1
|
Quinn L, Whitfield J, Alpers MP, Campbell T, Hummerich H, Pomat W, Siba P, Koki G, Moltke I, Collinge J, Hellenthal G, Mead S. Population structure and migration in the Eastern Highlands of Papua New Guinea, a region impacted by the kuru epidemic. Am J Hum Genet 2024; 111:668-679. [PMID: 38508194 PMCID: PMC11023820 DOI: 10.1016/j.ajhg.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Populations of the Eastern Highlands of Papua New Guinea (EHPNG, area 11,157 km2) lived in relative isolation from the rest of the world until the mid-20th century, and the region contains a wealth of linguistic and cultural diversity. Notably, several populations of EHPNG were devastated by an epidemic prion disease, kuru, which at its peak in the mid-twentieth century led to some villages being almost depleted of adult women. Until now, population genetic analyses to learn about genetic diversity, migration, admixture, and the impact of the kuru epidemic have been restricted to a small number of variants or samples. Here, we present a population genetic analysis of the region based on genome-wide genotype data of 943 individuals from 21 linguistic groups and 68 villages in EHPNG, including 34 villages in the South Fore linguistic group, the group most affected by kuru. We find a striking degree of genetic population structure in the relatively small region (average FST between linguistic groups 0.024). The genetic population structure correlates well with linguistic grouping, with some noticeable exceptions that reflect the clan system of community organization that has historically existed in EHPNG. We also detect the presence of migrant individuals within the EHPNG region and observe a significant excess of females among migrants compared to among non-migrants in areas of high kuru exposure (p = 0.0145, chi-squared test). This likely reflects the continued practice of patrilocality despite documented fears and strains placed on communities as a result of kuru and its associated skew in female incidence.
Collapse
Affiliation(s)
- Liam Quinn
- MRC Prion Unit at UCL, Institute of Prion Diseases, UCL, London, UK; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jerome Whitfield
- MRC Prion Unit at UCL, Institute of Prion Diseases, UCL, London, UK
| | - Michael P Alpers
- Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia; Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, Eastern Highlands Province, Papua New Guinea
| | - Tracy Campbell
- MRC Prion Unit at UCL, Institute of Prion Diseases, UCL, London, UK
| | - Holger Hummerich
- MRC Prion Unit at UCL, Institute of Prion Diseases, UCL, London, UK
| | - William Pomat
- Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, Eastern Highlands Province, Papua New Guinea
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, Eastern Highlands Province, Papua New Guinea
| | - George Koki
- Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, Eastern Highlands Province, Papua New Guinea
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - John Collinge
- MRC Prion Unit at UCL, Institute of Prion Diseases, UCL, London, UK.
| | - Garrett Hellenthal
- University College London Genetics Institute, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Simon Mead
- MRC Prion Unit at UCL, Institute of Prion Diseases, UCL, London, UK
| |
Collapse
|
2
|
Dalal V, Pasupuleti N, Chaubey G, Rai N, Shinde V. Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide. Genes (Basel) 2023; 14:479. [PMID: 36833406 PMCID: PMC9956214 DOI: 10.3390/genes14020479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.
Collapse
Affiliation(s)
- Vasundhra Dalal
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | | | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Niraj Rai
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, Lucknow 226007, Uttar Pradesh, India
| | - Vasant Shinde
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| |
Collapse
|
3
|
Crabtree SA, White DA, Bradshaw CJA, Saltré F, Williams AN, Beaman RJ, Bird MI, Ulm S. Landscape rules predict optimal superhighways for the first peopling of Sahul. Nat Hum Behav 2021; 5:1303-1313. [PMID: 33927367 DOI: 10.1038/s41562-021-01106-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 03/24/2021] [Indexed: 02/02/2023]
Abstract
Archaeological data and demographic modelling suggest that the peopling of Sahul required substantial populations, occurred rapidly within a few thousand years and encompassed environments ranging from hyper-arid deserts to temperate uplands and tropical rainforests. How this migration occurred and how humans responded to the physical environments they encountered have, however, remained largely speculative. By constructing a high-resolution digital elevation model for Sahul and coupling it with fine-scale viewshed analysis of landscape prominence, least-cost pedestrian travel modelling and high-performance computing, we create over 125 billion potential migratory pathways, whereby the most parsimonious routes traversed emerge. Our analysis revealed several major pathways-superhighways-transecting the continent, that we evaluated using archaeological data. These results suggest that the earliest Australian ancestors adopted a set of fundamental rules shaped by physiological capacity, attraction to visually prominent landscape features and freshwater distribution to maximize survival, even without previous experience of the landscapes they encountered.
Collapse
Affiliation(s)
- Stefani A Crabtree
- Department of Environment and Society, Utah State University, Logan, UT, USA. .,The Santa Fe Institute, Santa Fe, NM, USA. .,ARC Centre of Excellence for Australian Biodiversity and Heritage, James Cook University, Cairns, Queensland, Australia. .,Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), Paris, France.
| | - Devin A White
- Autonomous Sensing and Perception, Sandia National Laboratories, Albuquerque, NM, USA.,Department of Anthropology, University of Tennessee, Knoxville, Knoxville, TN, USA
| | - Corey J A Bradshaw
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Flinders University, Adelaide, South Australia, Australia.,Global Ecology Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Frédérik Saltré
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Flinders University, Adelaide, South Australia, Australia.,Global Ecology Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Alan N Williams
- Climate Change Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of New South Wales, Sydney, Australia.,EMM Consulting Pty Ltd, St Leonards, New South Wales, Australia
| | - Robin J Beaman
- College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Michael I Bird
- ARC Centre of Excellence for Australian Biodiversity and Heritage, James Cook University, Cairns, Queensland, Australia.,College of Science and Engineering, James Cook University, Cairns, Queensland, Australia
| | - Sean Ulm
- ARC Centre of Excellence for Australian Biodiversity and Heritage, James Cook University, Cairns, Queensland, Australia.,College of Arts, Society and Education, James Cook University, Cairns, Queensland, Australia
| |
Collapse
|
4
|
Rowold DJ, Chennakrishnaiah S, Gayden T, Luis JR, Alfonso-Sanchez MA, Bukhari A, Garcia-Bertrand R, Herrera RJ. The Y-chromosome of the Soliga, an ancient forest-dwelling tribe of South India. Gene 2021; 763S:100026. [PMID: 32550553 PMCID: PMC7286085 DOI: 10.1016/j.gene.2019.100026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 12/03/2019] [Accepted: 12/17/2019] [Indexed: 11/05/2022]
Abstract
A previous autosomal STR study provided evidence of a connection between the ancient Soliga tribe at the southern tip of the Indian subcontinent and Australian aboriginal populations, possibly reflecting an eastbound coastal migration circa (15 Kya). The Soliga are considered to be among India's earliest inhabitants. In this investigation, we focus on the Y chromosomal characteristics shared between the Soliga population and other Indian tribes as well as western Eurasia and Sub-Saharan Africa groups. Some noteworthy findings of this present analysis include the following: The three most frequent haplogroups detected in the Soliga population are F*, H1 and J2. F*, the oldest (43 to 63 Kya), has a significant frequency bias in favor of Indian tribes versus castes. This observation coupled with the fact that Y-STR haplotypes shared with sub-Saharan African populations are found only in F* males of the Soliga, Irula and Kurumba may indicate a unique genetic connection between these Indian tribes and sub-Saharan Africans. In addition, our study suggests that haplogroup H is confined mostly to South Asia and immediate neighbors and the H1 network may indicate minimal sharing of Y-STR haplotypes among South Asian collections, tribal and otherwise. Also, J2, brought into India by Neolithic farmers, is present at a significantly higher frequency in caste versus tribal communities. This last observation may reflect the marginalization of Indian tribes to isolated regions not ideal for agriculture. Hg F*, H1 and J2 of the Soliga population chronicle the demographic history of the Indian tribal communities. Frequency bias for F* in Indian tribes may be a result of genetic drift due isolation and low population growth. Sharing of Y-STR haplotypes among tribal populations may be indicative of a common source population.
