151
|
Jeong C, Wang K, Wilkin S, Taylor WTT, Miller BK, Bemmann JH, Stahl R, Chiovelli C, Knolle F, Ulziibayar S, Khatanbaatar D, Erdenebaatar D, Erdenebat U, Ochir A, Ankhsanaa G, Vanchigdash C, Ochir B, Munkhbayar C, Tumen D, Kovalev A, Kradin N, Bazarov BA, Miyagashev DA, Konovalov PB, Zhambaltarova E, Miller AV, Haak W, Schiffels S, Krause J, Boivin N, Erdene M, Hendy J, Warinner C. A Dynamic 6,000-Year Genetic History of Eurasia's Eastern Steppe. Cell 2020; 183:890-904.e29. [PMID: 33157037 PMCID: PMC7664836 DOI: 10.1016/j.cell.2020.10.015] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/12/2020] [Accepted: 10/07/2020] [Indexed: 12/22/2022]
Abstract
The Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region’s population history. Here, we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe. Genome-wide analysis of 214 ancient individuals from Mongolia and the Baikal region Three genetically distinct dairy pastoralist groups in Late Bronze Age Mongolia Xiongnu nomadic empire formed through mixing of distinct local and distant groups No selection on the lactase persistence alleles despite 5,000 years of dairy culture
Collapse
Affiliation(s)
- Choongwon Jeong
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Ke Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Shevan Wilkin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - William Timothy Treal Taylor
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Anthropology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Bryan K Miller
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jan H Bemmann
- Department of Archaeology and Anthropology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn 53113, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Chelsea Chiovelli
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Florian Knolle
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Sodnom Ulziibayar
- Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar 14200, Mongolia
| | | | - Diimaajav Erdenebaatar
- Department of Archaeology, Ulaanbaatar State University, Bayanzurkh district, Ulaanbaatar 13343, Mongolia
| | - Ulambayar Erdenebat
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Ayudai Ochir
- International Institute for the Study of Nomadic Civilizations, Ulaanbaatar 14200, Mongolia
| | - Ganbold Ankhsanaa
- National Centre for Cultural Heritage of Mongolia, Ulaanbaatar 14200, Mongolia
| | | | - Battuga Ochir
- Institute of History and Ethnology, Mongolian Academy of Sciences, Ulaanbaatar 14200, Mongolia
| | | | - Dashzeveg Tumen
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Alexey Kovalev
- Institute of Archaeology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nikolay Kradin
- Institute of History, Archaeology and Ethnology, Far East Branch of the Russian Academy of Sciences, Vladivostok 690001, Russia; Institute for Mongolian, Buddhist and Tibetan Studies, Siberian Branch of the Russian Academy of Sciences, Ulan-Ude 670047, Russia
| | - Bilikto A Bazarov
- Institute for Mongolian, Buddhist and Tibetan Studies, Siberian Branch of the Russian Academy of Sciences, Ulan-Ude 670047, Russia
| | - Denis A Miyagashev
- Institute for Mongolian, Buddhist and Tibetan Studies, Siberian Branch of the Russian Academy of Sciences, Ulan-Ude 670047, Russia
| | - Prokopiy B Konovalov
- Institute for Mongolian, Buddhist and Tibetan Studies, Siberian Branch of the Russian Academy of Sciences, Ulan-Ude 670047, Russia
| | - Elena Zhambaltarova
- Department of Museology and Heritage, Faculty of Social and Cultural Activities, Heritage, and Tourism, Federal State Budgetary Educational Institution of Higher Education, East Siberian State Institute of Culture, Ulan-Ude 670031, Russia
| | - Alicia Ventresca Miller
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Anthropology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Faculty of Biological Sciences, Friedrich Schiller University, Jena 02134, Germany
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Myagmar Erdene
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Jessica Hendy
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; BioArCh, Department of Archaeology, University of York, York YO10 5NG, UK
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Faculty of Biological Sciences, Friedrich Schiller University, Jena 02134, Germany; Department of Anthropology, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
152
|
Sun C, Kovacs P, Guiu-Jurado E. Genetics of Obesity in East Asians. Front Genet 2020; 11:575049. [PMID: 33193685 PMCID: PMC7606890 DOI: 10.3389/fgene.2020.575049] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
Obesity has become a public health problem worldwide. Compared with Europe, people in Asia tend to suffer from type 2 diabetes with a lower body mass index (BMI). Genome-wide association studies (GWASs) have identified over 750 loci associated with obesity. Although the majority of GWAS results were conducted in individuals of European ancestry, a recent GWAS in individuals of Asian ancestry has made a significant contribution to the identification of obesity susceptibility loci. Indeed, owing to the multifactorial character of obesity with a strong environmental component, the revealed loci may have distinct contributions in different ancestral genetic backgrounds and in different environments as presented through diet and exercise among other factors. Uncovering novel, yet unrevealed genes in non-European ancestries may further contribute to explaining the missing heritability for BMI. In this review, we aimed to summarize recent advances in obesity genetics in individuals of Asian ancestry. We therefore compared proposed mechanisms underlying susceptibility loci for obesity associated with individuals of European and Asian ancestries and discussed whether known genetic variants might explain ethnic differences in obesity risk. We further acknowledged that GWAS implemented in individuals of Asian ancestries have not only validated the potential role of previously specified obesity susceptibility loci but also exposed novel ones, which have been missed in the initial genetic studies in individuals of European ancestries. Thus, multi-ethnic studies have a great potential not only to contribute to a better understanding of the complex etiology of human obesity but also potentially of ethnic differences in the prevalence of obesity, which may ultimately pave new avenues in more targeted and personalized obesity treatments.
Collapse
Affiliation(s)
| | - Peter Kovacs
- Medical Department III – Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | | |
Collapse
|
153
|
Ma T, Rolett BV, Zheng Z, Zong Y. Holocene coastal evolution preceded the expansion of paddy field rice farming. Proc Natl Acad Sci U S A 2020; 117:24138-24143. [PMID: 32929013 PMCID: PMC7533829 DOI: 10.1073/pnas.1919217117] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 08/13/2020] [Indexed: 11/26/2022] Open
Abstract
Rice agriculture is the foundation of Asian civilizations south of the Yangtze River. Although rice history is well documented for its lower Yangtze homeland area, the early southward expansion of paddy rice farming is poorly known. Our study investigates this process using a compilation of paleoenvironmental proxies from coastal sediment cores from southeast China to Thailand and Island Southeast Asia. We propose that a shortage of land suitable for paddy fields, caused by marine transgression, constrained rice agriculture during the mid-Holocene. Rapid expansion of coastal plains, particularly in deltaic basins, over the past three millennia has coincided with increases in land suitable for rice cultivation. Our study also helps explain the past population movements of rice farmers.
Collapse
Affiliation(s)
- Ting Ma
- School of Earth Science and Engineering and School of Geography and Planning, Sun Yat-Sen University, 510275 Guangzhou, China
| | - Barry V Rolett
- Department of Anthropology, University of Hawai'i at Manoa, Honolulu, HI 96822;
| | - Zhuo Zheng
- School of Earth Science and Engineering and School of Geography and Planning, Sun Yat-Sen University, 510275 Guangzhou, China;
| | - Yongqiang Zong
- Department of Earth Sciences, University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
154
|
Gakuhari T, Nakagome S, Rasmussen S, Allentoft ME, Sato T, Korneliussen T, Chuinneagáin BN, Matsumae H, Koganebuchi K, Schmidt R, Mizushima S, Kondo O, Shigehara N, Yoneda M, Kimura R, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Tsurumoto T, Wakebe T, Shitara H, Hanihara T, Willerslev E, Sikora M, Oota H. Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations. Commun Biol 2020; 3:437. [PMID: 32843717 PMCID: PMC7447786 DOI: 10.1038/s42003-020-01162-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 07/16/2020] [Indexed: 12/28/2022] Open
Abstract
Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia. Takashi Gakuhari, Shigeki Nakagome et al. report the genomic analysis on a 2.5 kya individual from the ancient Jomon culture in present-day Japan. Phylogenetic analysis with comparison to other Eurasian sequences suggests early migration patterns in Asia and provides insight into the genetic affinities between peoples of the region.
Collapse
Affiliation(s)
- Takashi Gakuhari
- Center for Cultural Resource Studies, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan.,Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan.,Kitasato University School of Medicine, Sagamihara, Japan
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, the University of Dublin, Dublin, Ireland
| | - Simon Rasmussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Trace and Environmental DNA (TrEnD) laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Ryan Schmidt
- Kitasato University School of Medicine, Sagamihara, Japan
| | - Souichiro Mizushima
- Department of Anatomy, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Osamu Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nobuo Shigehara
- Nara National Research Institute for Cultural Properties, Nara, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Hajime Ishida
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | | | | | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | - Toshiyuki Tsurumoto
- Department of Macroscopic Anatomy, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Japan
| | - Tetsuaki Wakebe
- Department of Macroscopic Anatomy, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Japan
| | - Hiromi Shitara
- Department of Archaeology, The University of Tokyo, Tokyo, Japan
| | | | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,GeoGenetics Groups, Department of Zoology, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Hiroki Oota
- Kitasato University School of Medicine, Sagamihara, Japan. .,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
155
|
End of Green Sahara amplified mid- to late Holocene megadroughts in mainland Southeast Asia. Nat Commun 2020; 11:4204. [PMID: 32826905 PMCID: PMC7442841 DOI: 10.1038/s41467-020-17927-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/20/2020] [Indexed: 12/02/2022] Open
Abstract
Between 5 and 4 thousand years ago, crippling megadroughts led to the disruption of ancient civilizations across parts of Africa and Asia, yet the extent of these climate extremes in mainland Southeast Asia (MSEA) has never been defined. This is despite archeological evidence showing a shift in human settlement patterns across the region during this period. We report evidence from stalagmite climate records indicating a major decrease of monsoon rainfall in MSEA during the mid- to late Holocene, coincident with African monsoon failure during the end of the Green Sahara. Through a set of modeling experiments, we show that reduced vegetation and increased dust loads during the Green Sahara termination shifted the Walker circulation eastward and cooled the Indian Ocean, causing a reduction in monsoon rainfall in MSEA. Our results indicate that vegetation-dust climate feedbacks from Sahara drying may have been the catalyst for societal shifts in MSEA via ocean-atmospheric teleconnections. The mid-Holocene has seen a number of climate shifts, which have been associated with societal changes. Here, the authors investigate in a centuries long megadrought in Southeast Asia during the mid-Holocene, possibly caused by the end of the Green Sahara period.
