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King B, Greenhill SJ, Reid LA, Ross M, Walworth M, Gray RD. Bayesian phylogenetic analysis of Philippine languages supports a rapid migration of Malayo-Polynesian languages. Sci Rep 2024; 14:14967. [PMID: 38942799 PMCID: PMC11213883 DOI: 10.1038/s41598-024-65810-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 06/24/2024] [Indexed: 06/30/2024] Open
Abstract
The Philippines are central to understanding the expansion of the Austronesian language family from its homeland in Taiwan. It remains unknown to what extent the distribution of Malayo-Polynesian languages has been shaped by back migrations and language leveling events following the initial Out-of-Taiwan expansion. Other aspects of language history, including the effect of language switching from non-Austronesian languages, also remain poorly understood. Here we apply Bayesian phylogenetic methods to a core-vocabulary dataset of Philippine languages. Our analysis strongly supports a sister group relationship between the Sangiric and Minahasan groups of northern Sulawesi on one hand, and the rest of the Philippine languages on the other, which is incompatible with a simple North-to-South dispersal from Taiwan. We find a pervasive geographical signal in our results, suggesting a dominant role for cultural diffusion in the evolution of Philippine languages. However, we do find some support for a later migration of Gorontalo-Mongondow languages to northern Sulawesi from the Philippines. Subsequent diffusion processes between languages in Sulawesi appear to have led to conflicting data and a highly unstable phylogenetic position for Gorontalo-Mongondow. In the Philippines, language switching to Austronesian in 'Negrito' groups appears to have occurred at different time-points throughout the Philippines, and based on our analysis, there is no discernible effect of language switching on the basic vocabulary.
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Affiliation(s)
- Benedict King
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| | - Simon J Greenhill
- School of Biological Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Lawrence A Reid
- National Museum of the Philippines, 1000, Ermita, Manila, Metro Manila, Philippines
- Department of Linguistics, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Malcolm Ross
- School of Culture, History and Language, Australian National University, Canberra, 2601, Australia
| | - Mary Walworth
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Russell D Gray
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
- School of Psychology, University of Auckland, Auckland, 1142, New Zealand
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2
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Passmore S, Wood ALC, Barbieri C, Shilton D, Daikoku H, Atkinson QD, Savage PE. Global musical diversity is largely independent of linguistic and genetic histories. Nat Commun 2024; 15:3964. [PMID: 38729968 PMCID: PMC11087526 DOI: 10.1038/s41467-024-48113-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
Music is a universal yet diverse cultural trait transmitted between generations. The extent to which global musical diversity traces cultural and demographic history, however, is unresolved. Using a global musical dataset of 5242 songs from 719 societies, we identify five axes of musical diversity and show that music contains geographical and historical structures analogous to linguistic and genetic diversity. After creating a matched dataset of musical, genetic, and linguistic data spanning 121 societies containing 981 songs, 1296 individual genetic profiles, and 121 languages, we show that global musical similarities are only weakly and inconsistently related to linguistic or genetic histories, with some regional exceptions such as within Southeast Asia and sub-Saharan Africa. Our results suggest that global musical traditions are largely distinct from some non-musical aspects of human history.
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Affiliation(s)
- Sam Passmore
- Graduate School of Media and Governance, Keio University, Fujisawa, Japan.
- Evolution of Cultural Diversity Initiative (ECDI), Australian National University, Canberra, Australia.
| | | | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, 8057, Switzerland
- Centre for the Interdisciplinary Study of Language Evolution (ISLE), University of Zurich, Zurich, 8050, Switzerland
- Department of Life and Environmental Sciences, University of Cagliari, 09126, Cagliari, Italy
| | - Dor Shilton
- Cohn Institute for the History and Philosophy of Science and Ideas, Tel Aviv University, Tel Aviv, Israel
- Edelstein Centre for the History and Philosophy of Science, Technology, and Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hideo Daikoku
- Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | | | - Patrick E Savage
- School of Psychology, University of Auckland, Auckland, New Zealand.
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan.
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3
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Barron A. Applications of Microct Imaging to Archaeobotanical Research. JOURNAL OF ARCHAEOLOGICAL METHOD AND THEORY 2023:1-36. [PMID: 37359278 PMCID: PMC10225294 DOI: 10.1007/s10816-023-09610-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 04/05/2023] [Indexed: 06/28/2023]
Abstract
The potential applications of microCT scanning in the field of archaeobotany are only just beginning to be explored. The imaging technique can extract new archaeobotanical information from existing archaeobotanical collections as well as create new archaeobotanical assemblages within ancient ceramics and other artefact types. The technique could aid in answering archaeobotanical questions about the early histories of some of the world's most important food crops from geographical regions with amongst the poorest rates of archaeobotanical preservation and where ancient plant exploitation remains poorly understood. This paper reviews current uses of microCT imaging in the investigation of archaeobotanical questions, as well as in cognate fields of geosciences, geoarchaeology, botany and palaeobotany. The technique has to date been used in a small number of novel methodological studies to extract internal anatomical morphologies and three-dimensional quantitative data from a range of food crops, which includes sexually-propagated cereals and legumes, and asexually-propagated underground storage organs (USOs). The large three-dimensional, digital datasets produced by microCT scanning have been shown to aid in taxonomic identification of archaeobotanical specimens, as well as robustly assess domestication status. In the future, as scanning technology, computer processing power and data storage capacities continue to improve, the possible applications of microCT scanning to archaeobotanical studies will only increase with the development of machine and deep learning networks enabling the automation of analyses of large archaeobotanical assemblages.
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Affiliation(s)
- Aleese Barron
- School of Archaeology and Anthropology, Australian National University, Banks Building, Canberra, Canberra ACT 2601 Australia
- Department of Materials Physics, Research School of Physics, Australian National University, Canberra, Canberra ACT 2601 Australia
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4
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Markov I, Kharitonova K, Grigorenko EL. Language: Its Origin and Ongoing Evolution. J Intell 2023; 11:jintelligence11040061. [PMID: 37103246 PMCID: PMC10142271 DOI: 10.3390/jintelligence11040061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
With the present paper, we sought to use research findings to illustrate the following thesis: the evolution of language follows the principles of human evolution. We argued that language does not exist for its own sake, it is one of a multitude of skills that developed to achieve a shared communicative goal, and all its features are reflective of this. Ongoing emerging language adaptations strive to better fit the present state of the human species. Theories of language have evolved from a single-modality to multimodal, from human-specific to usage-based and goal-driven. We proposed that language should be viewed as a multitude of communication techniques that have developed and are developing in response to selective pressure. The precise nature of language is shaped by the needs of the species (arguably, uniquely H. sapiens) utilizing it, and the emergence of new situational adaptations, as well as new forms and types of human language, demonstrates that language includes an act driven by a communicative goal. This article serves as an overview of the current state of psycholinguistic research on the topic of language evolution.
