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Miyagawa S, DeSalle R, Nóbrega VA, Nitschke R, Okumura M, Tattersall I. Linguistic capacity was present in the Homo sapiens population 135 thousand years ago. Front Psychol 2025; 16:1503900. [PMID: 40134728 PMCID: PMC11933122 DOI: 10.3389/fpsyg.2025.1503900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 02/06/2025] [Indexed: 03/27/2025] Open
Abstract
Recent genome-level studies on the divergence of early Homo sapiens, based on single nucleotide polymorphisms, suggest that the initial population division within H. sapiens from the original stem occurred approximately 135 thousand years ago. Given that this and all subsequent divisions led to populations with full linguistic capacity, it is reasonable to assume that the potential for language must have been present at the latest by around 135 thousand years ago, before the first division occurred. Had linguistic capacity developed later, we would expect to find some modern human populations without language, or with some fundamentally different mode of communication. Neither is the case. While current evidence does not tell us exactly when language itself appeared, the genomic studies do allow a fairly accurate estimate of the time by which linguistic capacity must have been present in the modern human lineage. Based on the lower boundary of 135 thousand years ago for language, we propose that language may have triggered the widespread appearance of modern human behavior approximately 100 thousand years ago.
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Affiliation(s)
- Shigeru Miyagawa
- Department of Linguistics and Philosophy, Massachusetts Institute of Technology, Cambridge, MA, United States
- Biosciences Institute, University of São Paulo, São Paulo, Brazil
- Research Center for Super-Smart Society, Seikei University, Tokyo, Japan
| | - Rob DeSalle
- American Museum of Natural History, Institute for Comparative Genomics, New York, NY, United States
| | | | - Remo Nitschke
- Institute for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich, Switzerland
- Department of Linguistics, University of Arizona, Tucson, AZ, United States
| | - Mercedes Okumura
- Laboratory of Human Evolutionary Studies, Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Ian Tattersall
- American Museum of Natural History, Division of Anthropology, New York, NY, United States
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Kulaphisit M, Kampuansai J, Leecharoenkiat K, Wathikthinnakon M, Kangwanpong D, Munkongdee T, Svasti S, Fucharoen S, Smith DR, Lithanatudom P. A comprehensive ethnic-based analysis of alpha thalassaemia allelle frequency in northern Thailand. Sci Rep 2017; 7:4690. [PMID: 28680061 PMCID: PMC5498591 DOI: 10.1038/s41598-017-04957-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/22/2017] [Indexed: 12/25/2022] Open
Abstract
Alpha (α)-thalassaemia is one of the most prevalent hereditary blood disorders, commonly affecting Southeast Asian people, with the highest incidence (30–40%) being seen in northern Thailand. However, this high incidence was estimated without consideration of the variations between ethnic populations and the geographical location of the populations. To address this issue, a total of 688 samples from 13 different northern Thai ethnic groups (30 villages) categorized into three linguistic groups were genotyped for deletional alpha-thalassaemia (-α3.7, -α4.2, --SEA and --THAI) and/or non-deletional alpha-thalassaemia (αCS and αPS) via multiplex gap-PCR and dot-blot hybridization, respectively. Alpha+(-α3.7, -α4.2, αCS and αPS) and alpha°-thalassaemia (--SEA and --THAI) allele frequencies (with 95% Confidence Interval) were the highest in the Sino-Tibetan group [0.13 (0.08–0.18)] and the Tai-Kadai group [0.03 (0.02–0.05)], respectively. With regards to ethnicity, the varying allele frequency of α+ and α°-thalassaemia amongst a variety of ethnic groups was observed. The highest α+-thalassaemia allele frequency was found in the Paluang [0.21 (0.10–0.37)] while α°-thalassaemia allele frequency was the highest in the Yuan [0.04 (0.01–0.10)]. These detailed results of alpha thalassaemia allele frequency and genetic diversity amongst the northern Thai ethnic groups demonstrate the need for ethnicity based thalassaemia prevention programs.
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Affiliation(s)
- Mattapong Kulaphisit
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50300, Thailand
| | - Jatupol Kampuansai
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50300, Thailand
| | - Kamonlak Leecharoenkiat
- Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Methi Wathikthinnakon
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50300, Thailand
| | - Daoroong Kangwanpong
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50300, Thailand
| | - Thongperm Munkongdee
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakornpathom, 73170, Thailand
| | - Saovaros Svasti
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakornpathom, 73170, Thailand
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakornpathom, 73170, Thailand
| | - Duncan R Smith
- Molecular Pathology Laboratory, Institute of Molecular Biosciences, Mahidol University, Nakornpathom, 73170, Thailand
| | - Pathrapol Lithanatudom
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50300, Thailand.