Collapse
|
156
|
Mizuno F, Taniguchi Y, Kondo O, Hayashi M, Kurosaki K, Ueda S. A study of 8,300-year-old Jomon human remains in Japan using complete mitogenome sequences obtained by next-generation sequencing. Ann Hum Biol 2020; 47:555-559. [PMID: 32674620 DOI: 10.1080/03014460.2020.1797164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Ancient human remains have been assigned to their mitochondrial DNA (mtDNA) haplogroups. To obtain efficiently deep and reliable nucleotide sequences of ancient DNA of interest, we achieved target enrichment followed by next-generation sequencing (NGS). Complete mitochondrial genome (mitogenome) sequences were obtained for three human remains from the Iyai rock-shelter site of the Initial Jomon Period in Japan. All the Jomon mitogenomes belong to haplogroup N9b, but no sequences among them were identical. High genetic diversity was clarified even among the Jomon human remains belonging to haplogroup N9b, which has been described as a haplogroup representing the Jomon people.
Collapse
Affiliation(s)
- Fuzuki Mizuno
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Yasuhiro Taniguchi
- Department of Archaeology, Faculty of Letters, Kokugakuin University, Tokyo, Japan
| | - Osamu Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Michiko Hayashi
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Kunihiko Kurosaki
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
157
|
Johnson AF, Ngo LT. A commentary on "A Vietnamese human genetic variation database". Hum Mutat 2020; 41:1463-1464. [PMID: 32720373 DOI: 10.1002/humu.24035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/17/2020] [Accepted: 05/04/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Adam F Johnson
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam
| | - Linh T Ngo
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam
| |
Collapse
|
158
|
Le VS, Tran KT, Nguyen LT. Response to: A commentary on "A Vietnamese human genetic variation database". Hum Mutat 2020; 41:1461-1462. [PMID: 32720372 DOI: 10.1002/humu.24031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/20/2020] [Accepted: 05/04/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Vinh S Le
- Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam
| | - Kien T Tran
- Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam
| | - Liem T Nguyen
- Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam
| |
Collapse
|
159
|
Kutanan W, Shoocongdej R, Srikummool M, Hübner A, Suttipai T, Srithawong S, Kampuansai J, Stoneking M. Cultural variation impacts paternal and maternal genetic lineages of the Hmong-Mien and Sino-Tibetan groups from Thailand. Eur J Hum Genet 2020; 28:1563-1579. [PMID: 32690935 PMCID: PMC7576213 DOI: 10.1038/s41431-020-0693-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 06/17/2020] [Accepted: 06/26/2020] [Indexed: 11/09/2022] Open
Abstract
The Hmong-Mien (HM) and Sino-Tibetan (ST) speaking groups are known as hill tribes in Thailand; they were the subject of the first studies to show an impact of patrilocality vs. matrilocality on patterns of mitochondrial (mt) DNA vs. male-specific portion of the Y chromosome (MSY) variation. However, HM and ST groups have not been studied in as much detail as other Thai groups; here we report and analyze 234 partial MSY sequences (∼2.3 mB) and 416 complete mtDNA sequences from 14 populations that, when combined with our previous published data, provides the largest dataset yet for the hill tribes. We find a striking difference between Hmong and IuMien (Mien-speaking) groups: the Hmong are genetically different from both the IuMien and all other Thai groups, whereas the IuMien are genetically more similar to other linguistic groups than to the Hmong. In general, we find less of an impact of patrilocality vs. matrilocality on patterns of mtDNA vs. MSY variation than previous studies. However, there is a dramatic difference in the frequency of MSY and mtDNA lineages of Northeast Asian (NEA) origin vs. Southeast Asian (SEA) origin in HM vs. ST groups: HM groups have high frequencies of NEA MSY lineages but lower frequencies of NEA mtDNA lineages, while ST groups show the opposite. A potential explanation is that the ancestors of Thai HM groups were patrilocal, while the ancestors of Thai ST groups were matrilocal. Overall, these results attest to the impact of cultural practices on patterns of mtDNA vs. MSY variation.
Collapse
Affiliation(s)
- Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand. .,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| | - Rasmi Shoocongdej
- Department of Archaeology, Faculty of Archaeology, Silpakorn University, Bangkok, 10200, Thailand
| | - Metawee Srikummool
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Thanatip Suttipai
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Suparat Srithawong
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50202, Thailand.,Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, 50202, Thailand
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| |
Collapse
|
160
|
Zhang M, Fu Q. Human evolutionary history in Eastern Eurasia using insights from ancient DNA. Curr Opin Genet Dev 2020; 62:78-84. [PMID: 32688244 DOI: 10.1016/j.gde.2020.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/22/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022]
Abstract
Advances in ancient genomics are providing unprecedented insight into modern human history. Here, we review recent progress uncovering prehistoric populations in Eastern Eurasia based on ancient DNA studies from the Upper Pleistocene to the Holocene. Many ancient populations existed during the Upper Pleistocene of Eastern Eurasia-some with no substantial ancestry related to present-day populations, some with an affinity to East Asians, and some who contributed to Native Americans. By the Holocene, the genetic composition across East Asia greatly shifted, with several substantial migrations. Three are southward: an increase in northern East Asian-related ancestry in southern East Asia; movement of East Asian-related ancestry into Southeast Asia, mixing with Basal Asian ancestry; and movement of southern East Asian ancestry to islands of Southeast Asia and the Southwest Pacific through the expansion of Austronesians. We anticipate that additional ancient DNA will magnify our understanding of the genetic history in Eastern Eurasia.
Collapse
Affiliation(s)
- Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
161
|
Paleolithic genetic link between Southern China and Mainland Southeast Asia revealed by ancient mitochondrial genomes. J Hum Genet 2020; 65:1125-1128. [DOI: 10.1038/s10038-020-0796-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 12/26/2022]
|
162
|
Iwasaki RL, Ishiya K, Kanzawa-Kiriyama H, Kawai Y, Gojobori J, Satta Y. Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population. Genes (Basel) 2020; 11:genes11070775. [PMID: 32664326 PMCID: PMC7396988 DOI: 10.3390/genes11070775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 12/24/2022] Open
Abstract
A genome wide association study reported that the T allele of rs2294008 in a cancer-related gene, PSCA, is a risk allele for diffuse-type gastric cancer. This allele has the highest frequency (0.63) in Japanese in Tokyo (JPT) among 26 populations in the 1000 Genomes Project database. FST ≈ 0.26 at this single nucleotide polymorphism is one of the highest between JPT and the genetically close Han Chinese in Beijing (CHB). To understand the evolutionary history of the alleles in PSCA, we addressed: (i) whether the C non-risk allele at rs2294008 is under positive selection, and (ii) why the mainland Japanese population has a higher T allele frequency than other populations. We found that haplotypes harboring the C allele are composed of two subhaplotypes. We detected that positive selection on both subhaplotypes has occurred in the East Asian lineage. However, the selection on one of the subhaplotypes in JPT seems to have been relaxed or ceased after divergence from the continental population; this may have caused the elevation of T allele frequency. Based on simulations under the dual structure model (a specific demography for the Japanese) and phylogenetic analysis with ancient DNA, the T allele at rs2294008 might have had high frequency in the Jomon people (one of the ancestral populations of the modern Japanese); this may explain the high T allele frequency in the extant Japanese.
Collapse
Affiliation(s)
- Risa L. Iwasaki
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan; (R.L.I.); (J.G.)
| | - Koji Ishiya
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan;
| | | | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo 162-8655, Japan;
| | - Jun Gojobori
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan; (R.L.I.); (J.G.)
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan; (R.L.I.); (J.G.)
- Correspondence: ; Tel.: +81-46-858-1574
| |
Collapse
|
163
|
Othman SN, Chen YH, Chuang MF, Andersen D, Jang Y, Borzée A. Impact of the Mid-Pleistocene Revolution and Anthropogenic Factors on the Dispersion of Asian Black-Spined Toads ( Duttaphrynus melanostictus). Animals (Basel) 2020; 10:E1157. [PMID: 32650538 PMCID: PMC7401666 DOI: 10.3390/ani10071157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/28/2020] [Accepted: 07/01/2020] [Indexed: 11/28/2022] Open
Abstract
Divergence-time estimation critically improves the understanding of biogeography processes underlying the distribution of species, especially when fossil data is not available. We hypothesise that the Asian black-spined toad, Duttaphrynus melanostictus, expanded into the Eastern Indomalaya following the Quaternary glaciations with the subsequent colonisation of new landscapes during the Last Glacial Maximum. Divergence dating inferred from 364 sequences of mitochondrial tRNAGly ND3 supported the emergence of a common ancestor to the three D. melanostictus clades around 1.85 (±0.77) Ma, matching with the Lower to Mid-Pleistocene transition. Duttaphrynus melanostictus then dispersed into Southeast Asia from the central Indo-Pacific and became isolated in the Southern Sundaic and Wallacea regions 1.43 (±0.10) Ma through vicariance as a result of sea level oscillations. The clade on the Southeast Asian mainland then colonised the peninsula from Myanmar to Vietnam and expanded towards Southeastern China at the end of the Mid-Pleistocene Revolution 0.84 (±0.32) Ma. Population dynamics further highlight an expansion of the Southeast Asian mainland population towards Taiwan, the Northeastern edge of the species' range after the last interglacial, and during the emergence of the Holocene human settlements around 7000 BP. Thus, the current divergence of D. melanostictus into three segregated clades was mostly shaped by Quaternary glaciations, followed by natural dispersion events over land bridges and accelerated by anthropogenic activities.
