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Overview of the Americas’ First Peopling from a Patrilineal Perspective: New Evidence from the Southern Continent. Genes (Basel) 2022; 13:genes13020220. [PMID: 35205264 PMCID: PMC8871784 DOI: 10.3390/genes13020220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/24/2022] Open
Abstract
Uniparental genetic systems are unique sex indicators and complement the study of autosomal diversity by providing landmarks of human migrations that repeatedly shaped the structure of extant populations. Our knowledge of the variation of the male-specific region of the Y chromosome in Native Americans is still rather scarce and scattered, but by merging sequence information from modern and ancient individuals, we here provide a comprehensive and updated phylogeny of the distinctive Native American branches of haplogroups C and Q. Our analyses confirm C-MPB373, C-P39, Q-Z780, Q-M848, and Q-Y4276 as the main founding haplogroups and identify traces of unsuccessful (pre-Q-F1096) or extinct (C-L1373*, Q-YP4010*) Y-chromosome lineages, indicating that haplogroup diversity of the founder populations that first entered the Americas was greater than that observed in the Indigenous component of modern populations. In addition, through a diachronic and phylogeographic dissection of newly identified Q-M848 branches, we provide the first Y-chromosome insights into the early peopling of the South American hinterland (Q-BY104773 and Q-BY15730) and on overlying inland migrations (Q-BY139813).
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2
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Abstract
The peopling of Siberia and the Americas is intriguing for archaeologists, linguists, and human geneticists, but despite significant recent developments, many details remain controversial. Here, we provide insights based on genetic diversity within Helicobacter pylori, a bacterium that infects 50% of all humans. H. pylori strains were collected from across eastern Eurasia and the Americas. Sequence analyses indicated that Siberia contains both anciently diverged and recently admixed bacteria, supporting both human persistence over the last glacial maximum and more recent human recolonization. We inferred a single migration across the Bering land bridge, accompanied by a dramatic reduction in effective population size, followed by bidirectional Holocene gene flow between Asia and the Americas. The gastric bacterium Helicobacter pylori shares a coevolutionary history with humans that predates the out-of-Africa diaspora, and the geographical specificities of H. pylori populations reflect multiple well-known human migrations. We extensively sampled H. pylori from 16 ethnically diverse human populations across Siberia to help resolve whether ancient northern Eurasian populations persisted at high latitudes through the last glacial maximum and the relationships between present-day Siberians and Native Americans. A total of 556 strains were cultivated and genotyped by multilocus sequence typing, and 54 representative draft genomes were sequenced. The genetic diversity across Eurasia and the Americas was structured into three populations: hpAsia2, hpEastAsia, and hpNorthAsia. hpNorthAsia is closely related to the subpopulation hspIndigenousAmericas from Native Americans. Siberian bacteria were structured into five other subpopulations, two of which evolved through a divergence from hpAsia2 and hpNorthAsia, while three originated though Holocene admixture. The presence of both anciently diverged and recently admixed strains across Siberia support both Pleistocene persistence and Holocene recolonization. We also show that hspIndigenousAmericas is endemic in human populations across northern Eurasia. The evolutionary history of hspIndigenousAmericas was reconstructed using approximate Bayesian computation, which showed that it colonized the New World in a single migration event associated with a severe demographic bottleneck followed by low levels of recent admixture across the Bering Strait.
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Sun J, Ma PC, Cheng HZ, Wang CZ, Li YL, Cui YQ, Yao HB, Wen SQ, Wei LH. Post-last glacial maximum expansion of Y-chromosome haplogroup C2a-L1373 in northern Asia and its implications for the origin of Native Americans. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 174:363-374. [PMID: 33241578 DOI: 10.1002/ajpa.24173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 10/10/2020] [Accepted: 11/04/2020] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Subbranches of Y-chromosome haplogroup C2a-L1373 are founding paternal lineages in northern Asia and Native American populations. Our objective was to investigate C2a-L1373 differentiation in northern Asia and its implications for Native American origins. MATERIALS AND METHODS Sequences of rare subbranches (n = 43) and ancient individuals (n = 37) of C2a-L1373 (including P39 and MPB373), were used to construct phylogenetic trees with age estimation by BEAST software. RESULTS C2a-L1373 expanded rapidly approximately 17.7,000-14.3,000 years ago (kya) after the last glacial maximum (LGM), generating numerous sublineages which became founding paternal lineages of modern northern Asian and Native American populations (C2a-P39 and C2a-MPB373). The divergence pattern supports possible initiation of differentiation in low latitude regions of northern Asia and northward diffusion after the LGM. There is a substantial gap between the divergence times of C2a-MPB373 (approximately 22.4 or 17.7 kya) and C2a-P39 (approximately 14.3 kya), indicating two possible migration waves. DISCUSSION We discussed the decreasing time interval of "Beringian standstill" (2.5 ky or smaller) and its reduced significance. We also discussed the multiple possibilities for the peopling of the Americas: the "Long-term Beringian standstill model," the "Short-term Beringian standstill model," and the "Multiple waves of migration model." Our results support the argument from ancient DNA analyses that the direct ancestor group of Native Americans is an admixture of "Ancient Northern Siberians" and Paleolithic communities from the Amur region, which appeared during the post-LGM era, rather than ancient populations in greater Beringia, or an adjacent region, before the LGM.
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Affiliation(s)
- Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
- Xingyi Normal University for Nationalities, Xingyi, China
| | - Peng-Cheng Ma
- School of Life Sciences, Jilin University, Changchun, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Chi-Zao Wang
- Department of Radiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Yong-Lan Li
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, China
| | - Yin-Qiu Cui
- School of Life Sciences, Jilin University, Changchun, China
| | - Hong-Bin Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu University of Political Science and Law, Lanzhou, China
| | - Shao-Qing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
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4
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Vispute S, Khadilkar V, Khadilkar A, Ekbote V, Singh N, Chiplonkar S. Inter-regional differences in body proportions in Indian children and adolescents-a cross-sectional multicentric study. Ann Hum Biol 2020; 47:1-9. [PMID: 32013592 DOI: 10.1080/03014460.2019.1698656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Background: Sitting height (SH) and leg length (LL) help in assessing disproportionate growth. Anthropometric dissimilarity has been observed in different ethnicities.Aim: To (1) study sitting height and body proportions in children from different regions of India; and (2) compare sitting height and body proportions with data from other countries.Subjects and methods: This was a cross-sectional multicentric observational study, where 7961 (4328 boys) 3-18 year old children from five regions (north, south, east, west and central) were measured (height, weight and SH).Results: Boys from north India and girls from central India were taller and heavier (mean height 153.2 ± 18, 146.4 ± 11), while western boys and girls were the shortest (131.1 ± 20.7, 129.8 ± 19.5) (p < 0.05 for all). The highest SH was observed in the north (79.2 ± 8.5) and the lowest in the west (68.8 ± 9.1). Mean SH:LL ratio was highest in children from the northeast (1.13) followed by those from western, northern and central India (1.12, 1.10 and 1.07, respectively) and the ratio was the least in children from south India (1.05) (p < 0.0.5 for all except northeast and west). Children from the north and west were similar to the Dutch, children from the south were similar to South (black) Africans and the north-eastern children were similar to Chinese children.Conclusion: There were inter-regional differences in body proportions; similarities in body proportions with children from other ethnicities may throw light on the migration history of Indian people.
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Affiliation(s)
- Smruti Vispute
- Growth and Endocrine Unit, Hirabai Cowasji Jehangir Medical Research Institute, Jehangir Hospital, Pune, India
| | - Vaman Khadilkar
- Growth and Endocrine Unit, Hirabai Cowasji Jehangir Medical Research Institute, Jehangir Hospital, Pune, India
| | - Anuradha Khadilkar
- Growth and Endocrine Unit, Hirabai Cowasji Jehangir Medical Research Institute, Jehangir Hospital, Pune, India
| | - Veena Ekbote
- Growth and Endocrine Unit, Hirabai Cowasji Jehangir Medical Research Institute, Jehangir Hospital, Pune, India
| | - Narendra Singh
- Department of Anthropology, Assam University, Diphu, India
| | - Shashi Chiplonkar
- Growth and Endocrine Unit, Hirabai Cowasji Jehangir Medical Research Institute, Jehangir Hospital, Pune, India
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5
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HLA in Colombia Wayu from Guajira Peninsula Amerindians: Pacific Ocean relationships. Hum Immunol 2019; 80:93-94. [PMID: 30537523 DOI: 10.1016/j.humimm.2018.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/28/2018] [Accepted: 12/06/2018] [Indexed: 11/24/2022]
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6
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Bai H, Guo X, Narisu N, Lan T, Wu Q, Xing Y, Zhang Y, Bond SR, Pei Z, Zhang Y, Zhang D, Jirimutu J, Zhang D, Yang X, Morigenbatu M, Zhang L, Ding B, Guan B, Cao J, Lu H, Liu Y, Li W, Dang N, Jiang M, Wang S, Xu H, Wang D, Liu C, Luo X, Gao Y, Li X, Wu Z, Yang L, Meng F, Ning X, Hashenqimuge H, Wu K, Wang B, Suyalatu S, Liu Y, Ye C, Wu H, Leppälä K, Li L, Fang L, Chen Y, Xu W, Li T, Liu X, Xu X, Gignoux CR, Yang H, Brody LC, Wang J, Kristiansen K, Burenbatu B, Zhou H, Yin Y. Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia. Nat Genet 2018; 50:1696-1704. [PMID: 30397334 DOI: 10.1038/s41588-018-0250-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 09/03/2018] [Indexed: 12/30/2022]
Abstract
The genetic variation in Northern Asian populations is currently undersampled. To address this, we generated a new genetic variation reference panel by whole-genome sequencing of 175 ethnic Mongolians, representing six tribes. The cataloged variation in the panel shows strong population stratification among these tribes, which correlates with the diverse demographic histories in the region. Incorporating our results with the 1000 Genomes Project panel identifies derived alleles shared between Finns and Mongolians/Siberians, suggesting that substantial gene flow between northern Eurasian populations has occurred in the past. Furthermore, we highlight that North, East, and Southeast Asian populations are more aligned with each other than these groups are with South Asian and Oceanian populations.
