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Norasi E, Rastegar M, Hosseini SD, Aghcheli B, Tahamtan A. Prevalence of CCR5 Delta 32 Genetic Variant in the Turkmen Population of Golestan Province, Northeast of Iran. BIOMED RESEARCH INTERNATIONAL 2023; 2023:8823863. [PMID: 37388364 PMCID: PMC10307026 DOI: 10.1155/2023/8823863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/23/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023]
Abstract
The 32 bp deletion in the chemokine receptor (C-C motif) 5 gene (CCR5Δ32) is a natural loss of function polymorphism that prevents the protein from locating on the cell surface. This genetic variation acts as a double-edge sword in the pathogenesis/defense mechanism of different health conditions, such as viral infections, autoimmune diseases, and cancers. Here, we evaluated the prevalence of the CCR5Δ32 polymorphism in the Turkmen population of Golestan province, northeast of Iran. Blood samples were collected from 400 randomly selected Turkmen populations (199 women and 201 men), and genomic DNA was extracted. Characterization of CCR5Δ32 genotypes was performed by PCR using primers flanking the 32-nucleotide deletion in the CCR5 gene. The amplified DNA fragments were visualized on 2% agarose gel electrophoresis with cybergreen staining under UV light. All individuals were of Turkmen ethnicity and lived in the Golestan province, northeast of Iran. The mean age of all participants was 35.46 years, with a 20-45 year range. All the studied subjects were healthy without any severe conditions such as autoimmune disease and viral infections. All individuals had no history of HIV infection. The PCR product visualization showed that all the samples are at the 330 bp size, which means the CCR5Δ32 allele was utterly absent from the study population. The presence of the CCR5Δ32 allele among Turkmens may be attributed to the admixture with European descent people. We conclude that the CCR5Δ32 polymorphism may be absent in the Iranian Turkmen population, and further studies with a large population are needed.
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Affiliation(s)
- Elmira Norasi
- School of International, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mostafa Rastegar
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | | | - Bahman Aghcheli
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Alireza Tahamtan
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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Abstract
Geographic patterns in human genetic diversity carry footprints of population history and provide insights for genetic medicine and its application across human populations. Summarizing and visually representing these patterns of diversity has been a persistent goal for human geneticists, and has revealed that genetic differentiation is frequently correlated with geographic distance. However, most analytical methods to represent population structure do not incorporate geography directly, and it must be considered post hoc alongside a visual summary of the genetic structure. Here, we estimate "effective migration" surfaces to visualize how human genetic diversity is geographically structured. The results reveal local patterns of differentiation in detail and emphasize that while genetic similarity generally decays with geographic distance, the relationship is often subtly distorted. Overall, the visualizations provide a new perspective on genetics and geography in humans and insight to the geographic distribution of human genetic variation.
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Affiliation(s)
- Benjamin M Peter
- Department of Human Genetics, University of Chicago, Chicago, IL
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Desislava Petkova
- Wellcome Trust Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL
- Department of Ecology & Evolution, University of Chicago, Chicago, IL
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Kinney N, Kang L, Eckstrand L, Pulenthiran A, Samuel P, Anandakrishnan R, Varghese RT, Michalak P, Garner HR. Abundance of ethnically biased microsatellites in human gene regions. PLoS One 2019; 14:e0225216. [PMID: 31830051 PMCID: PMC6907796 DOI: 10.1371/journal.pone.0225216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022] Open
Abstract
Microsatellites-a type of short tandem repeat (STR)-have been used for decades as putatively neutral markers to study the genetic structure of diverse human populations. However, recent studies have demonstrated that some microsatellites contribute to gene expression, cis heritability, and phenotype. As a corollary, some microsatellites may contribute to differential gene expression and RNA/protein structure stability in distinct human populations. To test this hypothesis, we investigate genotype frequencies, functional relevance, and adaptive potential of microsatellites in five super-populations (ethnicities) drawn from the 1000 Genomes Project. We discover 3,984 ethnically-biased microsatellite loci (EBML); for each EBML at least one ethnicity has genotype frequencies statistically different from the remaining four. South Asian, East Asian, European, and American EBML show significant overlap; on the contrary, the set of African EBML is mostly unique. We cross-reference the 3,984 EBML with 2,060 previously identified expression STRs (eSTRs); repeats known to affect gene expression (64 total) are over-represented. The most significant pathway enrichments are those associated with the matrisome: a broad collection of genes encoding the extracellular matrix and its associated proteins. At least 14 of the EBML have established links to human disease. Analysis of the 3,984 EBML with respect to known selective sweep regions in the genome shows that allelic variation in some of them is likely associated with adaptive evolution.
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Affiliation(s)
- Nick Kinney
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
- Gibbs Cancer Center & Research Institute, Spartanburg, SC, United States of America
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
- Gibbs Cancer Center & Research Institute, Spartanburg, SC, United States of America
| | - Laurel Eckstrand
- Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, United States of America
| | - Arichanah Pulenthiran
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
| | - Peter Samuel
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
| | - Ramu Anandakrishnan
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
| | - Robin T. Varghese
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
| | - P. Michalak
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
- Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, United States of America
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Harold R. Garner
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States of America
- Gibbs Cancer Center & Research Institute, Spartanburg, SC, United States of America
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Tajbakhsh A, Fazeli M, Rezaee M, Ghasemi F, Heravi MM, Gholoobi A, Meshkat Z. Prevalence of CCR5delta32 in Northeastern Iran. BMC MEDICAL GENETICS 2019; 20:184. [PMID: 31730458 PMCID: PMC6858674 DOI: 10.1186/s12881-019-0913-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/25/2019] [Indexed: 12/16/2022]
Abstract
Background A 32-base pair deletion (∆32) in the open reading frame (ORF) of C-C motif chemokine receptor 5 (CCR5) seems to be a protective variant against immune system diseases, especially human immunodeficiency virus type 1 (HIV-1). We aimed to assess the frequency of CCR5∆32 in the healthy Iranian population. Methods In this study, 400 normal samples from Khorasan, northeastern Iran, were randomly selected. The frequency of CCR5∆32 carriers was investigated using PCR analysis. Allele prevalence and the fit to the Hardy-Weinberg equilibrium were analyzed. Results The prevalence of CCR5∆32 in the northeastern population of Iran was 0.016. Four hundred samples were studied, among which one with CCR5∆32/∆32 and 11 with CCR5Wild/∆32 genotype were detected. Conclusion This study was the first investigation for an assessment of the prevalence of CCR5∆32 in northeastern Iran. The low prevalence of CCR5∆32 allele in the Iranian population may result in the increased susceptibility to HIV-1. In addition, this prevalence is the same as that of reported in East Asia, while is lower than that in the Europeans.
