwan around 4,800-4,600 cal. BP, instead of the previous claim of 5,000 cal. BP. According to the rice grain metrics from three study sites of Zhiwuyuan, Dalongdong, and Anhe, the rice cultivated in northern and western-central Taiwan was mainly a short-grained type of the japonica subspecies, similar to the discoveries from the southeast coast of mainland China and the middle Yangtze valley. These new findings support the hypothesis that the southeast coast of mainland China was the origin of proto-Austronesian people who brought their crops and other cultural traditions across the Taiwan Strait 4,800 years ago and eventually farther into Island Southeast Asia.
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Affiliation(s)
- Zhenhua Deng
- Center for the Study of Chinese Archaeology, Peking University, Beijing, China
- School of Archaeology and Museology, Peking University, Beijing, China
| | - Su-chiu Kuo
- Institute of History and Philology, Academia Sinica, Taipei, Taiwan
| | | | - Hsiao-chun Hung
- Department of Archaeology and Natural History, The Australian National University, Canberra, ACT, Australia
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Karmin M, Flores RJ, Saag L, Hudjashov G, Brucato N, Crenna-Darusallam C, Larena M, Endicott PL, Jakobsson M, Lansing JS, Sudoyo H, Leavesley M, Metspalu M, Ricaut FX, Cox MP. Episodes of diversification and isolation in Island Southeast Asian and Near Oceanian male lineages. Mol Biol Evol 2022; 39:6539761. [PMID: 35294555 PMCID: PMC8926390 DOI: 10.1093/molbev/msac045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Island Southeast Asia (ISEA) and Oceania host one of the world’s richest assemblages of human phenotypic, linguistic, and cultural diversity. Despite this, the region’s male genetic lineages are globally among the last to remain unresolved. We compiled ∼9.7 Mb of Y chromosome (chrY) sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this data set allows us to fully resolve and date the regional chrY phylogeny. This new high-resolution tree confirms two main population bursts: multiple rapid diversifications following the region’s initial settlement ∼50 kya, and extensive expansions <6 kya. Notably, ∼40–25 kya the deep rooting local lineages of C-M130, M-P256, and S-B254 show almost no further branching events in ISEA, New Guinea, and Australia, matching a similar pause in diversification seen in maternal mitochondrial DNA lineages. The main local lineages start diversifying ∼25 kya, at the time of the last glacial maximum. This improved chrY topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and ISEA, potential interactions between Australia and the Papuan world, and a sustained period of diversification following the flooding of the ancient Sunda and Sahul continents as the insular landscape observed today formed. The high-resolution phylogeny of the chrY presented here thus enables a detailed exploration of past isolation, interaction, and change in one of the world’s least understood regions.
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Affiliation(s)
- Monika Karmin
- School of Natural Sciences, Massey University, Palmerston North, 4442, New Zealand
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
| | - Rodrigo J Flores
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
- Institute of Computer Science,University of Tartu, Tartu, 51009, Estonia
| | - Lauri Saag
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
| | - Georgi Hudjashov
- School of Natural Sciences, Massey University, Palmerston North, 4442, New Zealand
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
| | - Nicolas Brucato
- Laboratoire Evolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées,CNRS, IRD, UPS, Toulouse
| | - Chelzie Crenna-Darusallam
- Genome Diversity and Disease Laboratory, Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia
| | - Maximilian Larena
- Department of Organismal Biology, University of Uppsala, Uppsala, 75236, Sweden
| | - Phillip L Endicott
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
- Department Hommes Natures Societies, Musée de l’Homme, Paris, Ile de France, 75016, France
| | - Mattias Jakobsson
- Department of Organismal Biology, University of Uppsala, Uppsala, 75236, Sweden
| | | | - Herawati Sudoyo
- Genome Diversity and Disease Laboratory, Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia
- School of Humanities and Social Sciences, University of Papua New Guinea, National Capital District, Papua New Guinea
- CABAH and College of Arts, Society and Education, James Cook University, Cairns, QLD, 4870, Australia
| | - Matthew Leavesley
- School of Humanities and Social Sciences, University of Papua New Guinea, National Capital District, Papua New Guinea
- CABAH and College of Arts, Society and Education, James Cook University, Cairns, QLD, 4870, Australia
| | - Mait Metspalu
- Institute of Genomics,University of Tartu, Tartu, 51010, Estonia
| | - François-Xavier Ricaut
- Laboratoire Evolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées,CNRS, IRD, UPS, Toulouse
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, 4442, New Zealand
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Layos JKN, Godinez CJP, Liao LM, Yamamoto Y, Masangkay JS, Mannen H, Nishibori M. Origin and Demographic History of Philippine Pigs Inferred from Mitochondrial DNA. Front Genet 2022; 12:823364. [PMID: 35145546 PMCID: PMC8822243 DOI: 10.3389/fgene.2021.823364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 12/28/2021] [Indexed: 01/27/2023] Open
Abstract
The Philippines is a mega-diverse country that lies at the crossroads of past human migrations in the Asia-Pacific region and is believed to have never been connected to the Asian continent, even during the major sea-level subsidence of the Quaternary. As a result, the history of pig dispersal in the Philippines remains controversial, due to limited molecular studies and absence of archaeological evidence of pig domestication. This study provides the first comprehensive analysis of 184 complete mitochondrial DNA D-loop region from Philippine pigs to elucidate their early dispersal history by performing a phylogenetic comparison with wild boars and domestic pigs worldwide. The results showed a demographic signal of the ancestry of Philippine pigs that had a close genetic relationship with those from the mainland Southeast Asia and Northeast Asia, suggesting gene flow that may have resulted from human migration and trade. Here we have suggested two possible dispersal routes. One parallels the Neolithic expansion in Island Southeast Asia and Oceania via Northeast Asia, the other from the mainland Southeast Asia, into Palawan and Sulu Archipelago as early as prehistoric times via the Sundaic Region. Despite geographic barriers to migration, numerous genetic lineages have persisted across the Philippine islands, even justifying the recognition of a Philippine Lanyu subclade. The prehistoric population history suggests a demographic expansion that coincided with the interglacial periods of the Pleistocene and may have spread from the southern regions into the eastern and central regions of the Philippines. The intriguing signal of discrepancy discovered between the ancestral pattern and distribution range of the numerous endemic Philippine wild pigs opens a challenging new approach to illuminate complexity among these animals. Our study has contributed significantly towards completing the sparse molecular studies on Philippine pigs, an essential for creating win-win conservation measures.
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Affiliation(s)
- John King N. Layos
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- College of Agriculture and Forestry, Capiz State University, Mambusao, Philippines
- *Correspondence: John King N. Layos, ; Masahide Nishibori,
| | - Cyrill John P. Godinez
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Department of Animal Science, Visayas State University, Baybay City, Philippines
| | - Lawrence M. Liao
- Laboratory of Aquatic Botany, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yoshio Yamamoto
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Joseph S. Masangkay
- College of Veterinary Medicine, University of the Philippines, Los Baños, Philippines
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
- Department of Animal Science, Visayas State University, Baybay City, Philippines
- *Correspondence: John King N. Layos, ; Masahide Nishibori,
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