Collapse
Affiliation(s)
- Diane J Rowold
- Foundation for Applied Molecular Science (FfAME), Gainesville, FL 32601, USA; Department of Pediatrics, Nicklaus Children's Hospital, Miami, FL, USA
| | | | - Tenzin Gayden
- Department of Human Genetics, McGill University, Montreal, Canada
| | | | - Miguel A Alfonso-Sanchez
- Departamento de Genética y Antropología Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Bilbao, Spain
| | - Areej Bukhari
- Departamento de Genética y Antropología Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Bilbao, Spain
| | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
| |
Collapse
|
5
|
Brucato N, André M, Tsang R, Saag L, Kariwiga J, Sesuki K, Beni T, Pomat W, Muke J, Meyer V, Boland A, Deleuze JF, Sudoyo H, Mondal M, Pagani L, Romero IG, Metspalu M, Cox MP, Leavesley M, Ricaut FX. Papua New Guinean genomes reveal the complex settlement of north Sahul. Mol Biol Evol 2021; 38:5107-5121. [PMID: 34383935 PMCID: PMC8557464 DOI: 10.1093/molbev/msab238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The settlement of Sahul, the lost continent of Oceania, remains one of the most ancient and debated human migrations. Modern New Guineans inherited a unique genetic diversity tracing back 50,000 years, and yet there is currently no model reconstructing their past population dynamics. We generated 58 new whole genome sequences from Papua New Guinea, filling geographical gaps in previous sampling, specifically to address alternative scenarios of the initial migration to Sahul and the settlement of New Guinea. Here, we present the first genomic models for the settlement of northeast Sahul considering one or two migrations from Wallacea. Both models fit our dataset, reinforcing the idea that ancestral groups to New Guinean and Indigenous Australians split early, potentially during their migration in Wallacea where the northern route could have been favored. The earliest period of human presence in Sahul was an era of interactions and gene flow between related but already differentiated groups, from whom all modern New Guineans, Bismarck islanders and Indigenous Australians descend. The settlement of New Guinea was probably initiated from its southeast region, where the oldest archaeological sites have been found. This was followed by two migrations into the south and north lowlands that ultimately reached the west and east highlands. We also identify ancient gene flows between populations in New Guinea, Australia, East Indonesia and the Bismarck Archipelago, emphasizing the fact that the anthropological landscape during the early period of Sahul settlement was highly dynamic rather than the traditional view of extensive isolation.
Collapse
Affiliation(s)
- Nicolas Brucato
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Mathilde André
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France.,Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Roxanne Tsang
- School of Humanities, Languages and Social Science and Place, Evolution and Rock Art Heritage Unit, Griffith University Centre for Social and Cultural Research, Griffith University, Australia.,Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - Lauri Saag
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Jason Kariwiga
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea.,School of Social Science, University of Queensland, Australia, St Lucia, QLD 4072, Australia
| | - Kylie Sesuki
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - Teppsy Beni
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea
| | - William Pomat
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - John Muke
- Social Research Institute, Papua New Guinea
| | - Vincent Meyer
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057 Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057 Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, 91057 Evry, France
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia
| | - Mayukh Mondal
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Luca Pagani
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia.,Department of Biology, University of Padua, Italy
| | | | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu, Tartumaa 51010, Estonia
| | - Murray P Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Matthew Leavesley
- Strand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, PO Box 320, University 134, National Capital District, Papua New Guinea.,College of Arts, Society and Education, James Cook University, P.O. Box 6811, Cairns, Queensland, 4870, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New south Wales, 2522, Australia
| | - François-Xavier Ricaut
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| |
Collapse
|
6
|
Nagle N, van Oven M, Wilcox S, van Holst Pellekaan S, Tyler-Smith C, Xue Y, Ballantyne KN, Wilcox L, Papac L, Cooke K, van Oorschot RAH, McAllister P, Williams L, Kayser M, Mitchell RJ. Aboriginal Australian mitochondrial genome variation - an increased understanding of population antiquity and diversity. Sci Rep 2017; 7:43041. [PMID: 28287095 PMCID: PMC5347126 DOI: 10.1038/srep43041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/17/2017] [Indexed: 01/06/2023] Open
Abstract
Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 thousand years ago. Genetic studies, though limited, have demonstrated both the uniqueness and antiquity of Aboriginal Australian genomes. We have further resolved known Aboriginal Australian mitochondrial haplogroups and discovered novel indigenous lineages by sequencing the mitogenomes of 127 contemporary Aboriginal Australians. In particular, the more common haplogroups observed in our dataset included M42a, M42c, S, P5 and P12, followed by rarer haplogroups M15, M16, N13, O, P3, P6 and P8. We propose some major phylogenetic rearrangements, such as in haplogroup P where we delinked P4a and P4b and redefined them as P4 (New Guinean) and P11 (Australian), respectively. Haplogroup P2b was identified as a novel clade potentially restricted to Torres Strait Islanders. Nearly all Aboriginal Australian mitochondrial haplogroups detected appear to be ancient, with no evidence of later introgression during the Holocene. Our findings greatly increase knowledge about the geographic distribution and phylogenetic structure of mitochondrial lineages that have survived in contemporary descendants of Australia’s first settlers.
Collapse
Affiliation(s)
- Nano Nagle
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Mannis van Oven
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, The Netherlands
| | - Stephen Wilcox
- Australian Genome Research Facility, Melbourne, Victoria, Australia
| | - Sheila van Holst Pellekaan
- Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, Australia.,School of Biological Sciences, University of Sydney, Sydney, Australia
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Kaye N Ballantyne
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, The Netherlands.,Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Melbourne, Victoria, Australia
| | - Leah Wilcox
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Luka Papac
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Karen Cooke
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | - Roland A H van Oorschot
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Melbourne, Victoria, Australia
| | | | - Lesley Williams
- Community Elder and Cultural Advisor, Brisbane, Queensland, Australia
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, The Netherlands
| | - R John Mitchell
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, Victoria, Australia
| | | |
Collapse
|
7
|
Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia. Nature 2017; 544:180-184. [PMID: 28273067 DOI: 10.1038/nature21416] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/24/2017] [Indexed: 12/23/2022]
Abstract
Aboriginal Australians represent one of the longest continuous cultural complexes known. Archaeological evidence indicates that Australia and New Guinea were initially settled approximately 50 thousand years ago (ka); however, little is known about the processes underlying the enormous linguistic and phenotypic diversity within Australia. Here we report 111 mitochondrial genomes (mitogenomes) from historical Aboriginal Australian hair samples, whose origins enable us to reconstruct Australian phylogeographic history before European settlement. Marked geographic patterns and deep splits across the major mitochondrial haplogroups imply that the settlement of Australia comprised a single, rapid migration along the east and west coasts that reached southern Australia by 49-45 ka. After continent-wide colonization, strong regional patterns developed and these have survived despite substantial climatic and cultural change during the late Pleistocene and Holocene epochs. Remarkably, we find evidence for the continuous presence of populations in discrete geographic areas dating back to around 50 ka, in agreement with the notable Aboriginal Australian cultural attachment to their country.
Collapse
|
8
|
Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania. J Hum Genet 2016; 62:343-353. [PMID: 27904152 DOI: 10.1038/jhg.2016.147] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/21/2016] [Accepted: 10/27/2016] [Indexed: 12/30/2022]
Abstract
Aboriginal Australians are one of the more poorly studied populations from the standpoint of human evolution and genetic diversity. Thus, to investigate their genetic diversity, the possible date of their ancestors' arrival and their relationships with neighboring populations, we analyzed mitochondrial DNA (mtDNA) diversity in a large sample of Aboriginal Australians. Selected mtDNA single-nucleotide polymorphisms and the hypervariable segment haplotypes were analyzed in 594 Aboriginal Australians drawn from locations across the continent, chiefly from regions not previously sampled. Most (~78%) samples could be assigned to mtDNA haplogroups indigenous to Australia. The indigenous haplogroups were all ancient (with estimated ages >40 000 years) and geographically widespread across the continent. The most common haplogroup was P (44%) followed by S (23%) and M42a (9%). There was some geographic structure at the haplotype level. The estimated ages of the indigenous haplogroups range from 39 000 to 55 000 years, dates that fit well with the estimated date of colonization of Australia based on archeological evidence (~47 000 years ago). The distribution of mtDNA haplogroups in Australia and New Guinea supports the hypothesis that the ancestors of Aboriginal Australians entered Sahul through at least two entry points. The mtDNA data give no support to the hypothesis of secondary gene flow into Australia during the Holocene, but instead suggest long-term isolation of the continent.