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Kampuansai J, Völgyi A, Kutanan W, Kangwanpong D, Pamjav H. Autosomal STR variations reveal genetic heterogeneity in the Mon-Khmer speaking group of Northern Thailand. Forensic Sci Int Genet 2016; 27:92-99. [PMID: 28012377 DOI: 10.1016/j.fsigen.2016.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 11/05/2016] [Accepted: 11/28/2016] [Indexed: 12/01/2022]
Abstract
Since prehistoric times, Mon-Khmer speaking people have been recognized as indigenous ethnic groups living in northern Thailand. After the period of Tai colonization in the thirteenth century CE, the Mon-Khmer inhabitants were fragmented; some were expelled to rural areas while some were integrated into the mainstream of Tai society. Autosomal STR variations revealed that the present-day Mon-Khmer people could be genetically divided into two clusters. This finding appears to be consistent with the level of historical contact with the Tai majority ethnic groups. The cluster consisting of the Khamu, Lua, Paluang and Htin people, indicate that they have lived in remote areas and have had little historical contact with the Tai people. In this way, they appeared to have maintained aspects of their Mon-Khmer ancestral genetic bloodline but have genetically diverged from the Tai people. The cluster comprised of the Mon and Lawa people had an exclusively close relationship with the Tai people during the establishment of the prosperous Lan Na Kingdom. A fraction of the Tai genetic component investigated among the Mon people and some Lawa populations reflected the evidence of genetic admixture. However, some Lawa people, who have lived in the mountainous area of Mae Hong Son Province have exhibited a unique gene pool, which might have been shaped by the founder effect that occurred during their historical fragmentation. The rise of the genetic assimilation of the hill-tribe Karen people into the Mon-Khmer and the Tai gene pools indicated that different languages, cultures, and geographical distances have lost their power as barriers of inter-ethnic marriages in the present day.
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Affiliation(s)
- Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Antónia Völgyi
- DNA Laboratory, Institute of Forensic Medicine, Network of Foernsic Science Institutes, Ministry of Justice, Budapest, Hungary
| | - Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Daoroong Kangwanpong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Horolma Pamjav
- DNA Laboratory, Institute of Forensic Medicine, Network of Foernsic Science Institutes, Ministry of Justice, Budapest, Hungary.
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Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai-Kadai languages. Hum Genet 2016; 136:85-98. [PMID: 27837350 PMCID: PMC5214972 DOI: 10.1007/s00439-016-1742-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/27/2016] [Indexed: 11/30/2022]
Abstract
The Tai–Kadai (TK) language family is thought to have originated in southern China and spread to Thailand and Laos, but it is not clear if TK languages spread by demic diffusion (i.e., a migration of people from southern China) or by cultural diffusion, with native Austroasiatic (AA) speakers switching to TK languages. To address this and other questions, we obtained 1234 complete mtDNA genome sequences from 51 TK and AA groups from Thailand and Laos. We find high genetic heterogeneity across the region, with 212 different haplogroups, and significant genetic differentiation among different samples from the same ethnolinguistic group. TK groups are more genetically homogeneous than AA groups, with the latter exhibiting more ancient/basal mtDNA lineages, and showing more drift effects. Modeling of demic diffusion, cultural diffusion, and admixture scenarios consistently supports the spread of TK languages by demic diffusion.
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Kampuansai J, Kutanan W, Tassi F, Kaewgahya M, Ghirotto S, Kangwanpong D. Effect of migration patterns on maternal genetic structure: a case of Tai-Kadai migration from China to Thailand. J Hum Genet 2016; 62:223-228. [PMID: 27604557 DOI: 10.1038/jhg.2016.112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/25/2016] [Accepted: 07/30/2016] [Indexed: 11/09/2022]
Abstract
The migration of the Tai-Kadai speaking people from southern China to northern Thailand over the past hundreds of years has revealed numerous patterns that have likely been influenced by routes, purposes and periods of time. To study the effects of different migration patterns on Tai-Kadai maternal genetic structure, mitochondrial DNA hypervariable region I sequences from the Yong and the Lue people having well-documented histories in northern Thailand were analyzed. Although the Yong and Lue people were historically close relatives who shared Xishuangbanna Dai ancestors, significant genetic differences have been observed among them. The Yong people who have been known to practice mass migration have exhibited a closer genetic affinity to their Dai ancestors than have the Lue people. Genetic heterogeneity and a sudden reduced effective population size within the Lue group is likely a direct result of the circumstances of the founder effect.