Collapse
Affiliation(s)
- Siti N. Othman
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
| | - Yi-Huey Chen
- Department of Life Science, Chinese Culture University, Taipei 11114, Taiwan;
| | - Ming-Feng Chuang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Desiree Andersen
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
| | - Yikweon Jang
- Department of Life Sciences and Division of EcoScience, Ewha Womans University, Seoul 03760, Korea; (S.N.O.); (M.-F.C.); (D.A.); (Y.J.)
| | - Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| |
Collapse
|
164
|
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: 2.8] [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.
Collapse
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
| |
Collapse
|
165
|
Bellwood P. Some observations on the transeurasian language family, from the perspective of the Farming/Language Dispersal Hypothesis. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e37. [PMID: 37588353 PMCID: PMC10427460 DOI: 10.1017/ehs.2020.34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
During my attendance at the 'Transeurasian Millets and Beans, Words and Genes' conference in Jena (January 2019), Martine Robbeets invited me to comment on the articles that are published in this Special Collection in the journal Evolutionary Human Sciences. My comments are focused on the seven articles that deal with the 'Farming/Language Dispersal Hypothesis', one of the key theoretical constructs discussed during the conference. I consider how the hypothesis might aid an understanding of the prehistory and early history of the Transeurasian language family.
Collapse
Affiliation(s)
- Peter Bellwood
- School of Archaeology and Anthropology, Australian National University, Canberra, Australia
| |
Collapse
|
166
|
Abstract
In this special collection, we address the origin and dispersal of the Transeurasian languages, i.e. Japonic, Koreanic, Tungusic, Mongolic and Turkic, from an interdisciplinary perspective. Our key objective is to effectively synthesize linguistic, archaeological and genetic evidence in a single approach, for which we use the term 'triangulation'. The 10 articles collected in this volume contribute to the question of whether and to what extent the early spread of Transeurasian languages was driven by agriculture in general, and by economic reliance on millet cultivation in particular.
Collapse
Affiliation(s)
- Martine Robbeets
- Eurasia3angle Research group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen361005, China
| |
Collapse
|
167
|
Nägele K, Posth C, Iraeta Orbegozo M, Chinique de Armas Y, Hernández Godoy ST, González Herrera UM, Nieves-Colón MA, Sandoval-Velasco M, Mylopotamitaki D, Radzeviciute R, Laffoon J, Pestle WJ, Ramos-Madrigal J, Lamnidis TC, Schaffer WC, Carr RS, Day JS, Arredondo Antúnez C, Rangel Rivero A, Martínez-Fuentes AJ, Crespo-Torres E, Roksandic I, Stone AC, Lalueza-Fox C, Hoogland M, Roksandic M, Hofman CL, Krause J, Schroeder H. Genomic insights into the early peopling of the Caribbean. Science 2020; 369:456-460. [PMID: 32499399 DOI: 10.1126/science.aba8697] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/18/2020] [Indexed: 12/31/2022]
Abstract
The Caribbean was one of the last regions of the Americas to be settled by humans, but where they came from and how and when they reached the islands remain unclear. We generated genome-wide data for 93 ancient Caribbean islanders dating between 3200 and 400 calibrated years before the present and found evidence of at least three separate dispersals into the region, including two early dispersals into the Western Caribbean, one of which seems connected to radiation events in North America. This was followed by a later expansion from South America. We also detected genetic differences between the early settlers and the newcomers from South America, with almost no evidence of admixture. Our results add to our understanding of the initial peopling of the Caribbean and the movements of Archaic Age peoples in the Americas.
Collapse
Affiliation(s)
- Kathrin Nägele
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Jena, Germany.,Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Miren Iraeta Orbegozo
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Silvia Teresita Hernández Godoy
- Grupo de Investigación y Desarrollo, Dirección Provincial de Cultura, Matanzas, Cuba.,Universidad de Matanzas, Matanzas, Cuba
| | | | - Maria A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Marcela Sandoval-Velasco
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dorothea Mylopotamitaki
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rita Radzeviciute
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jason Laffoon
- Faculty of Archaeology, Leiden University, Leiden, Netherlands
| | | | - Jazmin Ramos-Madrigal
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - William C Schaffer
- Liberal Arts Department, Phoenix College, Phoenix, AZ, USA.,Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA
| | - Robert S Carr
- Archaeological and Historical Conservancy Inc., Davie, FL, USA
| | - Jane S Day
- Research Atlantica Inc., Boca Raton, FL, USA
| | | | - Armando Rangel Rivero
- Museo Antropológico Montané, Facultad de Biología, Universidad de La Habana, Havana, Cuba
| | | | - Edwin Crespo-Torres
- Departamento de Sociología y Antropología, Universidad de Puerto Rico Rio Piedras, San Juan, Puerto Rico
| | - Ivan Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, Spanish National Research Council (CSIC)-Universitat Pompeu Fabra, Barcelona, Spain
| | - Menno Hoogland
- Faculty of Archaeology, Leiden University, Leiden, Netherlands.,Royal Netherlands Institute of Southeast Asian and Caribbean Studies, Leiden, Netherlands
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada
| | - Corinne L Hofman
- Faculty of Archaeology, Leiden University, Leiden, Netherlands.,Royal Netherlands Institute of Southeast Asian and Caribbean Studies, Leiden, Netherlands
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Hannes Schroeder
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Faculty of Archaeology, Leiden University, Leiden, Netherlands
| |
Collapse
|
168
|
Chaubey G, van Driem G. Munda languages are father tongues, but Japanese and Korean are not. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e19. [PMID: 37588351 PMCID: PMC10427457 DOI: 10.1017/ehs.2020.14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Over two decades ago, it was observed that the linguistic affinity of the language spoken by a particular population tended to correlate with the predominant paternal, i.e. Y-chromosomal, lineage found in that population. Such correlations were found to be ubiquitous but not universal, and the striking exceptions to such conspicuous patterns of correlation between linguistic and genetic phylogeography elicit particular interest and beg for clarification. Within the Austroasiatic language family, the Munda languages are a clear-cut case of father tongues, whereas Japanese and Korean are manifestly not. In this study, the cases of Munda and Japanese are juxtaposed. A holistic understanding of these contrasting cases of ethnolinguistic prehistory with respect to the father tongue correlation will first necessitate a brief exposition of the phylogeography of the Y chromosomal lineage O. Then triangulation discloses some contours and particulars of both long lost episodes of ethnolinguistic prehistory.
Collapse
Affiliation(s)
- Gyaneshwer Chaubey
- Department of Zoology, Benaras Hindu University, Varanasi, Uttar Pradesh221005, India
| | - George van Driem
- Linguistics Institute, University of Bern, Länggassstrasse 49, CH 3012Bern, Switzerland
| |
Collapse
|
169
|
Uchiyama J, Gillam JC, Savelyev A, Ning C. Populations dynamics in Northern Eurasian forests: a long-term perspective from Northeast Asia. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e16. [PMID: 37588381 PMCID: PMC10427466 DOI: 10.1017/ehs.2020.11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The 'Northern Eurasian Greenbelt' (NEG) is the northern forest zone stretching from the Japanese Archipelago to Northern Europe. The NEG has created highly productive biomes for humanity to exploit since the end of the Pleistocene. This research explores how the ecological conditions in northern Eurasia contributed to and affected human migrations and cultural trajectories by synthesizing the complimentary viewpoints of environmental archaeology, Geographic Information Science (GIS), genetics and linguistics. First, the environmental archaeology perspective raises the possibility that the NEG functioned as a vessel fostering people to develop diverse cultures and engage in extensive cross-cultural exchanges. Second, geographical analysis of genomic data on mitochondrial DNA using GIS reveals the high probability that population dynamics in the southeastern NEG promoted the peopling of the Americas at the end of the Pleistocene. Finally, a linguistic examination of environmental- and landscape-related vocabulary of the proto-Turkic language groups enables the outline of their original cultural landscape and natural conditions, demonstrating significant cultural spheres, i.e. from southern Siberia to eastern Inner Mongolia during Neolithization. All of these results combine to suggest that the ecological complex in the southern edge of the NEG in northeast Asia played a significant role in peopling across the continents during prehistory.
Collapse
Affiliation(s)
- Junzo Uchiyama
- The Sainsbury Institute for the Study of Japanese Arts and Cultures, University of East Anglia, 64 The Close, NorwichNR1 4DH, UK
- Center for Cultural Resource Studies, Kanazawa University, Kakuma-machi, Kanazawa-shi, 920-1192, Japan
| | - J. Christopher Gillam
- Department of Sociology, Criminology and Anthropology, Winthrop University, 319 Kinard Hall, Rock Hill, SC29733, USA
| | - Alexander Savelyev
- Max Planck Institute for the Science of Human History, 07745Jena, Germany
- Institute of Linguistics, Russian Academy of Sciences, Bolshoy Kislovsky Pereulok 1/1, 125009Moscow, Russia
| | - Chao Ning
- Max Planck Institute for the Science of Human History, 07745Jena, Germany
| |
Collapse
|
170
|
de Boer E, Yang MA, Kawagoe A, Barnes GL. Japan considered from the hypothesis of farmer/language spread. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e13. [PMID: 37588377 PMCID: PMC10427481 DOI: 10.1017/ehs.2020.7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Formally, the Farming/Language Dispersal hypothesis as applied to Japan relates to the introduction of agriculture and spread of the Japanese language (between ca. 500 BC-AD 800). We review current data from genetics, archaeology, and linguistics in relation to this hypothesis. However, evidence bases for these disciplines are drawn from different periods. Genetic data have primarily been sampled from present-day Japanese and prehistoric Jōmon peoples (14,000-300 BC), preceding the introduction of rice agriculture. The best archaeological evidence for agriculture comes from western Japan during the Yayoi period (ca. 900 BC-AD 250), but little is known about northeastern Japan, which is a focal point here. And despite considerable hypothesizing about prehistoric language, the spread of historic languages/ dialects through the islands is more accessible but difficult to relate to prehistory. Though the lack of Yayoi skeletal material available for DNA analysis greatly inhibits direct study of how the pre-agricultural Jōmon peoples interacted with rice agriculturalists, our review of Jōmon genetics sets the stage for further research into their relationships. Modern linguistic research plays an unexpected role in bringing Izumo (Shimane Prefecture) and the Japan Sea coast into consideration in the populating of northeastern Honshu by agriculturalists beyond the Kantō region.