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Affiliation(s)
- Amir Tajbakhsh
- Department of Modern Sciences & Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mostafa Fazeli
- Department of Modern Sciences & Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehdi Rezaee
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Faezeh Ghasemi
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Mastoureh Momen Heravi
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, P.O Box: 9196773117, Mashhad, IR, Iran
| | - Aida Gholoobi
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Meshkat
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, P.O Box: 9196773117, Mashhad, IR, Iran.
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Lee AW, Navajas EE, Liu L. Clear differences in ovarian cancer incidence and trends by ethnicity among Asian Americans. Cancer Epidemiol 2019; 61:142-149. [PMID: 31254796 PMCID: PMC7428826 DOI: 10.1016/j.canep.2019.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/05/2019] [Accepted: 06/12/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND Across major races in the United States (U.S.), ovarian cancer incidence is low among Asian American women. However, this observation aggregates Asian Americans as a single group despite their heterogeneity. Disaggregating the ethnic Asian population will produce more useful information to better understand ovarian cancer incidence among Asian women in the U.S. METHODS Data from the Surveillance, Epidemiology, and End Results Program from 1990 to 2014 were used to compare age-adjusted incidence rates (AAIRs, per 100,000 women) for ovarian cancer for the six largest U.S. Asian ethnicities (Asian Indian/Pakistani, Chinese, Filipino, Japanese, Korean, Vietnamese) to non-Hispanic whites (NHWs). The race/ethnicity-specific AAIRs were calculated by time period and histotype. We examined the magnitude and direction of AAIR trends using average annual percent change (AAPC) statistics. RESULTS All Asian ethnicities had significantly lower ovarian cancer incidence rates than NHWs. However, among Asian ethnicities, Asian Indians/Pakistanis had the highest rate of ovarian cancer (AAIR = 10.51, 95% CI: 9.65-11.42) while Koreans had the lowest (AAIR = 7.23, 95% CI: 6.62-7.88). Clear cell ovarian cancer had significantly higher incidence rates among Chinese, Filipino, and Japanese women than NHW women (incidence rate ratio (IRR) = 1.49, 95% CI: 1.29-1.72, IRR = 1.30, 95% CI: 1.12-1.51, IRR = 1.64, 95% CI: 1.36-1.97, respectively). Incidence trends also differed by Asian ethnicity with significant decreases only observed for Chinese (AAPC = -1.49, 95% CI: -2.22 to -0.74) and Japanese (AAPC = -1.75, 95% CI: -2.57 to -0.92). CONCLUSIONS Examining Asian Americans as a single group results in missed ethnic-specific disparities in ovarian cancer, hence disaggregating this heterogeneous population in future research is warranted.
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Affiliation(s)
- Alice W Lee
- Department of Public Health, California State University, Fullerton, Fullerton, CA, United States.
| | - Emma E Navajas
- Department of Public Health, California State University, Fullerton, Fullerton, CA, United States
| | - Lihua Liu
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, United States
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Leow MKS. Characterization of the Asian Phenotype - An Emerging Paradigm with Clinicopathological and Human Research Implications. Int J Med Sci 2017; 14:639-647. [PMID: 28824295 PMCID: PMC5562114 DOI: 10.7150/ijms.18880] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/14/2017] [Indexed: 12/25/2022] Open
Abstract
Background: Modern medicine recognizes that salient, inherent variations between Caucasians and Asians exist. Radical changes are occurring in the health scene with increasing emphasis centered on the recognition of inter-individual variations unique to Asians that impact on medical management and outcomes. Aim: This review analyzes distinct features or outcomes in terms of epidemiology, disease thresholds, diagnostic cutoffs and treatment responses of Asian people compared with non-Asians. Methods: This review is based on a literature search via PubMed and MEDLINE for relevant articles related to the Asian phenotype and its impact on health and disease. Results: An 'Asian phenotype' could be characterized across the spectrum of biomedical disciplines and underscores the major challenges clinicians must face in their daily management of a cosmopolitan population and their extrapolation of research outcomes. Conclusion: Interventions for various ailments that have traditionally ignored population differences have now entered the age of personalized, stratified or precision medicine requiring an individualized approach being adopted as a new standard of care. Factoring in Asian phenotypes is essential for the medical research community and the development of improved clinical practice guidelines across a continuum of disciplines that will ultimately translate to better human health round the world.