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Affiliation(s)
- Ilia Markov
- Department of Psychology, University of Houston, Houston, TX 77204, USA
- Texas Institute for Measurement, Evaluation, and Statistics (TIMES), The University of Houston, Houston, TX 77204, USA
- Center for Cognitive Sciences, Sirius University for Science and Technology, Sochi 354340, Russia
| | | | - Elena L. Grigorenko
- Department of Psychology, University of Houston, Houston, TX 77204, USA
- Texas Institute for Measurement, Evaluation, and Statistics (TIMES), The University of Houston, Houston, TX 77204, USA
- Center for Cognitive Sciences, Sirius University for Science and Technology, Sochi 354340, Russia
- Baylor College of Medicine, Houston, TX 77030, USA
- Child Study Center and Haskins Laboratories, Yale University, New Haven, CT 06520, USA
- Rector’s Office, Moscow State University for Psychology and Education, Moscow 127051, Russia
- Correspondence:
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5
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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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6
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Karmin M, Flores R, 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:msac045. [PMID: 35294555 PMCID: PMC8926390 DOI: 10.1093/molbev/msac045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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, New Zealand
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Rodrigo Flores
- Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Lauri Saag
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Georgi Hudjashov
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Nicolas Brucato
- Laboratoire Evolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, Toulouse, France
| | - Chelzie Crenna-Darusallam
- Genome Diversity and Disease Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Maximilian Larena
- Department of Organismal Biology, University of Uppsala, Uppsala, Sweden
| | - Phillip L Endicott
- Institute of Genomics, University of Tartu, Tartu, Estonia
- Department Hommes Natures Societies, Musée de l’Homme, Paris, France
| | - Mattias Jakobsson
- Department of Organismal Biology, University of Uppsala, Uppsala, Sweden
| | - J Stephen Lansing
- Complexity Science Hub Vienna, Vienna, Austria
- Santa Fe Institute Center for Advanced Study in the Behavioral Sciences, Stanford University, Santa Fe, USA
| | - Herawati Sudoyo
- Genome Diversity and Disease Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - 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, Australia
| | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - François-Xavier Ricaut
- Laboratoire Evolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, Toulouse, France
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
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7
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Grimaldi IM, Van Andel TR, Denham TP. Looking beyond history: tracing the dispersal of the Malaysian complex of crops to Africa. AMERICAN JOURNAL OF BOTANY 2022; 109:193-208. [PMID: 35119100 DOI: 10.1002/ajb2.1821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
In his 1959 book, Africa: Its Peoples and Their Culture History, George P. Murdock suggested that a Malaysian complex of crops dispersed to Africa in ancient times across the Indian Ocean along the Sabaean Lane. The Malaysian complex comprised bananas, sugarcane, taro, three yam species, rice, Polynesian arrowroot, breadfruit, coconut, areca palm, and betel leaf. Except for rice, arrowroot, and potentially taro, most of these crops were domesticated in the Island Southeast Asia-New Guinea region, from where they dispersed to Africa. Our reassessment of agronomic, archaeological, classical, genetic, and historical sources shows that we need to go beneath standard historical narratives to recover a much more ancient and complex history of crop introductions to Africa. Despite considerable uncertainty and fragmented research, we were able to conclude that the Malaysian complex of crops did not arrive in Africa as a complete assemblage at one time or along one route. Multiple lines of evidence suggest that these crops arrived in Africa at different times and followed different pathways of introduction to the continent.
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Affiliation(s)
- Ilaria M Grimaldi
- Office of Innovation-Research and Extension (OINR), Food and Agriculture Organization of UN (FAO), Viale delle Terme di Caracalla, Rome, 00153, Italy
| | - Tinde R Van Andel
- Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands
| | - Tim P Denham
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT 2601, Australia
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8
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Alam O, Gutaker RM, Wu CC, Hicks KA, Bocinsky K, Castillo CC, Acabado S, Fuller D, d'Alpoim Guedes JA, Hsing YI, Purugganan MD. Genome analysis traces regional dispersal of rice in Taiwan and Southeast Asia. Mol Biol Evol 2021; 38:4832-4846. [PMID: 34240169 PMCID: PMC8557449 DOI: 10.1093/molbev/msab209] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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.
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Affiliation(s)
- Ornob Alam
- Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA
| | - Rafal M Gutaker
- Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA.,Royal Botanic Garden, Kew, Richmond, London, TW9 3AE UK
| | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan.,Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan
| | - Karen A Hicks
- Department of Biology, Kenyon College, Gambier, Ohio 43022 USA
| | | | | | - Stephen Acabado
- Department of Anthropology, University of California, Los Angeles, CA USA
| | - Dorian Fuller
- Institute of Archaeology, University College London, London, United Kingdom.,School of Cultural Heritage, North-West University, Xi'an, China
| | - Jade A d'Alpoim Guedes
- Department of Anthropology and Scripps Institution of Oceanography, University of California, San Diego, CA, USA
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA.,Institute for the Study of the Ancient World, New York University, New York, NY 10028 USA
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9
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The first quantitative assessment of radiocarbon chronologies for initial pottery in Island Southeast Asia supports multi-directional Neolithic dispersal. PLoS One 2021; 16:e0251407. [PMID: 34077445 PMCID: PMC8171956 DOI: 10.1371/journal.pone.0251407] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 04/27/2021] [Indexed: 11/29/2022] Open
Abstract
Neolithization, or the Holocene demographic expansion of farming populations, accounts for significant changes in human and animal biology, artifacts, languages, and cultures across the earth. For Island Southeast Asia, the orthodox Out of Taiwan hypothesis proposes that Neolithic expansion originated from Taiwan with populations moving south into Island Southeast Asia, while the Western Route Migration hypothesis suggests the earliest farming populations entered from Mainland Southeast Asia in the west. These hypotheses are also linked to competing explanations of the Austronesian expansion, one of the most significant population dispersals in the ancient world that influenced human and environmental diversity from Madagascar to Easter Island and Hawai‘i to New Zealand. The fundamental archaeological test of the Out of Taiwan and Western Route Migration hypotheses is the geographic and chronological distribution of initial pottery assemblages, but these data have never been quantitatively analyzed. Using radiocarbon determinations from 20 archaeological sites, we present a Bayesian chronological analysis of initial pottery deposition in Island Southeast Asia and western Near Oceania. Both site-scale and island-scale Bayesian models were produced in Oxcal using radiocarbon determinations that are most confidently associated with selected target events. Our results indicate multi-directional Neolithic dispersal in Island Southeast Asia, with the earliest pottery contemporaneously deposited in western Borneo and the northern Philippines. This work supports emerging research that identifies separate processes of biological, linguistic, and material culture change in Island Southeast Asia.