Collapse
Affiliation(s)
- Elisabeth de Boer
- Faculty of East Asian Studies, Ruhr-Universität Bochum, Bochum, Germany
| | - Melinda A. Yang
- Department of Biology, University of Richmond, Richmond, Virginia, USA
| | - Aileen Kawagoe
- Department of Social Studies, New International School of Japan, Tokyo, Japan
| | | |
Collapse
|
171
|
Gutaker RM, Groen SC, Bellis ES, Choi JY, Pires IS, Bocinsky RK, Slayton ER, Wilkins O, Castillo CC, Negrão S, Oliveira MM, Fuller DQ, Guedes JAD, Lasky JR, Purugganan MD. Genomic history and ecology of the geographic spread of rice. NATURE PLANTS 2020; 6:492-502. [PMID: 32415291 DOI: 10.1038/s41477-020-0659-6] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/02/2020] [Indexed: 05/22/2023]
Abstract
Rice (Oryza sativa) is one of the world's most important food crops, and is comprised largely of japonica and indica subspecies. Here, we reconstruct the history of rice dispersal in Asia using whole-genome sequences of more than 1,400 landraces, coupled with geographic, environmental, archaeobotanical and paleoclimate data. Originating around 9,000 yr ago in the Yangtze Valley, rice diversified into temperate and tropical japonica rice during a global cooling event about 4,200 yr ago. Soon after, tropical japonica rice reached Southeast Asia, where it rapidly diversified, starting about 2,500 yr BP. The history of indica rice dispersal appears more complicated, moving into China around 2,000 yr BP. We also identify extrinsic factors that influence genome diversity, with temperature being a leading abiotic factor. Reconstructing the dispersal history of rice and its climatic correlates may help identify genetic adaptations associated with the spread of a key domesticated species.
Collapse
Affiliation(s)
- Rafal M Gutaker
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Simon C Groen
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Emily S Bellis
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Jae Y Choi
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Inês S Pires
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Lisbon, Portugal
| | | | - Emma R Slayton
- Carnegie Mellon University Libraries, Pittsburgh, PA, USA
| | - Olivia Wilkins
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Cristina C Castillo
- Institute of Archaeology, University College London, London, United Kingdom
- School of Cultural Heritage, North-West University, Xi'an, China
| | - Sónia Negrão
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Dorian Q 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
| | - Jesse R Lasky
- Department of Biology, Pennsylvania State University, University Park, PA, USA.
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.
- Institute for the Study of the Ancient World, New York University, New York, NY, USA.
| |
Collapse
|
172
|
Zhang X, Li C, Zhou Y, Huang J, Yu T, Liu X, Shi H, Liu H, Chia S, Huang S, Guo Y, Shoocongdej R, Ji X, Su B. A Matrilineal Genetic Perspective of Hanging Coffin Custom in Southern China and Northern Thailand. iScience 2020; 23:101032. [PMID: 32304863 PMCID: PMC7163074 DOI: 10.1016/j.isci.2020.101032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/06/2020] [Accepted: 03/30/2020] [Indexed: 01/16/2023] Open
Abstract
Hanging Coffin is a unique and ancient burial custom that has been practiced in southern China, Southeast Asia, and near Oceania regions for more than 3,000 years. Here, we conducted mitochondrial whole-genome analyses of 41 human remains sampled from 13 Hanging Coffin sites in southern China and northern Thailand, which were dated between ∼2,500 and 660 years before present. We found that there were genetic connections between the Hanging Coffin people living in different geographic regions. Notably, the matrilineal genetic diversity of the Hanging Coffin people from southern China is much higher than those from northern Thailand, consistent with the hypothesized single origin of the Hanging Coffin custom in southern China about 3,600 years ago, followed by its dispersal in southern China through demic diffusion, whereas the major dispersal pattern in Southeast Asia is cultural assimilation in the past 2,000 years.
Collapse
Affiliation(s)
- Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Chunmei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Yanan Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiahui Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tengsong Yu
- Zhaotong Institute of Cultural Relics Protection and Archaeology, Zhaoyang, Yunnan 657200, China
| | - Xu Liu
- Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China
| | - Hong Shi
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming 650228, China
| | - Hong Liu
- International Joint Research Center for Karstology, Yunnan University, Kunming, 650223, China
| | - Stephen Chia
- Center for Global Archaeological Research, University of Science Malaysia, Penang, Malaysia
| | - Shenmin Huang
- Key Laboratory of Environmental Change and Resources Use in Baibu Gulf, Ministry of Education, Nanning Normal University, Nanning, Guangxi 530001, China
| | - Yaozheng Guo
- Youjiang Nationalities Museum, Baise, Guangxi 533000, China
| | - Rasmi Shoocongdej
- Department of Archaeology, Faculty of Archaeology, Silpakorn University, Bangkok 10200, Thailand.
| | - Xueping Ji
- Yunnan Institute of Cultural Relics and Archaeology, Kunming 650118, China; School of Geoscience, Yunnan University, Kunming 650091, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| |
Collapse
|
173
|
Sufriyana H, Wu YW, Su ECY. Artificial intelligence-assisted prediction of preeclampsia: Development and external validation of a nationwide health insurance dataset of the BPJS Kesehatan in Indonesia. EBioMedicine 2020; 54:102710. [PMID: 32283530 PMCID: PMC7152721 DOI: 10.1016/j.ebiom.2020.102710] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/24/2020] [Accepted: 02/24/2020] [Indexed: 02/06/2023] Open
Abstract
Background We developed and validated an artificial intelligence (AI)-assisted prediction of preeclampsia applied to a nationwide health insurance dataset in Indonesia. Methods The BPJS Kesehatan dataset have been preprocessed using a nested case-control design into preeclampsia/eclampsia (n = 3318) and normotensive pregnant women (n = 19,883) from all women with one pregnancy. The dataset provided 95 features consisting of demographic variables and medical histories started from 24 months to event and ended by delivery as the event. Six algorithms were compared by area under the receiver operating characteristics curve (AUROC) with a subgroup analysis by time to the event. We compared our model to similar prediction models from systematically reviewed studies. In addition, we conducted a text mining analysis based on natural language processing techniques to interpret our modeling results. Findings The best model consisted of 17 predictors extracted by a random forest algorithm. Nine∼12 months to the event was the period that had the best AUROC in external validation by either geographical (0.88, 95% confidence interval (CI) 0.88–0.89) or temporal split (0.86, 95% CI 0.85–0.86). We compared this model to prediction models in seven studies from 869 records in PUBMED, EMBASE, and SCOPUS. This model outperformed the previous models in terms of the precision, sensitivity, and specificity in all validation sets. Interpretation Our low-cost model improved preliminary prediction to decide pregnant women that will be predicted by the models with high specificity and advanced predictors. Funding This work was supported by grant no. MOST108-2221-E-038-018 from the Ministry of Science and Technology of Taiwan.
Collapse
Affiliation(s)
- Herdiantri Sufriyana
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Department of Medical Physiology, College of Medicine, University of Nahdlatul Ulama Surabaya, Surabaya 60237, Indonesia.
| | - Yu-Wei Wu
- Department of Medical Physiology, College of Medicine, University of Nahdlatul Ulama Surabaya, Surabaya 60237, Indonesia; Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei 11031, Taiwan.
| | - Emily Chia-Yu Su
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei 11031, Taiwan; Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei 11031, Taiwan.
| |
Collapse
|
174
|
Beyond broad strokes: sociocultural insights from the study of ancient genomes. Nat Rev Genet 2020; 21:355-366. [DOI: 10.1038/s41576-020-0218-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2020] [Indexed: 01/01/2023]
|
175
|
Inferring the population history of Tai-Kadai-speaking people and southernmost Han Chinese on Hainan Island by genome-wide array genotyping. Eur J Hum Genet 2020; 28:1111-1123. [PMID: 32123326 DOI: 10.1038/s41431-020-0599-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 12/19/2019] [Accepted: 02/04/2020] [Indexed: 11/08/2022] Open
Abstract
Hainan Island, located between East Asia and Southeast Asia, represents an ideal region for the study of the genetic architecture of geographically isolated populations. However, the genetic structure and demographic history of the indigenous Tai-Kadai-speaking Hlai people and recent expanded southernmost Han Chinese on this island are poorly characterized due to a lack of genetic data. Thus, we collected and genotyped 36 Qiongzhong Hlai and 48 Haikou Han individuals at 497,637 single nucleotide polymorphisms (SNPs). We applied principal component analysis, ADMIXTURE, symmetrical D-statistics, admixture-f3 statistics, qpWave, and qpAdm analysis to infer the population history. Our results revealed the East Asian populations are characterized by a north-south genetic cline with Hlai at the southernmost end. We have not detected recent gene flow from neighboring populations into Hlai, therefore, we used Hlai as an unadmixed proxy to model the admixture history of mainland Tai-Kadai-speaking populations and southern Han Chinese. The mainland Tai-Kadai-speaking populations are suggested deriving a larger number of their ancestry from Hlai-related lineage, but also having admixture from South Asian-related or other neighboring populations. The Hlai group is also suggested to contribute about half of the ancestry to Han Chinese in Hainan. The complex patterns of genetic structure in East Asia were shaped via language categories, geographical boundaries, and large southward population movements with language dispersal and agriculture propagation.