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Affiliation(s)
- Melvin Khee-Shing Leow
- Clinical Investigator, Singapore Institute for Clinical Sciences, ASTAR; Deputy Director, Clinical Nutrition Research Centre (CNRC), Singapore; Senior Consultant Endocrinologist, Tan Tock Seng Hospital; Clinician Scientist, National Healthcare Group (NHG); Clinical Associate Professor, National University of Singapore; Adjunct Associate Professor, Duke-NUS Graduate Medical School, Singapore; Associate Professor, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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Marrero P, Abu-Amero KK, Larruga JM, Cabrera VM. Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia. BMC Evol Biol 2016; 16:246. [PMID: 27832758 PMCID: PMC5105315 DOI: 10.1186/s12862-016-0816-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/28/2016] [Indexed: 11/23/2022] Open
Abstract
Background From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia. To contrast both hypothesis, here we reanalyzed the phylogeography and respective ages of mtDNA haplogroups belonging to macrohaplogroup M in different regions of Eurasia and Australasia. Results The macrohaplogroup M has a historical implantation in West Eurasia, including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. Moreover, there is a significant positive correlation between the age of the M haplogroups and its longitudinal geographical distribution. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side. Conclusions The existence of a northern route, previously proposed for the mtDNA macrohaplogroup N, is confirmed here for the macrohaplogroup M. Both mtDNA macrolineages seem to have differentiated in South East Asia from ancestral L3 lineages. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0816-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patricia Marrero
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, Norfolk, UK
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain.
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Distribution of DI*A and DI*B Allele Frequencies and Comparisons among Central Thai and Other Populations. PLoS One 2016; 11:e0165134. [PMID: 27764238 PMCID: PMC5072727 DOI: 10.1371/journal.pone.0165134] [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: 07/14/2016] [Accepted: 10/06/2016] [Indexed: 12/29/2022] Open
Abstract
Alloantibodies to the Diego (DI) blood group system, anti-Dia and anti-Dib are clinically significant in causing hemolytic transfusion reactions (HTRs) and hemolytic disease of the fetus and newborn (HDFN), especially in Asian populations with Mongolian ancestry. This study aimed to report the frequency of the DI*A and DI*B alleles in a Central Thai population and to compare them with those of other populations previously published. Altogether, 1,011 blood samples from unrelated healthy blood donors at the National Blood Centre, Thai Red Cross Society, Bangkok were included. Only 391 samples were tested with anti-Dia by conventional tube technique. All samples were genotyped for DI*A and DI*B alleles using an in-house polymerase chain reaction with sequence-specific primer (PCR-SSP) technique. The DI phenotyping and genotyping results were in 100% concordance. The DI*A and DI*B allele frequencies among 1,011 Central Thais were 0.0183 (37/2,022) and 0.9817 (1,985/2,022), respectively. Allele frequencies were compared between Central Thai and other populations. Our data shows that DI*A and DI*B allele frequencies are similar to Southeast Asian, Brazilian, Southern Brazilian and American Native populations; whereas, these frequencies significantly differ from those reported in East Asian, Italian, Alaska Native/Aleut, Hawaiian/Pacific Islander and Filipino populations (P<0.05), corresponding to the results of a matrix of geometric genetic distances. This study confirms that the prevalence of DI*A and DI*B alleles among Central Thais is similar to Southeast Asians and different to others populations of the world. A PCR-based identification of DI genotyping should overcome some of the serological limitations in transfusion medicine and provides a complementary tool for further population-genetic studies.
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Rare Helicobacter pylori Virulence Genotypes in Bhutan. Sci Rep 2016; 6:22584. [PMID: 26931643 PMCID: PMC4773856 DOI: 10.1038/srep22584] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 02/17/2016] [Indexed: 12/21/2022] Open
Abstract
Both the prevalence of Helicobacter pylori infection and the incidence of gastric cancer are high in Bhutan. The high incidence of atrophic gastritis and gastric cancer suggest the phylogeographic origin of an infection with a more virulent strain of H. pylori. More than 90% of Bhutanese strains possessed the highly virulent East Asian-type CagA and all strains had the most virulent type of vacA (s1 type). More than half also had multiple repeats in East Asian-type CagA, which are rare in other countries and are reported characteristictly found in assciation with atrophic gastritis and gastric cancer consistent with Bhutanese strains having multiple H. pylori virulence factors associated with an increase in gastric cancer risk. Phylogeographic analyses showed that most Bhutanese strains belonged to the East Asian population type with some strains (17.5%) sharing East Asian and Amerindian components. Only 9.5% belonged to the European type consistant with H. pylori in Bhutan representing an intermediate evolutionary stage between H. pylori from European and East Asian countries.
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A comparison of worldwide phonemic and genetic variation in human populations. Proc Natl Acad Sci U S A 2015; 112:1265-72. [PMID: 25605893 DOI: 10.1073/pnas.1424033112] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Worldwide patterns of genetic variation are driven by human demographic history. Here, we test whether this demographic history has left similar signatures on phonemes-sound units that distinguish meaning between words in languages-to those it has left on genes. We analyze, jointly and in parallel, phoneme inventories from 2,082 worldwide languages and microsatellite polymorphisms from 246 worldwide populations. On a global scale, both genetic distance and phonemic distance between populations are significantly correlated with geographic distance. Geographically close language pairs share significantly more phonemes than distant language pairs, whether or not the languages are closely related. The regional geographic axes of greatest phonemic differentiation correspond to axes of genetic differentiation, suggesting that there is a relationship between human dispersal and linguistic variation. However, the geographic distribution of phoneme inventory sizes does not follow the predictions of a serial founder effect during human expansion out of Africa. Furthermore, although geographically isolated populations lose genetic diversity via genetic drift, phonemes are not subject to drift in the same way: within a given geographic radius, languages that are relatively isolated exhibit more variance in number of phonemes than languages with many neighbors. This finding suggests that relatively isolated languages are more susceptible to phonemic change than languages with many neighbors. Within a language family, phoneme evolution along genetic, geographic, or cognate-based linguistic trees predicts similar ancestral phoneme states to those predicted from ancient sources. More genetic sampling could further elucidate the relative roles of vertical and horizontal transmission in phoneme evolution.