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10
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Abstract
A key link to understand human history in Island Southeast Asia is the Philippine archipelago and its poorly investigated genetic diversity. We analyzed the most comprehensive set of population-genomic data for the Philippines: 1,028 individuals covering 115 indigenous communities. We demonstrate that the Philippines were populated by at least five waves of human migration. The Cordillerans migrated into the Philippines prior to the arrival of rice agriculture, where some remain as the least admixed East Asians carrying an ancestry shared by all Austronesian-speaking populations, thereby challenging an exclusive out-of-Taiwan model of joint farming–language–people dispersal. Altogether, our findings portray the Philippines as a crucial gateway, with a multilayered history, that ultimately changed the genetic landscape of the Asia-Pacific region. Island Southeast Asia has recently produced several surprises regarding human history, but the region’s complex demography remains poorly understood. Here, we report ∼2.3 million genotypes from 1,028 individuals representing 115 indigenous Philippine populations and genome-sequence data from two ∼8,000-y-old individuals from Liangdao in the Taiwan Strait. We show that the Philippine islands were populated by at least five waves of human migration: initially by Northern and Southern Negritos (distantly related to Australian and Papuan groups), followed by Manobo, Sama, Papuan, and Cordilleran-related populations. The ancestors of Cordillerans diverged from indigenous peoples of Taiwan at least ∼8,000 y ago, prior to the arrival of paddy field rice agriculture in the Philippines ∼2,500 y ago, where some of their descendants remain to be the least admixed East Asian groups carrying an ancestry shared by all Austronesian-speaking populations. These observations contradict an exclusive “out-of-Taiwan” model of farming–language–people dispersal within the last four millennia for the Philippines and Island Southeast Asia. Sama-related ethnic groups of southwestern Philippines additionally experienced some minimal South Asian gene flow starting ∼1,000 y ago. Lastly, only a few lowlanders, accounting for <1% of all individuals, presented a low level of West Eurasian admixture, indicating a limited genetic legacy of Spanish colonization in the Philippines. Altogether, our findings reveal a multilayered history of the Philippines, which served as a crucial gateway for the movement of people that ultimately changed the genetic landscape of the Asia-Pacific region.
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11
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Deng Z, Hung HC, Carson MT, Oktaviana AA, Hakim B, Simanjuntak T. Validating earliest rice farming in the Indonesian Archipelago. Sci Rep 2020; 10:10984. [PMID: 32620777 PMCID: PMC7335082 DOI: 10.1038/s41598-020-67747-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/28/2020] [Indexed: 11/26/2022] Open
Abstract
Preserved ancient botanical evidence in the form of rice phytoliths has confirmed that people farmed domesticated rice (Oryza sativa) in the interior of Sulawesi Island, Indonesia, by at least 3,500 years ago. This discovery helps to resolve a mystery about one of the region's major events in natural and cultural history, by documenting when rice farming spread into Indonesia, ultimately from a source in mainland China. At the Minanga Sipakko site in Sulawesi, preserved leaf and husk phytoliths of rice show the diagnostic morphology of domesticated varieties, and the discarded husks indicate on-site processing of the crops. The phytoliths were contained within an undisturbed, subsurface archaeological layer of red-slipped pottery, a marker for an evidently sudden cultural change in the region that multiple radiocarbon results extend back to 3,500 years ago. The results from Minanga Sipakko allow factual evaluation of previously untested hypotheses about the timing, geographic pattern, and cultural context of the spread of rice farming into Indonesia, as well as the contribution of external immigrants in this process.
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Affiliation(s)
- Zhenhua Deng
- Center for the Study of Chinese Archaeology, Peking University, Beijing, 100871, China.
- School of Archaeology and Museology, Peking University, Beijing, 100871, China.
| | - Hsiao-Chun Hung
- Department of Archaeology and Natural History, Australian National University, Canberra, ACT 2061, Australia.
| | - Mike T Carson
- Micronesian Area Research Center, University of Guam, Mangilao, Guam, 96913, USA
| | - Adhi Agus Oktaviana
- Center for Prehistoric and Austronesian Studies, and National Center for Archaeology, Jalan Raya Condet Pejaten 4, Jakarta, 12510, Indonesia
| | - Budianto Hakim
- Balai Arkeologi Makassar, Jl. Pajjaiang No.13, Sudiang Raya, Kota Makassar, Sulawesi Selatan, 90242, Indonesia
| | - Truman Simanjuntak
- Center for Prehistoric and Austronesian Studies, and National Center for Archaeology, Jalan Raya Condet Pejaten 4, Jakarta, 12510, Indonesia
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12
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Papuan mitochondrial genomes and the settlement of Sahul. J Hum Genet 2020; 65:875-887. [PMID: 32483274 PMCID: PMC7449881 DOI: 10.1038/s10038-020-0781-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/29/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023]
Abstract
New Guineans represent one of the oldest locally continuous populations outside Africa, harboring among the greatest linguistic and genetic diversity on the planet. Archeological and genetic evidence suggest that their ancestors reached Sahul (present day New Guinea and Australia) by at least 55,000 years ago (kya). However, little is known about this early settlement phase or subsequent dispersal and population structuring over the subsequent period of time. Here we report 379 complete Papuan mitochondrial genomes from across Papua New Guinea, which allow us to reconstruct the phylogenetic and phylogeographic history of northern Sahul. Our results support the arrival of two groups of settlers in Sahul within the same broad time window (50–65 kya), each carrying a different set of maternal lineages and settling Northern and Southern Sahul separately. Strong geographic structure in northern Sahul remains visible today, indicating limited dispersal over time despite major climatic, cultural, and historical changes. However, following a period of isolation lasting nearly 20 ky after initial settlement, environmental changes postdating the Last Glacial Maximum stimulated diversification of mtDNA lineages and greater interactions within and beyond Northern Sahul, to Southern Sahul, Wallacea and beyond. Later, in the Holocene, populations from New Guinea, in contrast to those of Australia, participated in early interactions with incoming Asian populations from Island Southeast Asia and continuing into Oceania.