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Affiliation(s)
- Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Francesca Tassi
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Massupa Kaewgahya
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Silvia Ghirotto
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Daoroong Kangwanpong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
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Di Lorenzo P, Lancioni H, Ceccobelli S, Curcio L, Panella F, Lasagna E. Uniparental genetic systems: a male and a female perspective in the domestic cattle origin and evolution. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Lithanatudom P, Khampan P, Smith DR, Svasti S, Fucharoen S, Kangwanpong D, Kampuansai J. The prevalence of alpha-thalassemia amongst Tai and Mon-Khmer ethnic groups residing in northern Thailand: A population-based study. ACTA ACUST UNITED AC 2016; 21:480-5. [PMID: 27077764 DOI: 10.1080/10245332.2016.1148374] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Northern Thailand is one of the highest α-thalassemia incidence areas where 30-40% of inhabitants have been reported to carry aberrant α-globin genes. However, all previous α-thalassemia prevalence surveys in northern Thailand have been undertaken without consideration of ethnicity. Here we report the prevalence of α-thalassemia genes in 4 Tai (Yong, Yuan, Khuen, Lue) and 4 Mon-Khmer speaking populations (Blang, Mon, Paluang, Lawa). METHODS DNA extracted from 141 individuals was genotyped for 4 α-thalassemia deletional types (--(SEA), --(THAI), -α(3.7), -α(4.2)) using MultiplexGap-PCR analysis and 2 non-deletional types (Hb CS, Hb Pakse) using dot-blot hybridization technique. RESULTS AND DISCUSSION A total of 33 α-thalassemia carrying individuals (23.4%) were detected of which 32 were heterozygotes and one was a homozygote. The most common α-thalassemia detected were -α(3.7) (17.7%) and --(SEA) (3.5%), while Hb CS was detected in 2.1% of cases. No occurrence of --(THAI), -α(4.2) and Hb Pakse was observed. The prevalence of α-thalassemia carriers varied between the different ethnic groups, with the Yuan having the highest prevalence of α-thalassemia carriers (50%) while the Lawa had the lowest prevalence (0%). The Paluang had a high prevalence (42%) of a single deletion type (-α(3.7)) possibly related to the endogamous marriage traditions of this ethnic group. CONCLUSION The extreme variation of α-thalassemia prevalence among the different ethnic groups highlights the significantly different genetic backgrounds found in these peoples, as consequences of dissimilar cultures. Our study suggests that ethnicity must be considered in any of the disease-causing allele prevalence surveys in this region.
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Affiliation(s)
- Pathrapol Lithanatudom
- a Department of Biology, Faculty of Science , Chiang Mai University , Chiang Mai 50202 , Thailand
| | - Pornnapa Khampan
- b Thalassemia Research Center, Institute of Molecular Biosciences , Mahidol University , Salaya , Nakhonpathom 73170 , Thailand
| | - Duncan R Smith
- c Molecular Pathology Laboratory, Institute of Molecular Biosciences , Mahidol University , Salaya , Nakhonpathom 73170 , Thailand
| | - Saovaros Svasti
- b Thalassemia Research Center, Institute of Molecular Biosciences , Mahidol University , Salaya , Nakhonpathom 73170 , Thailand
| | - Suthat Fucharoen
- b Thalassemia Research Center, Institute of Molecular Biosciences , Mahidol University , Salaya , Nakhonpathom 73170 , Thailand
| | - Daoroong Kangwanpong
- a Department of Biology, Faculty of Science , Chiang Mai University , Chiang Mai 50202 , Thailand
| | - Jatupol Kampuansai
- a Department of Biology, Faculty of Science , Chiang Mai University , Chiang Mai 50202 , Thailand
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Landouré G, Samassékou O, Traoré M, Meilleur KG, Guinto CO, Burnett BG, Sumner CJ, Fischbeck KH. Genetics and genomic medicine in Mali: challenges and future perspectives. Mol Genet Genomic Med 2016; 4:126-34. [PMID: 27066513 PMCID: PMC4799869 DOI: 10.1002/mgg3.212] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 02/11/2016] [Accepted: 02/11/2016] [Indexed: 11/14/2022] Open
Abstract
Genetics and genomic medicine in Mali: challenges and future perspectives.