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Kim H, Yoo WG, Park J, Kim H, Kang BC. Semantic Modeling for SNPs Associated with Ethnic Disparities in HapMap Samples. Genomics Inform 2014; 12:35-41. [PMID: 24748859 PMCID: PMC3990764 DOI: 10.5808/gi.2014.12.1.35] [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: 11/19/2013] [Revised: 12/23/2013] [Accepted: 12/24/2013] [Indexed: 11/20/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) have been emerging out of the efforts to research human diseases and ethnic disparities. A semantic network is needed for in-depth understanding of the impacts of SNPs, because phenotypes are modulated by complex networks, including biochemical and physiological pathways. We identified ethnicity-specific SNPs by eliminating overlapped SNPs from HapMap samples, and the ethnicity-specific SNPs were mapped to the UCSC RefGene lists. Ethnicity-specific genes were identified as follows: 22 genes in the USA (CEU) individuals, 25 genes in the Japanese (JPT) individuals, and 332 genes in the African (YRI) individuals. To analyze the biologically functional implications for ethnicity-specific SNPs, we focused on constructing a semantic network model. Entities for the network represented by "Gene," "Pathway," "Disease," "Chemical," "Drug," "ClinicalTrials," "SNP," and relationships between entity-entity were obtained through curation. Our semantic modeling for ethnicity-specific SNPs showed interesting results in the three categories, including three diseases ("AIDS-associated nephropathy," "Hypertension," and "Pelvic infection"), one drug ("Methylphenidate"), and five pathways ("Hemostasis," "Systemic lupus erythematosus," "Prostate cancer," "Hepatitis C virus," and "Rheumatoid arthritis"). We found ethnicity-specific genes using the semantic modeling, and the majority of our findings was consistent with the previous studies - that an understanding of genetic variability explained ethnicity-specific disparities.
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Affiliation(s)
- Hyoyoung Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Korea
| | - Won Gi Yoo
- Codes Division, Insilicogen, Inc., Suwon 441-813, Korea
| | - Junhyung Park
- Codes Division, Insilicogen, Inc., Suwon 441-813, Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-742, Korea
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Tateno Y, Komiyama T, Katoh T, Munkhbat B, Oka A, Haida Y, Kobayashi H, Tamiya G, Inoko H. Divergence of East Asians and Europeans estimated using male- and female-specific genetic markers. Genome Biol Evol 2014; 6:466-73. [PMID: 24589501 PMCID: PMC3971580 DOI: 10.1093/gbe/evu027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To study the male and female lineages of East Asian and European humans, we have sequenced 25 short tandem repeat markers on 453 Y-chromosomes and collected sequences of 72 complete mitochondrial genomes to construct independent phylogenetic trees for male and female lineages. The results indicate that East Asian individuals fall into two clades, one that includes East Asian individuals only and a second that contains East Asian and European individuals. Surprisingly, the European individuals did not form an independent clade, but branched within in the East Asians. We then estimated the divergence time of the root of the European clade as ∼41,000 years ago. These data indicate that, contrary to traditional views, Europeans diverged from East Asians around that time. We also address the origin of the Ainu lineage in northern Japan.
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Affiliation(s)
- Yoshio Tateno
- School of New Biology, Daegu Gyoungbuk Institute of Science and Technology, Daegu, Republic of Korea
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Zhang G, Muglia LJ, Chakraborty R, Akey JM, Williams SM. Signatures of natural selection on genetic variants affecting complex human traits. Appl Transl Genom 2013; 2:78-94. [PMID: 27896059 PMCID: PMC5121263 DOI: 10.1016/j.atg.2013.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/14/2013] [Indexed: 01/04/2023]
Abstract
It has recently been hypothesized that polygenic adaptation, resulting in modest allele frequency changes at many loci, could be a major mechanism behind the adaptation of complex phenotypes in human populations. Here we leverage the large number of variants that have been identified through genome-wide association (GWA) studies to comprehensively study signatures of natural selection on genetic variants associated with complex traits. Using population differentiation based methods, such as FST and phylogenetic branch length analyses, we systematically examined nearly 1300 SNPs associated with 38 complex phenotypes. Instead of detecting selection signatures at individual variants, we aimed to identify combined evidence of natural selection by aggregating signals across many trait associated SNPs. Our results have revealed some general features of polygenic selection on complex traits associated variants. First, natural selection acting on standing variants associated with complex traits is a common phenomenon. Second, characteristics of selection for different polygenic traits vary both temporarily and geographically. Third, some studied traits (e.g. height and urate level) could have been the primary targets of selection, as indicated by the significant correlation between the effect sizes and the estimated strength of selection in the trait associated variants; however, for most traits, the allele frequency changes in trait associated variants might have been driven by the selection on other correlated phenotypes. Fourth, the changes in allele frequencies as a result of selection can be highly stochastic, such that, polygenic adaptation may accelerate differentiation in allele frequencies among populations, but generally does not produce predictable directional changes. Fifth, multiple mechanisms (pleiotropy, hitchhiking, etc) may act together to govern the changes in allele frequencies of genetic variants associated with complex traits.
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Affiliation(s)
- Ge Zhang
- Human Genetics Division, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Louis J. Muglia
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center and March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
| | - Ranajit Chakraborty
- Center for Computational Genomics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Scott M. Williams
- Department of Genetics and Institute for Quantitative Biomedical Sciences, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
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Badro DA, Douaihy B, Haber M, Youhanna SC, Salloum A, Ghassibe-Sabbagh M, Johnsrud B, Khazen G, Matisoo-Smith E, Soria-Hernanz DF, Wells RS, Tyler-Smith C, Platt DE, Zalloua PA. Y-chromosome and mtDNA genetics reveal significant contrasts in affinities of modern Middle Eastern populations with European and African populations. PLoS One 2013; 8:e54616. [PMID: 23382925 PMCID: PMC3559847 DOI: 10.1371/journal.pone.0054616] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 12/13/2012] [Indexed: 11/21/2022] Open
Abstract
The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations.