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13
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Hamilton MJ, Walker RS. Nonlinear diversification rates of linguistic phylogenies over the Holocene. PLoS One 2019; 14:e0213126. [PMID: 31314806 PMCID: PMC6636708 DOI: 10.1371/journal.pone.0213126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/20/2019] [Indexed: 11/25/2022] Open
Abstract
The expansion of the human species out of Africa in the Pleistocene, and the subsequent development of agriculture in the Holocene, resulted in waves of linguistic diversification and replacement across the planet. Analogous to the growth of populations or the speciation of biological organisms, languages diversify over time to form phylogenies of language families. However, the dynamics of this diversification process are unclear. Bayesian methods applied to lexical and phonetic data have created dated linguistic phylogenies for 18 language families encompassing ~3,000 of the world's ~7,000 extant languages. In this paper we use these phylogenies to quantify how fast languages expand and diversify through time both within and across language families. The overall diversification rate of languages in our sample is ~0.001 yr-1 (or a doubling time of ~700 yr) over the last 6,000 years with evidence for nonlinear dynamics in language diversification rates over time, where both within and across language families, diversity initially increases rapidly and then slows. The expansion, evolution, and diversification of languages as they spread around the planet was a non-constant process.
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Affiliation(s)
- Marcus J. Hamilton
- Department of Anthropology, University of Texas at San Antonio, San Antonio, TX, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, NM, United States of America
| | - Robert S. Walker
- Department of Anthropology, University of Missouri, Columbia, MO, United States of America
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Affiliation(s)
- Hao-Li Lin
- Institute of Anthropology, National Tsing Hua University, Hsinchu, Taiwan
| | - Richard Scaglion
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA
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Spehar SN, Sheil D, Harrison T, Louys J, Ancrenaz M, Marshall AJ, Wich SA, Bruford MW, Meijaard E. Orangutans venture out of the rainforest and into the Anthropocene. SCIENCE ADVANCES 2018; 4:e1701422. [PMID: 29963619 PMCID: PMC6021148 DOI: 10.1126/sciadv.1701422] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
Conservation benefits from understanding how adaptability and threat interact to determine a taxon's vulnerability. Recognizing how interactions with humans have shaped taxa such as the critically endangered orangutan (Pongo spp.) offers insights into this relationship. Orangutans are viewed as icons of wild nature, and most efforts to prevent their extinction have focused on protecting minimally disturbed habitat, with limited success. We synthesize fossil, archeological, genetic, and behavioral evidence to demonstrate that at least 70,000 years of human influence have shaped orangutan distribution, abundance, and ecology and will likely continue to do so in the future. Our findings indicate that orangutans are vulnerable to hunting but appear flexible in response to some other human activities. This highlights the need for a multifaceted, landscape-level approach to orangutan conservation that leverages sound policy and cooperation among government, private sector, and community stakeholders to prevent hunting, mitigate human-orangutan conflict, and preserve and reconnect remaining natural forests. Broad cooperation can be encouraged through incentives and strategies that focus on the common interests and concerns of different stakeholders. Orangutans provide an illustrative example of how acknowledging the long and pervasive influence of humans can improve strategies to preserve biodiversity in the Anthropocene.
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Affiliation(s)
- Stephanie N. Spehar
- Anthropology Program, University of Wisconsin Oshkosh, Oshkosh, WI 54901, USA
| | - Douglas Sheil
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Terry Harrison
- Department of Anthropology, New York University, New York, NY 10003, USA
| | - Julien Louys
- Australian Research Center for Human Evolution, Environmental Futures Research Institute, Griffith University, Brisbane, Queensland, Australia
| | - Marc Ancrenaz
- Borneo Futures, Bandar Seri Begawan, BE1518 Brunei Darussalam
- Kinabatangan Orang-Utan Conservation Programme, Kota Kinabalu, Sabah, Malaysia
| | - Andrew J. Marshall
- Department of Anthropology, Department of Ecology and Evolutionary Biology, Program in the Environment, and School for Environment and Sustainability, University of Michigan, Ann Arbor, MI 48109, USA
| | - Serge A. Wich
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool L3 3AF, UK
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, Amsterdam 1098, Netherlands
| | - Michael W. Bruford
- Sustainable Places Research Institute and School of Biosciences, Cardiff University, Cardiff, UK
| | - Erik Meijaard
- Borneo Futures, Bandar Seri Begawan, BE1518 Brunei Darussalam
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
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16
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Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles. Sci Rep 2018; 8:1823. [PMID: 29379068 PMCID: PMC5789021 DOI: 10.1038/s41598-018-20026-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/11/2018] [Indexed: 12/14/2022] Open
Abstract
The debate concerning the origin of the Polynesian speaking peoples has been recently reinvigorated by genetic evidence for secondary migrations to western Polynesia from the New Guinea region during the 2nd millennium BP. Using genome-wide autosomal data from the Leeward Society Islands, the ancient cultural hub of eastern Polynesia, we find that the inhabitants' genomes also demonstrate evidence of this episode of admixture, dating to 1,700-1,200 BP. This supports a late settlement chronology for eastern Polynesia, commencing ~1,000 BP, after the internal differentiation of Polynesian society. More than 70% of the autosomal ancestry of Leeward Society Islanders derives from Island Southeast Asia with the lowland populations of the Philippines as the single largest potential source. These long-distance migrants into Polynesia experienced additional admixture with northern Melanesians prior to the secondary migrations of the 2nd millennium BP. Moreover, the genetic diversity of mtDNA and Y chromosome lineages in the Leeward Society Islands is consistent with linguistic evidence for settlement of eastern Polynesia proceeding from the central northern Polynesian outliers in the Solomon Islands. These results stress the complex demographic history of the Leeward Society Islands and challenge phylogenetic models of cultural evolution predicated on eastern Polynesia being settled from Samoa.