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Affiliation(s)
- Guida Landouré
- Service de NeurologieCentre Hospitalier Universitaire du Point "G"BamakoMali; Neurogenetics BranchNational Institute of Neurological Disorders and Stroke (NINDS)National Institutes of Health (NIH)BethesdaMaryland
| | - Oumar Samassékou
- Manitoba Institute of cell BiologyUniversity of ManibotaWinnipegCanada; Service de cytogenetique et de biologie reproductiveInstitut National de Recherche en Santé Publique (INRSP)BamakoMali
| | - Mahamadou Traoré
- Service de cytogenetique et de biologie reproductive Institut National de Recherche en Santé Publique (INRSP) Bamako Mali
| | - Katherine G Meilleur
- Tissue Injury Branch National Institute of Nursing Research (NINR) NIH Bethesda Maryland
| | - Cheick Oumar Guinto
- Service de Neurologie Centre Hospitalier Universitaire du Point "G" Bamako Mali
| | - Barrington G Burnett
- Departments of Anatomy, Physiology and Genetics Uniformed Services University of the Health Sciences (USUHS) Bethesda Maryland
| | | | - Kenneth H Fischbeck
- Neurogenetics Branch National Institute of Neurological Disorders and Stroke (NINDS) National Institutes of Health (NIH) Bethesda Maryland
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Kundu S, Ghosh SK. Trend of different molecular markers in the last decades for studying human migrations. Gene 2014; 556:81-90. [PMID: 25510397 DOI: 10.1016/j.gene.2014.12.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 12/07/2014] [Accepted: 12/11/2014] [Indexed: 12/15/2022]
Abstract
Anatomically modern humans are known to have widely migrated throughout history. Different scientific evidences suggest that the entire human population descended from just several thousand African migrants. About 85,000 years ago, the first wave of human migration was out of Africa, that followed the coasts through the Middle East, into Southern Asia via Sri Lanka, and in due course around Indonesia and into Australia. Another wave of migration between 40,000 and 12,000 years ago brought humans northward into Europe. However, the frozen north limited human expansion in Europe, and created a land bridge, "Bering land bridge", connecting Asia with North America about 25,000 years ago. Although fossil data give the most direct information about our past, it has certain anomalies. So, molecular archeologists are now using different molecular markers to trace the "most recent common ancestor" and also the migration pattern of modern humans. In this study, we have studied the trend of molecular markers and also the methodologies implemented in the last decades (2003-2014). From our observation, we can say that D-loop region of mtDNA and Y chromosome based markers are predominant. Nevertheless, mtDNA, especially the D-loop region, has some unique features, which makes it a more effective marker for tracing prehistoric footprints of modern human populations. Although, natural selection should also be taken into account in studying mtDNA based human migration. As per technology is concerned, Sanger sequencing is the major technique that is being used in almost all studies. But, the emergence of different cost-effective-and-easy-to-handle NGS platforms has increased its popularity over Sanger sequencing in studying human migration.
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Affiliation(s)
- Sharbadeb Kundu
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Pin-788011 Assam, India
| | - Sankar Kumar Ghosh
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Pin-788011 Assam, India.
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10
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Disotell TR. Archaic human genomics. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 149 Suppl 55:24-39. [PMID: 23124308 DOI: 10.1002/ajpa.22159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 12/18/2022]
Abstract
For much of the 20th century, the predominant view of human evolutionary history was derived from the fossil record. Homo erectus was seen arising in Africa from an earlier member of the genus and then spreading throughout the Old World and into the Oceania. A regional continuity model of anagenetic change from H. erectus via various intermediate archaic species into the modern humans in each of the regions inhabited by H. erectus was labeled the multiregional model of human evolution (MRE). A contrasting model positing a single origin, in Africa, of anatomically modern H. sapiens with some populations later migrating out of Africa and replacing the local archaic populations throughout the world with complete replacement became known as the recent African origin (RAO) model. Proponents of both models used different interpretations of the fossil record to bolster their views for decades. In the 1980s, molecular genetic techniques began providing evidence from modern human variation that allowed not only the different models of modern human origins to be tested but also the exploration demographic history and the types of selection that different regions of the genome and even specific traits had undergone. The majority of researchers interpreted these data as strongly supporting the RAO model, especially analyses of mitochondrial DNA (mtDNA). Extrapolating backward from modern patterns of variation and using various calibration points and substitution rates, a consensus arose that saw modern humans evolving from an African population around 200,000 years ago. Much later, around 50,000 years ago, a subset of this population migrated out of Africa replacing Neanderthals in Europe and western Asia as well as archaics in eastern Asia and Oceania. mtDNA sequences from more than two-dozen Neanderthals and early modern humans re-enforced this consensus. In 2010, however, the complete draft genomes of Neanderthals and of heretofore unknown hominins from Siberia, called Denisovans, demonstrated gene flow between these archaic human species and modern Eurasians but not sub-Saharan Africans. Although the levels of gene flow may be very limited, this unexpected finding does not fit well with either the RAO model or MRE model. More thorough sampling of modern human diversity, additional fossil discoveries, and the sequencing of additional hominin fossils are necessary to throw light onto our origins and our history.