Collapse
|
9
|
Nagle N, Ballantyne KN, van Oven M, Tyler-Smith C, Xue Y, Taylor D, Wilcox S, Wilcox L, Turkalov R, van Oorschot RA, McAllister P, Williams L, Kayser M, Mitchell RJ. Antiquity and diversity of aboriginal Australian Y-chromosomes. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:367-81. [DOI: 10.1002/ajpa.22886] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 10/01/2015] [Accepted: 10/08/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Nano Nagle
- Department of Biochemistry and Genetics; La Trobe Institute of Molecular Sciences, La Trobe University; Melbourne VIC Australia
| | - Kaye N. Ballantyne
- Victorian Police Forensic Services Department; Office of the Chief Forensic Scientist; Melbourne VIC Australia
- Department of Forensic Molecular Biology; Erasmus MC University Medical Center; Rotterdam The Netherlands
| | - Mannis van Oven
- Department of Forensic Molecular Biology; Erasmus MC University Medical Center; Rotterdam The Netherlands
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute; Welcome Trust Genome Campus; Hinxton Cambridgeshire UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute; Welcome Trust Genome Campus; Hinxton Cambridgeshire UK
| | - Duncan Taylor
- Forensic Science South Australia; 21 Divett Place Adelaide SA 5000 Australia
- School of Biological Sciences; Flinders University; Adelaide SA 5001 Australia
| | - Stephen Wilcox
- Australian Genome Research Facility; Melbourne VIC Australia
| | - Leah Wilcox
- Department of Biochemistry and Genetics; La Trobe Institute of Molecular Sciences, La Trobe University; Melbourne VIC Australia
| | - Rust Turkalov
- Australian Genome Research Facility; Melbourne VIC Australia
| | - Roland A.H. van Oorschot
- Victorian Police Forensic Services Department; Office of the Chief Forensic Scientist; Melbourne VIC Australia
| | | | - Lesley Williams
- Department of Communities; Child Safety and Disability Services, Queensland Government; Brisbane QLD Australia
| | - Manfred Kayser
- Department of Forensic Molecular Biology; Erasmus MC University Medical Center; Rotterdam The Netherlands
| | - Robert J. Mitchell
- Department of Biochemistry and Genetics; La Trobe Institute of Molecular Sciences, La Trobe University; Melbourne VIC Australia
| | | |
Collapse
|
10
|
Pugach I, Stoneking M. Genome-wide insights into the genetic history of human populations. INVESTIGATIVE GENETICS 2015; 6:6. [PMID: 25834724 PMCID: PMC4381409 DOI: 10.1186/s13323-015-0024-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 03/05/2015] [Indexed: 12/21/2022]
Abstract
Although mtDNA and the non-recombining Y chromosome (NRY) studies continue to provide valuable insights into the genetic history of human populations, recent technical, methodological and computational advances and the increasing availability of large-scale, genome-wide data from contemporary human populations around the world promise to reveal new aspects, resolve finer points, and provide a more detailed look at our past demographic history. Genome-wide data are particularly useful for inferring migrations, admixture, and fine structure, as well as for estimating population divergence and admixture times and fluctuations in effective population sizes. In this review, we highlight some of the stories that have emerged from the analyses of genome-wide SNP genotyping data concerning the human history of Southern Africa, India, Oceania, Island South East Asia, Europe and the Americas and comment on possible future study directions. We also discuss advantages and drawbacks of using SNP-arrays, with a particular focus on the ascertainment bias, and ways to circumvent it.
Collapse
Affiliation(s)
- Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany
| |
Collapse
|
11
|
Gomes SM, Bodner M, Souto L, Zimmermann B, Huber G, Strobl C, Röck AW, Achilli A, Olivieri A, Torroni A, Côrte-Real F, Parson W. Human settlement history between Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic mtDNA diversity. BMC Genomics 2015; 16:70. [PMID: 25757516 PMCID: PMC4342813 DOI: 10.1186/s12864-014-1201-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 12/22/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Distinct, partly competing, "waves" have been proposed to explain human migration in(to) today's Island Southeast Asia and Australia based on genetic (and other) evidence. The paucity of high quality and high resolution data has impeded insights so far. In this study, one of the first in a forensic environment, we used the Ion Torrent Personal Genome Machine (PGM) for generating complete mitogenome sequences via stand-alone massively parallel sequencing and describe a standard data validation practice. RESULTS In this first representative investigation on the mitochondrial DNA (mtDNA) variation of East Timor (Timor-Leste) population including >300 individuals, we put special emphasis on the reconstruction of the initial settlement, in particular on the previously poorly resolved haplogroup P1, an indigenous lineage of the Southwest Pacific region. Our results suggest a colonization of southern Sahul (Australia) >37 kya, limited subsequent exchange, and a parallel incubation of initial settlers in northern Sahul (New Guinea) followed by westward migrations <28 kya. CONCLUSIONS The temporal proximity and possible coincidence of these latter dispersals, which encompassed autochthonous haplogroups, with the postulated "later" events of (South) East Asian origin pinpoints a highly dynamic migratory phase.
Collapse
Affiliation(s)
- Sibylle M Gomes
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal.
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Luis Souto
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal.
- Cencifor Centro de Ciências Forenses, Coimbra, Portugal.
| | - Bettina Zimmermann
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Alexander W Röck
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy.
- Dipartimento di Chimica, Biologia e Biotecnologie, University of Perugia, Perugia, Italy.
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy.
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy.
| | | | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
- Penn State Eberly College of Science, University Park, PA, USA.
| |
Collapse
|
12
|
Pugach I, Delfin F, Gunnarsdóttir E, Kayser M, Stoneking M. Genome-wide data substantiate Holocene gene flow from India to Australia. Proc Natl Acad Sci U S A 2013; 110:1803-8. [PMID: 23319617 PMCID: PMC3562786 DOI: 10.1073/pnas.1211927110] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early "southern route" migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.
Collapse
Affiliation(s)
- Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
| | | | | | | | | |
Collapse
|
13
|
Yong E. Aboriginal Australian genomes reveal Indian ancestry. Nature 2013. [DOI: 10.1038/nature.2013.12219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
14
|
Reich D, Patterson N, Kircher M, Delfin F, Nandineni MR, Pugach I, Ko AMS, Ko YC, Jinam TA, Phipps ME, Saitou N, Wollstein A, Kayser M, Pääbo S, Stoneking M. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am J Hum Genet 2011; 89:516-28. [PMID: 21944045 DOI: 10.1016/j.ajhg.2011.09.005] [Citation(s) in RCA: 280] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 09/08/2011] [Accepted: 09/08/2011] [Indexed: 01/10/2023] Open
Abstract
It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a "Negrito" group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.
Collapse
Affiliation(s)
- David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Ballantyne KN, van Oven M, Ralf A, Stoneking M, Mitchell RJ, van Oorschot RAH, Kayser M. MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania. Forensic Sci Int Genet 2011; 6:425-36. [PMID: 21940232 DOI: 10.1016/j.fsigen.2011.08.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/18/2011] [Accepted: 08/25/2011] [Indexed: 01/22/2023]
Abstract
Human mitochondrial DNA (mtDNA) is a convenient marker for tracing matrilineal bio-geographic ancestry and is widely applied in forensic, genealogical and anthropological studies. In forensic applications, DNA-based ancestry inference can be useful for finding unknown suspects by concentrating police investigations in cases where autosomal STR profiling was unable to provide a match, or can help provide clues in missing person identification. Although multiplexed mtDNA single nucleotide polymorphism (SNP) assays to infer matrilineal ancestry at a (near) continental level are already available, such tools are lacking for the Oceania region. Here, we have developed a hierarchical system of three SNaPshot multiplexes for genotyping 26 SNPs defining all major mtDNA haplogroups for Oceania (including Australia, Near Oceania and Remote Oceania). With this system, it was possible to conclusively assign 74% of Oceanian individuals to their Oceanian matrilineal ancestry in an established literature database (after correcting for obvious external admixture). Furthermore, in a set of 161 genotyped individuals collected in Australia, Papua New Guinea and Fiji, 87.6% were conclusively assigned an Oceanian matrilineal origin. For the remaining 12.4% of the genotyped samples either a Eurasian origin was detected indicating likely European admixture (1.9%), the identified haplogroups are shared between Oceania and S/SE-Asia (5%), or the SNPs applied did not allow a geographic inference to be assigned (5.6%). Sub-regional assignment within Oceania was possible for 32.9% of the individuals genotyped: 49.5% of Australians were assigned an Australian origin and 13.7% of the Papua New Guineans were assigned a Near Oceanian origin, although none of the Fijians could be assigned a specific Remote Oceanian origin. The low assignment rates of Near and Remote Oceania are explained by recent migrations from Asia via Near Oceania into Remote Oceania. Combining the mtDNA multiplexes for Oceania introduced here with those we developed earlier for all other continental regions, global matrilineal bio-geographic ancestry assignment from DNA is now achievable in a highly efficient way that is also suitable for applications with limited material such as forensic case work.