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Corny J, Galland M, Arzarello M, Bacon AM, Demeter F, Grimaud-Hervé D, Higham C, Matsumura H, Nguyen LC, Nguyen TKT, Nguyen V, Oxenham M, Sayavongkhamdy T, Sémah F, Shackelford LL, Détroit F. Dental phenotypic shape variation supports a multiple dispersal model for anatomically modern humans in Southeast Asia. J Hum Evol 2017; 112:41-56. [PMID: 29037415 DOI: 10.1016/j.jhevol.2017.08.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 01/05/2023]
Abstract
The population history of anatomically modern humans (AMH) in Southeast Asia (SEA) is a highly debated topic. The impact of sea level variations related to the Last Glacial Maximum (LGM) and the Neolithic diffusion on past population dispersals are two key issues. We have investigated competing AMH dispersal hypotheses in SEA through the analysis of dental phenotype shape variation on the basis of very large archaeological samples employing two complementary approaches. We first explored the structure of between- and within-group shape variation of permanent human molar crowns. Second, we undertook a direct test of competing hypotheses through a modeling approach. Our results identify a significant LGM-mediated AMH expansion and a strong biological impact of the spread of Neolithic farmers into SEA during the Holocene. The present work thus favors a "multiple AMH dispersal" hypothesis for the population history of SEA, reconciling phenotypic and recent genomic data.
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Affiliation(s)
- Julien Corny
- Aix Marseille Université, CNRS, EFS, ADES UMR 7268, 13916, Marseille, France.
| | - Manon Galland
- University College Dublin, School of Archaeology, Belfield, Dublin 4, Ireland; Muséum national d'Histoire naturelle, Musée de l'Homme, Département Homme et environnement, CNRS, UMR 7206, 75116, Paris, France
| | - Marta Arzarello
- Università degli Studi di Ferrara, Dipartimento Studi Umanistici, 44121, Ferrara, Italy
| | - Anne-Marie Bacon
- Université Paris-Descartes, Faculté de chirurgie dentaire, UMR 5288 CNRS, AMIS, 92120, Montrouge, France
| | - Fabrice Demeter
- Muséum national d'Histoire naturelle, Musée de l'Homme, Département Homme et environnement, CNRS, UMR 7206, 75116, Paris, France; Center for GeoGenetics, Copenhagen, Denmark
| | - Dominique Grimaud-Hervé
- Muséum national d'Histoire naturelle, Musée de l'Homme, Département Homme et environnement, CNRS, UMR 7194, 75116, Paris, France
| | - Charles Higham
- University of Otago, Department of Anthropology and Archaeology, Dunedin 9054, New Zealand
| | - Hirofumi Matsumura
- Sapporo Medical University, School of Health Science, Sapporo 060-8556, Japan
| | | | | | - Viet Nguyen
- Center for Southeast Asian Prehistory, 96/203 Hoang Quoc Viet, Hanoi, Viet Nam
| | - Marc Oxenham
- Australian National University, School of Archaeology and Anthropology, Canberra ACT 0200, Australia
| | - Thongsa Sayavongkhamdy
- Department of National Heritage, Ministry of Information and Culture, Vientiane, Lao People's Democratic Republic
| | - François Sémah
- Muséum national d'Histoire naturelle, Musée de l'Homme, Département Homme et environnement, CNRS, UMR 7194, 75116, Paris, France
| | | | - Florent Détroit
- Muséum national d'Histoire naturelle, Musée de l'Homme, Département Homme et environnement, CNRS, UMR 7194, 75116, Paris, France
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18
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Barron A, Turner M, Beeching L, Bellwood P, Piper P, Grono E, Jones R, Oxenham M, Kien NKT, Senden T, Denham T. MicroCT reveals domesticated rice (Oryza sativa) within pottery sherds from early Neolithic sites (4150-3265 cal BP) in Southeast Asia. Sci Rep 2017; 7:7410. [PMID: 28785094 PMCID: PMC5547045 DOI: 10.1038/s41598-017-04338-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/16/2017] [Indexed: 11/14/2022] Open
Abstract
Rice (Oryza sativa) was domesticated in the Yangtze Valley region at least 6000–8000 years ago, yet the timing of dispersal of domesticated rice to Southeast Asia is contentious. Often rice is not well-preserved in archaeobotanical assemblages at early Neolithic sites in the wet tropics of Southeast Asia and consequently rice impressions in pottery have been used as a proxy for rice cultivation despite their uncertain taxonomic and domestication status. In this research, we use microCT technology to determine the 3D microscale morphology of rice husk and spikelet base inclusions within pottery sherds from early Neolithic sites in Vietnam. In contrast to surface impressions, microCT provides images of the entire husk and spikelet base preserved within the pottery, including the abscission scar characteristic of domesticated rice. This research demonstrates the potential of microCT to be a new, non-destructive method for the identification of domesticated plant remains within pottery sherds, especially in contexts where archaeobotanical preservation is poor and chaff-tempered sherds are rare and unavailable for destructive analysis. The method has the potential to greatly advance the understanding of crop domestication and agricultural dispersal for ceramic cultures in different parts of the world.
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Affiliation(s)
- Aleese Barron
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, 2601, Australia
| | - Michael Turner
- National Laboratory for X-ray Computed Tomography, Australian National University, Canberra, ACT, 2601, Australia
| | - Levi Beeching
- National Laboratory for X-ray Computed Tomography, Australian National University, Canberra, ACT, 2601, Australia
| | - Peter Bellwood
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, 2601, Australia
| | - Philip Piper
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, 2601, Australia
| | - Elle Grono
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, 2601, Australia
| | - Rebecca Jones
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, 2601, Australia
| | - Marc Oxenham
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, 2601, Australia
| | - Nguyen Khanh Trung Kien
- Centre for Archaeological Studies, Southern Institute for Social Sciences, Ho Chi Minh City, Vietnam
| | - Tim Senden
- Research School of Physics and Engineering, Australian National University, Canberra, ACT, 2601, Australia
| | - Tim Denham
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, 2601, Australia.
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20
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Brandão A, Eng KK, Rito T, Cavadas B, Bulbeck D, Gandini F, Pala M, Mormina M, Hudson B, White J, Ko TM, Saidin M, Zafarina Z, Oppenheimer S, Richards MB, Pereira L, Soares P. Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia. Hum Genet 2016; 135:363-376. [PMID: 26875094 PMCID: PMC4796337 DOI: 10.1007/s00439-016-1640-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/21/2016] [Indexed: 12/30/2022]
Abstract
There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the "out-of-Taiwan" mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20% of mtDNA lineages in the modern ISEA pool result from the "out-of-Taiwan" dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6-7 ka, where rice-farming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA.