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Affiliation(s)
- Haihua Bai
- School of Life Science, Inner Mongolia University for the Nationalities, Tongliao, China.,Inner Mongolia Engineering Research Center of Personalized Medicine, Tongliao, China
| | - Xiaosen Guo
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Narisu Narisu
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tianming Lan
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Qizhu Wu
- Affiliated Hospital of Inner Mongolia University for the Nationalities, Tongliao, China
| | - Yanping Xing
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yong Zhang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Stephen R Bond
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhili Pei
- College of Computer Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Yanru Zhang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Dandan Zhang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jirimutu Jirimutu
- College of Mathematics, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Dong Zhang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xukui Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Morigenbatu Morigenbatu
- College of Mongolian Studies, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Li Zhang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Bingyi Ding
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Baozhu Guan
- Inner Mongolia International Mongolian Hospital, Hohhot, China
| | - Junwei Cao
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Haorong Lu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | - Yiyi Liu
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Wangsheng Li
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Ningxin Dang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Mingyang Jiang
- College of Computer Science and Technology, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Shenyuan Wang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Huixin Xu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Dingzhu Wang
- College of Mongolian Studies, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Chunxia Liu
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xin Luo
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Ying Gao
- School of Life Science, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Xueqiong Li
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zongze Wu
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Liqing Yang
- Affiliated Hospital of Inner Mongolia University for the Nationalities, Tongliao, China
| | - Fanhua Meng
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaolian Ning
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | | | - Kaifeng Wu
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Bo Wang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Suyalatu Suyalatu
- School of Life Science, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Yingchun Liu
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Chen Ye
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Huiguang Wu
- School of Life Science, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Kalle Leppälä
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Lu Li
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Lin Fang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yujie Chen
- School of Life Science, Inner Mongolia University for the Nationalities, Tongliao, China
| | - Wenhao Xu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,College of Life Science and Technology, Huazhong Agricultural University, No.1 Shizishan Street, Wuhan, China
| | - Tao Li
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Lawrence C Brody
- Gene and Environment Interaction Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Burenbatu Burenbatu
- Affiliated Hospital of Inner Mongolia University for the Nationalities, Tongliao, China.
| | - Huanmin Zhou
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, China.
| | - Ye Yin
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark. .,BGI Genomics, BGI-Shenzhen, Shenzhen, China. .,School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China.
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7
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Genetic variation in populations from central Argentina based on mitochondrial and Y chromosome DNA evidence. J Hum Genet 2018; 63:493-507. [DOI: 10.1038/s10038-017-0406-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 12/06/2017] [Accepted: 12/12/2017] [Indexed: 12/29/2022]
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8
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Arnaiz-Villena A, Enriquez-de-Salamanca M, Palacio-Gruber J, Juarez I, Muñiz E, Nieto J, Campos C, Martin-Villa JM. HLA-G in Amerindians: Epidemiology and Worldwide Population Comparison. ACTA ACUST UNITED AC 2018. [DOI: 10.2174/1874220301805010001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:HLA-G molecules are immunosuppressive and avoid fetal rejection by giving negative signals to maternal immune system from fetal trophoblast cell surface. HLA-G genes have been associated to different pathologies: Spontaneous abortions, autoimmunity, tumor progression, transplant rejection and infection. In addition, different World populations show remarkable different HLA-G allele frequencies in the allele that does not produce a full HLA-G molecule (HLA-G*05N); this allele is almost absent in studied Amerindians.Objectives:The aim is to study HLA-A.-B,-DRB1 and –G alleles and extended haplotypes in Amerindians for the first time. This may be useful to asses HLA-G epidemiology, association to disease and Preventive Medicine in Amerindians.Methods:HLA-A,-B and -DRB1 have been typed by using standard automatic protocols. HLA-G alleles have been detected by direct HLA-G exon 2, exon 3 and exon 4 DNA sequencing. Computer calculations have been done by specific standard methods.Results:HLA-A,-B,-DRB1 and –G extended haplotypes have been calculated in Amerindians for the first time. Also, their HLA-G frequencies have been compared with worldwide populations.Conclusion:Low frequencies of null HLA-G*01:05N allele are found in Amerindians. The extended haplotypes with this allele bear other typical Amerindian HLA-DRB1 alleles and its origin is discussed. HLA-G allele frequency profile is closer to that of Europeans than to that of Far East Asians. Our findings are useful to Preventive Medicine and Epidemiology associated to Fertility and HLA-G associated pathology and transplantation.
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9
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Distribution of KIR genes and KIR2DS4 gene variants in two Mexican Mestizo populations. Hum Immunol 2017; 78:614-620. [PMID: 28734803 DOI: 10.1016/j.humimm.2017.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 07/15/2017] [Accepted: 07/16/2017] [Indexed: 12/24/2022]
Abstract
Killer immunoglobulin-like receptors (KIR) are transmembrane proteins that regulate NK and T cell subsets by recognizing HLA-I molecules as ligands. The KIR gene family consists of 16 genes, located at chromosome 19q13.4. KIR gene frequencies vary among populations. In Mexico, HLA and genetic ancestry studies show that Mestizo populations have different genetic backgrounds based on admixture with European, African, and Asian ancestry. This study aimed to evaluate the frequencies of KIR genes and genotypes in Guerrero and Jalisco, two Mexican Mestizo populations located in the south and the west of the country, respectively, and to compare these frequencies with those of other populations. KIR genotyping was performed by SSP-PCR. We observed that KIR gene frequencies were similar in both populations. There were 24 genotypes observed in Guerrero, 38 genotypes observed in Jalisco, 15 genotypes shared in both populations and 32 genotypes unique to one population or the other. In 10 individuals, nine novel genotypes were identified. KIR2DS4 gene variants showed significant differences: The KIR2DS4full gene was more common in Guerrero (p<0.0001), and the KIR2DS4del variant was more common in Jalisco (p<0.05). Differences in KIR2DS4 gene variants and genotypic profiles could be influenced by the genetic admixture in both regions.
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10
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Arnaiz-Villena A, Enriquez-de-Salamanca M, Palacio-Grüber J, Campos C, Camacho A, Martin-Villa JM, Martinez-Quiles N, Gomez-Casado E, Muñiz E. Characterisation and functional implications of the two new HLA-G alleles found in Amerindian and Caribbean populations. Hum Immunol 2016; 77:812-6. [PMID: 26796363 DOI: 10.1016/j.humimm.2016.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/05/2016] [Accepted: 01/07/2016] [Indexed: 01/17/2023]
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11
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New native South American Y chromosome lineages. J Hum Genet 2016; 61:593-603. [PMID: 27030145 DOI: 10.1038/jhg.2016.26] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/23/2016] [Accepted: 02/22/2016] [Indexed: 11/09/2022]
Abstract
Many single-nucleotide polymorphisms (SNPs) in the non-recombining region of the human Y chromosome have been described in the last decade. High-coverage sequencing has helped to characterize new SNPs, which has in turn increased the level of detail in paternal phylogenies. However, these paternal lineages still provide insufficient information on population history and demography, especially for Native Americans. The present study aimed to identify informative paternal sublineages derived from the main founder lineage of the Americas-haplogroup Q-L54-in a sample of 1841 native South Americans. For this purpose, we used a Y-chromosomal genotyping multiplex platform and conventional genotyping methods to validate 34 new SNPs that were identified in the present study by sequencing, together with many Y-SNPs previously described in the literature. We updated the haplogroup Q phylogeny and identified two new Q-M3 and three new Q-L54*(xM3) sublineages defined by five informative SNPs, designated SA04, SA05, SA02, SA03 and SA29. Within the Q-M3, sublineage Q-SA04 was mostly found in individuals from ethnic groups belonging to the Tukanoan linguistic family in the northwest Amazon, whereas sublineage Q-SA05 was found in Peruvian and Bolivian Amazon ethnic groups. Within Q-L54*, the derived sublineages Q-SA03 and Q-SA02 were exclusively found among Coyaima individuals (Cariban linguistic family) from Colombia, while Q-SA29 was found only in Maxacali individuals (Jean linguistic family) from southeast Brazil. Furthermore, we validated the usefulness of several published SNPs among indigenous South Americans. This new Y chromosome haplogroup Q phylogeny offers an informative paternal genealogy to investigate the pre-Columbian history of South America.Journal of Human Genetics advance online publication, 31 March 2016; doi:10.1038/jhg.2016.26.
