101
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Jernvall J, Thesleff I. Tooth shape formation and tooth renewal: evolving with the same signals. Development 2012; 139:3487-97. [PMID: 22949612 DOI: 10.1242/dev.085084] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Teeth are found in almost all vertebrates, and they therefore provide a general paradigm for the study of epithelial organ development and evolution. Here, we review the developmental mechanisms underlying changes in tooth complexity and tooth renewal during evolution, focusing on recent studies of fish, reptiles and mammals. Mammals differ from other living vertebrates in that they have the most complex teeth with restricted capacity for tooth renewal. As we discuss, however, limited tooth replacement in mammals has been compensated for in some taxa by the evolution of continuously growing teeth, the development of which appears to reuse the regulatory pathways of tooth replacement.
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Affiliation(s)
- Jukka Jernvall
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, PO Box 56, FIN 00014, Finland.
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102
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Jinam T, Nishida N, Hirai M, Kawamura S, Oota H, Umetsu K, Kimura R, Ohashi J, Tajima A, Yamamoto T, Tanabe H, Mano S, Suto Y, Kaname T, Naritomi K, Yanagi K, Niikawa N, Omoto K, Tokunaga K, Saitou N. The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations. J Hum Genet 2012; 57:787-95. [PMID: 23135232 DOI: 10.1038/jhg.2012.114] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The Japanese Archipelago stretches over 4000 km from north to south, and is the homeland of the three human populations; the Ainu, the Mainland Japanese and the Ryukyuan. The archeological evidence of human residence on this Archipelago goes back to >30 000 years, and various migration routes and root populations have been proposed. Here, we determined close to one million single-nucleotide polymorphisms (SNPs) for the Ainu and the Ryukyuan, and compared these with existing data sets. This is the first report of these genome-wide SNP data. Major findings are: (1) Recent admixture with the Mainland Japanese was observed for more than one third of the Ainu individuals from principal component analysis and frappe analyses; (2) The Ainu population seems to have experienced admixture with another population, and a combination of two types of admixtures is the unique characteristics of this population; (3) The Ainu and the Ryukyuan are tightly clustered with 100% bootstrap probability followed by the Mainland Japanese in the phylogenetic trees of East Eurasian populations. These results clearly support the dual structure model on the Japanese Archipelago populations, though the origins of the Jomon and the Yayoi people still remain to be solved.
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103
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Peter BM, Huerta-Sanchez E, Nielsen R. Distinguishing between selective sweeps from standing variation and from a de novo mutation. PLoS Genet 2012; 8:e1003011. [PMID: 23071458 PMCID: PMC3469416 DOI: 10.1371/journal.pgen.1003011] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Accepted: 08/20/2012] [Indexed: 01/22/2023] Open
Abstract
An outstanding question in human genetics has been the degree to which adaptation occurs from standing genetic variation or from de novo mutations. Here, we combine several common statistics used to detect selection in an Approximate Bayesian Computation (ABC) framework, with the goal of discriminating between models of selection and providing estimates of the age of selected alleles and the selection coefficients acting on them. We use simulations to assess the power and accuracy of our method and apply it to seven of the strongest sweeps currently known in humans. We identify two genes, ASPM and PSCA, that are most likely affected by selection on standing variation; and we find three genes, ADH1B, LCT, and EDAR, in which the adaptive alleles seem to have swept from a new mutation. We also confirm evidence of selection for one further gene, TRPV6. In one gene, G6PD, neither neutral models nor models of selective sweeps fit the data, presumably because this locus has been subject to balancing selection.
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Affiliation(s)
- Benjamin M Peter
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA.
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104
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Créton M, van den Boogaard MJ, Maal T, Verhamme L, Fennis W, Carels C, Kuijpers-Jagtman AM, Cune M. Three-dimensional analysis of tooth dimensions in the MSX1-missense mutation. Clin Oral Investig 2012; 17:1437-45. [PMID: 22936299 DOI: 10.1007/s00784-012-0828-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Accepted: 08/07/2012] [Indexed: 11/26/2022]
Abstract
OBJECTIVES A novel, 3D technique to measure the differences in tooth crown morphology between the MSX1 cases and non-affected controls was designed to get a better understanding of dental phenotype-genotype associations. MATERIALS AND METHODS Eight Dutch subjects from a single family with tooth agenesis, all with an established nonsense mutation c.332 C > A, p. Ser 111 Stop in exon 1 of MSX1, were compared with unaffected controls regarding several aspects of tooth crown morphology of incisor and molar teeth. A novel method of quantitative three-dimensional analysis was used to detect differences. RESULTS Statistically significant shape differences were observed for the maxillary incisor in the MSX1 family compared with the controls on the following parameters: surface area, buccolingual dimension, squareness, and crown volume (P ≤ 0.002). Molar crown shape was unaffected. CONCLUSIONS A better understanding of dental phenotype-genotype associations may contribute to earlier diagnosis of some multiple-anomaly congenital syndromes involving dental anomalies. CLINICAL RELEVANCE A "shape database" that includes associated gene mutations resulting from developmental syndromes may facilitate the genetic identification of hypodontia cases.