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Affiliation(s)
| | | | - Marc Haber
- The Lebanese American University, Chouran, Beirut, Lebanon
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | | | | | | | - Brian Johnsrud
- Modern Thought and Literature, Stanford University, Stanford, California, United States of America
| | - Georges Khazen
- The Lebanese American University, Chouran, Beirut, Lebanon
| | - Elizabeth Matisoo-Smith
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand
| | - David F. Soria-Hernanz
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
| | - R. Spencer Wells
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Daniel E. Platt
- Computational Biology Centre, IBM TJ Watson Research Centre, Yorktown Heights, New York, United States of America
| | - Pierre A. Zalloua
- The Lebanese American University, Chouran, Beirut, Lebanon
- Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet 2012; 8:e1002967. [PMID: 23166502 PMCID: PMC3499260 DOI: 10.1371/journal.pgen.1002967] [Citation(s) in RCA: 1443] [Impact Index Per Article: 120.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 08/08/2012] [Indexed: 11/29/2022] Open
Abstract
Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In our model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data, we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and "ancient" Asian breeds. Software implementing the model described here, called TreeMix, is available at http://treemix.googlecode.com.
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Affiliation(s)
- Joseph K. Pickrell
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Jonathan K. Pritchard
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America
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The local origin of the Tibetan pig and additional insights into the origin of Asian pigs. PLoS One 2011; 6:e28215. [PMID: 22163285 PMCID: PMC3233571 DOI: 10.1371/journal.pone.0028215] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 11/03/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The domestic pig currently indigenous to the Tibetan highlands is supposed to have been introduced during a continuous period of colonization by the ancestors of modern Tibetans. However, there is no direct genetic evidence of either the local origin or exotic migration of the Tibetan pig. METHODS AND FINDINGS We analyzed mtDNA hypervariable segment I (HVI) variation of 218 individuals from seven Tibetan pig populations and 1,737 reported mtDNA sequences from domestic pigs and wild boars across Asia. The Bayesian consensus tree revealed a main haplogroup M and twelve minor haplogroups, which suggested a large number of small scale in situ domestication episodes. In particular, haplogroups D1 and D6 represented two highly divergent lineages in the Tibetan highlands and Island Southeastern Asia, respectively. Network analysis of haplogroup M further revealed one main subhaplogroup M1 and two minor subhaplogroups M2 and M3. Intriguingly, M2 was mainly distributed in Southeastern Asia, suggesting for a local origin. Similar with haplogroup D6, M3 was mainly restricted in Island Southeastern Asia. This pattern suggested that Island Southeastern Asia, but not Southeastern Asia, might be the center of domestication of the so-called Pacific clade (M3 and D6 here) described in previous studies. Diversity gradient analysis of major subhaplogroup M1 suggested three local origins in Southeastern Asia, the middle and downstream regions of the Yangtze River, and the Tibetan highlands, respectively. CONCLUSIONS We identified two new origin centers for domestic pigs in the Tibetan highlands and in the Island Southeastern Asian region.
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Group XV phospholipase A₂, a lysosomal phospholipase A₂. Prog Lipid Res 2010; 50:1-13. [PMID: 21074554 DOI: 10.1016/j.plipres.2010.10.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 10/29/2010] [Accepted: 10/30/2010] [Indexed: 12/21/2022]
Abstract
A phospholipase A₂ was identified from MDCK cell homogenates with broad specificity toward glycerophospholipids including phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and phosphatidylglycerol. The phospholipase has the unique ability to transacylate short chain ceramides. This phospholipase is calcium-independent, localized to lysosomes, and has an acidic pH optimum. The enzyme was purified from bovine brain and found to be a water-soluble glycoprotein consisting of a single peptide chain with a molecular weight of 45 kDa. The primary structure deduced from the DNA sequences is highly conserved between chordates. The enzyme was named lysosomal phospholipase A₂ (LPLA₂) and subsequently designated group XV phospholipase A₂. LPLA₂ has 49% of amino acid sequence identity to lecithin-cholesterol acyltransferase and is a member of the αβ-hydrolase superfamily. LPLA₂ is highly expressed in alveolar macrophages. A marked accumulation of glycerophospholipids and extensive lamellar inclusion bodies, a hallmark of cellular phospholipidosis, is observed in alveolar macrophages in LPLA₂(-/-) mice. This defect can also be reproduced in macrophages that are exposed to cationic amphiphilic drugs such as amiodarone. In addition, older LPLA₂(-/-) mice develop a phenotype similar to human autoimmune disease. These observations indicate that LPLA₂ may play a primary role in phospholipid homeostasis, drug toxicity, and host defense.
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Martínez-Cruz B, Vitalis R, Ségurel L, Austerlitz F, Georges M, Théry S, Quintana-Murci L, Hegay T, Aldashev A, Nasyrova F, Heyer E. In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations. Eur J Hum Genet 2010; 19:216-23. [PMID: 20823912 DOI: 10.1038/ejhg.2010.153] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Located in the Eurasian heartland, Central Asia has played a major role in both the early spread of modern humans out of Africa and the more recent settlements of differentiated populations across Eurasia. A detailed knowledge of the peopling in this vast region would therefore greatly improve our understanding of range expansions, colonizations and recurrent migrations, including the impact of the historical expansion of eastern nomadic groups that occurred in Central Asia. However, despite its presumable importance, little is known about the level and the distribution of genetic variation in this region. We genotyped 26 Indo-Iranian- and Turkic-speaking populations, belonging to six different ethnic groups, at 27 autosomal microsatellite loci. The analysis of genetic variation reveals that Central Asian diversity is mainly shaped by linguistic affiliation, with Turkic-speaking populations forming a cluster more closely related to East-Asian populations and Indo-Iranian speakers forming a cluster closer to Western Eurasians. The scattered position of Uzbeks across Turkic- and Indo-Iranian-speaking populations may reflect their origins from the union of different tribes. We propose that the complex genetic landscape of Central Asian populations results from the movements of eastern, Turkic-speaking groups during historical times, into a long-lasting group of settled populations, which may be represented nowadays by Tajiks and Turkmen. Contrary to what is generally thought, our results suggest that the recurrent expansions of eastern nomadic groups did not result in the complete replacement of local populations, but rather into partial admixture.