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Affiliation(s)
- Todd R Disotell
- Center for Study of Human Origins, Department of Anthropology, New York University, New York, NY 10003, USA.
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Veeramah KR, Wegmann D, Woerner A, Mendez FL, Watkins JC, Destro-Bisol G, Soodyall H, Louie L, Hammer MF. An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC-based analysis of autosomal resequencing data. Mol Biol Evol 2011; 29:617-30. [PMID: 21890477 DOI: 10.1093/molbev/msr212] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Sub-Saharan Africa has consistently been shown to be the most genetically diverse region in the world. Despite the fact that a substantial portion of this variation is partitioned between groups practicing a variety of subsistence strategies and speaking diverse languages, there is currently no consensus on the genetic relationships of sub-Saharan African populations. San (a subgroup of KhoeSan) and many Pygmy groups maintain hunter-gatherer lifestyles and cluster together in autosomal-based analysis, whereas non-Pygmy Niger-Kordofanian speakers (non-Pygmy NKs) predominantly practice agriculture and show substantial genetic homogeneity despite their wide geographic range throughout sub-Saharan Africa. However, KhoeSan, who speak a set of relatively unique click-based languages, have long been thought to be an early branch of anatomically modern humans based on phylogenetic analysis. To formally test models of divergence among the ancestors of modern African populations, we resequenced a sample of San, Eastern, and Western Pygmies and non-Pygmy NKs individuals at 40 nongenic (∼2 kb) regions and then analyzed these data within an Approximate Bayesian Computation (ABC) framework. We find substantial support for a model of an early divergence of KhoeSan ancestors from a proto-Pygmy-non-Pygmy NKs group ∼110 thousand years ago over a model incorporating a proto-KhoeSan-Pygmy hunter-gatherer divergence from the ancestors of non-Pygmy NKs. The results of our analyses are consistent with previously identified signals of a strong bottleneck in Mbuti Pygmies and a relatively recent expansion of non-Pygmy NKs. We also develop a number of methodologies that utilize "pseudo-observed" data sets to optimize our ABC-based inference. This approach is likely to prove to be an invaluable tool for demographic inference using genome-wide resequencing data.
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Affiliation(s)
- Krishna R Veeramah
- Arizona Research Laboratories Division of Biotechnology, University of Arizona, Arizona, USA
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Kutanan W, Kampuansai J, Fuselli S, Nakbunlung S, Seielstad M, Bertorelle G, Kangwanpong D. Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand. BMC Genet 2011; 12:56. [PMID: 21672265 PMCID: PMC3126721 DOI: 10.1186/1471-2156-12-56] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 06/15/2011] [Indexed: 11/12/2022] Open
Abstract
Background The Mon-Khmer speaking peoples inhabited northern Thailand before the arrival of the Tai speaking people from southern China in the thirteenth century A.D. Historical and anthropological evidence suggests a close relationship between the Mon-Khmer groups and the present day majority northern Thai groups. In this study, mitochondrial and Y-chromosomal DNA polymorphisms in more than 800 volunteers from eight Mon-Khmer and ten Tai speaking populations were investigated to estimate the degree of genetic divergence between these major linguistic groups and their internal structure. Results A large fraction of genetic variation is observed within populations (about 80% and 90% for mtDNA and the Y-chromosome, respectively). The genetic divergence between populations is much higher in Mon-Khmer than in Tai speaking groups, especially at the paternally inherited markers. The two major linguistic groups are genetically distinct, but only for a marginal fraction (1 to 2%) of the total genetic variation. Genetic distances between populations correlate with their linguistic differences, whereas the geographic distance does not explain the genetic divergence pattern. Conclusions The Mon-Khmer speaking populations in northern Thailand exhibited the genetic divergence among each other and also when compared to Tai speaking peoples. The different drift effects and the post-marital residence patterns between the two linguistic groups are the explanation for a small but significant fraction of the genetic variation pattern within and between them.