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12
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Coevolution of genes and languages and high levels of population structure among the highland populations of Daghestan. J Hum Genet 2015; 61:181-91. [PMID: 26607180 DOI: 10.1038/jhg.2015.132] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/11/2015] [Accepted: 10/08/2015] [Indexed: 01/29/2023]
Abstract
As a result of the combination of great linguistic and cultural diversity, the highland populations of Daghestan present an excellent opportunity to test the hypothesis of language-gene coevolution at a fine geographic scale. However, previous genetic studies generally have been restricted to uniparental markers and have not included many of the key populations of the region. To improve our understanding of the genetic structure of Daghestani populations and to investigate possible correlations between genetic and linguistic variation, we analyzed ~550,000 autosomal single nucleotide polymorphisms, phylogenetically informative Y chromosome markers and mtDNA haplotypes in 21 ethnic Daghestani groups. We found high levels of population structure in Daghestan consistent with the hypothesis of long-term isolation among populations of the highland Caucasus. Highland Daghestani populations exhibit extremely high levels of between-population diversity for all genetic systems tested, leading to some of the highest FST values observed for any region of the world. In addition, we find a significant positive correlation between gene and language diversity, suggesting that these two aspects of human diversity have coevolved as a result of historical patterns of social interaction among highland farmers at the community level. Finally, our data are consistent with the hypothesis that most Daghestanian-speaking groups descend from a common ancestral population (~6000-6500 years ago) that spread to the Caucasus by demic diffusion followed by population fragmentation and low levels of gene flow.
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13
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Latitude has more significant impact on prevalence of multiple sclerosis than ultraviolet level or sunshine duration in Japanese population. Neurol Sci 2015; 36:1147-51. [PMID: 25754614 DOI: 10.1007/s10072-015-2150-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
Higher latitude is known to be associated with higher prevalence of multiple sclerosis (MS). We investigated the degree of impact of latitude, ultraviolet (UV) radiation, and sunshine on the prevalence of MS in Japan, which has 47 prefectures with a variety of climates. MS prevalence in each prefecture was collected from database of the Ministry of Health, Labour, and Welfare of Japan. Latitude of each prefecture was represented by that of the capital city. Data of UV radiation level and annual actual sunshine duration were obtained from databases of Japan Meteorological Agency. We performed linear correlation analyses of MS prevalence against latitude, UV radiation, and annual actual sunshine duration. MS prevalence significantly correlated to latitude (Pearson's correlation, r = 0.69, p < 0.001) and UV radiation level (r = -0.65, p < 0.001) but not to annual actual sunshine duration (r = -0.37, p = 0.011). Stepwise multiple linear regression analyses revealed significant correlation between MS prevalence and only latitude (p < 0.001). While our result shows that both latitude and the UV intensity have significant relationship to MS prevalence, the stronger relevance of the former suggests an existence of risk factors other than UV radiation.
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Karafet TM, Bulayeva KB, Bulayev OA, Gurgenova F, Omarova J, Yepiskoposyan L, Savina OV, Veeramah KR, Hammer MF. Extensive genome-wide autozygosity in the population isolates of Daghestan. Eur J Hum Genet 2015; 23:1405-12. [PMID: 25604856 DOI: 10.1038/ejhg.2014.299] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 12/09/2014] [Accepted: 12/19/2014] [Indexed: 01/01/2023] Open
Abstract
Isolated populations are valuable resources for mapping disease genes, as inbreeding increases genome-wide homozygosity and enhances the ability to map disease alleles on a genetically uniform background within a relatively homogenous environment. The populations of Daghestan are thought to have resided in the Caucasus Mountains for hundreds of generations and are characterized by a high prevalence of certain complex diseases. To explore the extent to which their unique population history led to increased levels of inbreeding, we genotyped >550 000 autosomal single-nucleotide polymorphisms (SNPs) in a set of 14 population isolates speaking Nakh-Daghestanian (ND) languages. The ND-speaking populations showed greatly elevated coefficients of inbreeding, very high numbers and long lengths of Runs of Homozygosity, and elevated linkage disequilibrium compared with surrounding groups from the Caucasus, the Near East, Europe, Central and South Asia. These results are consistent with the hypothesis that most ND-speaking groups descend from a common ancestral population that fragmented into a series of genetic isolates in the Daghestanian highlands. They have subsequently maintained a long-term small effective population size as a result of constant inbreeding and very low levels of gene flow. Given these findings, Daghestanian population isolates are likely to be useful for mapping genes associated with complex diseases.
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Affiliation(s)
- Tatiana M Karafet
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ, USA
| | - Kazima B Bulayeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Oleg A Bulayev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Farida Gurgenova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Jamilia Omarova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Levon Yepiskoposyan
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Olga V Savina
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ, USA
| | | | - Michael F Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ, USA
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15
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Hallast P, Batini C, Zadik D, Maisano Delser P, Wetton JH, Arroyo-Pardo E, Cavalleri GL, de Knijff P, Destro Bisol G, Dupuy BM, Eriksen HA, Jorde LB, King TE, Larmuseau MH, López de Munain A, López-Parra AM, Loutradis A, Milasin J, Novelletto A, Pamjav H, Sajantila A, Schempp W, Sears M, Tolun A, Tyler-Smith C, Van Geystelen A, Watkins S, Winney B, Jobling MA. The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades. Mol Biol Evol 2014; 32:661-73. [PMID: 25468874 PMCID: PMC4327154 DOI: 10.1093/molbev/msu327] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes.
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Affiliation(s)
- Pille Hallast
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Daniel Zadik
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | | | - Jon H Wetton
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Eduardo Arroyo-Pardo
- Laboratory of Forensic and Population Genetics, Department of Toxicology and Health Legislation, Faculty of Medicine, Complutense University, Madrid, Spain
| | - Gianpiero L Cavalleri
- Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Giovanni Destro Bisol
- Istituto Italiano di Antropologia, Rome, Italy Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Berit Myhre Dupuy
- Division of Forensic Sciences, Norwegian Institute of Public Health, Oslo, Norway
| | - Heidi A Eriksen
- Centre of Arctic Medicine, Thule Institute, University of Oulu, Oulu, Finland Utsjoki Health Care Centre, Utsjoki, Finland
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT
| | - Turi E King
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Maarten H Larmuseau
- Laboratory of Forensic Genetics and Molecular Archaeology, KU Leuven, Leuven, Belgium Department of Imaging & Pathology, Biomedical Forensic Sciences, KU Leuven, Leuven, Belgium Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Ana M López-Parra
- Laboratory of Forensic and Population Genetics, Department of Toxicology and Health Legislation, Faculty of Medicine, Complutense University, Madrid, Spain
| | | | - Jelena Milasin
- School of Dental Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | | | - Horolma Pamjav
- Network of Forensic Science Institutes, Institute of Forensic Medicine, Budapest, Hungary
| | - Antti Sajantila
- Department of Forensic Medicine, Hjelt Institute, University of Helsinki, Helsinki, Finland Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas
| | - Werner Schempp
- Institute of Human Genetics, University of Freiburg, Freiburg, Germany
| | - Matt Sears
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Aslıhan Tolun
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | | | - Anneleen Van Geystelen
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Scott Watkins
- Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT
| | - Bruce Winney
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester, United Kingdom
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16
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Ruiz-Linares A. How genes have illuminated the history of early Americans and Latino Americans. Cold Spring Harb Perspect Biol 2014; 7:cshperspect.a008557. [PMID: 25256008 DOI: 10.1101/cshperspect.a008557] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The American continent currently accounts for ∼15% of the world population. Although first settled thousands of years ago and fitting its label as "the New World," the European colonial expansion initiated in the late 15th century resulted in people from virtually every corner of the globe subsequently settling in the Americas. The arrival of large numbers of immigrants led to a dramatic decline of the Native American population and extensive population mixing. A salient feature of the current human population of the Americas is, thus, its great diversity. The genetic variation of the Native peoples that recent immigrants encountered had been shaped by demographic events acting since the initial peopling of the continent. Similarly, but on a compressed timescale, the colonial history of the Americas has had a major impact on the genetic makeup of the current population of the continent. A range of genetic analyses has been used to study both the ancient settlement of the continent and more recent history of population mixing. Here, I show how these two strands of research overlap and make use of results from other scientific disciplines to produce a fuller picture of the settlement of the continent at different time periods. The biological diversity of the Americas also provides prominent examples of the complex interaction between biological and social factors in constructing human identities and of the difficulties in defining human populations.
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Affiliation(s)
- Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
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17
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Medina LSJ, Muzzio M, Schwab M, Costantino MLB, Barreto G, Bailliet G. Human Y-chromosome SNP characterization by multiplex amplified product-length polymorphism analysis. Electrophoresis 2014; 35:2524-7. [PMID: 24846779 DOI: 10.1002/elps.201400020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 05/12/2014] [Accepted: 05/12/2014] [Indexed: 11/09/2022]
Abstract
We designed an allele-specific amplification protocol to optimize Y-chromosome SNP typing, which is an unavoidable step for defining the phylogenetic status of paternal lineages. It allows the simultaneous highly specific definition of up to six mutations in a single reaction by amplification fragment length polymorphism (AFLP) without the need of specialized equipment, at a considerably lower cost than that based on single-base primer extension (SNaPshot™) technology or PCR-RFLP systems, requiring as little as 0.5 ng DNA and compatible with the small fragments characteristic of low-quality DNA. By designation of two primers recognizing the derived and ancestral state for each SNP, which can be differentiated by size by the addition of a noncomplementary nucleotide tail, we could define major Y clades E, F, K, R, Q, and subhaplogroups R1, R1a, R1b, R1b1b, R1b1c, J1, J2, G1, G2, I1, Q1a3, and Q1a3a1 through amplification fragments that ranged between 60 and 158bp.