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Affiliation(s)
- Andreia Brandão
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK
- ICBAS (Instituto Ciências Biomédicas Abel Salazar), Universidade do Porto, Rua de Jorge Viterbo Ferreira n.º 228, 4050-313, Porto, Portugal
| | - Ken Khong Eng
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Centre for Global Archaeological Research, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Teresa Rito
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Bruno Cavadas
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal
| | - David Bulbeck
- Department of Archaeology and Natural History, College of Asia and the Pacific, The Australian National University, Acton ACT, Canberra, 2601, Australia
| | - Francesca Gandini
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK
| | - Maru Mormina
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Department of Applied Social Studies, University of Winchester, Sparkford Road, Winchester, SO22 4NR, UK
| | - Bob Hudson
- Archaeology Department, University of Sydney, New South Wales, 2006, Australia
| | - Joyce White
- Department of Anthropology, University of Pennsylvania Museum, 3260 South St., Philadelphia, USA
| | - Tsang-Ming Ko
- Department of Obstetrics and Gynecology, National Taiwan University, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Mokhtar Saidin
- Centre for Global Archaeological Research, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Zainuddin Zafarina
- Malaysian Institute of Pharmaceuticals and Nutraceuticals Malaysia, National Institutes of Biotechnology Malaysia, Penang, Malaysia
- Human Identification Unit, School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Stephen Oppenheimer
- School of Anthropology, Institute of Human Sciences, The Pauling Centre, University of Oxford, 58a Banbury Road, Oxford, OX2 6QS, UK
| | - Martin B Richards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK.
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Luísa Pereira
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal
- Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Pedro Soares
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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21
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Resolving the ancestry of Austronesian-speaking populations. Hum Genet 2016; 135:309-26. [PMID: 26781090 PMCID: PMC4757630 DOI: 10.1007/s00439-015-1620-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 11/18/2015] [Indexed: 01/17/2023]
Abstract
There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The "out-of-Taiwan" model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion.
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22
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Paquette AM, Harahap A, Laosombat V, Patnode JM, Satyagraha A, Sudoyo H, Thompson MK, Yusoff NM, Wilder JA. The evolutionary origins of Southeast Asian Ovalocytosis. INFECTION GENETICS AND EVOLUTION 2015; 34:153-9. [PMID: 26047685 DOI: 10.1016/j.meegid.2015.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/25/2015] [Accepted: 06/01/2015] [Indexed: 11/30/2022]
Abstract
Southeast Asian Ovalocytosis (SAO) is a common red blood cell disorder that is maintained as a balanced polymorphism in human populations. In individuals heterozygous for the SAO-causing mutation there are minimal detrimental effects and well-documented protection from severe malaria caused by Plasmodium vivax and Plasmodium falciparum; however, the SAO-causing mutation is fully lethal in utero when homozygous. The present-day high frequency of SAO in Island Southeast Asia indicates the trait is maintained by strong heterozygote advantage. Our study elucidates the evolutionary origin of SAO by characterizing DNA sequence variation in a 9.5 kilobase region surrounding the causal mutation in the SLC4A1 gene. We find substantial haplotype diversity among SAO chromosomes and estimate the age of the trait to be approximately 10,005 years (95% CI: 4930-23,200 years). This date is far older than any other human malaria-resistance trait examined previously in Southeast Asia, and considerably pre-dates the widespread adoption of agriculture associated with the spread of speakers of Austronesian languages some 4000 years ago. Using a genealogy-based method we find no evidence of historical positive selection acting on SAO (s=0.0, 95% CI: 0.0-0.03), in sharp contrast to the strong present-day selection coefficient (e.g., 0.09) estimated from the frequency of this recessively lethal trait. This discrepancy may be due to a recent increase in malaria-driven selection pressure following the spread of agriculture, with SAO targeted as a standing variant by positive selection in malarial populations.
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Affiliation(s)
- A M Paquette
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - A Harahap
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - V Laosombat
- Division of Pediatric Hematology & Oncology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkla 90110, Thailand
| | - J M Patnode
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - A Satyagraha
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - H Sudoyo
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - M K Thompson
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - N M Yusoff
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Kepala Batas, Pulau Pinang, Malaysia
| | - J A Wilder
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA.
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23
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Kusuma P, Cox MP, Pierron D, Razafindrazaka H, Brucato N, Tonasso L, Suryadi HL, Letellier T, Sudoyo H, Ricaut FX. Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations. BMC Genomics 2015; 16:191. [PMID: 25880430 PMCID: PMC4373124 DOI: 10.1186/s12864-015-1394-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/24/2015] [Indexed: 11/18/2022] Open
Abstract
Background Linguistic, cultural and genetic characteristics of the Malagasy suggest that both Africans and Island Southeast Asians were involved in the colonization of Madagascar. Populations from the Indonesian archipelago played an especially important role because linguistic evidence suggests that the Malagasy language branches from the Southeast Barito language family of southern Borneo, Indonesia, with the closest language spoken today by the Ma’anyan. To test for a genetic link between Malagasy and these linguistically related Indonesian populations, we studied the Ma’anyan and other Indonesian ethnic groups (including the sea nomad Bajo) that, from their historical and linguistic contexts, may be modern descendants of the populations that helped enact the settlement of Madagascar. Result A combination of phylogeographic analysis of genetic distances, haplotype comparisons and inference of parental populations by linear optimization, using both maternal and paternal DNA lineages, suggests that Malagasy derive from multiple regional sources in Indonesia, with a focus on eastern Borneo, southern Sulawesi and the Lesser Sunda islands. Conclusion Settlement may have been mediated by ancient sea nomad movements because the linguistically closest population, Ma’anyan, has only subtle genetic connections to Malagasy, whereas genetic links with other sea nomads are more strongly supported. Our data hint at a more complex scenario for the Indonesian settlement of Madagascar than has previously been recognized. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1394-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pradiptajati Kusuma
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France. .,Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
| | - Denis Pierron
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
| | - Harilanto Razafindrazaka
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
| | - Nicolas Brucato
- Center for Linguistics, University of Leiden, Leiden, Netherlands.
| | - Laure Tonasso
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
| | - Helena Loa Suryadi
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
| | - Thierry Letellier
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia. .,Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia.
| | - François-Xavier Ricaut
- Laboratoire d'Anthropologie Moléculaire et Imagérie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.
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Lipson M, Loh PR, Patterson N, Moorjani P, Ko YC, Stoneking M, Berger B, Reich D. Reconstructing Austronesian population history in Island Southeast Asia. Nat Commun 2014; 5:4689. [PMID: 25137359 PMCID: PMC4143916 DOI: 10.1038/ncomms5689] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 07/14/2014] [Indexed: 12/22/2022] Open
Abstract
Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the ‘Austronesian expansion,’ which began 4,000–5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia. Populations speaking Austronesian languages are numerous and widespread, but their history remains controversial. Here, the authors analyse genetic data from Southeast Asia and show that all populations harbour ancestry most closely related to aboriginal Taiwanese, while some also contain a component closest to Austro-Asiatic speakers.