Collapse
Affiliation(s)
- Kaye N Ballantyne
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
16
|
Smith HF. The role of genetic drift in shaping modern human cranial evolution: a test using microevolutionary modeling. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2011; 2011:145262. [PMID: 21461369 PMCID: PMC3065169 DOI: 10.4061/2011/145262] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 01/03/2011] [Accepted: 01/14/2011] [Indexed: 11/20/2022]
Abstract
The means by which various microevolutionary processes have acted in the past to produce patterns of cranial variation that characterize modern humans is not thoroughly understood. Applying a microevolutionary framework, within- and among-population variance/covariance (V/CV) structure was compared for several functional and developmental modules of the skull across a worldwide sample of modern humans. V/CV patterns in the basicranium, temporal bone, and face are proportional within and among groups, which is consistent with a hypothesis of neutral evolution; however, mandibular morphology deviated from this pattern. Degree of intergroup similarity in facial, temporal bone, and mandibular morphology is significantly correlated with geographic distance; however, much of the variance remains unexplained. These findings provide insight into the evolutionary history of modern human cranial variation by identifying signatures of genetic drift, gene flow, and migration and set the stage for inferences regarding selective pressures that early humans encountered since their initial migrations around the world.
Collapse
Affiliation(s)
- Heather F Smith
- Department of Anatomy, Arizona College of Osteopathic Medicine, Midwestern University, 19555 North 59th Avenue, Glendale, AZ 85308, USA
| |
Collapse
|
17
|
The Soliga, an isolated tribe from Southern India: genetic diversity and phylogenetic affinities. J Hum Genet 2011; 56:258-69. [PMID: 21307856 DOI: 10.1038/jhg.2010.173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
India's role in the dispersal of modern humans can be explored by investigating its oldest inhabitants: the tribal people. The Soliga people of the Biligiri Rangana Hills, a tribal community in Southern India, could be among the country's first settlers. This forest-bound, Dravidian speaking group, lives isolated, practicing subsistence-level agriculture under primitive conditions. The aim of this study is to examine the phylogenetic relationships of the Soligas in relation to 29 worldwide, geographically targeted, reference populations. For this purpose, we employed a battery of 15 hypervariable autosomal short tandem repeat loci as markers. The Soliga tribe was found to be remarkably different from other Indian populations including other southern Dravidian-speaking tribes. In contrast, the Soliga people exhibited genetic affinity to two Australian aboriginal populations. This genetic similarity could be attributed to the 'Out of Africa' migratory wave(s) along the southern coast of India that eventually reached Australia. Alternatively, the observed genetic affinity may be explained by more recent migrations from the Indian subcontinent into Australia.
Collapse
|
18
|
Ancient voyaging and Polynesian origins. Am J Hum Genet 2011; 88:239-47. [PMID: 21295281 DOI: 10.1016/j.ajhg.2011.01.009] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 01/13/2011] [Accepted: 01/14/2011] [Indexed: 01/02/2023] Open
Abstract
The "Polynesian motif" defines a lineage of human mtDNA that is restricted to Austronesian-speaking populations and is almost fixed in Polynesians. It is widely thought to support a rapid dispersal of maternal lineages from Taiwan ~4000 years ago (4 ka), but the chronological resolution of existing control-region data is poor, and an East Indonesian origin has also been proposed. By analyzing 157 complete mtDNA genomes, we show that the motif itself most likely originated >6 ka in the vicinity of the Bismarck Archipelago, and its immediate ancestor is >8 ka old and virtually restricted to Near Oceania. This indicates that Polynesian maternal lineages from Island Southeast Asia gained a foothold in Near Oceania much earlier than dispersal from either Taiwan or Indonesia 3-4 ka would predict. However, we find evidence in minor lineages for more recent two-way maternal gene flow between Island Southeast Asia and Near Oceania, likely reflecting movements along a "voyaging corridor" between them, as previously proposed on archaeological grounds. Small-scale mid-Holocene movements from Island Southeast Asia likely transmitted Austronesian languages to the long-established Southeast Asian colonies in the Bismarcks carrying the Polynesian motif, perhaps also providing the impetus for the expansion into Polynesia.
Collapse
|
19
|
Genomic screening by 454 pyrosequencing identifies a new human IGHV gene and sixteen other new IGHV allelic variants. Immunogenetics 2011; 63:259-65. [PMID: 21249354 DOI: 10.1007/s00251-010-0510-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 12/31/2010] [Indexed: 02/02/2023]
Abstract
Complete and accurate knowledge of the genes and allelic variants of the human immunoglobulin gene loci is critical for studies of B cell repertoire development and somatic point mutation, but evidence from studies of VDJ rearrangements suggests that our knowledge of the available immunoglobulin gene repertoire is far from complete. The reported repertoire has changed little over the last 15 years. This is, in part, a consequence of the inefficiencies involved in searching for new members of large, multigenic gene families by cloning and sequencing. The advent of high-throughput sequencing provides a new avenue by which the germline repertoire can be explored. In this report, we describe pyrosequencing studies of the heavy chain IGHV1, IGHV3 and IGHV4 gene subgroups in ten Papua New Guineans. Thousands of 454 reads aligned with complete identity to 51 previously reported functional IGHV genes and allelic variants. A new gene, IGHV3-NL1*01, was identified, which differs from the nearest previously reported gene by 15 nucleotides. Sixteen new IGHV alleles were also identified, 15 of which varied from previously reported functional IGHV genes by between one and four nucleotides, while one sequence appears to be a functional variant of the pseudogene IGHV3-25. BLAST searches suggest that at least six of these new genes are carried within the relatively well-studied populations of North America, Europe or Asia. This study substantially expands the known immunoglobulin gene repertoire and demonstrates that genetic variation of immunoglobulin genes can now be efficiently explored in different human populations using high-throughput pyrosequencing.
Collapse
|
20
|
McEvoy BP, Lind JM, Wang ET, Moyzis RK, Visscher PM, van Holst Pellekaan SM, Wilton AN. Whole-genome genetic diversity in a sample of Australians with deep Aboriginal ancestry. Am J Hum Genet 2010; 87:297-305. [PMID: 20691402 DOI: 10.1016/j.ajhg.2010.07.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 06/30/2010] [Accepted: 07/16/2010] [Indexed: 12/19/2022] Open
Abstract
Australia was probably settled soon after modern humans left Africa, but details of this ancient migration are not well understood. Debate centers on whether the Pleistocene Sahul continent (composed of New Guinea, Australia, and Tasmania) was first settled by a single wave followed by regional divergence into Aboriginal Australian and New Guinean populations (common origin) or whether different parts of the continent were initially populated independently. Australia has been the subject of relatively few DNA studies even though understanding regional variation in genomic structure and diversity will be important if disease-association mapping methods are to be successfully evaluated and applied across populations. We report on a genome-wide investigation of Australian Aboriginal SNP diversity in a sample of participants from the Riverine region. The phylogenetic relationship of these Aboriginal Australians to a range of other global populations demonstrates a deep common origin with Papuan New Guineans and Melanesians, with little evidence of substantial later migration until the very recent arrival of European colonists. The study provides valuable and robust insights into an early and important phase of human colonization of the globe. A broader survey of Australia, including diverse geographic sample populations, will be required to fully appreciate the continent's unique population history and consequent genetic heritage, as well as the importance of both to the understanding of health issues.