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Affiliation(s)
- Laura Smeldy Jurado Medina
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT- CONICET-La Plata/CICPBA, La Plata, Argentina
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18
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Strong genetic admixture in the Altai at the Middle Bronze Age revealed by uniparental and ancestry informative markers. Forensic Sci Int Genet 2014; 12:199-207. [PMID: 25016250 DOI: 10.1016/j.fsigen.2014.05.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 05/21/2014] [Accepted: 05/25/2014] [Indexed: 11/21/2022]
Abstract
The Altai Mountains have been a long-term boundary zone between the Eurasian Steppe populations and South and East Asian populations. To disentangle some of the historical population movements in this area, 14 ancient human specimens excavated in the westernmost part of the Mongolian Altai were studied. Thirteen of them were dated from the Middle to the End of the Bronze Age and one of them to the Eneolithic period. The environmental conditions encountered in this region led to the good preservation of DNA in the human remains. Therefore, a multi-markers approach was adopted for the genetic analysis of identity, ancestry and phenotype markers. Mitochondrial DNA analyses revealed that the ancient Altaians studied carried both Western (H, U, T) and Eastern (A, C, D) Eurasian lineages. In the same way, the patrilineal gene pool revealed the presence of different haplogroups (Q1a2a1-L54, R1a1a1b2-Z93 and C), probably marking different origins for the male paternal lineages. To go further in the search of the origin of these ancient specimens, phenotypical characters (i.e. hair and eye color) were determined. For this purpose, we adapted the HIrisPlex assay recently described to MALDI-TOF mass spectrometry. In addition, some ancestry informative markers were analyzed with this assay. The results revealed mixed phenotypes among this group confirming the probable admixed ancestry of the studied Altaian population at the Middle Bronze Age. The good results obtained from ancient DNA samples suggest that this approach might be relevant for forensic casework too.
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Herrera B, Hanihara T, Godde K. Comparability of multiple data types from the bering strait region: Cranial and dental metrics and nonmetrics, mtDNA, and Y-chromosome DNA. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 154:334-48. [DOI: 10.1002/ajpa.22513] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 03/03/2014] [Accepted: 03/04/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Brianne Herrera
- Department of Anthropology; The Ohio State University; Columbus OH
| | - Tsunehiko Hanihara
- Department of Anatomy and Biological Anthropology; Saga Medical School; Saga Japan
| | - Kanya Godde
- Sociology and Anthropology Department; University of La Verne; La Verne CA
- Department of Anthropology; University of Tennessee; Knoxville TN
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20
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Khurana P, Aggarwal A, Mitra S, Italia YM, Saraswathy KN, Chandrasekar A, Kshatriya GK. Y chromosome haplogroup distribution in Indo-European speaking tribes of Gujarat, western India. PLoS One 2014; 9:e90414. [PMID: 24614885 PMCID: PMC3948632 DOI: 10.1371/journal.pone.0090414] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/01/2014] [Indexed: 11/20/2022] Open
Abstract
The present study was carried out in the Indo-European speaking tribal population groups of Southern Gujarat, India to investigate and reconstruct their paternal population structure and population histories. The role of language, ethnicity and geography in determining the observed pattern of Y haplogroup clustering in the study populations was also examined. A set of 48 bi-allelic markers on the non-recombining region of Y chromosome (NRY) were analysed in 284 males; representing nine Indo-European speaking tribal populations. The genetic structure of the populations revealed that none of these groups was overtly admixed or completely isolated. However, elevated haplogroup diversity and FST value point towards greater diversity and differentiation which suggests the possibility of early demographic expansion of the study groups. The phylogenetic analysis revealed 13 paternal lineages, of which six haplogroups: C5, H1a*, H2, J2, R1a1* and R2 accounted for a major portion of the Y chromosome diversity. The higher frequency of the six haplogroups and the pattern of clustering in the populations indicated overlapping of haplogroups with West and Central Asian populations. Other analyses undertaken on the population affiliations revealed that the Indo-European speaking populations along with the Dravidian speaking groups of southern India have an influence on the tribal groups of Gujarat. The vital role of geography in determining the distribution of Y lineages was also noticed. This implies that although language plays a vital role in determining the distribution of Y lineages, the present day linguistic affiliation of any population in India for reconstructing the demographic history of the country should be considered with caution.
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Affiliation(s)
- Priyanka Khurana
- Department of Anthropology, School of Applied Sciences, Dr. Harisingh Gour University, Sagar, Madhya Pradesh, India
| | - Aastha Aggarwal
- South Asia Network for Chronic Disease, Public Health Foundation of India, Delhi, India
| | - Siuli Mitra
- Department of Anthropology, University of Delhi, Delhi, India
| | - Yazdi M. Italia
- Valsad Raktdan Kendra, R.N.C. Free Eye Hospital Complex, Valsad, Gujarat, India
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21
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Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, Bustamante CD. Reconstructing Native American migrations from whole-genome and whole-exome data. PLoS Genet 2013; 9:e1004023. [PMID: 24385924 PMCID: PMC3873240 DOI: 10.1371/journal.pgen.1004023] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 10/29/2013] [Indexed: 12/12/2022] Open
Abstract
There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and especially Native American ancestry to these populations. Estimated Native American ancestry is in MXL, in CLM, and in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas thousand years ago (kya), supports that the MXL Ancestors split kya, with a subsequent split of the ancestors to CLM and PUR kya. The model also features effective populations of in Mexico, in Colombia, and in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations. Populations of the Americas have a rich and heterogeneous genetic and cultural heritage that draws from a diversity of pre-Columbian Native American, European, and African populations. Characterizing this diversity facilitates the development of medical genetics research in diverse populations and the transfer of medical knowledge across populations. It also represents an opportunity to better understand the peopling of the Americas, from the crossing of Beringia to the post-Columbian era. Here, we take advantage sequencing of individuals of Colombian (CLM), Mexican (MXL), and Puerto Rican (PUR) origin by the 1000 Genomes project to improve our demographic models for the peopling of the Americas. The divergence among African, European, and Native American ancestors to these populations enables us to infer the continent of origin at each locus in the sampled genomes. The resulting patterns of ancestry suggest complex post-Columbian migration histories, starting later in CLM than in MXL and PUR. Whereas European ancestral segments show evidence of relatedness, a demographic model of synonymous variation suggests that the Native American Ancestors to MXL, PUR, and CLM panels split within a few hundred years over 12 thousand years ago. Together with early archeological sites in South America, these results support rapid divergence during the initial peopling of the Americas.
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Affiliation(s)
- Simon Gravel
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
- * E-mail:
| | - Fouad Zakharia
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Andres Moreno-Estrada
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Jake K. Byrnes
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Ancestry.com DNA LLC, San Francisco, California, United States of America
| | - Marina Muzzio
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE). CCT- CONICET-La Plata, Argentina and Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina
| | | | - Eimear E. Kenny
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Department of Genetics and Genomic Sciences, The Charles Bronfman Institute for Personalized Medicine, Center for Statistical Genetics, and Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Christopher R. Gignoux
- Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America
| | - Brian K. Maples
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Wilfried Guiblet
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Julie Dutil
- Department of Biochemistry, Ponce School of Medicine and Health Sciences, Ponce, Puerto Rico
| | - Marc Via
- Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America
- Department of Psychiatry and Clinical Psychobiology, University of Barcelona, Barcelona, Spain
| | - Karla Sandoval
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | | | | | - Taras K. Oleksyk
- Department of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto Rico
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Esteban G. Burchard
- Department of Bioengineering and Therapeutic Sciences and Medicine, Univeristy of California San Francisco, San Francisco, California, United States of America
| | | | - Carlos D. Bustamante
- Department of Genetics, Stanford University, Stanford, California, United States of America
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Pacheco CM, Daley SM, Brown T, Filippi M, Greiner KA, Daley CM. Moving forward: breaking the cycle of mistrust between American Indians and researchers. Am J Public Health 2013; 103:2152-9. [PMID: 24134368 DOI: 10.2105/ajph.2013.301480] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
American Indians (AIs) have some of the poorest documented health outcomes of any racial/ethnic group. Research plays a vital role in addressing these health disparities. Historical and recent instances of unethical research, specifically the Havasupai diabetes project, have generated mistrust in AI communities. To address the concerns about unethical research held by some AIs in the Heartland (Midwest), the Center for American Indian Community Health (CAICH) has launched a series of efforts to inform AIs about research participants' rights. CAICH educates health researchers about the importance of learning and respecting a community's history, culture, values, and wishes when engaging in research with that community. Through community-based participatory research, CAICH is also empowering AIs to assert their rights as research participants.