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Affiliation(s)
- Mark Lipson
- Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Po-Ru Loh
- 1] Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2]
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Priya Moorjani
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [3]
| | - Ying-Chin Ko
- Graduate Institute of Clinical Medical Science, China Medical University, Taichung 40402, Taiwan
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Bonnie Berger
- 1] Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - David Reich
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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Zeng Z, Rowold DJ, Garcia-Bertrand R, Calderon S, Regueiro M, Li L, Zhong M, Herrera RJ. Taiwanese aborigines: genetic heterogeneity and paternal contribution to Oceania. Gene 2014; 542:240-7. [PMID: 24613753 DOI: 10.1016/j.gene.2014.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
Abstract
In the present study, for the first time, 293 Taiwanese aboriginal males from all nine major tribes (Ami, Atayal, Bunun, Rukai, Paiwan, Saisat, Puyuma, Tsou, Yami) were genotyped with 17 YSTR loci in a attend to reveal migrational patterns connected with the Austronesian expansion. We investigate the paternal genetic relationships of these Taiwanese aborigines to 42 Asia-Pacific reference populations, geographically selected to reflect various locations within the Austronesian domain. The Tsou and Puyuma tribes exhibit the lowest (0.1851) and the highest (0.5453) average total genetic diversity, respectively. Further, the fraction of unique haplotypes is also relatively high in the Puyuma (86.7%) and low in Tsou (33.3%) suggesting different demographic histories. Multidimensional scaling (MDS) and analysis of molecular variance (AMOVA) revealed several notable findings: 1) the Taiwan indigenous populations are highly diverse. In fact, the level of inter-population heterogeneity displayed by the Taiwanese aboriginal populations is close to that exhibited among all 51 Asia-Pacific populations examined; 2) the asymmetrical contribution of the Taiwanese aborigines to the Oceanic groups. Ami, Bunun and Saisiyat tribes exhibit the strongest paternal links to the Solomon and Polynesian island communities, whereas most of the remaining Taiwanese aboriginal groups are more genetically distant to these Oceanic inhabitants; 3) the present YSTR analyses does not reveal a strong paternal affinity of the nine Taiwanese tribes to their continental Asian neighbors. Overall, our current findings suggest that, perhaps, only a few of the tribes were involved in the migration out of Taiwan.
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Affiliation(s)
- Zhaoshu Zeng
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, China
| | - Diane J Rowold
- Foundation for Applied Molecular Science (FfAME), Gainesville, FL 32601, USA
| | | | - Silvia Calderon
- Department of Dentistry, New York University, New York, NY, USA
| | | | - Li Li
- Department of Obstetrics & Gynecology, Zhengzhou Central Hospital, Zhengzhou University, China
| | - Mingxia Zhong
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, China
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Reid LA. Who are the Philippine Negritos? Evidence from Language. Hum Biol 2013; 85:329-58. [DOI: 10.3378/027.085.0316] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
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Mirabal S, Cadenas AM, Garcia-Bertrand R, Herrera RJ. Ascertaining the role of Taiwan as a source for the Austronesian expansion. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 150:551-64. [PMID: 23440864 DOI: 10.1002/ajpa.22226] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 12/14/2012] [Indexed: 01/15/2023]
Abstract
Taiwanese aborigines have been deemed the ancestors of Austronesian speakers which are currently distributed throughout two-thirds of the globe. As such, understanding their genetic distribution and diversity as well as their relationship to mainland Asian groups is important to consolidating the numerous models that have been proposed to explain the dispersal of Austronesian speaking peoples into Oceania. To better understand the role played by the aboriginal Taiwanese in this diaspora, we have analyzed a total of 451 individuals belonging to nine of the tribes currently residing in Taiwan, namely the Ami, Atayal, Bunun, Paiwan, Puyuma, Rukai, Saisiyat, Tsou, and the Yami from Orchid Island off the coast of Taiwan across 15 autosomal short tandem repeat loci. In addition, we have compared the genetic profiles of these tribes to populations from mainland China as well as to collections at key points throughout the Austronesian domain. While our results suggest that Daic populations from Southern China are the likely forefathers of the Taiwanese aborigines, populations within Taiwan show a greater genetic impact on groups at the extremes of the current domain than populations from Indonesia, Mainland, or Southeast Asia lending support to the "Out of Taiwan" hypothesis. We have also observed that specific Taiwanese aboriginal groups (Paiwan, Puyuma, and Saisiyat), and not all tribal populations, have highly influenced genetic distributions of Austronesian populations in the pacific and Madagascar suggesting either an asymmetric migration out of Taiwan or the loss of certain genetic signatures in some of the Taiwanese tribes due to endogamy, isolation, and/or drift.
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Affiliation(s)
- Sheyla Mirabal
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL 33199, USA
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Genetic dating indicates that the Asian-Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion. Proc Natl Acad Sci U S A 2012; 109:4574-9. [PMID: 22396590 DOI: 10.1073/pnas.1118892109] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the Austronesian expansion had a major impact on the languages of Island Southeast Asia, controversy still exists over the genetic impact of this expansion. The coexistence of both Asian and Papuan genetic ancestry in Eastern Indonesia provides a unique opportunity to address this issue. Here, we estimate recombination breakpoints in admixed genomes based on genome-wide SNP data and date the genetic admixture between populations of Asian vs. Papuan ancestry in Eastern Indonesia. Analyses of two genome-wide datasets indicate an eastward progression of the Asian admixture signal in Eastern Indonesia beginning about 4,000-3,000 y ago, which is in excellent agreement with inferences based on Austronesian languages. The average rate of spread of Asian genes in Eastern Indonesia was about 0.9 km/y. Our results indicate that the Austronesian expansion had a strong genetic as well as linguistic impact on Island Southeast Asia, and they significantly advance our understanding of the biological origins of human populations in the Asia-Pacific region.