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Affiliation(s)
- Marijn Créton
- Department of Oral and Maxillofacial Surgery, Prosthodontics and Special Dental Care, University Medical Centre Utrecht, Utrecht, The Netherlands.
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105
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Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S. A high-coverage genome sequence from an archaic Denisovan individual. Science 2012; 338:222-6. [PMID: 22936568 DOI: 10.1126/science.1224344] [Citation(s) in RCA: 1090] [Impact Index Per Article: 90.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.
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Affiliation(s)
- Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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106
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Lee WC, Yamaguchi T, Watanabe C, Kawaguchi A, Takeda M, Kim YI, Haga S, Tomoyasu Y, Ishida H, Maki K, Park SB, Kimura R. Association of common PAX9 variants with permanent tooth size variation in non-syndromic East Asian populations. J Hum Genet 2012; 57:654-9. [DOI: 10.1038/jhg.2012.90] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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107
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Komazaki Y, Fujiwara T, Ogawa T, Sato M, Suzuki K, Yamagata Z, Moriyama K. Prevalence and gender comparison of malocclusion among Japanese adolescents: A population-based study. J World Fed Orthod 2012. [DOI: 10.1016/j.ejwf.2012.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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108
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Effects of an Asian-specific nonsynonymous EDAR variant on multiple dental traits. J Hum Genet 2012; 57:508-14. [DOI: 10.1038/jhg.2012.60] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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109
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Cobourne MT, Sharpe PT. Diseases of the tooth: the genetic and molecular basis of inherited anomalies affecting the dentition. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 2:183-212. [DOI: 10.1002/wdev.66] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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110
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Genetic differences in the two main groups of the Japanese population based on autosomal SNPs and haplotypes. J Hum Genet 2012; 57:326-34. [PMID: 22456480 DOI: 10.1038/jhg.2012.26] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Although the Japanese population has a rather low genetic diversity, we recently confirmed the presence of two main clusters (the Hondo and Ryukyu clusters) through principal component analysis of genome-wide single-nucleotide polymorphism (SNP) genotypes. Understanding the genetic differences between the two main clusters requires further genome-wide analyses based on a dense SNP set and comparison of haplotype frequencies. In the present study, we determined haplotypes for the Hondo cluster of the Japanese population by detecting SNP homozygotes with 388,591 autosomal SNPs from 18,379 individuals and estimated the haplotype frequencies. Haplotypes for the Ryukyu cluster were inferred by a statistical approach using the genotype data from 504 individuals. We then compared the haplotype frequencies between the Hondo and Ryukyu clusters. In most genomic regions, the haplotype frequencies in the Hondo and Ryukyu clusters were very similar. However, in addition to the human leukocyte antigen region on chromosome 6, other genomic regions (chromosomes 3, 4, 5, 7, 10 and 12) showed dissimilarities in haplotype frequency. These regions were enriched for genes involved in the immune system, cell-cell adhesion and the intracellular signaling cascade. These differentiated genomic regions between the Hondo and Ryukyu clusters are of interest because they (1) should be examined carefully in association studies and (2) likely contain genes responsible for morphological or physiological differences between the two groups.
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111
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Townsend G, Bockmann M, Hughes T, Brook A. Genetic, environmental and epigenetic influences on variation in human tooth number, size and shape. Odontology 2011; 100:1-9. [DOI: 10.1007/s10266-011-0052-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 11/19/2011] [Indexed: 11/24/2022]
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112
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Hu M, Ayub Q, Guerra-Assunção JA, Long Q, Ning Z, Huang N, Romero IG, Mamanova L, Akan P, Liu X, Coffey AJ, Turner DJ, Swerdlow H, Burton J, Quail MA, Conrad DF, Enright AJ, Tyler-Smith C, Xue Y. Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data. Hum Genet 2011; 131:665-74. [PMID: 22057783 PMCID: PMC3325425 DOI: 10.1007/s00439-011-1111-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2011] [Accepted: 10/24/2011] [Indexed: 11/25/2022]
Abstract
We have investigated whether regions of the genome showing signs of positive selection in scans based on haplotype structure also show evidence of positive selection when sequence-based tests are applied, whether the target of selection can be localized more precisely, and whether such extra evidence can lead to increased biological insights. We used two tools: simulations under neutrality or selection, and experimental investigation of two regions identified by the HapMap2 project as putatively selected in human populations. Simulations suggested that neutral and selected regions should be readily distinguished and that it should be possible to localize the selected variant to within 40 kb at least half of the time. Re-sequencing of two ~300 kb regions (chr4:158Mb and chr10:22Mb) lacking known targets of selection in HapMap CHB individuals provided strong evidence for positive selection within each and suggested the micro-RNA gene hsa-miR-548c as the best candidate target in one region, and changes in regulation of the sperm protein gene SPAG6 in the other.