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Affiliation(s)
- Christina M Pacheco
- Christina M. Pacheco, Travis Brown, Melissa Filippi, K. Allen Greiner, and Christine M. Daley are with the Center for American Indian Community Health, University of Kansas Medical Center, Kansas City. Sean M. Daley is with the Center for American Indian Studies, Johnson County Community College, Overland Park, KS
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23
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Y-chromosome diversity in the Kalmyks at the ethnical and tribal levels. J Hum Genet 2013; 58:804-11. [DOI: 10.1038/jhg.2013.108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/16/2013] [Accepted: 09/27/2013] [Indexed: 01/15/2023]
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Villanea FA, Bolnick DA, Monroe C, Worl R, Cambra R, Leventhal A, Kemp BM. Brief communication: Evolution of a specific O allele (O1vG542A) supports unique ancestry of Native Americans. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 151:649-57. [PMID: 23868176 DOI: 10.1002/ajpa.22292] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 04/16/2013] [Indexed: 11/09/2022]
Abstract
In this study, we explore the geographic and temporal distribution of a unique variant of the O blood group allele called O1v(G542A) , which has been shown to be shared among Native Americans but is rare in other populations. O1v(G542A) was previously reported in Native American populations in Mesoamerica and South America, and has been proposed as an ancestry informative marker. We investigated whether this allele is also found in the Tlingit and Haida, two contemporary indigenous populations from Alaska, and a pre-Columbian population from California. If O1v(G542A) is present in Na-Dene speakers (i.e., Tlingits), it would indicate that Na-Dene speaking groups share close ancestry with other Native American groups and support a Beringian origin of the allele, consistent with the Beringian Incubation Model. If O1v(G542A) is found in pre-Columbian populations, it would further support a Beringian origin of the allele, rather than a more recent introduction of the allele into the Americas via gene flow from one or more populations which have admixed with Native Americans over the past five centuries. We identified this allele in one Na-Dene population at a frequency of 0.11, and one ancient California population at a frequency of 0.20. Our results support a Beringian origin of O1v(G542A) , which is distributed today among all Native American groups that have been genotyped in appreciable numbers at this locus. This result is consistent with the hypothesis that Na-Dene and other Native American populations primarily derive their ancestry from a single source population.
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Affiliation(s)
- Fernando A Villanea
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4910, USA
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25
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Pauro M, García A, Nores R, Demarchi DA. Analysis of Uniparental Lineages in Two Villages of Santiago del Estero, Argentina, Seat of Pueblos de Indios in Colonial Times. Hum Biol 2013; 85:699-720. [DOI: 10.3378/027.085.0504] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2013] [Indexed: 11/05/2022]
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Schurr TG, Dulik MC, Cafaro TA, Suarez MF, Urrets-Zavalia JA, Serra HM. Genetic background and climatic droplet keratopathy incidence in a Mapuche population from Argentina. PLoS One 2013; 8:e74593. [PMID: 24040292 PMCID: PMC3764023 DOI: 10.1371/journal.pone.0074593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/05/2013] [Indexed: 11/18/2022] Open
Abstract
Purpose To determine whether the incidence of and susceptibility to climatic droplet keratopathy (CDK), an acquired, often bilateral degenerative corneal disease, is influenced by the genetic background of the individuals who exhibit the disorder. Methods To determine whether the disease expression was influenced by the genetic ancestry of CDK cases in native Mapuche of the northwest area of Patagonia in Argentina, we examined mitochondrial DNA and Y-chromosome variation in 53 unrelated individuals. Twenty-nine of them were part of the CDK (patient) population, while 24 were part of the control group. The analysis revealed the maternal and paternal lineages that were present in the two study groups. Results This analysis demonstrated that nearly all persons had a Native American mtDNA background, whereas 50% of the CDK group and 37% of the control group had Native American paternal ancestry, respectively. There was no significant difference in the frequencies of mtDNA haplogroups between the CDK patient and control groups. Although the Y-chromosome data revealed differences in specific haplogroup frequencies between these two groups, there was no statistically significant relationship between individual paternal genetic backgrounds and the incidence or stage of disease. Conclusions These results indicate a lack of correlation between genetic ancestry as represented by haploid genetic systems and the incidence of CDK in Mapuche populations. In addition, the mtDNA appears to play less of a role in CDK expression than for other complex diseases linked to bioenergetic processes. However, further analysis of the mtDNA genome sequence and other genes involved in corneal function may reveal the more precise role that mitochondria play in the expression of CDK.
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Affiliation(s)
- Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew C. Dulik
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Thamara A. Cafaro
- CIBICI (Centro de Investigaciones en Bioquímica Clínica e Inmunología), Faculty of Chemistry, National University of Córdoba, Córdoba, Argentina
| | - María F. Suarez
- CIBICI (Centro de Investigaciones en Bioquímica Clínica e Inmunología), Faculty of Chemistry, National University of Córdoba, Córdoba, Argentina
| | | | - Horacio M. Serra
- CIBICI (Centro de Investigaciones en Bioquímica Clínica e Inmunología), Faculty of Chemistry, National University of Córdoba, Córdoba, Argentina
- * E-mail:
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Battaglia V, Grugni V, Perego UA, Angerhofer N, Gomez-Palmieri JE, Woodward SR, Achilli A, Myres N, Torroni A, Semino O. The first peopling of South America: new evidence from Y-chromosome haplogroup Q. PLoS One 2013; 8:e71390. [PMID: 23990949 PMCID: PMC3749222 DOI: 10.1371/journal.pone.0071390] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/03/2013] [Indexed: 01/13/2023] Open
Abstract
Recent progress in the phylogenetic resolution of the Y-chromosome phylogeny permits the male demographic dynamics and migratory events that occurred in Central and Southern America after the initial human spread into the Americas to be investigated at the regional level. To delve further into this issue, we examined more than 400 Native American Y chromosomes (collected in the region ranging from Mexico to South America) belonging to haplogroup Q – virtually the only branch of the Y phylogeny observed in modern-day Amerindians of Central and South America – together with 27 from Mongolia and Kamchatka. Two main founding lineages, Q1a3a1a-M3 and Q1a3a1-L54(xM3), were detected along with novel sub-clades of younger age and more restricted geographic distributions. The first was also observed in Far East Asia while no Q1a3a1-L54(xM3) Y chromosome was found in Asia except the southern Siberian-specific sub-clade Q1a3a1c-L330. Our data not only confirm a southern Siberian origin of ancestral populations that gave rise to Paleo-Indians and the differentiation of both Native American Q founding lineages in Beringia, but support their concomitant arrival in Mesoamerica, where Mexico acted as recipient for the first wave of migration, followed by a rapid southward migration, along the Pacific coast, into the Andean region. Although Q1a3a1a-M3 and Q1a3a1-L54(xM3) display overlapping general distributions, they show different patterns of evolution in the Mexican plateau and the Andean area, which can be explained by local differentiations due to demographic events triggered by the introduction of agriculture and associated with the flourishing of the Great Empires.
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Affiliation(s)
- Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
| | - Viola Grugni
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
| | - Ugo Alessandro Perego
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | - Norman Angerhofer
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | | | - Scott Ray Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- AncestryDNA, Provo, Utah, United States of America
| | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Natalie Myres
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- AncestryDNA, Provo, Utah, United States of America
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
- Centro Interdipartimentale “Studi di Genere”, Università di Pavia, Pavia, Italy
- * E-mail:
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Fedorova SA, Reidla M, Metspalu E, Metspalu M, Rootsi S, Tambets K, Trofimova N, Zhadanov SI, Kashani BH, Olivieri A, Voevoda MI, Osipova LP, Platonov FA, Tomsky MI, Khusnutdinova EK, Torroni A, Villems R. Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia. BMC Evol Biol 2013; 13:127. [PMID: 23782551 PMCID: PMC3695835 DOI: 10.1186/1471-2148-13-127] [Citation(s) in RCA: 66] [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: 02/08/2013] [Accepted: 06/10/2013] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Sakha--an area connecting South and Northeast Siberia--is significant for understanding the history of peopling of Northeast Eurasia and the Americas. Previous studies have shown a genetic contiguity between Siberia and East Asia and the key role of South Siberia in the colonization of Siberia. RESULTS We report the results of a high-resolution phylogenetic analysis of 701 mtDNAs and 318 Y chromosomes from five native populations of Sakha (Yakuts, Evenks, Evens, Yukaghirs and Dolgans) and of the analysis of more than 500,000 autosomal SNPs of 758 individuals from 55 populations, including 40 previously unpublished samples from Siberia. Phylogenetically terminal clades of East Asian mtDNA haplogroups C and D and Y-chromosome haplogroups N1c, N1b and C3, constituting the core of the gene pool of the native populations from Sakha, connect Sakha and South Siberia. Analysis of autosomal SNP data confirms the genetic continuity between Sakha and South Siberia. Maternal lineages D5a2a2, C4a1c, C4a2, C5b1b and the Yakut-specific STR sub-clade of Y-chromosome haplogroup N1c can be linked to a migration of Yakut ancestors, while the paternal lineage C3c was most likely carried to Sakha by the expansion of the Tungusic people. MtDNA haplogroups Z1a1b and Z1a3, present in Yukaghirs, Evens and Dolgans, show traces of different and probably more ancient migration(s). Analysis of both haploid loci and autosomal SNP data revealed only minor genetic components shared between Sakha and the extreme Northeast Siberia. Although the major part of West Eurasian maternal and paternal lineages in Sakha could originate from recent admixture with East Europeans, mtDNA haplogroups H8, H20a and HV1a1a, as well as Y-chromosome haplogroup J, more probably reflect an ancient gene flow from West Eurasia through Central Asia and South Siberia. CONCLUSIONS Our high-resolution phylogenetic dissection of mtDNA and Y-chromosome haplogroups as well as analysis of autosomal SNP data suggests that Sakha was colonized by repeated expansions from South Siberia with minor gene flow from the Lower Amur/Southern Okhotsk region and/or Kamchatka. The minor West Eurasian component in Sakha attests to both recent and ongoing admixture with East Europeans and an ancient gene flow from West Eurasia.