Collapse
Affiliation(s)
- Brian P McEvoy
- Queensland Institute of Medical Research, Brisbane, Queensland 4006, Australia.
| | | | | | | | | | | | | |
Collapse
|
21
|
Kivisild T, Villems R, Jorde LB, Bamshad M, Kumar S, Hedrick P, Dowling T, Stoneking M, Parsons TJ, Irwin JA, Awadalla P, Eyre-Walker A, Smith JM. Questioning evidence for recombination in human mitochondrial DNA. Science 2010; 288:1931a. [PMID: 17835098 DOI: 10.1126/science.288.5473.1931a] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
22
|
Abstract
The human history of Oceania is unique in the way that it encompasses both the first out-of-Africa expansion of modern humans to New Guinea and Australia as well as the last regional human occupation of Polynesia. Other anthropological peculiarities of Oceania include features like the extraordinarily rich linguistic diversity especially of New Guinea with about 1,000 often very distinct languages, the independent and early development of agriculture in the highlands of New Guinea about 10,000 years ago, or the long-term isolation of the entire region from the outside world, which lasted as long as until the 1930s for most of the interior of New Guinea. This review will provide an overview on the genetic aspects of human population history of Oceania and how some of the anthropological peculiarities are reflected in human genetic data. Due to current data availability it will mostly focus on insights from sex-specifically inherited mitochondrial DNA and Y-chromosomal DNA, whereas more genome-wide autosomal DNA data are soon expected to add additional details or may correct views obtained from these two, albeit highly complex, genetic loci.
Collapse
Affiliation(s)
- Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
| |
Collapse
|
23
|
Davidson I. The Colonization of Australia and Its Adjacent Islands and the Evolution of Modern Cognition. CURRENT ANTHROPOLOGY 2010. [DOI: 10.1086/650694] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
24
|
|
25
|
Kumar S, Ravuri RR, Koneru P, Urade BP, Sarkar BN, Chandrasekar A, Rao VR. Reconstructing Indian-Australian phylogenetic link. BMC Evol Biol 2009; 9:173. [PMID: 19624810 PMCID: PMC2720955 DOI: 10.1186/1471-2148-9-173] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 07/22/2009] [Indexed: 11/10/2022] Open
Abstract
Background An early dispersal of biologically and behaviorally modern humans from their African origins to Australia, by at least 45 thousand years via southern Asia has been suggested by studies based on morphology, archaeology and genetics. However, mtDNA lineages sampled so far from south Asia, eastern Asia and Australasia show non-overlapping distributions of haplogroups within pan Eurasian M and N macrohaplogroups. Likewise, support from the archaeology is still ambiguous. Results In our completely sequenced 966-mitochondrial genomes from 26 relic tribes of India, we have identified seven genomes, which share two synonymous polymorphisms with the M42 haplogroup, which is specific to Australian Aborigines. Conclusion Our results showing a shared mtDNA lineage between Indians and Australian Aborigines provides direct genetic evidence of an early colonization of Australia through south Asia, following the "southern route".
Collapse
Affiliation(s)
- Satish Kumar
- Anthropological Survey of India, 27 Jawaharlal Nehru Road, Kolkata, India.
| | | | | | | | | | | | | |
Collapse
|
26
|
The evolution and diversity of TNF block haplotypes in European, Asian and Australian Aboriginal populations. Genes Immun 2009; 10:607-15. [DOI: 10.1038/gene.2009.45] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
27
|
Mona S, Grunz KE, Brauer S, Pakendorf B, Castrì L, Sudoyo H, Marzuki S, Barnes RH, Schmidtke J, Stoneking M, Kayser M. Genetic Admixture History of Eastern Indonesia as Revealed by Y-Chromosome and Mitochondrial DNA Analysis. Mol Biol Evol 2009; 26:1865-77. [PMID: 19414523 DOI: 10.1093/molbev/msp097] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Stefano Mona
- Department of Forensic Molecular Biology, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Moodley Y, Linz B, Yamaoka Y, Windsor HM, Breurec S, Wu JY, Maady A, Bernhöft S, Thiberge JM, Phuanukoonnon S, Jobb G, Siba P, Graham DY, Marshall BJ, Achtman M. The peopling of the Pacific from a bacterial perspective. Science 2009; 323:527-30. [PMID: 19164753 DOI: 10.1126/science.1166083] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Two prehistoric migrations peopled the Pacific. One reached New Guinea and Australia, and a second, more recent, migration extended through Melanesia and from there to the Polynesian islands. These migrations were accompanied by two distinct populations of the specific human pathogen Helicobacter pylori, called hpSahul and hspMaori, respectively. hpSahul split from Asian populations of H. pylori 31,000 to 37,000 years ago, in concordance with archaeological history. The hpSahul populations in New Guinea and Australia have diverged sufficiently to indicate that they have remained isolated for the past 23,000 to 32,000 years. The second human expansion from Taiwan 5000 years ago dispersed one of several subgroups of the Austronesian language family along with one of several hspMaori clades into Melanesia and Polynesia, where both language and parasite have continued to diverge.
Collapse
Affiliation(s)
- Yoshan Moodley
- Max-Planck-Institut für Infektionsbiologie, Department of Molecular Biology, Charitéplatz 1, 10117 Berlin, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Bellis C, Cox HC, Dyer TD, Charlesworth JC, Begley KN, Quinlan S, Lea RA, Heath SC, Blangero J, Griffiths LR. Linkage mapping of CVD risk traits in the isolated Norfolk Island population. Hum Genet 2008; 124:543-52. [PMID: 18975005 DOI: 10.1007/s00439-008-0580-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Accepted: 10/21/2008] [Indexed: 01/04/2023]
Abstract
To understand the underlying genetic architecture of cardiovascular disease (CVD) risk traits, we undertook a genome-wide linkage scan to identify CVD quantitative trait loci (QTLs) in 377 individuals from the Norfolk Island population. The central aim of this research focused on the utilization of a genetically and geographically isolated population of individuals from Norfolk Island for the purposes of variance component linkage analysis to identify QTLs involved in CVD risk traits. Substantial evidence supports the involvement of traits such as systolic and diastolic blood pressures, high-density lipoprotein-cholesterol, low-density lipoprotein-cholesterol, body mass index and triglycerides as important risk factors for CVD pathogenesis. In addition to the environmental influences of poor diet, reduced physical activity, increasing age, cigarette smoking and alcohol consumption, many studies have illustrated a strong involvement of genetic components in the CVD phenotype through family and twin studies. We undertook a genome scan using 400 markers spaced approximately 10 cM in 600 individuals from Norfolk Island. Genotype data was analyzed using the variance components methods of SOLAR. Our results gave a peak LOD score of 2.01 localizing to chromosome 1p36 for systolic blood pressure and replicated previously implicated loci for other CVD relevant QTLs.
Collapse
Affiliation(s)
- C Bellis
- Genomics Research Centre, Griffith Institute for Health and Medical Research, Griffith University, Gold Coast PMB 50, GCMC Bundall 9726, Gold Coast, Australia.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Vilar MG, Kaneko A, Hombhanje FW, Tsukahara T, Hwaihwanje I, Lum JK. Reconstructing the origin of the Lapita Cultural Complex: mtDNA analyses of East Sepik Province, PNG. J Hum Genet 2008; 53:698-708. [PMID: 18498001 DOI: 10.1007/s10038-008-0301-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 04/29/2008] [Indexed: 10/22/2022]
Abstract
The colonization of Oceania occurred in two waves. By 32,000 BP, humans had reached New Guinea and settled all intervisible islands east to the Solomon Islands. Around 3,500 BP, a distinct intrusive group from Southeast Asia reached coastal New Guinea, integrated their components with indigenous resources, and gave rise to the Lapita Cultural Complex. Within 2,500 years, Lapita and its descendant cultures colonized the Pacific. To uncover the origin of the Lapita Cultural Complex, we analyzed the hypervariable region I of the mitochondrial deoxyribonucleic acid (mtDNA) in 219 individuals from eight East Sepik Province villages: two villages in each of four environmental zones. Same-zone villages spoke different languages: one Austronesian and three Papuan (Arapesh, Abelam, and Boiken). Our analysis examined whether language or geography better predicted gene flow. In general, language better predicted genetic affinities. Boiken villages across all four zones showed no significant genetic difference (F(ST) P value > 0.05). In contrast, the Austronesian village was significantly different to most other villages (P < 0.05). Only the mountains and coast showed zonal gene flow (P > 0.05). We interpret the data to reflect limited gene flow inland by Austronesians overshadowed by a regional displacement by inland Boiken speakers migrating seaward. These results are consistent with oral histories and ethnographic accounts.