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Affiliation(s)
- Wibhu Kutanan
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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Babiker HM, Schlebusch CM, Hassan HY, Jakobsson M. Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci. INVESTIGATIVE GENETICS 2011; 2:12. [PMID: 21542921 PMCID: PMC3118356 DOI: 10.1186/2041-2223-2-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Accepted: 05/04/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region. RESULT We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE) was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia. CONCLUSION We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.
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Affiliation(s)
- Hiba Ma Babiker
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
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Y-chromosomal evidence of a pastoralist migration through Tanzania to southern Africa. Proc Natl Acad Sci U S A 2008; 105:10693-8. [PMID: 18678889 DOI: 10.1073/pnas.0801184105] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although geneticists have extensively debated the mode by which agriculture diffused from the Near East to Europe, they have not directly examined similar agropastoral diffusions in Africa. It is unclear, for example, whether early instances of sheep, cows, pottery, and other traits of the pastoralist package were transmitted to southern Africa by demic or cultural diffusion. Here, we report a newly discovered Y-chromosome-specific polymorphism that defines haplogroup E3b1f-M293. This polymorphism reveals the monophyletic relationship of the majority of haplotypes of a previously paraphyletic clade, E3b1-M35*, that is widespread in Africa and southern Europe. To elucidate the history of the E3b1f haplogroup, we analyzed this haplogroup in 13 populations from southern and eastern Africa. The geographic distribution of the E3b1f haplogroup, in association with the microsatellite diversity estimates for populations, is consistent with an expansion through Tanzania to southern-central Africa. The data suggest this dispersal was independent of the migration of Bantu-speaking peoples along a similar route. Instead, the phylogeography and microsatellite diversity of the E3b1f lineage correlate with the arrival of the pastoralist economy in southern Africa. Our Y-chromosomal evidence supports a demic diffusion model of pastoralism from eastern to southern Africa approximately 2,000 years ago.
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Watkins WS, Rogers AR, Ostler CT, Wooding S, Bamshad MJ, Brassington AME, Carroll ML, Nguyen SV, Walker JA, Prasad BVR, Reddy PG, Das PK, Batzer MA, Jorde LB. Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms. Genome Res 2003; 13:1607-18. [PMID: 12805277 PMCID: PMC403734 DOI: 10.1101/gr.894603] [Citation(s) in RCA: 169] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2002] [Accepted: 04/22/2003] [Indexed: 11/24/2022]
Abstract
We examine the distribution and structure of human genetic diversity for 710 individuals representing 31 populations from Africa, East Asia, Europe, and India using 100 Alu insertion polymorphisms from all 22 autosomes. Alu diversity is highest in Africans (0.349) and lowest in Europeans (0.297). Alu insertion frequency is lowest in Africans (0.463) and higher in Indians (0.544), E. Asians (0.557), and Europeans (0.559). Large genetic distances are observed among African populations and between African and non-African populations. The root of a neighbor-joining network is located closest to the African populations. These findings are consistent with an African origin of modern humans and with a bottleneck effect in the human populations that left Africa to colonize the rest of the world. Genetic distances among all pairs of populations show a significant product-moment correlation with geographic distances (r = 0.69, P < 0.00001). F(ST), the proportion of genetic diversity attributable to population subdivision is 0.141 for Africans/E. Asians/Europeans, 0.047 for E. Asians/Indians/Europeans, and 0.090 for all 31 populations. Resampling analyses show that approximately 50 Alu polymorphisms are sufficient to obtain accurate and reliable genetic distance estimates. These analyses also demonstrate that markers with higher F(ST) values have greater resolving power and produce more consistent genetic distance estimates.