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Affiliation(s)
- Sardana A Fedorova
- Department of Molecular Genetics, Yakut Research Center of Complex Medical Problems, Russian Academy of Medical Sciences and North-Eastern Federal University, Yakutsk, Russia
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Maere Reidla
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Ene Metspalu
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | | | | | | | - Natalya Trofimova
- Institute of Biochemistry and Genetics, Ufa Scientific Center, Russian Academy of Sciences, Ufa, Russia
| | - Sergey I Zhadanov
- Department of Anthropology, University of Pennsylvania, Philadelphia, USA
| | | | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Mikhail I Voevoda
- Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia
| | - Ludmila P Osipova
- Institute of Genetics and Cytology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Fedor A Platonov
- Institute of Health, North-East Federal University, Yakutsk, Russia
| | - Mikhail I Tomsky
- Department of Molecular Genetics, Yakut Research Center of Complex Medical Problems, Russian Academy of Medical Sciences and North-Eastern Federal University, Yakutsk, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center, Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Richard Villems
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
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HLA genetic profile of Mapuche (Araucanian) Amerindians from Chile. Mol Biol Rep 2013; 40:4257-67. [PMID: 23666052 DOI: 10.1007/s11033-013-2509-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 04/27/2013] [Indexed: 10/26/2022]
Abstract
Amerindian Mapuche (Araucanians) are now living in Chile and Argentina at both sides of Andean Mountains. They are anthropologically and genetically different from southernmost South America Patagonian Amerindians. Most of the HLA alleles found in our Mapuche sample are frequent or very frequent in North and South America Amerindians: (1) Class I: A*02:01, A*03:01, A*68:01, B*39:09, B*51:01, (2) Class II: DRB1*03:01, DRB1*04:03, DRB1*07:01, DRB1*08:02, DRB1*14:02, DRB1*16:02. One of the nine most frequent extended haplotypes seems to be from European origin, suggesting the existence of a degree of admixture with Europeans in our Mapuche sample. It has been calculated of about 11 % admixture. Three of the extended haplotypes are also found in other Amerindians and five of them are newly found in Mapuche Amerindians: A*68:01-B*39:09-DRB1*08:02-DQB1*04:02; A*68:01-B*51:01-DRB1*04:03-DQB1*03:02; A*29:01-B*08:01-DRB1*03:01-DQB1*02:01; A*02:01-B*15:01-DRB1*04:03-DQB1*03:02; A*33:01-B*14:02-DRB1*07:01-DQB1*03:03. The medical importance of calculating HLA profile is discussed on the diagnostic (HLA and disease) and therapeutical bases of HLA pharmacogenomics and on the construction of a virtual transplantation HLA list profile. Also, anthropological conclusions are drawn.
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Gubina MA, Damba LD, Babenko VN, Romaschenko AG, Voevoda MI. Haplotype diversity in mtDNA and Y-chromosome in populations of Altai-Sayan region. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795412120034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Regueiro M, Alvarez J, Rowold D, Herrera RJ. On the origins, rapid expansion and genetic diversity of Native Americans from hunting-gatherers to agriculturalists. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 150:333-48. [PMID: 23283701 DOI: 10.1002/ajpa.22207] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 11/08/2012] [Indexed: 11/05/2022]
Abstract
Given the importance of Y-chromosome haplogroup Q to better understand the source populations of contemporary Native Americans, we studied 8 biallelic and 17 microsatellite polymorphisms on the background of 128 Q Y-chromosomes from geographically targeted populations. The populations examined in this study include three from the Tuva Republic in Central Asia (Bai-Tai, Kungurtug, and Toora-Hem, n = 146), two from the northeastern tip of Siberia (New Chaplino and Chukchi, n = 32), and two from Mesoamerica (Mayans from Yucatan, Mexico n = 72, and Mayans from the Guatemalan Highlands, n = 43). We also see evidence of a dramatic Mesoamerican post-migration population growth in the ubiquitous and diverse Y-STR profiles of the Mayan and other Mesoamerican populations. In the case of the Mayans, this demographic growth was most likely fueled by the agricultural- and trade-based subsistence adopted during the Pre-Classic, Classic and Post-Classic periods of their empire. The limited diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined, may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. Furthermore, our data illustrate how a sociocultural characteristic such as mode of subsistence may be of impact on the genetic structure of populations. We analyzed our genetic data using Multidimensional Scaling Analysis of populations, Principal Component Analysis of individuals, Median-joining networks of M242, M346, L54, and M3 individuals, age estimations based on microsatellite variation utilizing genealogical and evolutionary mutation rates/generation times and estimation of Y- STR average gene diversity indices.
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Affiliation(s)
- Maria Regueiro
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL 33199, USA
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Arrival of Paleo-Indians to the southern cone of South America: new clues from mitogenomes. PLoS One 2012; 7:e51311. [PMID: 23240014 PMCID: PMC3519775 DOI: 10.1371/journal.pone.0051311] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 10/31/2012] [Indexed: 11/19/2022] Open
Abstract
With analyses of entire mitogenomes, studies of Native American mitochondrial DNA (mtDNA) variation have entered the final phase of phylogenetic refinement: the dissection of the founding haplogroups into clades that arose in America during and after human arrival and spread. Ages and geographic distributions of these clades could provide novel clues on the colonization processes of the different regions of the double continent. As for the Southern Cone of South America, this approach has recently allowed the identification of two local clades (D1g and D1j) whose age estimates agree with the dating of the earliest archaeological sites in South America, indicating that Paleo-Indians might have reached that region from Beringia in less than 2000 years. In this study, we sequenced 46 mitogenomes belonging to two additional clades, termed B2i2 (former B2l) and C1b13, which were recently identified on the basis of mtDNA control-region data and whose geographical distributions appear to be restricted to Chile and Argentina. We confirm that their mutational motifs most likely arose in the Southern Cone region. However, the age estimate for B2i2 and C1b13 (11–13,000 years) appears to be younger than those of other local clades. The difference could reflect the different evolutionary origins of the distinct South American-specific sub-haplogroups, with some being already present, at different times and locations, at the very front of the expansion wave in South America, and others originating later in situ, when the tribalization process had already begun. A delayed origin of a few thousand years in one of the locally derived populations, possibly in the central part of Chile, would have limited the geographical and ethnic diffusion of B2i2 and explain the present-day occurrence that appears to be mainly confined to the Tehuelche and Araucanian-speaking groups.
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Abstract
The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved1–5. One contentious issue is whether the settlement occurred via a single6–8 or multiple streams of migration from Siberia9–15. The pattern of dispersals within the Americas is also poorly understood. To address these questions at higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. We show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call “First American”. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan-speakers on both sides of the Panama Isthmus, who have ancestry from both North and South America.
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Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations. Proc Natl Acad Sci U S A 2012; 109:8471-6. [PMID: 22586127 DOI: 10.1073/pnas.1118760109] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
For decades, the peopling of the Americas has been explored through the analysis of uniparentally inherited genetic systems in Native American populations and the comparison of these genetic data with current linguistic groupings. In northern North America, two language families predominate: Eskimo-Aleut and Na-Dene. Although the genetic evidence from nuclear and mtDNA loci suggest that speakers of these language families share a distinct biological origin, this model has not been examined using data from paternally inherited Y chromosomes. To test this hypothesis and elucidate the migration histories of Eskimoan- and Athapaskan-speaking populations, we analyzed Y-chromosomal data from Inuvialuit, Gwich'in, and Tłįch populations living in the Northwest Territories of Canada. Over 100 biallelic markers and 19 chromosome short tandem repeats (STRs) were genotyped to produce a high-resolution dataset of Y chromosomes from these groups. Among these markers is an SNP discovered in the Inuvialuit that differentiates them from other Aboriginal and Native American populations. The data suggest that Canadian Eskimoan- and Athapaskan-speaking populations are genetically distinct from one another and that the formation of these groups was the result of two population expansions that occurred after the initial movement of people into the Americas. In addition, the population history of Athapaskan speakers is complex, with the Tłįch being distinct from other Athapaskan groups. The high-resolution biallelic data also make clear that Y-chromosomal diversity among the first Native Americans was greater than previously recognized.
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Sandoval K, Moreno-Estrada A, Mendizabal I, Underhill PA, Lopez-Valenzuela M, Peñaloza-Espinosa R, Lopez-Lopez M, Buentello-Malo L, Avelino H, Calafell F, Comas D. Y-chromosome diversity in Native Mexicans reveals continental transition of genetic structure in the Americas. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 148:395-405. [PMID: 22576278 DOI: 10.1002/ajpa.22062] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 02/29/2012] [Indexed: 12/11/2022]
Abstract
The genetic characterization of Native Mexicans is important to understand multiethnic based features influencing the medical genetics of present Mexican populations, as well as to the reconstruct the peopling of the Americas. We describe the Y-chromosome genetic diversity of 197 Native Mexicans from 11 populations and 1,044 individuals from 44 Native American populations after combining with publicly available data. We found extensive heterogeneity among Native Mexican populations and ample segregation of Q-M242* (46%) and Q-M3 (54%) haplogroups within Mexico. The northernmost sampled populations falling outside Mesoamerica (Pima and Tarahumara) showed a clear differentiation with respect to the other populations, which is in agreement with previous results from mtDNA lineages. However, our results point toward a complex genetic makeup of Native Mexicans whose maternal and paternal lineages reveal different narratives of their population history, with sex-biased continental contributions and different admixture proportions. At a continental scale, we found that Arctic populations and the northernmost groups from North America cluster together, but we did not find a clear differentiation within Mesoamerica and the rest of the continent, which coupled with the fact that the majority of individuals from Central and South American samples are restricted to the Q-M3 branch, supports the notion that most Native Americans from Mesoamerica southwards are descendants from a single wave of migration. This observation is compatible with the idea that present day Mexico might have constituted an area of transition in the diversification of paternal lineages during the colonization of the Americas.