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Increased Y-chromosome resolution of haplogroup O suggests genetic ties between the Ami aborigines of Taiwan and the Polynesian Islands of Samoa and Tonga. Gene 2012; 492:339-48. [DOI: 10.1016/j.gene.2011.10.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 10/13/2011] [Accepted: 10/18/2011] [Indexed: 11/22/2022]
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Sheppard PJ. Lapita Colonization across the Near/Remote Oceania Boundary. CURRENT ANTHROPOLOGY 2011. [DOI: 10.1086/662201] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Wilder JA, Cox MP, Paquette AM, Alford R, Satyagraha AW, Harahap A, Sudoyo H. Genetic continuity across a deeply divergent linguistic contact zone in North Maluku, Indonesia. BMC Genet 2011; 12:100. [PMID: 22098696 PMCID: PMC3252253 DOI: 10.1186/1471-2156-12-100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 11/18/2011] [Indexed: 12/03/2022] Open
Abstract
Background The islands of North Maluku, Indonesia occupy a central position in the major prehistoric dispersal streams that shaped the peoples of Island Southeast Asia and the Pacific. Within this region a linguistic contact zone exists where speakers of Papuan and Austronesian languages reside in close proximity. Here we use population genetic data to assess the extent to which North Maluku populations experienced admixture of Asian genetic material, and whether linguistic boundaries reflect genetic differentiation today. Results Autosomal and X-linked markers reveal overall Asian admixture of 67% in North Maluku, demonstrating a substantial contribution of genetic material into the region from Asia. We observe no evidence of population structure associated with ethnicity or language affiliation. Conclusions Our data support a model of widespread Asian admixture in North Maluku, likely mediated by the expansion of Austronesian-speaking peoples into the region during the mid Holocene. In North Maluku there is no genetic differentiation in terms of Austronesian- versus Papuan-speakers, suggesting extensive gene flow across linguistic boundaries. In a regional context, our results illuminate a major genetic divide at the Molucca Sea, between the islands of Sulawesi and North Maluku. West of this divide, populations exhibit predominantly Asian ancestry, with very little contribution of Papuan genetic material. East of the Molucca Sea, populations show diminished rates of Asian admixture and substantial persistence of Papuan genetic diversity.
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Affiliation(s)
- Jason A Wilder
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA.
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Bellwood P. Holocene Population History in the Pacific Region as a Model for Worldwide Food Producer Dispersals. CURRENT ANTHROPOLOGY 2011. [DOI: 10.1086/658181] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Denham T. Early Agriculture and Plant Domestication in New Guinea and Island Southeast Asia. CURRENT ANTHROPOLOGY 2011. [DOI: 10.1086/658682] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Stoneking M, Krause J. Learning about human population history from ancient and modern genomes. Nat Rev Genet 2011; 12:603-14. [PMID: 21850041 DOI: 10.1038/nrg3029] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Genome-wide data, both from SNP arrays and from complete genome sequencing, are becoming increasingly abundant and are now even available from extinct hominins. These data are providing new insights into population history; in particular, when combined with model-based analytical approaches, genome-wide data allow direct testing of hypotheses about population history. For example, genome-wide data from both contemporary populations and extinct hominins strongly support a single dispersal of modern humans from Africa, followed by two archaic admixture events: one with Neanderthals somewhere outside Africa and a second with Denisovans that (so far) has only been detected in New Guinea. These new developments promise to reveal new stories about human population history, without having to resort to storytelling.
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Affiliation(s)
- Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany.
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Delfin F, Myles S, Choi Y, Hughes D, Illek R, van Oven M, Pakendorf B, Kayser M, Stoneking M. Bridging Near and Remote Oceania: mtDNA and NRY Variation in the Solomon Islands. Mol Biol Evol 2011; 29:545-64. [DOI: 10.1093/molbev/msr186] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Ancient voyaging and Polynesian origins. Am J Hum Genet 2011; 88:239-47. [PMID: 21295281 DOI: 10.1016/j.ajhg.2011.01.009] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 01/13/2011] [Accepted: 01/14/2011] [Indexed: 01/02/2023] Open
Abstract
The "Polynesian motif" defines a lineage of human mtDNA that is restricted to Austronesian-speaking populations and is almost fixed in Polynesians. It is widely thought to support a rapid dispersal of maternal lineages from Taiwan ~4000 years ago (4 ka), but the chronological resolution of existing control-region data is poor, and an East Indonesian origin has also been proposed. By analyzing 157 complete mtDNA genomes, we show that the motif itself most likely originated >6 ka in the vicinity of the Bismarck Archipelago, and its immediate ancestor is >8 ka old and virtually restricted to Near Oceania. This indicates that Polynesian maternal lineages from Island Southeast Asia gained a foothold in Near Oceania much earlier than dispersal from either Taiwan or Indonesia 3-4 ka would predict. However, we find evidence in minor lineages for more recent two-way maternal gene flow between Island Southeast Asia and Near Oceania, likely reflecting movements along a "voyaging corridor" between them, as previously proposed on archaeological grounds. Small-scale mid-Holocene movements from Island Southeast Asia likely transmitted Austronesian languages to the long-established Southeast Asian colonies in the Bismarcks carrying the Polynesian motif, perhaps also providing the impetus for the expansion into Polynesia.
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Walker RS, Ribeiro LA. Bayesian phylogeography of the Arawak expansion in lowland South America. Proc Biol Sci 2011; 278:2562-7. [PMID: 21247954 DOI: 10.1098/rspb.2010.2579] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic inference based on language is a vital tool for tracing the dynamics of human population expansions. The timescale of agriculture-based expansions around the world provides an informative amount of linguistic change ideal for reconstructing phylogeographies. Here we investigate the expansion of Arawak, one of the most widely dispersed language families in the Americas, scattered from the Antilles to Argentina. It has been suggested that Northwest Amazonia is the Arawak homeland based on the large number of diverse languages in the region. We generate language trees by coding cognates of basic vocabulary words for 60 Arawak languages and dialects to estimate the phylogenetic relationships among Arawak societies, while simultaneously implementing a relaxed random walk model to infer phylogeographic history. Estimates of the Arawak homeland exclude Northwest Amazonia and are bi-modal, with one potential homeland on the Atlantic seaboard and another more likely origin in Western Amazonia. Bayesian phylogeography better supports a Western Amazonian origin, and consequent dispersal to the Caribbean and across the lowlands. Importantly, the Arawak expansion carried with it not only language but also a number of cultural traits that contrast Arawak societies with other lowland cultures.
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Affiliation(s)
- Robert S Walker
- Department of Anthropology, University of Missouri, MO, USA.
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Affiliation(s)
- V. Kirch Patrick
- Departments of Anthropology and Integrative Biology, University of California, Berkeley, California 94720;
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