Collapse
|
176
|
Hudson MJ, Nakagome S, Whitman JB. The evolving Japanese: the dual structure hypothesis at 30. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e6. [PMID: 37588379 PMCID: PMC10427290 DOI: 10.1017/ehs.2020.6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The population history of Japan has been one of the most intensively studied anthropological questions anywhere in the world, with a huge literature dating back to the nineteenth century and before. A growing consensus over the 1980s that the modern Japanese comprise an admixture of a Neolithic population with Bronze Age migrants from the Korean peninsula was crystallised in Kazurō Hanihara's influential 'dual structure hypothesis' published in 1991. Here, we use recent research in biological anthropology, historical linguistics and archaeology to evaluate this hypothesis after three decades. Although the major assumptions of Hanihara's model have been supported by recent work, we discuss areas where new findings have led to a re-evaluation of aspects of the hypothesis and emphasise the need for further research in key areas including ancient DNA and archaeology.
Collapse
Affiliation(s)
- Mark J. Hudson
- Eurasia3angle Research Group, Max Planck Institute for the Science of Human History, Kahlaische straße 10, 07745Jena, Germany
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, 150-162 Pearse Street, Dublin, Ireland
| | - John B. Whitman
- Department of Linguistics, Cornell University, 203 Morrill Hall, Ithaca, NY14853, USA
| |
Collapse
|
177
|
Kutanan W, Kampuansai J, Srikummool M, Brunelli A, Ghirotto S, Arias L, Macholdt E, Hübner A, Schröder R, Stoneking M. Contrasting Paternal and Maternal Genetic Histories of Thai and Lao Populations. Mol Biol Evol 2020; 36:1490-1506. [PMID: 30980085 PMCID: PMC6573475 DOI: 10.1093/molbev/msz083] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The human demographic history of Mainland Southeast Asia (MSEA) has not been well studied; in particular, there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of ∼2.3 mB from 914 males and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major Mainland Southeast Asia families: Austroasiatic, Tai-Kadai, and Sino-Tibetan. Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* [O-M95*] and O2a* [O-M324*]) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyze complete mitochondrial DNA genome sequences published previously from the same groups and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of postmarital residence pattern on genetic diversity in patrilocal versus matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic (∼10 ka), with two later major male-specific expansions during the Neolithic period (∼4–5 ka) and the Bronze/Iron Age (∼2.0–2.5 ka). These two later expansions are characteristic of the modern Austroasiatic and Tai-Kadai groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion, and cultural diffusion) of major Thai groups and find different results from mitochondrial DNA simulations, supporting contrasting male and female genetic histories.
Collapse
Affiliation(s)
- Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Metawee Srikummool
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Andrea Brunelli
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Silvia Ghirotto
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Leonardo Arias
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Enrico Macholdt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| |
Collapse
|
178
|
The paternal and maternal genetic history of Vietnamese populations. Eur J Hum Genet 2019; 28:636-645. [PMID: 31827276 PMCID: PMC7171127 DOI: 10.1038/s41431-019-0557-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/14/2019] [Accepted: 11/17/2019] [Indexed: 11/08/2022] Open
Abstract
Vietnam exhibits great cultural and linguistic diversity, yet the genetic history of Vietnamese populations remains poorly understood. Previous studies focused mostly on the majority Kinh group, and thus the genetic diversity of the many other groups has not yet been investigated. Here we analyze complete mtDNA genome sequences and ~2.3 Mb sequences of the male-specific portion of the Y chromosome from the Kinh and 16 minority populations, encompassing all five language families present in Vietnam. We find highly variable levels of diversity within and between groups that do not correlate with either geography or language family. In particular, the Mang and Sila have undergone recent, independent bottlenecks, while the majority group, Kinh, exhibits low levels of differentiation with other groups. The two Austronesian-speaking groups, Giarai and Ede, show a potential impact of matrilocality on their patterns of variation. Overall, we find that isolation, coupled with limited contact involving some groups, has been the major factor influencing the genetic structure of Vietnamese populations, and that there is substantial genetic diversity that is not represented by the Kinh.
Collapse
|
179
|
McHugo GP, Dover MJ, MacHugh DE. Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics. BMC Biol 2019; 17:98. [PMID: 31791340 PMCID: PMC6889691 DOI: 10.1186/s12915-019-0724-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.
Collapse
Affiliation(s)
- Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Michael J Dover
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland.
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland.
| |
Collapse
|
180
|
Zhang C, Gao Y, Ning Z, Lu Y, Zhang X, Liu J, Xie B, Xue Z, Wang X, Yuan K, Ge X, Pan Y, Liu C, Tian L, Wang Y, Lu D, Hoh BP, Xu S. PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations. Genome Biol 2019; 20:215. [PMID: 31640808 PMCID: PMC6805450 DOI: 10.1186/s13059-019-1838-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 09/26/2019] [Indexed: 12/23/2022] Open
Abstract
Despite the tremendous growth of the DNA sequencing data in the last decade, our understanding of the human genome is still in its infancy. To understand the implications of genetic variants in the light of population genetics and molecular evolution, we developed a database, PGG.SNV ( https://www.pggsnv.org ), which gives much higher weight to previously under-investigated indigenous populations in Asia. PGG.SNV archives 265 million SNVs across 220,147 present-day genomes and 1018 ancient genomes, including 1009 newly sequenced genomes, representing 977 global populations. Moreover, estimation of population genetic diversity and evolutionary parameters is available in PGG.SNV, a unique feature compared with other databases.
Collapse
Affiliation(s)
- Chao Zhang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
- Present Address: Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yang Gao
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zhilin Ning
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
| | - Yan Lu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
| | - Xiaoxi Zhang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jiaojiao Liu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Bo Xie
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
| | - Zhe Xue
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
| | - Xiaoji Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
| | - Kai Yuan
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
| | - Xueling Ge
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
| | - Yuwen Pan
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
| | - Chang Liu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
| | - Lei Tian
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
| | - Yuchen Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
| | - Dongsheng Lu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
| | - Boon-Peng Hoh
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China
- Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, Cheras, 56000, Kuala Lumpur, Malaysia
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- Collaborative Innovation Center of Genetics and Development, Shanghai, 200438, China.
| |
Collapse
|
181
|
Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore. Cell 2019; 179:736-749.e15. [DOI: 10.1016/j.cell.2019.09.019] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 06/24/2019] [Accepted: 09/19/2019] [Indexed: 12/19/2022]
|
182
|
Ishiya K, Mizuno F, Wang L, Ueda S. MitoIMP: A Computational Framework for Imputation of Missing Data in Low-Coverage Human Mitochondrial Genome. Bioinform Biol Insights 2019; 13:1177932219873884. [PMID: 31523131 PMCID: PMC6732850 DOI: 10.1177/1177932219873884] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 08/13/2019] [Indexed: 11/16/2022] Open
Abstract
The incompleteness of partial human mitochondrial genome sequences makes it difficult to perform relevant comparisons among multiple resources. To deal with this issue, we propose a computational framework for deducing missing nucleotides in the human mitochondrial genome. We applied it to worldwide mitochondrial haplogroup lineages and assessed its performance. Our approach can deduce the missing nucleotides with a precision of 0.99 or higher in most human mitochondrial DNA lineages. Furthermore, although low-coverage mitochondrial genome sequences often lead to a blurred relationship in the multidimensional scaling analysis, our approach can correct this positional arrangement according to the corresponding mitochondrial DNA lineages. Therefore, our framework will provide a practical solution to compensate for the lack of genome coverage in partial and fragmented human mitochondrial genome sequences. In this study, we developed an open-source computer program, MitoIMP, implementing our imputation procedure. MitoIMP is freely available from https://github.com/omics-tools/mitoimp.
Collapse
Affiliation(s)
- Koji Ishiya
- Computational Bio Big Data Open Innovation Lab (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST)-Waseda University, Tokyo, Japan
| | - Fuzuki Mizuno
- Department of Legal Medicine, School of Medicine, Toho University, Tokyo, Japan
| | - Li Wang
- School of Medicine, Hangzhou Normal University, Zhejiang, China
| | - Shintaroh Ueda
- Department of Legal Medicine, School of Medicine, Toho University, Tokyo, Japan.,School of Medicine, Hangzhou Normal University, Zhejiang, China.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
183
|
Samper Carro SC, Gilbert F, Bulbeck D, O'Connor S, Louys J, Spooner N, Questiaux D, Arnold L, Price GJ, Wood R, Mahirta. Somewhere beyond the sea: Human cranial remains from the Lesser Sunda Islands (Alor Island, Indonesia) provide insights on Late Pleistocene peopling of Island Southeast Asia. J Hum Evol 2019; 134:102638. [PMID: 31446971 DOI: 10.1016/j.jhevol.2019.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 07/05/2019] [Accepted: 07/06/2019] [Indexed: 01/29/2023]
Abstract
The migration of anatomically modern humans (AMH) from Africa to every inhabitable continent included their dispersal through Island Southeast Asia (ISEA) to Australia. Significantly, this involved overwater dispersal through the Lesser Sunda Islands between Sunda (continental Southeast Asia) and Sahul (Australia and New Guinea). However, the timing and direction of this movement is still debated. Here, we report on human skeletal material recovered from excavations at two rockshelters, known locally as Tron Bon Lei, on Alor Island, Indonesia. The remains, dated to the Late Pleistocene, are the first anatomically modern human remains recovered in Wallacea dated to this period and are associated with cultural material demonstrating intentional burial. The human remains from Tron Bon Lei represent a population osteometrically distinct from Late Pleistocene Sunda and Sahul AMH. Instead, morphometrically, they appear more similar to Holocene populations in the Lesser Sundas. Thus, they may represent the remains of a population originally from Sunda whose Lesser Sunda Island descendants survived into the Holocene.