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Affiliation(s)
- Karla Sandoval
- Institut de Biologia Evolutiva, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
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Bisso-Machado R, Bortolini MC, Salzano FM. Uniparental genetic markers in South Amerindians. Genet Mol Biol 2012; 35:365-87. [PMID: 22888284 PMCID: PMC3389523 DOI: 10.1590/s1415-47572012005000027] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 01/12/2012] [Indexed: 12/25/2022] Open
Abstract
A comprehensive review of uniparental systems in South Amerindians was undertaken. Variability in the Y-chromosome haplogroups were assessed in 68 populations and 1,814 individuals whereas that of Y-STR markers was assessed in 29 populations and 590 subjects. Variability in the mitochondrial DNA (mtDNA) haplogroup was examined in 108 populations and 6,697 persons, and sequencing studies used either the complete mtDNA genome or the highly variable segments 1 and 2. The diversity of the markers made it difficult to establish a general picture of Y-chromosome variability in the populations studied. However, haplogroup Q1a3a* was almost always the most prevalent whereas Q1a3* occurred equally in all regions, which suggested its prevalence among the early colonizers. The STR allele frequencies were used to derive a possible ancient Native American Q-clade chromosome haplotype and five of six STR loci showed significant geographic variation. Geographic and linguistic factors moderately influenced the mtDNA distributions (6% and 7%, respectively) and mtDNA haplogroups A and D correlated positively and negatively, respectively, with latitude. The data analyzed here provide rich material for understanding the biological history of South Amerindians and can serve as a basis for comparative studies involving other types of data, such as cultural data.
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Affiliation(s)
- Rafael Bisso-Machado
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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O'Rourke D, Enk J. Genetics, Geography, and Human Variation. Hum Biol 2012. [DOI: 10.1002/9781118108062.ch4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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He Y, Wang WR, Xu S, Jin L, Snp Consortium PA. Paleolithic Contingent in Modern Japanese: Estimation and Inference using Genome-wide Data. Sci Rep 2012; 2:355. [PMID: 22482036 PMCID: PMC3320058 DOI: 10.1038/srep00355] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 03/21/2012] [Indexed: 01/15/2023] Open
Abstract
The genetic origins of Japanese populations have been controversial. Upper Paleolithic Japanese, i.e. Jomon, developed independently in Japanese islands for more than 10,000 years until the isolation was ended with the influxes of continental immigrants about 2,000 years ago. However, the knowledge of origin of Jomon and its contribution to the genetic pool of contemporary Japanese is still limited, albeit the extensive studies using mtDNA and Y chromosomes. In this report, we aimed to infer the origin of Jomon and to estimate its contribution to Japanese by fitting an admixture model with missing data from Jomon to a genome-wide data from 94 worldwide populations. Our results showed that the genetic contributions of Jomon, the Paleolithic contingent in Japanese, are 54.3∼62.3% in Ryukyuans and 23.1∼39.5% in mainland Japanese, respectively. Utilizing inferred allele frequencies of the Jomon population, we further showed the Paleolithic contingent in Japanese had a Northeast Asia origin.
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Mitochondrial DNA and Y chromosome variation provides evidence for a recent common ancestry between Native Americans and Indigenous Altaians. Am J Hum Genet 2012; 90:229-46. [PMID: 22281367 DOI: 10.1016/j.ajhg.2011.12.014] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 12/06/2011] [Accepted: 12/19/2011] [Indexed: 11/20/2022] Open
Abstract
The Altai region of southern Siberia has played a critical role in the peopling of northern Asia as an entry point into Siberia and a possible homeland for ancestral Native Americans. It has an old and rich history because humans have inhabited this area since the Paleolithic. Today, the Altai region is home to numerous Turkic-speaking ethnic groups, which have been divided into northern and southern clusters based on linguistic, cultural, and anthropological traits. To untangle Altaian genetic histories, we analyzed mtDNA and Y chromosome variation in northern and southern Altaian populations. All mtDNAs were assayed by PCR-RFLP analysis and control region sequencing, and the nonrecombining portion of the Y chromosome was scored for more than 100 biallelic markers and 17 Y-STRs. Based on these data, we noted differences in the origin and population history of Altaian ethnic groups, with northern Altaians appearing more like Yeniseian, Ugric, and Samoyedic speakers to the north, and southern Altaians having greater affinities to other Turkic speaking populations of southern Siberia and Central Asia. Moreover, high-resolution analysis of Y chromosome haplogroup Q has allowed us to reshape the phylogeny of this branch, making connections between populations of the New World and Old World more apparent and demonstrating that southern Altaians and Native Americans share a recent common ancestor. These results greatly enhance our understanding of the peopling of Siberia and the Americas.
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Mendez FL, Watkins JC, Hammer MF. Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations. Mol Biol Evol 2012; 29:1513-20. [PMID: 22319157 DOI: 10.1093/molbev/msr301] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recent analysis of DNA extracted from two Eurasian forms of archaic human shows that more genetic variants are shared with humans currently living in Eurasia than with anatomically modern humans in sub-Saharan Africa. Although these genome-wide average measures of genetic similarity are consistent with the hypothesis of archaic admixture in Eurasia, analyses of individual loci exhibiting the signal of archaic introgression are needed to test alternative hypotheses and investigate the admixture process. Here, we provide a detailed sequence analysis of the innate immune gene OAS1, a locus with a divergent Melanesian haplotype that is very similar to the Denisova sequence from the Altai region of Siberia. We resequenced a 7-kb region encompassing the OAS1 gene in 88 individuals from six Old World populations (San, Biaka, Mandenka, French Basque, Han Chinese, and Papua New Guineans) and discovered previously unknown and ancient genetic variation. The 5' region of this gene has unusual patterns of diversity, including 1) higher levels of nucleotide diversity in Papuans than in sub-Saharan Africans, 2) very deep ancestry with an estimated time to the most recent common ancestor of >3 myr, and 3) a basal branching pattern with Papuan individuals on either side of the rooted network. A global geographic survey of >1,500 individuals showed that the divergent Papuan haplotype is nearly restricted to populations from eastern Indonesia and Melanesia. Polymorphic sites within this haplotype are shared with the draft Denisova genome over a span of ∼90 kb and are associated with an extended block of linkage disequilibrium, supporting the hypothesis that this haplotype introgressed from an archaic source that likely lived in Eurasia.
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Affiliation(s)
- Fernando L Mendez
- Department of Ecology and Evolutionary Biology, University of Arizona, USA
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Arnaiz-Villena A, Parga-Lozano C, Moreno E, Areces C, Rey D, Gomez-Prieto P. The Origin of Amerindians and the Peopling of the Americas According to HLA Genes: Admixture with Asian and Pacific People. Curr Genomics 2011; 11:103-14. [PMID: 20885818 PMCID: PMC2874220 DOI: 10.2174/138920210790886862] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Revised: 12/01/2009] [Accepted: 12/08/2009] [Indexed: 11/22/2022] Open
Abstract
The classical three-waves theory of American peopling through Beringia was based on a mixed anthropological and linguistic methodology. The use of mtDNA, Y chromosome and other DNA markers offers different results according to the different markers and methodologies chosen by different authors. At present, the peopling of Americas remains uncertain, regarding: time of population, number of peopling waves and place of peopling entrance among other related issues. In the present review, we have gathered most available HLA data already obtained about First Native American populations, which raise some doubts about the classical three waves of American peopling hypothesis. In summary, our conclusions are: 1) North West Canadian Athabaskans have had gene flow with: a) close neighboring populations, b) Amerindians, c) Pacific Islanders including East Australians and d) Siberians; 2) Beringia was probably not the only entrance of people to America: Pacific Ocean boat trips may have contributed to the HLA genetic American profile (or the opposite could also be true); 3) Amerindians entrance to America may have been different to that of Athabaskans and Eskimos and Amerindians may have been in their lands long before Athabaskans and Eskimos because they present and altogether different set of HLA-DRB1 allele frequencies; 4) Amerindians show very few “particular alleles”, almost all are shared with other Amerindians, Athabaskans and Pacific Islanders, including East Australians and Siberians; 5) Our results do not support the three waves model of American peopling, but another model where the people entrance is not only Beringia, but also Pacific Coast. Reverse migration (America to Asia) is not discarded and different movements of people in either direction in different times are supported by the Athabaskan population admixture with Asian-Pacific population and with Amerindians, 6) HLA variability is more common than allele veriability in Amerindians. Finally, it is shown that gene genealogy analises should be completed with allele frequency analyses in population relatednes and migrations studies.