Collapse
Affiliation(s)
- Miguel G Vilar
- Laboratory of Evolutionary Anthropology and Health, Binghamton University, Binghamton, NY, USA. .,Department of Anthropology, Binghamton University, Binghamton, NY, 13902-6000, USA.
| | - Akira Kaneko
- Malaria Research Unit, Unit for Infectious Diseases, Department of Medicine, Karolinska University Hospital, Stockholm, Sweden.,Department of International Affairs and Tropical Medicine, Tokyo's Women's Medical University, Tokyo, Japan
| | - Francis W Hombhanje
- Faculty of Health Sciences, Divine Word University, Madang, Papua New Guinea
| | - Takahiro Tsukahara
- Department of International Affairs and Tropical Medicine, Tokyo's Women's Medical University, Tokyo, Japan
| | | | - J Koji Lum
- Laboratory of Evolutionary Anthropology and Health, Binghamton University, Binghamton, NY, USA.,Department of Anthropology, Binghamton University, Binghamton, NY, 13902-6000, USA.,Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
| |
Collapse
|
31
|
Habgood PJ, Franklin NR. The revolution that didn't arrive: A review of Pleistocene Sahul. J Hum Evol 2008; 55:187-222. [PMID: 18485448 DOI: 10.1016/j.jhevol.2007.11.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Revised: 06/12/2007] [Accepted: 11/15/2007] [Indexed: 10/22/2022]
Abstract
There is a "package" of cultural innovations that are claimed to reflect modern human behaviour. The introduction of the "package" has been associated with the Middle-to-Upper Palaeolithic transition and the appearance in Europe of modern humans. It has been proposed that modern humans spread from Africa with the "package" and colonised not only Europe but also southern Asia and Australia (McBrearty and Brooks, 2000; Mellars, 2006a). In order to evaluate this proposal, we explore the late Pleistocene archaeological record of Sahul, the combined landmass of Australia and Papua New Guinea, for indications of these cultural innovations at the earliest sites. It was found that following initial occupation of the continent by anatomically and behaviourally modern humans, the components were gradually assembled over a 30,000-year period. We discount the idea that the "package" was lost en route to Sahul and assess the possibility that the "package" was not integrated within the material culture of the initial colonising groups because they may not have been part of a rapid colonisation process from Africa. As the cultural innovations appear at different times and locations within Sahul, the proposed "package" of archaeologically visible traits cannot be used to establish modern human behaviour. Whilst the potential causal role of increasing population densities/pressure in the appearance of the "package" of modern human behaviour in the archaeological record is acknowledged, it is not seen as the sole explanation because the individual components of the "package" appear at sites that are widely separated in space and time.
Collapse
Affiliation(s)
- Phillip J Habgood
- School of Social Science, University of Queensland, Brisbane QLD 4072, Australia
| | | |
Collapse
|
32
|
Ricaut FX, Thomas T, Arganini C, Staughton J, Leavesley M, Bellatti M, Foley R, Mirazon Lahr M. Mitochondrial DNA variation in Karkar Islanders. Ann Hum Genet 2008; 72:349-67. [PMID: 18307577 DOI: 10.1111/j.1469-1809.2008.00430.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We analyzed 375 base pairs (bp) of the first hypervariable region (HVS-I) of the mitochondrial DNA (mtDNA) control region and intergenic COII/tRNALys 9-bp deletion from 47 Karkar Islanders (north coast of Papua New Guinea) belonging to the Waskia Papuan language group. To address questions concerning the origin and evolution of this population we compared the Karkar mtDNA haplotypes and haplogroups to those of neighbouring East Asians and Oceanic populations. The results of the phylogeographic analysis show grouping in three different clusters of the Karkar Islander mtDNA lineages: one group of lineages derives from the first Pleistocene settlers of New Guinea-Island Melanesia, a second set derives from more recent arrivals of Austronesian speaking populations, and the third contains lineages specific to the Karkar Islanders, but still rooted to Austronesian and New Guinea-Island Melanesia populations. Our results suggest (i) the absence of a strong association between language and mtDNA variation and, (ii) reveal that the mtDNA haplogroups F1a1, M7b1 and E1a, which probably originated in Island Southeast Asia and may be considered signatures of Austronesian population movements, are preserved in the Karkar Islanders but absent in other New Guinea-Island Melanesian populations. These findings indicate that the Karkar Papuan speakers retained a certain degree of their own genetic uniqueness and a high genetic diversity. We present a hypothesis based on archaeological, linguistic and environmental datasets to argue for a succession of (partial) depopulation and repopulation and expansion events, under conditions of structured interaction, which may explain the variability expressed in the Karkar mtDNA.
Collapse
Affiliation(s)
- F X Ricaut
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, CB2 1QH, United Kingdom.
| | | | | | | | | | | | | | | |
Collapse
|
33
|
Alfonso-Sánchez MA, Pérez-Miranda AM, Herrera RJ. Autosomal microsatellite variability of the Arrernte people of Australia. Am J Hum Biol 2007; 20:91-9. [PMID: 17957762 DOI: 10.1002/ajhb.20685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The genomic diversity of the Arrernte people of Australia or caterpillar people was investigated utilizing 13 autosomal short tandem repeat (STR) markers. Significant departures from Hardy-Weinberg equilibrium were detected at the D18S51, TPOX and CSF1PO loci, which persisted after applying the Bonferroni correction. Gene diversity values oscillate between 0.6302 (CSF1PO) and 0.8731 (D21S11). Observed heterozygosity (Ho) ranges from 0.2632 (D18S51) to 0.8333 (vWA) and is lower than the expected heterozygosity (He) for 12 of the 13 loci analyzed. The genetic relationships of the Arrernte with Middle Eastern, East Asian, South Asian and Indian populations were analyzed by distance-based methods, including Neighbor-Joining trees and nonmetric multidimensional scaling. In addition, the genetic contribution of the populations included in the analysis to the Arrernte gene pool was estimated utilizing weighted least square coefficients. Although the Arrernte population exhibits a remarkable level of genetic differentiation, results of the phylogeographic analyses based on autosomal microsatellite data suggest a certain degree of genetic relatedness between the Arrernte tribe of Australia and populations from the Indian subcontinent. In contrast, the STR diversity analyses failed to detect substantial East Asian contribution to the genetic background of the Arrernte group.
Collapse
Affiliation(s)
- M A Alfonso-Sánchez
- Molecular Biology and Human Diversity Laboratory, Department of Biological Sciences, Florida International University, Miami, Florida 33199, USA
| | | | | |
Collapse
|
34
|
Walsh SJ, Mitchell RJ, Watson N, Buckleton JS. A comprehensive analysis of microsatellite diversity in Aboriginal Australians. J Hum Genet 2007; 52:712-728. [PMID: 17628738 DOI: 10.1007/s10038-007-0172-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 06/18/2007] [Indexed: 10/23/2022]
Abstract
Indigenous Australians have a unique evolutionary history that has resulted in a complex system of inter and intra-tribal relationships. While a number of studies have examined the population genetics of indigenous Australians, most have used a single sample to illuminate details of the global dispersal of modern humans and few studies have focussed on the population genetic features of the widely dispersed communities of the indigenous population. In this study we examine the largest Aboriginal Australian sample yet analysed (N = 8,868) at fifteen hypervariable autosomal microsatellite loci. A comprehensive analysis of differentiation indicates different levels of heterogeneity among indigenous peoples from traditional regions of Aboriginal Australia. The most genetically differentiated populations inhabit the North of the country, in particular the Tiwi of Melville and Bathurst islands, Arnhem Land (itself divided into West and East Arnhem), and Fitzmaurice regions. These tribal groups are most differentiated from other Aboriginal Australian tribes, especially those of the Central Desert regions, and also show marked heterogeneity from one another. These genetic findings are supportive of observations of body measurements, skin colour, and dermatoglyphic features which also vary substantially between tribes of the North (e.g. Arnhem Land) and Central Australian regions and, more specifically, between the Tiwi and West and East Arnhem tribes. This study provides the most comprehensive survey of the population genetics of Aboriginal Australia.
Collapse
Affiliation(s)
- Simon J Walsh
- Forensic and Technical Services, Australian Federal Police, GPO Box 401, Canberra, ACT, 2601, Australia.