Collapse
Affiliation(s)
- Sofía C Samper Carro
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, 2601, Australia; School of Archaeology and Anthropology, College of Arts and Social Sciences, Australian National University, Canberra, 2601, Australia; Centre d'Estudis del Patrimoni Arqueològic de la Prehistòria, Facultat de Lletres-Edifici B, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Felicity Gilbert
- School of Archaeology and Anthropology, College of Arts and Social Sciences, Australian National University, Canberra, 2601, Australia
| | - David Bulbeck
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, 2601, Australia
| | - Sue O'Connor
- Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, 2601, Australia; ARC Centre of Excellence for Australian Biodiversity and Heritage, Australian National University, Canberra, 2601, Australia
| | - Julien Louys
- Australian Research Centre of Human Evolution (ARCHE), Environmental Futures Research Institute, Griffith University, Nathan, 4111, Australia
| | - Nigel Spooner
- Institute for Photonics and Advanced Sensing & School of Physical Sciences, University of Adelaide, SA, 5005, Australia; Defence Science and Technology Group, PO Box 1500, Edinburgh, SA, 5111, UK
| | - Danielle Questiaux
- Institute for Photonics and Advanced Sensing & School of Physical Sciences, University of Adelaide, SA, 5005, Australia
| | - Lee Arnold
- Institute for Photonics and Advanced Sensing & School of Physical Sciences, University of Adelaide, SA, 5005, Australia
| | - Gilbert J Price
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, 4072, Australia
| | - Rachel Wood
- Earth Chemistry, Research School of Earth Sciences, Australian National University, Canberra, 2601, Australia
| | - Mahirta
- Jurusan Arkeologi, Fakultas Ilmu Budaya, Universitas Gadja Madja, Bulaksumur, Yogjakarta, 55281, Indonesia
| |
Collapse
|
184
|
Bokelmann L, Hajdinjak M, Peyrégne S, Brace S, Essel E, de Filippo C, Glocke I, Grote S, Mafessoni F, Nagel S, Kelso J, Prüfer K, Vernot B, Barnes I, Pääbo S, Meyer M, Stringer C. A genetic analysis of the Gibraltar Neanderthals. Proc Natl Acad Sci U S A 2019; 116:15610-15615. [PMID: 31308224 PMCID: PMC6681707 DOI: 10.1073/pnas.1903984116] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Forbes' Quarry and Devil's Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes' Quarry and Devil's Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes' Quarry individual. We confirm that the Forbes' Quarry individual was a female and the Devil's Tower individual a male. We also show that the Forbes' Quarry individual is genetically more similar to the ∼120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ∼60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ∼49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes' Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation.
Collapse
Affiliation(s)
- Lukas Bokelmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany;
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Selina Brace
- Centre for Human Evolution Research, Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Isabelle Glocke
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Steffi Grote
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Ian Barnes
- Centre for Human Evolution Research, Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany;
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Chris Stringer
- Centre for Human Evolution Research, Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
| |
Collapse
|
185
|
Abstract
The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace's Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic.
Collapse
|
186
|
Le VS, Tran KT, Bui HTP, Le HTT, Nguyen CD, Do DH, Ly HTT, Pham LTD, Dao LTM, Nguyen LT. A Vietnamese human genetic variation database. Hum Mutat 2019; 40:1664-1675. [PMID: 31180159 DOI: 10.1002/humu.23835] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/14/2019] [Accepted: 06/05/2019] [Indexed: 12/29/2022]
Abstract
Large scale human genome projects have created tremendous human genome databases for some well-studied populations. Vietnam has about 95 million people (the 14th largest country by population in the world) of which more than 86% are Kinh people. To date, genetic studies for Vietnamese people mostly rely on genetic information from other populations. Building a Vietnamese human genetic variation database is a must for properly interpreting Vietnamese genetic variants. To this end, we sequenced 105 whole genomes and 200 whole exomes of 305 unrelated Kinh Vietnamese (KHV) people. We also included 101 other previously published KHV genomes to build a Vietnamese human genetic variation database of 406 KHV people. The KHV database contains 24.81 million variants (22.47 million single nucleotide polymorphisms (SNPs) and 2.34 million indels) of which 0.71 million variants are novel. It includes more than 99.3% of variants with a frequency of >1% in the KHV population. Noticeably, the KHV database revealed 107 variants reported in the human genome mutation database as pathological mutations with a frequency above 1% in the KHV population. The KHV database (available at https://genomes.vn) would be beneficial for genetic studies and medical applications not only for the Vietnamese population but also for other closely related populations.
Collapse
Affiliation(s)
- Vinh S Le
- Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam.,Department of Gene Technology, Vinmec International Hospital Times City, Hanoi, Vietnam.,Faculty of Information Technology, University of Engineering and Technology, Vietnam National University Hanoi, Hanoi, Vietnam
| | - Kien T Tran
- Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam
| | - Hoa T P Bui
- Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam.,Department of Gene Technology, Vinmec International Hospital Times City, Hanoi, Vietnam.,School of Environment and Life Science, University of Salford, Manchester, United Kingdom
| | - Huong T T Le
- Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam.,Department of Gene Technology, Vinmec International Hospital Times City, Hanoi, Vietnam
| | - Canh D Nguyen
- Faculty of Information Technology, University of Engineering and Technology, Vietnam National University Hanoi, Hanoi, Vietnam
| | - Duong H Do
- Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam.,Department of Gene Technology, Vinmec International Hospital Times City, Hanoi, Vietnam
| | - Ha T T Ly
- Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam.,Department of Gene Technology, Vinmec International Hospital Times City, Hanoi, Vietnam
| | - Linh T D Pham
- Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam
| | - Lan T M Dao
- Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam
| | - Liem T Nguyen
- Vinmec Research Institute of Stem Cell and Gene Technology, Hanoi, Vietnam
| |
Collapse
|
187
|
Population genetics, diversity and forensic characteristics of Tai–Kadai-speaking Bouyei revealed by insertion/deletions markers. Mol Genet Genomics 2019; 294:1343-1357. [DOI: 10.1007/s00438-019-01584-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 05/30/2019] [Indexed: 12/13/2022]
|
188
|
Jeong C, Balanovsky O, Lukianova E, Kahbatkyzy N, Flegontov P, Zaporozhchenko V, Immel A, Wang CC, Ixan O, Khussainova E, Bekmanov B, Zaibert V, Lavryashina M, Pocheshkhova E, Yusupov Y, Agdzhoyan A, Koshel S, Bukin A, Nymadawa P, Turdikulova S, Dalimova D, Churnosov M, Skhalyakho R, Daragan D, Bogunov Y, Bogunova A, Shtrunov A, Dubova N, Zhabagin M, Yepiskoposyan L, Churakov V, Pislegin N, Damba L, Saroyants L, Dibirova K, Atramentova L, Utevska O, Idrisov E, Kamenshchikova E, Evseeva I, Metspalu M, Outram AK, Robbeets M, Djansugurova L, Balanovska E, Schiffels S, Haak W, Reich D, Krause J. The genetic history of admixture across inner Eurasia. Nat Ecol Evol 2019; 3:966-976. [PMID: 31036896 PMCID: PMC6542712 DOI: 10.1038/s41559-019-0878-2] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 03/18/2019] [Indexed: 12/29/2022]
Abstract
The indigenous populations of inner Eurasia-a huge geographic region covering the central Eurasian steppe and the northern Eurasian taiga and tundra-harbour tremendous diversity in their genes, cultures and languages. In this study, we report novel genome-wide data for 763 individuals from Armenia, Georgia, Kazakhstan, Moldova, Mongolia, Russia, Tajikistan, Ukraine and Uzbekistan. We furthermore report additional damage-reduced genome-wide data of two previously published individuals from the Eneolithic Botai culture in Kazakhstan (~5,400 BP). We find that present-day inner Eurasian populations are structured into three distinct admixture clines stretching between various western and eastern Eurasian ancestries, mirroring geography. The Botai and more recent ancient genomes from Siberia show a decrease in contributions from so-called 'ancient North Eurasian' ancestry over time, which is detectable only in the northern-most 'forest-tundra' cline. The intermediate 'steppe-forest' cline descends from the Late Bronze Age steppe ancestries, while the 'southern steppe' cline further to the south shows a strong West/South Asian influence. Ancient genomes suggest a northward spread of the southern steppe cline in Central Asia during the first millennium BC. Finally, the genetic structure of Caucasus populations highlights a role of the Caucasus Mountains as a barrier to gene flow and suggests a post-Neolithic gene flow into North Caucasus populations from the steppe.
Collapse
Affiliation(s)
- Choongwon Jeong
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
- Eurasia3angle Research Group, Max Planck Institute for the Science of Human History, Jena, Germany.