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Affiliation(s)
- A Arnaiz-Villena
- Department Immunology, University Complutense, The Madrid Regional Blood Center, Madrid, Spain
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Klyosov AA. Biological chemistry as a foundation of DNA genealogy: the emergence of "molecular history". BIOCHEMISTRY (MOSCOW) 2011; 76:517-33. [PMID: 21639832 DOI: 10.1134/s0006297911050026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This paper presents the basis of DNA genealogy, a new field of science, which is currently emerging as an unusual blend of biochemistry, history, linguistics, and chemical kinetics. The methodology of the new approach is comprised of chemical (biological) kinetics applied to a pattern of mutations in non-recombinant fragments of DNA (Y chromosome and mtDNA, the latter not being considered in this overview). The goal of the analysis is to translate DNA mutation patterns into time spans to the most recent common ancestors of a given population or tribe and to the dating of ancient migration routes. To illustrate this approach, time spans to the common ancestors are calculated for ethnic Russians, that is Eastern Slavs (R1a1 tribe), Western Slavs (I1 and I2 tribes), and Northern (or Uralic) Slavs (N1c tribe), which were found to live around 4600 years before present (R1a1), 3650 ybp (I1), 3000 and 10,500 ybp (I2, two principal DNA lineages), and 3525 ybp (N1c) (confidence intervals are given in the main text). The data were compared with the respective dates for the nearest common ancestor of the R1a1 "Indo-European" population in India, who lived 4050 years before present, whose descendants represent the majority of the upper castes in India today (up to 72%). Furthermore, it was found that the haplotypes of ethnic Russians of the R1a1 haplogroup (up to 62% of the population in the Russian Federation) and those of the R1a1 Indians (more than 100 million today) are practically identical to each other, up to 67-marker haplotypes. This essentially solves a 200-year-old mystery of who were the Aryans who arrived in India around 3500 years before the present. Haplotypes and time spans to the ancient common ancestors were also compared for the ethnic Russians of haplogroups I1 and I2, on one hand, and the respective I1 and I2 populations in Eastern and Western Europe and Scandinavia, on the other. It is suggested that the approach described in this overview lays the foundation for "molecular history", in which the principal tool is high-technology analysis of DNA molecules of both our contemporaries and excavated ancient DNA samples, along with their biological kinetics.
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Affiliation(s)
- A A Klyosov
- MIR International, Inc., Newton, Massachusetts 02459, USA.
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Geppert M, Baeta M, Núñez C, Martínez-Jarreta B, Zweynert S, Cruz OWV, González-Andrade F, González-Solorzano J, Nagy M, Roewer L. Hierarchical Y-SNP assay to study the hidden diversity and phylogenetic relationship of native populations in South America. Forensic Sci Int Genet 2011; 5:100-4. [DOI: 10.1016/j.fsigen.2010.08.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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SEGUCHI NORIKO, MCKEOWN ASHLEY, SCHMIDT RYAN, UMEDA HIDEYUKI, BRACE CLORING. An alternative view of the peopling of South America: Lagoa Santa in craniometric perspective. ANTHROPOL SCI 2011. [DOI: 10.1537/ase.090921] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- NORIKO SEGUCHI
- Department of Anthropology, University of Montana, Missoula
| | - ASHLEY MCKEOWN
- Department of Anthropology, University of Montana, Missoula
| | - RYAN SCHMIDT
- Department of Anthropology, University of Montana, Missoula
| | - HIDEYUKI UMEDA
- Department of Astronomy, Faculty of Science, The University of Tokyo, Tokyo
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Ding QL, Wang CC, Farina SE, Li H. Mapping Human Genetic Diversity on the Japanese Archipelago. ACTA ACUST UNITED AC 2011. [DOI: 10.4236/aa.2011.12004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Parga-Lozano C, Rey-Medrano D, Gomez-Prieto P, Areces C, Moscoso J, Abd-El-Fatah-Khalil S, Moreno E, Arnaiz-Villena A. HLA genes in Amerindian immigrants to Madrid (Spain): epidemiology and a virtual transplantation waiting list: Amerindians in Madrid (Spain). Mol Biol Rep 2010; 38:2263-71. [PMID: 20931290 DOI: 10.1007/s11033-010-0357-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 09/22/2010] [Indexed: 11/28/2022]
Abstract
Amerindians immigrated to Madrid (Spain) region are about 10% of the present day population. Amerindians are believed to be the first American inhabitants, before Na-Dene speakers, Aleuts and Eskimo. They may initially have arrived to America from Siberia and also from other parts of Pacific Sea (South Asia, Polynesia and Australia). Nowadays, they populate America from Canada to Tierra del Fuego (South America tip South). Most Amerindian immigrants to Madrid have come from Andean Countries in the last 10 years (mainly Ecuador, Bolivia, Peru and Colombia). They show an HLA profile with "quasi-specific alleles", which makes them different to the rest of the World. In the present work, we have aimed to determine the immigrants HLA profile in order to establish a virtual transplantation waiting list which may be useful for their therapeutic transplants, particularly bone marrow transplantation. This would be carried out together with Amerindian immigrants to other parts of Spain and with their own countries in order to build up transplantation programs. Specific epidemiology programs on HLA linked disease will also be established. Immigrant volunteer unrelated blood donors contributed to the present study. HLA typing was performed by standard methods and their HLA profile obtained and obtained and compared with 15,108 HLA chromosomes from the rest of the World, including Spaniards. The immigrants showed a typical Amerindian profile similar to isolated Amerindian ethnic groups and altogether different to other World inhabitants (including Spaniards). These are the first bases to set up transplantation and epidemiology studies in collaboration with their original population in America. Finally, the HLA profile found in these Amerindians does not indicate their American specific original area, as it is expected from previous studies, i.e.: they do not relate more with Andean than with other Amerindians in Neighbour Joining dendrograms or correspondence analyses.
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Affiliation(s)
- Carlos Parga-Lozano
- Department of Immunology, Facultad de Medicina, University Complutense, Universidad Complutense, and Department of Hepatic Surgery, Hospital 12 de Octubre, Avda. Complutense s/n, 28040, Madrid, Spain
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Silvera C, Vargas-Alarcon G, Areces C, Rey D, Parga-Lozano C, Gomez-Prieto P, Barbolla L, Martinez-Laso J, Arnaiz-Villena A. HLA genes in Wayu Amerindians from Colombia. Immunol Invest 2010; 40:92-100. [PMID: 20923327 DOI: 10.3109/08820139.2010.517390] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Amerindians origins and prehistory are still debated. HLA profile is different to all other World populations, although they have particular alleles in common with Asians, Australians and Pacific Islanders. In the present work, HLA-A, -B, -DRB1, -DQB1 alleles have been studied in Wayu Amerindians from Colombia. HLA alleles haplotypes, genetic distances and NJ dendrograms were calculated by Arlequin and DISPAN software. Only a few both class I and class II alleles have been observed. Most common extended haplotypes include: A*24-B*51-DRB1*0403-DQB1*0302, A*2-B*15-DRB1*1602-DQB1*0301, A*2-B*35-DRB1*0407-DQB1*0302, but also A*68-B*15-DRB1*0403-DQB1*0302. No trace of Caucasoid or Negroid admixture is detected. The Wayu HLA profile is typical from Amerindians and shows how languages and genes do not correlated particularly in this case (i.e., Wayu closest HLA genetic group is North Argentinian Guarani group). Results obtained in this work may be useful for future transplant programs and also for HLA linked diseases and individualized pharmacogenetics.
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Affiliation(s)
- Carlos Silvera
- Department of Genetics, Universidad del Norte, Barranquilla, Colombia
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Yang NN, Mazières S, Bravi C, Ray N, Wang S, Burley MW, Bedoya G, Rojas W, Parra MV, Molina JA, Gallo C, Poletti G, Hill K, Hurtado AM, Petzl-Erler ML, Tsuneto LT, Klitz W, Barrantes R, Llop E, Rothhammer F, Labuda D, Salzano FM, Bortolini MC, Excoffier L, Dugoujon JM, Ruiz-Linares A. Contrasting patterns of nuclear and mtDNA diversity in Native American populations. Ann Hum Genet 2010; 74:525-38. [PMID: 20887376 DOI: 10.1111/j.1469-1809.2010.00608.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We report an integrated analysis of nuclear (autosomal, X- and Y-chromosome) short tandem repeat (STR) data and mtDNA D-loop sequences obtained in the same set of 22 Native populations from across the Americas. A north to south gradient of decreasing population diversity was observed, in agreement with a settlement of the Americas from the extreme northwest of the continent. This correlation is stronger with "least cost distances," which consider the coasts as facilitators of migration. Continent-wide estimates of population structure are highest for the Y-chromosome and lowest for the autosomes, consistent with the effective size of the different marker systems examined. Population differentiation is highest in East South America and lowest in Meso America and the Andean region. Regional analyses suggest a deviation from mutation-drift equilibrium consistent with population expansion in Meso America and the Andes and population contraction in Northwest and East South America. These data hint at an early divergence of Andean and non-Andean South Americans and at a contrasting demographic history for populations from these regions.
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Affiliation(s)
- Ning Ning Yang
- Department of Genetics, Evolution and Environment, University College London, UK
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Ramalho RF, Santos EJ, Guerreiro JF, Meyer D. Balanced polymorphism in bottlenecked populations: The case of the CCR5 5′ cis-regulatory region in Amazonian Amerindians. Hum Immunol 2010; 71:922-8. [DOI: 10.1016/j.humimm.2010.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 05/20/2010] [Accepted: 05/26/2010] [Indexed: 11/28/2022]
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