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Affiliation(s)
- Begoña Martínez-Cruz
- Muséum National d'Histoire Naturelle - Centre National de la Recherche Scientifique-Université Paris 7, UMR 7206, Éco-Anthropologie et Ethnobiologie, Paris, France
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19
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Jin HJ, Tyler-Smith C, Kim W. The peopling of Korea revealed by analyses of mitochondrial DNA and Y-chromosomal markers. PLoS One 2009; 4:e4210. [PMID: 19148289 PMCID: PMC2615218 DOI: 10.1371/journal.pone.0004210] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 12/08/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The Koreans are generally considered a northeast Asian group because of their geographical location. However, recent findings from Y chromosome studies showed that the Korean population contains lineages from both southern and northern parts of East Asia. To understand the genetic history and relationships of Korea more fully, additional data and analyses are necessary. METHODOLOGY AND RESULTS We analyzed mitochondrial DNA (mtDNA) sequence variation in the hypervariable segments I and II (HVS-I and HVS-II) and haplogroup-specific mutations in coding regions in 445 individuals from seven east Asian populations (Korean, Korean-Chinese, Mongolian, Manchurian, Han (Beijing), Vietnamese and Thais). In addition, published mtDNA haplogroup data (N = 3307), mtDNA HVS-I sequences (N = 2313), Y chromosome haplogroup data (N = 1697) and Y chromosome STR data (N = 2713) were analyzed to elucidate the genetic structure of East Asian populations. All the mtDNA profiles studied here were classified into subsets of haplogroups common in East Asia, with just two exceptions. In general, the Korean mtDNA profiles revealed similarities to other northeastern Asian populations through analysis of individual haplogroup distributions, genetic distances between populations or an analysis of molecular variance, although a minor southern contribution was also suggested. Reanalysis of Y-chromosomal data confirmed both the overall similarity to other northeastern populations, and also a larger paternal contribution from southeastern populations. CONCLUSION The present work provides evidence that peopling of Korea can be seen as a complex process, interpreted as an early northern Asian settlement with at least one subsequent male-biased southern-to-northern migration, possibly associated with the spread of rice agriculture.
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Affiliation(s)
- Han-Jun Jin
- Department of Biological Sciences, Dankook University, Cheonan, Korea
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Wook Kim
- Department of Biological Sciences, Dankook University, Cheonan, Korea
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Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms. BMC Genet 2008; 9:86. [PMID: 19077280 PMCID: PMC2621241 DOI: 10.1186/1471-2156-9-86] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Accepted: 12/12/2008] [Indexed: 02/04/2023] Open
Abstract
Background Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations. Results We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (RST = 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu RST = 0.96%, Andhra Pradesh RST = 0.77%) exceeds the estimate of variation between these geographically separated groups (RST = 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data. Conclusion Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions.
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21
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Tian C, Kosoy R, Lee A, Ransom M, Belmont JW, Gregersen PK, Seldin MF. Analysis of East Asia genetic substructure using genome-wide SNP arrays. PLoS One 2008; 3:e3862. [PMID: 19057645 PMCID: PMC2587696 DOI: 10.1371/journal.pone.0003862] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 11/10/2008] [Indexed: 11/19/2022] Open
Abstract
Accounting for population genetic substructure is important in reducing type 1 errors in genetic studies of complex disease. As efforts to understand complex genetic disease are expanded to different continental populations the understanding of genetic substructure within these continents will be useful in design and execution of association tests. In this study, population differentiation (Fst) and Principal Components Analyses (PCA) are examined using >200 K genotypes from multiple populations of East Asian ancestry. The population groups included those from the Human Genome Diversity Panel [Cambodian, Yi, Daur, Mongolian, Lahu, Dai, Hezhen, Miaozu, Naxi, Oroqen, She, Tu, Tujia, Naxi, Xibo, and Yakut], HapMap [ Han Chinese (CHB) and Japanese (JPT)], and East Asian or East Asian American subjects of Vietnamese, Korean, Filipino and Chinese ancestry. Paired Fst (Wei and Cockerham) showed close relationships between CHB and several large East Asian population groups (CHB/Korean, 0.0019; CHB/JPT, 00651; CHB/Vietnamese, 0.0065) with larger separation with Filipino (CHB/Filipino, 0.014). Low levels of differentiation were also observed between Dai and Vietnamese (0.0045) and between Vietnamese and Cambodian (0.0062). Similarly, small Fst's were observed among different presumed Han Chinese populations originating in different regions of mainland of China and Taiwan (Fst's <0.0025 with CHB). For PCA, the first two PC's showed a pattern of relationships that closely followed the geographic distribution of the different East Asian populations. PCA showed substructure both between different East Asian groups and within the Han Chinese population. These studies have also identified a subset of East Asian substructure ancestry informative markers (EASTASAIMS) that may be useful for future complex genetic disease association studies in reducing type 1 errors and in identifying homogeneous groups that may increase the power of such studies.