- Centre for Forensic Science, UTS, PO Box 123, Broadway, NSW, 2007, Australia.
| | - R John Mitchell
- Department of Human Genetics, LaTrobe University, Melbourne, Australia
| | | | | |
Collapse
|
35
|
Hudjashov G, Kivisild T, Underhill PA, Endicott P, Sanchez JJ, Lin AA, Shen P, Oefner P, Renfrew C, Villems R, Forster P. Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. Proc Natl Acad Sci U S A 2007; 104:8726-30. [PMID: 17496137 PMCID: PMC1885570 DOI: 10.1073/pnas.0702928104] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Published and new samples of Aboriginal Australians and Melanesians were analyzed for mtDNA (n=172) and Y variation (n=522), and the resulting profiles were compared with the branches known so far within the global mtDNA and the Y chromosome tree. (i) All Australian lineages are confirmed to fall within the mitochondrial founder branches M and N and the Y chromosomal founders C and F, which are associated with the exodus of modern humans from Africa approximately 50-70,000 years ago. The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event approximately 50,000 years ago, in agreement with current archaeological evidence. (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged approximately 8,000 years ago, thus calling into question that certain significant developments in later Australian prehistory (the emergence of a backed-blade lithic industry, and the linguistic dichotomy) were externally motivated.
Collapse
Affiliation(s)
- Georgi Hudjashov
- Estonian Biocentre and Tartu University, Department of Evolutionary Biology, Riia 23, 51010 Tartu, Estonia
| | - Toomas Kivisild
- Estonian Biocentre and Tartu University, Department of Evolutionary Biology, Riia 23, 51010 Tartu, Estonia
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge CB2 1QH, United Kingdom
- To whom correspondence may be addressed. E-mail: or
| | - Peter A. Underhill
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120
| | - Phillip Endicott
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
| | - Juan J. Sanchez
- National Institute of Toxicology and Forensic Science, Canary Islands Delegation, Campus de Ciencias de la Salud, 38320 La Laguna, Tenerife, Spain
| | - Alice A. Lin
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120
| | - Peidong Shen
- Stanford Genome Technology Center, Palo Alto, CA 94304
| | - Peter Oefner
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany
| | - Colin Renfrew
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, United Kingdom; and
- To whom correspondence may be addressed. E-mail: or
| | - Richard Villems
- Estonian Biocentre and Tartu University, Department of Evolutionary Biology, Riia 23, 51010 Tartu, Estonia
| | - Peter Forster
- Department of Forensic Science and Chemistry, Faculty of Science and Technology, Anglia Ruskin University, East Road, Cambridge CB1 1PT, United Kingdom
| |
Collapse
|
36
|
Friedlaender JS, Friedlaender FR, Hodgson JA, Stoltz M, Koki G, Horvat G, Zhadanov S, Schurr TG, Merriwether DA. Melanesian mtDNA complexity. PLoS One 2007; 2:e248. [PMID: 17327912 PMCID: PMC1803017 DOI: 10.1371/journal.pone.0000248] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2006] [Accepted: 02/05/2007] [Indexed: 12/02/2022] Open
Abstract
Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA) sequences from hypervariable regions 1 and 2 (HVR1 and HVR2) from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups). Persistent differences between shore and inland groups in effective population sizes and marital migration rates probably cause these differences. We also add 16 whole sequences to the Melanesian mtDNA phylogenies. We identify the likely origins of a number of the haplogroups and ancient branches in specific islands, point to some ancient mtDNA connections between Near Oceania and Australia, and show additional Holocene connections between Island Southeast Asia/Taiwan and Island Melanesia with branches of haplogroup E. Coalescence estimates based on synonymous transitions in the coding region suggest an initial settlement and expansion in the region at approximately 30-50,000 years before present (YBP), and a second important expansion from Island Southeast Asia/Taiwan during the interval approximately 3,500-8,000 YBP. However, there are some important variance components in molecular dating that have been overlooked, and the specific nature of ancestral (maternal) Austronesian influence in this region remains unresolved.
Collapse
Affiliation(s)
- Jonathan S Friedlaender
- Anthropology Department, Temple University, Philadelphia, Pennsylvania, United States of America.
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Alvarez-Iglesias V, Jaime JC, Carracedo A, Salas A. Coding region mitochondrial DNA SNPs: targeting East Asian and Native American haplogroups. Forensic Sci Int Genet 2006; 1:44-55. [PMID: 19083727 DOI: 10.1016/j.fsigen.2006.09.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 09/15/2006] [Accepted: 09/17/2006] [Indexed: 11/30/2022]
Abstract
We have developed a single PCR multiplex SNaPshot reaction that consists of 32 coding region SNPs that allows (i) increasing the discrimination power of the mitochondrial DNA (mtDNA) typing in forensic casework, and (ii) haplogroup assignments of mtDNA profiles in both human population studies (e.g. anthropological) and medical research. The selected SNPs target the East Asian phylogeny, including its Native American derived branches. We have validated this multiplex assay by genotyping a sample of East Asians (Taiwanese) and Native Americans (Argentineans). In addition to the coding SNP typing, we have sequenced the complete control region for the same samples. The genotyping results (control region plus SNaPshot profiles) are in good agreement with previous human population genetic studies (based on e.g. complete sequencing) and the known mtDNA phylogeny. We observe that the SNaPshot method is reliable, rapid, and cost effective in comparison with other techniques of multiplex SNP genotyping. We discuss the advantages of our SNP genotyping selection with respect to previous attempts, and we highlight the importance of using the known mtDNA phylogeny as a framework for SNP profile interpretation and as a tool to minimize genotyping errors.
Collapse
Affiliation(s)
- V Alvarez-Iglesias
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Galicia, Spain
| | | | | | | |
Collapse
|
38
|
van Holst Pellekaan SM, Ingman M, Roberts-Thomson J, Harding RM. Mitochondrial genomics identifies major haplogroups in Aboriginal Australians. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2006; 131:282-94. [PMID: 16596590 DOI: 10.1002/ajpa.20426] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We classified diversity in eight new complete mitochondrial genome sequences and 41 partial sequences from living Aboriginal Australians into five haplogroups. Haplogroup AuB belongs to global lineage M, and AuA, AuC, AuD, and AuE to N. Within N, we recognize subdivisions, assigning AuA to haplogroup S, AuD to haplogroup O, AuC to P4, and AuE to P8. On available evidence, (S)AuA and (M)AuB are widespread in Australia. (P4)AuC is found in the Riverine region of western New South Wales, and was identified by others in northern Australia. (O)AuD and (P8)AuE were clearly identified only from central Australia. Our eight Australian full mt genome sequences, combined with 20 others (Ingman and Gyllensten 2003 Genome Res. 13:1600-1606) and compared with full mt genome sequences from regions to the north that include Papua New Guinea, Malaya, and Andaman and Nicobar Islands, show that ancestral connections between regions are deep and limited to clustering at the level of the N and M macrohaplogroups. The Australian-specific distribution of the five haplogroups identified indicates genetic isolation over a long period. Ancestral connections within Australia are deeper than those reflected by known linguistic or culturally based affinities. Applying a coalescence analysis to a gene tree for the coding regions of the eight genomic sequences, we made estimates of time depth that support a continuity of presence for the descendants of a founding population already established by 40,000 years ago.
Collapse
Affiliation(s)
- Sheila M van Holst Pellekaan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales 2052, Australia.
| | | | | | | |
Collapse
|
39
|
Boldt ABW, Culpi L, Tsuneto LT, de Souza IR, Kun JFJ, Petzl-Erler ML. Diversity of the MBL2 gene in various Brazilian populations and the case of selection at the mannose-binding lectin locus. Hum Immunol 2006; 67:722-34. [PMID: 17002903 DOI: 10.1016/j.humimm.2006.05.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Accepted: 05/10/2006] [Indexed: 11/15/2022]
Abstract
The mannose binding lectin (MBL2) polymorphism is responsible for a common immunodeficiency in the human species. There were suggestions that the MBL2 polymorphism has been under balancing selection, based on the high global frequency of alleles generating MBL deficiency and on the worldwide distribution of diseases negatively associated with them. To describe the distribution of MBL2 allelic haplotypes in Brazilian populations and to discuss the evolution of this polymorphism, we analyzed six South Brazilian populations (152 Guarani Amerindian, 239 Kaingang Amerindian, 107 admixed, Brazilian 32 Afro-Brazilian, 202 Euro-Brazilian and 16 Oriental-Brazilian). Eight haplotypes were observed: MBL2*HYPA, LYQA, LYPA, LXPA, LYPB, LYQC, HYPD, and LYPD. In addition, through sequencing of the promoter and exon 1 from Amerindian and Oriental individuals, three new single-nucleotide polymorphisms (SNPs) were found in the MBL2 promoter region in the Kaingang. Analysis of the sequencing data by neutrality tests (Tajima's D and Fu and Li's D* and F*) revealed no deviation from selective neutrality equilibrium in the Guarani and Kaingang. Significant Fay and Wu's H results are explained by the recent gene flow in these populations. Contrarily to previous thoughts, stochastic evolutionary factors seem therefore to have had a predominant role in shaping the MBL2 polymorphism, at least in the Amerindians.