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
| | - Oleg Balanovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Federal State Budgetary Institution 'Research Centre for Medical Genetics', Moscow, Russia
| | - Elena Lukianova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Nurzhibek Kahbatkyzy
- Department of Population Genetics, Institute of General Genetics and Cytology, Science Committee, Ministry of Education and Science of the Republic of Kazakhstan, Almaty, Kazakhstan
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Faculty of Science, University of South Bohemia and Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic
| | - Valery Zaporozhchenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Federal State Budgetary Institution 'Research Centre for Medical Genetics', Moscow, Russia
| | - Alexander Immel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Chuan-Chao Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, China
| | - Olzhas Ixan
- Department of Population Genetics, Institute of General Genetics and Cytology, Science Committee, Ministry of Education and Science of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Elmira Khussainova
- Department of Population Genetics, Institute of General Genetics and Cytology, Science Committee, Ministry of Education and Science of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Bakhytzhan Bekmanov
- Department of Population Genetics, Institute of General Genetics and Cytology, Science Committee, Ministry of Education and Science of the Republic of Kazakhstan, Almaty, Kazakhstan
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Victor Zaibert
- Institute of Archeology and Steppe Civilization, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | | | - Yuldash Yusupov
- Institute of Strategic Research of the Republic of Bashkortostan, Ufa, Russia
| | - Anastasiya Agdzhoyan
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Federal State Budgetary Institution 'Research Centre for Medical Genetics', Moscow, Russia
| | - Sergey Koshel
- Faculty of Geography, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Shahlo Turdikulova
- Center for Advanced Technologies, Ministry of Innovational Development, Tashkent, Uzbekistan
| | - Dilbar Dalimova
- Center for Advanced Technologies, Ministry of Innovational Development, Tashkent, Uzbekistan
| | | | - Roza Skhalyakho
- Federal State Budgetary Institution 'Research Centre for Medical Genetics', Moscow, Russia
| | - Denis Daragan
- Federal State Budgetary Institution 'Research Centre for Medical Genetics', Moscow, Russia
| | - Yuri Bogunov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Federal State Budgetary Institution 'Research Centre for Medical Genetics', Moscow, Russia
| | - Anna Bogunova
- Federal State Budgetary Institution 'Research Centre for Medical Genetics', Moscow, Russia
| | - Alexandr Shtrunov
- Federal State Budgetary Institution 'Research Centre for Medical Genetics', Moscow, Russia
| | - Nadezhda Dubova
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | - Maxat Zhabagin
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Vladimir Churakov
- Udmurt Institute of History, Language and Literature, Udmurt Federal Research Center, Ural Branch, Russian Academy of Sciences, Izhevsk, Russia
| | - Nikolay Pislegin
- Udmurt Institute of History, Language and Literature, Udmurt Federal Research Center, Ural Branch, Russian Academy of Sciences, Izhevsk, Russia
| | - Larissa Damba
- Research Institute of Medical and Social Problems and Control, Healthcare Department of Tuva Republic, Kyzyl, Russia
| | | | - Khadizhat Dibirova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Federal State Budgetary Institution 'Research Centre for Medical Genetics', Moscow, Russia
| | | | - Olga Utevska
- V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | - Eldar Idrisov
- Astrakhan Branch, Russian Presidential Academy of National Economy and Public Administration under the President of the Russian Federation, Astrakhan, Russia
| | | | - Irina Evseeva
- Northern State Medical University, Arkhangelsk, Russia
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Alan K Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Martine Robbeets
- Eurasia3angle Research Group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Leyla Djansugurova
- Department of Population Genetics, Institute of General Genetics and Cytology, Science Committee, Ministry of Education and Science of the Republic of Kazakhstan, Almaty, Kazakhstan
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Elena Balanovska
- Federal State Budgetary Institution 'Research Centre for Medical Genetics', Moscow, Russia
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
| |
Collapse
|
189
|
Abstract
Rushton and Jensen argued that cognitive ability differs between human populations. But why are such differences expectable? Their answer: as modern humans spread out of Africa and into northern Eurasia, they entered colder and more seasonal climates that selected for the ability to plan ahead, in order to store food, make clothes, and build shelters for winter. This cold winter theory is supported by research on Paleolithic humans and recent hunter-gatherers. Tools become more diverse and complex as effective temperature decreases, apparently because food has to be obtained during limited periods and over large areas. There is also more storage of food and fuel and greater use of untended traps and snares. Finally, shelters have to be sturdier, and clothing more cold-resistant. The resulting cognitive demands are met primarily by women because the lack of opportunities for food gathering pushes them into more cognitively demanding tasks, like garment making, needlework, weaving, leatherworking, pottery, and kiln operation. The northern tier of Paleolithic Eurasia thus produced the “Original Industrial Revolution”—an explosion of creativity that preadapted its inhabitants for later developments, i.e., farming, more complex technology and social organization, and an increasingly future-oriented culture. Over time, these humans would spread south, replacing earlier populations that could less easily exploit the possibilities of the new cultural environment. As this environment developed further, it selected for further increases in cognitive ability. Indeed, mean intelligence seems to have risen during recorded history at temperate latitudes in Europe and East Asia. There is thus no unified theory for the evolution of human intelligence. A key stage was adaptation to cold winters during the Paleolithic, but much happened later.
Collapse
|
190
|
Jacobs GS, Hudjashov G, Saag L, Kusuma P, Darusallam CC, Lawson DJ, Mondal M, Pagani L, Ricaut FX, Stoneking M, Metspalu M, Sudoyo H, Lansing JS, Cox MP. Multiple Deeply Divergent Denisovan Ancestries in Papuans. Cell 2019; 177:1010-1021.e32. [DOI: 10.1016/j.cell.2019.02.035] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/07/2019] [Accepted: 02/21/2019] [Indexed: 12/29/2022]
|
191
|
Ralph PL. An empirical approach to demographic inference with genomic data. Theor Popul Biol 2019; 127:91-101. [PMID: 30978307 DOI: 10.1016/j.tpb.2019.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/21/2019] [Accepted: 03/27/2019] [Indexed: 01/20/2023]
Abstract
Inference with population genetic data usually treats the population pedigree as a nuisance parameter, the unobserved product of a past history of random mating. However, the history of genetic relationships in a given population is a fixed, unobserved object, and so an alternative approach is to treat this network of relationships as a complex object we wish to learn about, by observing how genomes have been noisily passed down through it. This paper explores this point of view, showing how to translate questions about population genetic data into calculations with a Poisson process of mutations on all ancestral genomes. This method is applied to give a robust interpretation to the f4 statistic used to identify admixture, and to design a new statistic that measures covariances in mean times to most recent common ancestor between two pairs of sequences. The method more generally interprets population genetic statistics in terms of sums of specific functions over ancestral genomes, thereby providing concrete, broadly interpretable interpretations for these statistics. This provides a method for describing demographic history without simplified demographic models. More generally, it brings into focus the population pedigree, which is averaged over in model-based demographic inference.
Collapse
Affiliation(s)
- Peter L Ralph
- Institute of Ecology and Evolution, Departments of Mathematics and Biology, University of Oregon, Eugene, OR, USA.
| |
Collapse
|
192
|
The Promise of Paleogenomics Beyond Our Own Species. Trends Genet 2019; 35:319-329. [PMID: 30954285 DOI: 10.1016/j.tig.2019.02.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/18/2019] [Accepted: 02/25/2019] [Indexed: 02/06/2023]
Abstract
Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions.
Collapse
|
193
|
Prohaska A, Racimo F, Schork AJ, Sikora M, Stern AJ, Ilardo M, Allentoft ME, Folkersen L, Buil A, Moreno-Mayar JV, Korneliussen T, Geschwind D, Ingason A, Werge T, Nielsen R, Willerslev E. Human Disease Variation in the Light of Population Genomics. Cell 2019; 177:115-131. [DOI: 10.1016/j.cell.2019.01.052] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 01/25/2023]
|
194
|
Curnoe D, Datan I, Goh HM, Sauffi MS. Femur associated with the Deep Skull from the West Mouth of the Niah Caves (Sarawak, Malaysia). J Hum Evol 2019; 127:133-148. [PMID: 30777354 DOI: 10.1016/j.jhevol.2018.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 01/06/2023]
Abstract
The skeletal remains of Pleistocene anatomically modern humans are rare in island Southeast Asia. Moreover, continuing doubts over the dating of most of these finds has left the arrival time for the region's earliest inhabitants an open question. The unique biogeography of island Southeast Asia also raises questions about the physical and cultural adaptations of early anatomically modern humans, especially within the setting of rainforest inhabitation. Within this context the Deep Skull from the West Mouth of the Niah Caves continues to figure prominently owing to its relative completeness and the greater certainty surrounding its geological age. Recovered along with this partial cranium in 1958 were several postcranial bones including a partial femur which until now has received little attention. Here we provide a description and undertake a comparison of the Deep Skull femur finding it to be very small in all of its cross-sectional dimensions. We note a number of size and shape similarities to the femora of Indigenous Southeast Asians, especially Aeta people from the Philippines. We estimate its stature to have been roughly 145-146 cm and body mass around 35 kg, confirming similarities to Aeta females. Its extreme gracility indicated by low values for a range of biomechanical parameters taken midshaft meets expectations for a very small (female) Paleolithic East Asian. Interestingly, the second moment of area about the mediolateral axis is enlarged relative to the second moment of area about the anteroposterior axis, which could potentially signal a difference in activity levels or lifestyle compared with other Paleolithic femora. However, it might also be the result of sexual dimorphism in these parameters as well as possibly reflecting changes associated with aging.
Collapse
Affiliation(s)
- Darren Curnoe
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Palaeontology, Geobiology and Earth Archives Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Ipoi Datan
- Sarawak Museum Department, Jalan Barak, Kuching, Sarawak, 93000, Malaysia
| | - Hsiao Mei Goh
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Palaeontology, Geobiology and Earth Archives Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia; Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, 11800, Malaysia
| | - Mohammed S Sauffi
- Sarawak Museum Department, Jalan Barak, Kuching, Sarawak, 93000, Malaysia
| |
Collapse
|
195
|
Yeo LF, Aghakhanian FF, Tan JSY, Gan HM, Phipps ME. Health and saliva microbiomes of a semi-urbanized indigenous tribe in Peninsular Malaysia. F1000Res 2019; 8:175. [PMID: 31275564 PMCID: PMC6544134 DOI: 10.12688/f1000research.17706.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/02/2019] [Indexed: 10/13/2023] Open
Abstract
Background: The indigenous people of Peninsular Malaysia, also known as Orang Asli, have gradually been urbanized. A shift towards non-communicable diseases commonly associated with sedentary lifestyles have been reported in many tribes. This study engaged with a semi-urbanized Temiar tribe from Kampong Pos Piah, Perak, who are experiencing an epidemiological transition. Methods: Weight, height, waist circumference, blood pressure, HbA1C and lipid levels were measured as indicators of cardio-metabolic health. DNA was extracted from saliva using salting-out method followed by PCR amplification of the V3-V4 region of the 16S rRNA gene and sequencing on Illumina MiSeq. Microbiome analysis was conducted on Qiime v1.9. Statistical analysis was conducted using Qiime v1.9 and R. Results: The study revealed that 60.4% of the Temiar community were overweight/obese, with a higher prevalence among women. HbA1C levels showed that 45% of Temiar had pre-diabetes. Insulin resistance was identified in 21% of Temiar by using a surrogate marker, TG/HDL. In total, 56.5% of Temiar were pre-hypertensive, and the condition was prevalent across all age-groups. The saliva microbiome profiles of Temiar revealed significant differences by gender, BMI, abdominal obesity as well as smoking status. The relative abundance of Bifidobacterium was increased in men whereas Prevotella, Capnocytophaga, Leptotrichia, Neisseria and Streptococcus were increased in women. Proteobacteria was significantly depleted in smokers. Conclusions: Temiar from Pos Piah had a high prevalence of cardio-metabolic risks, including general and abdominal obesity, pre-diabetes, prehypertension and hypertension. This phenomenon has not been previously reported in this tribe. The saliva microbiome profiles were significantly different for individuals of different gender, BMI scores, abdominal obesity and smoking status.