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Affiliation(s)
- Chao Tian
- Rowe Program in Human Genetics, Departments of Biochemistry and Medicine, University of California Davis, Davis, California, United States of America
| | - Roman Kosoy
- Rowe Program in Human Genetics, Departments of Biochemistry and Medicine, University of California Davis, Davis, California, United States of America
| | - Annette Lee
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, New York, United States of America
| | - Michael Ransom
- Rowe Program in Human Genetics, Departments of Biochemistry and Medicine, University of California Davis, Davis, California, United States of America
| | - John W. Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Peter K. Gregersen
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, New York, United States of America
| | - Michael F. Seldin
- Rowe Program in Human Genetics, Departments of Biochemistry and Medicine, University of California Davis, Davis, California, United States of America
- * E-mail:
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Hughes AL, Welch R, Puri V, Matthews C, Haque K, Chanock SJ, Yeager M. Genome-wide SNP typing reveals signatures of population history. Genomics 2008; 92:1-8. [PMID: 18485661 DOI: 10.1016/j.ygeno.2008.03.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Revised: 02/11/2008] [Accepted: 03/03/2008] [Indexed: 10/22/2022]
Abstract
Single-nucleotide polymorphism (SNP) arrays have become a popular technology for disease-association studies, but they also have potential for studying the genetic differentiation of human populations. Application of the Affymetrix GeneChip Human Mapping 500K Array Set to a population of 102 individuals representing the major ethnic groups in the United States (African, Asian, European, and Hispanic) revealed patterns of gene diversity and genetic distance that reflected population history. We analyzed allelic frequencies at 388,654 autosomal SNP sites that showed some variation in our study population and 10% or fewer missing values. Despite the small size (23-31 individuals) of each subpopulation, there were no fixed differences at any site between any two subpopulations. As expected from the African origin of modern humans, greater gene diversity was seen in Africans than in either Asians or Europeans, and the genetic distance between the Asian and the European populations was significantly lower than that between either of these two populations and Africans. Principal components analysis applied to a correlation matrix among individuals was able to separate completely the major continental groups of humans (Africans, Asians, and Europeans), while Hispanics overlapped all three of these groups. Genes containing two or more markers with extraordinarily high genetic distance between subpopulations were identified as candidate genes for health differences between subpopulations. The results show that, even with modest sample sizes, genome-wide SNP genotyping technologies have great promise for capturing signatures of gene frequency difference between human subpopulations, with applications in areas as diverse as forensics and the study of ethnic health disparities.
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Affiliation(s)
- Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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Li D, Li H, Ou C, Lu Y, Sun Y, Yang B, Qin Z, Zhou Z, Li S, Jin L. Paternal genetic structure of Hainan aborigines isolated at the entrance to East Asia. PLoS One 2008; 3:e2168. [PMID: 18478090 PMCID: PMC2374892 DOI: 10.1371/journal.pone.0002168] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Accepted: 04/01/2008] [Indexed: 11/25/2022] Open
Abstract
Background At the southern entrance to East Asia, early population migration has affected most of the Y-chromosome variations of East Asians. Methodology/Principal Findings To assess the isolated genetic structure of Hainan Island and the original genetic structure at the southern entrance, we studied the Y chromosome diversity of 405 Hainan Island aborigines from all the six populations, who have little influence of the recent mainland population relocations and admixtures. Here we report that haplogroups O1a* and O2a* are dominant among Hainan aborigines. In addition, the frequency of the mainland dominant haplogroup O3 is quite low among these aborigines, indicating that they have lived rather isolated. Clustering analyses suggests that the Hainan aborigines have been segregated since about 20 thousand years ago, after two dominant haplogroups entered East Asia (31 to 36 thousand years ago). Conclusions/Significance Our results suggest that Hainan aborigines have been isolated at the entrance to East Asia for about 20 thousand years, whose distinctive genetic characteristics could be used as important controls in many population genetic studies.
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Affiliation(s)
- Dongna Li
- Department of Biology, Hainan Medical College, Haikou, Hainan, China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
| | - Caiying Ou
- Department of Biology, Hainan Medical College, Haikou, Hainan, China
| | - Yan Lu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuantian Sun
- Department of Biology, Hainan Medical College, Haikou, Hainan, China
| | - Bo Yang
- Department of Anatomy, Third Military Medical University, Chongqing, China
| | - Zhendong Qin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhenjian Zhou
- Department of Biology, Hainan Medical College, Haikou, Hainan, China
| | - Shilin Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
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Mitochondrial DNA structure in the Arabian Peninsula. BMC Evol Biol 2008; 8:45. [PMID: 18269758 PMCID: PMC2268671 DOI: 10.1186/1471-2148-8-45] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Accepted: 02/12/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Two potential migratory routes followed by modern humans to colonize Eurasia from Africa have been proposed. These are the two natural passageways that connect both continents: the northern route through the Sinai Peninsula and the southern route across the Bab al Mandab strait. Recent archaeological and genetic evidence have favored a unique southern coastal route. Under this scenario, the study of the population genetic structure of the Arabian Peninsula, the first step out of Africa, to search for primary genetic links between Africa and Eurasia, is crucial. The haploid and maternally inherited mitochondrial DNA (mtDNA) molecule has been the most used genetic marker to identify and to relate lineages with clear geographic origins, as the African Ls and the Eurasian M and N that have a common root with the Africans L3. RESULTS To assess the role of the Arabian Peninsula in the southern route, we genetically analyzed 553 Saudi Arabs using partial (546) and complete mtDNA (7) sequencing, and compared the lineages obtained with those present in Africa, the Near East, central, east and southeast Asia and Australasia. The results showed that the Arabian Peninsula has received substantial gene flow from Africa (20%), detected by the presence of L, M1 and U6 lineages; that an 18% of the Arabian Peninsula lineages have a clear eastern provenance, mainly represented by U lineages; but also by Indian M lineages and rare M links with Central Asia, Indonesia and even Australia. However, the bulk (62%) of the Arabian lineages has a Northern source. CONCLUSION Although there is evidence of Neolithic and more recent expansions in the Arabian Peninsula, mainly detected by (preHV)1 and J1b lineages, the lack of primitive autochthonous M and N sequences, suggests that this area has been more a receptor of human migrations, including historic ones, from Africa, India, Indonesia and even Australia, than a demographic expansion center along the proposed southern coastal route.