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Affiliation(s)
- Min Hu
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | | | - Quan Long
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Gregor Mendel Institut für Molekulare Pflanzenbiologie GmbH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Zemin Ning
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Ni Huang
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Irene Gallego Romero
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Lira Mamanova
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Pelin Akan
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Science for Life Laboratory, Royal Institute of Technology, 171 65 Stockholm, Sweden
| | - Xin Liu
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Alison J. Coffey
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Daniel J. Turner
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Oxford Nanopore Technologies Ltd., Oxford, UK
| | - Harold Swerdlow
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - John Burton
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Michael A. Quail
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Donald F. Conrad
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
- Present Address: Department of Genetics, Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO USA
| | - Anton J. Enright
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD UK
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA UK
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113
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Delgado-Burbano ME, Scott GR, Turner CG. The Uto-Aztecan premolar among North and South Amerindians: Geographic variation and genetics. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 143:570-8. [PMID: 20623681 DOI: 10.1002/ajpa.21351] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The Uto-Aztecan premolar (UAP) is a dental polymorphism characterized by an exaggerated distobuccal rotation of the paracone in combination with the presence of a fossa at the intersection of the distal occlusal ridge and distal marginal ridge of upper first premolars. This trait is important because, unlike other dental variants, it has been found exclusively in Native American populations. However, the trait's temporal and geographic variation has never been fully documented. The discovery of a Uto-Aztecan premolar in a prehistoric skeletal series from northern South America calls into question the presumed linguistic and geographic limits of this trait. We examined published and unpublished data for this rare but highly distinctive trait in samples representing over 5,000 Native Americans from North and South America. Our findings in living Southwest Amerindian populations corroborate the notion that the variable goes beyond the bounds of the Uto-Aztecan language family. It is found in prehistoric Native Americans from South America, eastern North America, Northern and Central Mexico, and in living and prehistoric populations in the American Southwest that are not members of the Uto-Aztecan language stock. The chronology of samples, its geographic distribution, and trait frequencies suggests a North American origin (Southwest) for UAP perhaps between 15,000 BP and 4,000 BP and a rapid and widespread dispersal into South America during the late Holocene. Family data indicate that it may represent an autosomal recessive mutation that occurred after the peopling of the Americas as its geographic range appears to be limited to North and South Amerindian populations.
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Affiliation(s)
- Miguel E Delgado-Burbano
- CONICET, División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s / n. La Plata 1900, Argentina.
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114
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SAITOU NARUYA, KIMURA RYOSUKE, FUKASE HITOSHI, YOGI AKIRA, MURAYAMA SADAYUKI, ISHIDA HAJIME. Advanced CT images reveal nonmetric cranial variations in living humans. ANTHROPOL SCI 2011. [DOI: 10.1537/ase.100928] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- NARUYA SAITOU
- Division of Population Genetics, National Institute of Genetics, Mishima
| | - RYOSUKE KIMURA
- Transdisciplinary Research Organization for Subtropics and Island Studies, University of the Ryukyus, Okinawa
| | - HITOSHI FUKASE
- Department of Human Biology and Anatomy, Faculty of Medicine, University of the Ryukyus, Okinawa
| | - AKIRA YOGI
- Department of Radiology, Faculty of Medicine, University of the Ryukyus, Okinawa
| | - SADAYUKI MURAYAMA
- Department of Radiology, Faculty of Medicine, University of the Ryukyus, Okinawa
| | - HAJIME ISHIDA
- Department of Human Biology and Anatomy, Faculty of Medicine, University of the Ryukyus, Okinawa
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115
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Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MTP, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TFG, Ramsey CB, Hansen TVO, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Pontén T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 2010; 463:757-62. [PMID: 20148029 DOI: 10.1038/nature08835] [Citation(s) in RCA: 461] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 01/18/2010] [Indexed: 12/29/2022]
Abstract
We report here the genome sequence of an ancient human. Obtained from approximately 4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20x, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.
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Affiliation(s)
- Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark and Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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