Collapse
Affiliation(s)
- Li-Fang Yeo
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
- Tropical Medicine and Biology Platform, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
| | - Farhang F. Aghakhanian
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
- Tropical Medicine and Biology Platform, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
| | - James S. Y. Tan
- Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Han Ming Gan
- School of Life & Env Sciences, Deakin University, Geelong Waurn Ponds Campus, Australia
| | - Maude E. Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
| |
Collapse
|
196
|
Yeo LF, Aghakhanian FF, Tan JSY, Gan HM, Phipps ME. Health and saliva microbiomes of a semi-urbanized indigenous tribe in Peninsular Malaysia. F1000Res 2019; 8:175. [PMID: 31275564 PMCID: PMC6544134 DOI: 10.12688/f1000research.17706.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/30/2019] [Indexed: 12/20/2022] Open
Abstract
Background: The indigenous people of Peninsular Malaysia, also known as Orang Asli, have gradually been urbanized. A shift towards non-communicable diseases commonly associated with sedentary lifestyles have been reported in many tribes. This study engaged with a semi-urbanized Temiar tribe from Kampong Pos Piah, Perak, who are experiencing an epidemiological transition. Methods: Weight, height, waist circumference, blood pressure, HbA1C and lipid levels were measured as indicators of cardio-metabolic health. DNA was extracted from saliva using salting-out method followed by PCR amplification of the V3-V4 region of the 16S rRNA gene and sequencing on Illumina MiSeq. Microbiome analysis was conducted on Qiime v1.9. Statistical analysis was conducted using Qiime v1.9 and R. Results: The study revealed that 60.4% of the Temiar community were overweight/obese, with a higher prevalence among women. HbA1C levels showed that 45% of Temiar had pre-diabetes. Insulin resistance was identified in 21% of Temiar by using a surrogate marker, TG/HDL. In total, 56.5% of Temiar were pre-hypertensive, and the condition was prevalent across all age-groups. The saliva microbiome profiles of Temiar revealed significant differences by gender, BMI, abdominal obesity as well as smoking status. The relative abundance of Bifidobacterium, bacteria commonly found in dairy products, was increased in men. Prevotella, associated with consumption of plant-rich diets, was increased in women. Mogibacteriacea and Mycoplasma levels were significantly elevated in overweight individuals. Proteobacteria was significantly depleted in smokers. Conclusions: Temiar from Pos Piah had a high prevalence of cardio-metabolic risks, including general and abdominal obesity, pre-diabetes, prehypertension and hypertension. This phenomenon has not been previously reported in this tribe. The saliva microbiome profiles were significantly different for individuals of different gender, BMI scores and abdominal obesity and smoking status.
Collapse
Affiliation(s)
- Li-Fang Yeo
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
- Tropical Medicine and Biology Platform, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
| | - Farhang F. Aghakhanian
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
- Tropical Medicine and Biology Platform, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
| | - James S. Y. Tan
- Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Han Ming Gan
- School of Life & Env Sciences, Deakin University, Geelong Waurn Ponds Campus, Australia
| | - Maude E. Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
| |
Collapse
|
197
|
Yeo LF, Aghakhanian FF, Tan JSY, Gan HM, Phipps ME. Health and saliva microbiomes of a semi-urbanized indigenous tribe in Peninsular Malaysia. F1000Res 2019; 8:175. [PMID: 31275564 PMCID: PMC6544134 DOI: 10.12688/f1000research.17706.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/23/2019] [Indexed: 01/05/2023] Open
Abstract
Background: The indigenous people of Peninsular Malaysia, also known as Orang Asli, have gradually been urbanized. A shift towards non-communicable diseases commonly associated with sedentary lifestyles have been reported in many tribes. This study engaged with a semi-urbanized Temiar tribe from Kampong Pos Piah, Perak, who are experiencing an epidemiological transition. Methods: Weight, height, waist circumference, blood pressure, HbA1C and lipid levels were measured as indicators of cardio-metabolic health. DNA was extracted from saliva using salting-out method followed by PCR amplification of the V3-V4 region of the 16S rRNA gene and sequencing on Illumina MiSeq. Microbiome analysis was conducted on Qiime v1.9. Statistical analysis was conducted using Qiime v1.9 and R. Results: The study revealed that 60.4% of the Temiar community were overweight/obese, with a higher prevalence among women. HbA1C levels showed that 45% of Temiar had pre-diabetes. Insulin resistance was identified in 21% of Temiar by using a surrogate marker, TG/HDL. In total, 56.5% of Temiar were pre-hypertensive, and the condition was prevalent across all age-groups. The saliva microbiome profiles of Temiar revealed significant differences by gender, BMI, abdominal obesity as well as smoking status. The relative abundance of the genus Bifidobacterium was increased in men whereas the genera Prevotella, Capnocytophaga, Leptotrichia, Neisseria and Streptococcus were increased in women. Proteobacteria was significantly depleted in smokers. Conclusions: Temiar from Pos Piah had a high prevalence of cardio-metabolic risks, including general and abdominal obesity, pre-diabetes, prehypertension and hypertension. This phenomenon has not been previously reported in this tribe. The saliva microbiome profiles were significantly different for individuals of different gender, BMI, abdominal obesity and smoking status.
Collapse
Affiliation(s)
- Li-Fang Yeo
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
- Tropical Medicine and Biology Platform, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
| | - Farhang F. Aghakhanian
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
- Tropical Medicine and Biology Platform, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
| | - James S. Y. Tan
- Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Han Ming Gan
- School of Life & Env Sciences, Deakin University, Geelong Waurn Ponds Campus, Australia
| | - Maude E. Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University, Bandar Sunway, Selangor, 46150, Malaysia
| |
Collapse
|
198
|
Craniometrics Reveal "Two Layers" of Prehistoric Human Dispersal in Eastern Eurasia. Sci Rep 2019; 9:1451. [PMID: 30723215 PMCID: PMC6363732 DOI: 10.1038/s41598-018-35426-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/31/2018] [Indexed: 12/22/2022] Open
Abstract
This cranio-morphometric study emphasizes a “two-layer model” for eastern Eurasian anatomically modern human (AMH) populations, based on large datasets of 89 population samples including findings directly from ancient archaeological contexts. Results suggest that an initial “first layer” of AMH had related closely to ancestral Andaman, Australian, Papuan, and Jomon groups who likely entered this region via the Southeast Asian landmass, prior to 65–50 kya. A later “second layer” shared strong cranial affinities with Siberians, implying a Northeast Asian source, evidenced by 9 kya in central China and then followed by expansions of descendant groups into Southeast Asia after 4 kya. These two populations shared limited initial exchange, and the second layer grew at a faster rate and in greater numbers, linked with contexts of farming that may have supported increased population densities. Clear dichotomization between the two layers implies a temporally deep divergence of distinct migration routes for AMH through both southern and northern Eurasia.
Collapse
|
199
|
Tran HL, Nguyen HT, Pham TT, Nguyen MH, Hoang H, Chu HH. Allele frequencies for 22 autosomal STRs in the Kinh population in Vietnam. Int J Legal Med 2019; 133:1761-1762. [PMID: 30612322 DOI: 10.1007/s00414-018-01996-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/19/2018] [Indexed: 10/27/2022]
Abstract
We collected and analysed the autosomal STR data of 2040 unrelated Kinh individuals living in Vietnam. Allele frequencies and forensic parameters were calculated, showing high values for the combined powers of discrimination and exclusion. Phylogenetic analysis was performed to determine the genetic relationship of the Kinh population with other Asian populations.
Collapse
Affiliation(s)
- Huyen Linh Tran
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam
| | - Hong Trang Nguyen
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam
| | - Thanh Tung Pham
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam
| | - Mau Hung Nguyen
- Centre of DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha Hoang
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam
| | - Hoang Ha Chu
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, 100000, Vietnam. .,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
| |
Collapse
|
200
|
KANZAWA-KIRIYAMA HIDEAKI, JINAM TIMOTHYA, KAWAI YOSUKE, SATO TAKEHIRO, HOSOMICHI KAZUYOSHI, TAJIMA ATSUSHI, ADACHI NOBORU, MATSUMURA HIROFUMI, KRYUKOV KIRILL, SAITOU NARUYA, SHINODA KENICHI. Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan. ANTHROPOL SCI 2019. [DOI: 10.1537/ase.190415] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
| | - TIMOTHY A. JINAM
- Division of Population Genetics, National Institute of Genetics, Mishima
| | - YOSUKE KAWAI
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo
| | - TAKEHIRO SATO
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa
| | - KAZUYOSHI HOSOMICHI
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa
| | - ATSUSHI TAJIMA
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa
| | - NOBORU ADACHI
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo
| | - HIROFUMI MATSUMURA
- Second Division of Physical Therapy, School of Health Sciences, Sapporo Medical University, Sapporo
| | - KIRILL KRYUKOV
- Department of Molecular Life Science, School of Medicine, Tokai University, Isehara
| | - NARUYA SAITOU
- Division of Population Genetics, National Institute of Genetics, Mishima
| | - KEN-ICHI SHINODA
- Department of Anthropology, National Museum of Nature and Science, Tsukuba
| |
Collapse
|