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Affiliation(s)
- W Scott Watkins
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
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Kayser M, Brauer S, Schädlich H, Prinz M, Batzer MA, Zimmerman PA, Boatin BA, Stoneking M. Y chromosome STR haplotypes and the genetic structure of U.S. populations of African, European, and Hispanic ancestry. Genome Res 2003; 13:624-34. [PMID: 12671003 PMCID: PMC430174 DOI: 10.1101/gr.463003] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To investigate geographic structure within U.S. ethnic populations, we analyzed 1705 haplotypes on the basis of 9 short tandem repeat (STR) loci on the Y-chromosome from 9-11 groups each of African-Americans, European-Americans, and Hispanics. There were no significant differences in the distribution of Y-STR haplotypes among African-American groups, whereas European-American and Hispanic groups did exhibit significant geographic heterogeneity. However, the significant heterogeneity resulted from one sample; removal of that sample in each case eliminated the significant heterogeneity. Multidimensional scaling analysis of R(ST) values indicated that African-American groups formed a distinct cluster, whereas there was some intermingling of European-American and Hispanic groups. MtDNA data exist for many of these same groups; estimates of the European-American genetic contribution to the African-American gene pool were 27.5%-33.6% for the Y-STR haplotypes and 9%-15.4% for the mtDNA types. The lack of significant geographic heterogeneity among Y-STR and mtDNA haplotypes in U.S ethnic groups means that forensic DNA databases do not need to be constructed for separate geographic regions of the U.S. Moreover, absence of significant geographic heterogeneity for these two loci means that regional variation in disease susceptibility within ethnic groups is more likely to reflect cultural/environmental factors, rather than any underlying genetic heterogeneity.
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Affiliation(s)
- Manfred Kayser
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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Wells RS, Yuldasheva N, Ruzibakiev R, Underhill PA, Evseeva I, Blue-Smith J, Jin L, Su B, Pitchappan R, Shanmugalakshmi S, Balakrishnan K, Read M, Pearson NM, Zerjal T, Webster MT, Zholoshvili I, Jamarjashvili E, Gambarov S, Nikbin B, Dostiev A, Aknazarov O, Zalloua P, Tsoy I, Kitaev M, Mirrakhimov M, Chariev A, Bodmer WF. The Eurasian heartland: a continental perspective on Y-chromosome diversity. Proc Natl Acad Sci U S A 2001; 98:10244-9. [PMID: 11526236 PMCID: PMC56946 DOI: 10.1073/pnas.171305098] [Citation(s) in RCA: 290] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nonrecombining portion of the human Y chromosome has proven to be a valuable tool for the study of population history. The maintenance of extended haplotypes characteristic of particular geographic regions, despite extensive admixture, allows complex demographic events to be deconstructed. In this study we report the frequencies of 23 Y-chromosome biallelic polymorphism haplotypes in 1,935 men from 49 Eurasian populations, with a particular focus on Central Asia. These haplotypes reveal traces of historical migrations, and provide an insight into the earliest patterns of settlement of anatomically modern humans on the Eurasian continent. Central Asia is revealed to be an important reservoir of genetic diversity, and the source of at least three major waves of migration leading into Europe, the Americas, and India. The genetic results are interpreted in the context of Eurasian linguistic patterns.
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Affiliation(s)
- R S Wells
- Imperial Cancer Research Fund Cancer and Immunogenetics Laboratory and Wellcome Trust Centre for Human Genetics, University of Oxford, Headington OX3 9DS, United Kingdom.
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18
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Abstract
The origins and affinities of the ∼1 billion people living on the subcontinent of India have long been contested. This is owing, in part, to the many different waves of immigrants that have influenced the genetic structure of India. In the most recent of these waves, Indo-European-speaking people from West Eurasia entered India from the Northwest and diffused throughout the subcontinent. They purportedly admixed with or displaced indigenous Dravidic-speaking populations. Subsequently they may have established the Hindu caste system and placed themselves primarily in castes of higher rank. To explore the impact of West Eurasians on contemporary Indian caste populations, we compared mtDNA (400 bp of hypervariable region 1 and 14 restriction site polymorphisms) and Y-chromosome (20 biallelic polymorphisms and 5 short tandem repeats) variation in ∼265 males from eight castes of different rank to ∼750 Africans, Asians, Europeans, and other Indians. For maternally inherited mtDNA, each caste is most similar to Asians. However, 20%–30% of Indian mtDNA haplotypes belong to West Eurasian haplogroups, and the frequency of these haplotypes is proportional to caste rank, the highest frequency of West Eurasian haplotypes being found in the upper castes. In contrast, for paternally inherited Y-chromosome variation each caste is more similar to Europeans than to Asians. Moreover, the affinity to Europeans is proportionate to caste rank, the upper castes being most similar to Europeans, particularly East Europeans. These findings are consistent with greater West Eurasian male admixture with castes of higher rank. Nevertheless, the mitochondrial genome and the Y chromosome each represents only a single haploid locus and is more susceptible to large stochastic variation, bottlenecks, and selective sweeps. Thus, to increase the power of our analysis, we assayed 40 independent, biparentally inherited autosomal loci (1 LINE-1 and 39 Aluelements) in all of the caste and continental populations (∼600 individuals). Analysis of these data demonstrated that the upper castes have a higher affinity to Europeans than to Asians, and the upper castes are significantly more similar to Europeans than are the lower castes. Collectively, all five datasets show a trend toward upper castes being more similar to Europeans, whereas lower castes are more similar to Asians. We conclude that Indian castes are most likely to be of proto-Asian origin with West Eurasian admixture resulting in rank-related and sex-specific differences in the genetic affinities of castes to Asians and Europeans.