Collapse
Affiliation(s)
- A B W Boldt
- Kun Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | | | | | | | | | | |
Collapse
|
40
|
Souto L, Rocha A, Pires A, Ferreira E, Kayser M, Amorim A, Côrte-Real F, Vieira D. Mitochondrial DNA variability in populations from East Timor (Timor Leste). ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.ics.2005.11.060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
41
|
|
42
|
|
43
|
Excavating the mitochondrial genome identifies major haplogroups in Aboriginal Australians. ACTA ACUST UNITED AC 2006. [DOI: 10.3828/bfarm.2006.1.3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
44
|
Ricaut FX, Bellatti M, Lahr MM. Ancient mitochondrial DNA from Malaysian hair samples: Some indications of Southeast Asian population movements. Am J Hum Biol 2006; 18:654-67. [PMID: 16917897 DOI: 10.1002/ajhb.20535] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The late Pleistocene and early Holocene population history of Southeast Asia is not well-known. Our study provides new data on mitochondrial DNA (mtDNA) lineages of the aboriginal inhabitants of the Malay Peninsula, and through an extensive comparison to the known mtDNA diversity in Southeast and East Asia, provides some new insights into the origins and historical geography of certain mtDNA lineages in the region. We extracted DNA from hair samples (dating back 100 years) preserved in the Duckworth Collection and belonging to two Peninsular Malaysian individuals identified as "Negrito." Ancient DNA was analyzed by sequencing hypervariable region I (HVS-I) of the mtDNA control region and the mtDNA region V length polymorphism. The results show that the maternal lineages of these individuals belong to a recently defined haplogroup B sub-branch called B4c2. A comparison of mitochondrial haplotypes and haplogroups with those of 10,349 East Asian individuals indicates their very restricted geographical distribution (southwestern China, Southeast Asia Peninsula, and Indonesia). Recalculation of the B4c2 age across all of East Asia ( approximately 13,000 years) and in different subregions/populations suggests its rapid diffusion in Southeast Asia between the end of the Last Glacial Maximum and the Neolithic expansion of the Holocene.
Collapse
Affiliation(s)
- François-X Ricaut
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge CB2 1QH, United Kingdom.
| | | | | |
Collapse
|
45
|
Green H, Curnoe D. Mandibular fossa of fossil Australians. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2005; 56:233-47. [PMID: 16325487 DOI: 10.1016/j.jchb.2005.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2004] [Accepted: 06/10/2005] [Indexed: 11/30/2022]
Abstract
Many questions about the skeletal adaptations and morphology of hunter-gatherers on the Australian continent remain unanswered. One anatomical region receiving little research in Australian fossils to date is the mandibular fossa. Here we report a study of three size dimensions, three shape indices and three morphological (non-metric) features of the mandibular fossa in 11 fossil Australians comparing them with modern Australo-Melanesian samples. We find broad similarities in past and modern populations in this region. Early and modern Australians and modern Papua New Guineans have elongate, broad and shallow fossae. All three populations show similarity in articular tubercle size, but postglenoid tubercle and entoglenoid process sizes show unexpected affinities. We also test for the possible presence of temporal trends in mandibular fossa size among fossil Australians. Our analyses indicate that none are present.
Collapse
Affiliation(s)
- Hayley Green
- Department of Anatomy, University of New South Wales, Sydney NSW 2052, Australia.
| | | |
Collapse
|
46
|
McElreavey K, Quintana-Murci L. A population genetics perspective of the Indus Valley through uniparentally-inherited markers. Ann Hum Biol 2005; 32:154-62. [PMID: 16096211 DOI: 10.1080/03014460500076223] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Analysis of mtDNA and Y-chromosome variation in the Indo-Gangetic plains shows that it was a region where genetic components of different geographical origins (from west, east and south) met. The genetic architecture of the populations now living in the area comprise genetic components dating back to different time-periods during the Palaeolithic and the Neolithic. mtDNA data analysis has demonstrated a number of deep-rooting lineages of Pleistocene origin that may be witness to the arrival of the first settlers of South and Southwest Asia after humans left Africa around 60,000 YBP. In addition, comparisons of Y-chromosome and mtDNA data have indicated a number of recent and sexually asymmetrical demographic events, such as the migrations of the Parsis from Iran to India, and the maternal traces of the East African slave trade.
Collapse
Affiliation(s)
- K McElreavey
- Reproduction, Fertility and Populations, Institut Pasteur, Paris, France.
| | | |
Collapse
|
47
|
James H, Petraglia M. Modern Human Origins and the Evolution of Behavior in the Later Pleistocene Record of South Asia. CURRENT ANTHROPOLOGY 2005. [DOI: 10.1086/444365] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
48
|
Merriwether DA, Hodgson JA, Friedlaender FR, Allaby R, Cerchio S, Koki G, Friedlaender JS. Ancient mitochondrial M haplogroups identified in the Southwest Pacific. Proc Natl Acad Sci U S A 2005; 102:13034-9. [PMID: 16150714 PMCID: PMC1201611 DOI: 10.1073/pnas.0506195102] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Based on whole mtDNA sequencing of 14 samples from Northern Island Melanesia, we characterize three formerly unresolved branches of macrohaplogroup M that we call haplogroups M27, M28, and M29. Our 1,399 mtDNA control region sequences and a literature search indicate these haplogroups have extremely limited geographical distributions. Their coding region variation suggests diversification times older than the estimated date for the initial settlement of Northern Island Melanesia. This finding indicates that they were among the earliest mtDNA variants to appear in these islands or in the ancient continent of Sahul. These haplogroups from Northern Island Melanesia extend the existing schema for macrohaplogroup M, with many independent branches distributed across Asia, East Africa, Australia, and Near Oceania.
Collapse
Affiliation(s)
- D Andrew Merriwether
- Department of Anthropology, Binghamton University, Binghamton, NY 13902-6000, USA.
| | | | | | | | | | | | | |
Collapse
|
49
|
Abstract
Several unique properties of human mitochondrial DNA (mtDNA), including its high copy number, maternal inheritance, lack of recombination, and high mutation rate, have made it the molecule of choice for studies of human population history and evolution. Here we review the current state of knowledge concerning these properties, how mtDNA variation is studied, what we have learned, and what the future likely holds. We conclude that increasingly, mtDNA studies are (and should be) supplemented with analyses of the Y-chromosome and other nuclear DNA variation. Some serious issues need to be addressed concerning nuclear inserts, database quality, and the possible influence of selection on mtDNA variation. Nonetheless, mtDNA studies will continue to play an important role in such areas as examining socio-cultural influences on human genetic variation, ancient DNA, certain forensic DNA applications, and in tracing personal genetic history.
Collapse
Affiliation(s)
- Brigitte Pakendorf
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
| | | |
Collapse
|
50
|
Inferring the population structure and demography of Drosophila ananassae from multilocus data. Genetics 2005; 168:1975-85. [PMID: 15611168 DOI: 10.1534/genetics.104.031567] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inferring the origin, population structure, and demographic history of a species is a major objective of population genetics. Although many organisms have been analyzed, the genetic structures of subdivided populations are not well understood. Here we analyze Drosophila ananassae, a highly substructured, cosmopolitan, and human-commensal species distributed in the tropical, subtropical, and mildly temperate regions of the world. We adopt a multilocus approach (with 10 neutral loci) using 16 population samples covering almost the entire species range (Asia, Australia, and America). Analyzed with our recently developed Bayesian method, 5 populations in Southeast Asia are found to be central, while the other 11 are peripheral. These 5 central populations were sampled from localities that belonged to a single landmass ("Sundaland") during the late Pleistocene ( approximately 18,000 years ago), when sea level was approximately 120 m below the present level. The inferred migration routes of D. ananassae out of Sundaland seem to parallel those of humans in this region. Strong evidence for a population size expansion is seen particularly in the ancestral populations.
Collapse
|