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Zhivotovsky LA. Estimating divergence time with the use of microsatellite genetic distances: impacts of population growth and gene flow. Mol Biol Evol 2001; 18:700-9. [PMID: 11319254 DOI: 10.1093/oxfordjournals.molbev.a003852] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genetic distances play an important role in estimating divergence time of bifurcated populations. However, they can be greatly affected by demographic processes, such as migration and population dynamics, which complicate their interpretation. For example, the widely used distance for microsatellite loci, (deltamu)2, assumes constant population size, no gene flow, and mutation-drift equilibrium. It is shown here that (deltamu)2 strongly underestimates divergence time if populations are growing and/or connected by gene flow. In recent publications, the average estimate of divergence time between African and non-African populations obtained by using (deltamu)2 is about 34,000 years, although archaeological data show a much earlier presence of modern humans out of Africa. I introduce a different estimator of population separation time based on microsatellite statistics, T(D), that does not assume mutation-drift equilibrium, is independent of population dynamics in the absence of gene flow, and is robust to weak migration flow for growing populations. However, it requires a knowledge of the variance in the number of repeats at the beginning of population separation, V(0). One way to overcome this problem is to find minimal and maximal bounds for the variance and thus obtain the earliest and latest bounds for divergence time (this is not a confidence interval, and it simply reflects an uncertainty about the value of V(0) in an ancestral population). Another way to avoid the uncertainty is to choose from among present populations a reference whose variation is presumably close to what it might have been in an ancestral population. A different approach for using T(D) is to estimate the time difference between adjacent nodes on a phylogenetic population tree. Using data on variation at autosomal short tandem repeat loci with di-, tri-, and tetranucleotide repeats in worldwide populations, T(D) gives an estimate of 57,000 years for the separation of the out-of-Africa branch of modern humans from Africans based on the value of V(0) in the Southern American Indian populations; the earliest bound for this event has been estimated to be about 135,000 years. The data also suggest that the Asian and European populations diverged from each other about 20,000 years, after the occurrence of the out-of-Africa branch.
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Affiliation(s)
- L A Zhivotovsky
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
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Abstract
Population genetics has emerged as a powerful tool for unraveling human history. In addition to the study of mitochondrial and autosomal DNA, attention has recently focused on Y-chromosome variation. Ambiguities and inaccuracies in data analysis, however, pose an important obstacle to further development of the field. Here we review the methods available for genealogical inference using Y-chromosome data. Approaches can be divided into those that do and those that do not use an explicit population model in genealogical inference. We describe the strengths and weaknesses of these model-based and model-free approaches, as well as difficulties associated with the mutation process that affect both methods. In the case of genealogical inference using microsatellite loci, we use coalescent simulations to show that relatively simple generalizations of the mutation process can greatly increase the accuracy of genealogical inference. Because model-free and model-based approaches have different biases and limitations, we conclude that there is considerable benefit in the continued use of both types of approaches.
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Affiliation(s)
- M P Stumpf
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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Abstract
Naming new human species may seem to be a harmless endeavor, of little interest to all but a few specialists playing out the consequences of different evolutionary explanations of phyletic variation, but it has significant implications in how humanity is viewed because studies of race and human evolution are inexorably linked. When essentialist approaches are used to interpret variation in the past as taxonomic rather than populational, as increasingly has been the case, it serves to underscore a typological view of modern human variation.
In terms of how they are treated in analysis, there often seems to be no difference between the species, subspecies, or paleodemes of the past and the populations or races whose interrelationships and demographic history are discussed today. This is not inconsequential because both history and current practice shows that science, especially anthropology, is not isolated from society.
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