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Genetic determinants of basal C-reactive protein expression in Filipino systemic lupus erythematosus families. Genes Immun 2008; 9:153-60. [PMID: 18216863 DOI: 10.1038/sj.gene.6364459] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Basal C-reactive protein (CRP) is a heritable trait associated with long-term cardiovascular disease risk. Existing studies leave ambiguity over the key functional polymorphisms and fail to adjust for trans-acting effects. In a novel cohort of 285 Filipino systemic lupus erythematosus probands and their first-degree relatives, we quantified serum CRP and typed a dense map of CRP single-nucleotide polymorphisms (SNPs), along with SNPs in the interleukin-1 beta, interleukin-6 and apolipoprotein E genes. Ten CRP SNPs demonstrated association with basal CRP in a regression model (P=0.011-0.002). These delineated two haplotypes associated with high and low basal CRP expression (P=0.002). Differences in allele frequency were seen compared with Caucasian populations, enabling us to argue for an independent genetic effect from a phylogenetically distinct haplotype tagged by SNP rs1800947. We demonstrated an association between Apo epsilon 2 and higher basal CRP. Interleukin-6 genotype was associated with basal CRP, highlighting a role for acute-phase cytokines even in basal expression. Identifying these trans-acting variants may improve the use of basal CRP as a predictor cardiovascular risk, and increase our power to detect associations between CRP and disease.
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Zhang F, Su B, Zhang YP, Jin L. Genetic studies of human diversity in East Asia. Philos Trans R Soc Lond B Biol Sci 2007; 362:987-95. [PMID: 17317646 PMCID: PMC2435565 DOI: 10.1098/rstb.2007.2028] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic history and designing and interpreting genetic studies of human diseases, in recent years researchers in China have made substantial efforts to collect samples and generate data especially for markers on Y chromosomes and mtDNA. The hallmark of these efforts is the discovery and confirmation of consistent distinction between northern and southern East Asian populations at genetic markers across the genome. With the confirmation of an African origin for East Asian populations and the observation of a dominating impact of the gene flow entering East Asia from the south in early human settlement, interpretation of the north-south division in this context poses the challenge to the field. Other areas of interest that have been studied include the gene flow between East Asia and its neighbouring regions (i.e. Central Asia, the Sub-continent, America and the Pacific Islands), the origin of Sino-Tibetan populations and expansion of the Chinese.
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Affiliation(s)
- Feng Zhang
- Institute of Genetics, School of Life Sciences, Fudan UniversityShanghai 200433, People's Republic of China
| | - Bing Su
- Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunming 650223, People's Republic of China
| | - Ya-ping Zhang
- Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunming 650223, People's Republic of China
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan UniversityKunming 650091, People's Republic of China
| | - Li Jin
- Institute of Genetics, School of Life Sciences, Fudan UniversityShanghai 200433, People's Republic of China
- CAS-MPG Partner Institute of Computational Biology, Chinese Academy of SciencesShanghai 200031, People's Republic of China
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Bazrgar M, Karimi M, Fathzadeh M, Senemar S, Peiravian F, Shojaee A, Saadat M. Apolipoprotein E polymorphism in Southern Iran: E4 allele in the lowest reported amounts. Mol Biol Rep 2007; 35:495-9. [PMID: 17594534 DOI: 10.1007/s11033-007-9113-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 05/31/2007] [Indexed: 01/18/2023]
Abstract
BACKGROUND Apolipoprotein E (apoE) with three major alleles E2, E3 and E4 is one of the critical genes in lipid metabolism. Common apoE alleles are in association with an increase in risk for central nervous and cardiovascular diseases such as Alzheimer's disease, dementia, multiple sclerosis, atherosclerosis, coronary heart disease, hyperlipoproteinemia and stroke. ApoE3 is known as the most frequent allele in all populations, while association of apoE gene polymorphism with reported diseases have mostly been related to other two major alleles especially apoE4. OBJECTIVE To determine of apoE alleles frequencies in Southern Iran and comparison of those frequencies with other populations. METHODS DNA was extracted from the whole blood of 198 healthy unrelated candidates from population of Fars Province, Southern Iran, for apoE genotyping who were checked up by a physician. The frequencies of apoE alleles were compared with other populations by chi(2) test. RESULTS The frequencies of E2, E3 and E4 were 0.063, 0.886 and 0.051 respectively. These values were similar to those reported from populations of Kuwait, Oman, Lebanon, India, Turkey, Greece, Spain, Sardinia Islands of Italy and two Iranian populations but were different from South of Italy and Caucasians in other Europe regions, American, American-Indian, African, East Asian and Saudi populations (P < 0.05). CONCLUSION The frequency of E4 allele as a genetic risk factor for some multifactorial diseases in the population of Southern Iran is in the lowest reported amounts in the world. Iranian population has Caucasoid origin but differs from some Caucasian populations in Europe and America. The results of present study are in agreement with the historical evidences which show admixture of Iranian population with other populations and some studies based on genetic polymorphisms in the population of Southern Iran.
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Affiliation(s)
- Masood Bazrgar
- Human Genetic Research Group, Iranian Academic Center for Education, Culture & Research, Fars Province Branch, Zand Ave., P.O. Box: 71345-1463, Shiraz, Iran.
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Gayden T, Cadenas AM, Regueiro M, Singh NB, Zhivotovsky LA, Underhill PA, Cavalli-Sforza LL, Herrera RJ. The Himalayas as a directional barrier to gene flow. Am J Hum Genet 2007; 80:884-94. [PMID: 17436243 PMCID: PMC1852741 DOI: 10.1086/516757] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Accepted: 02/23/2007] [Indexed: 11/03/2022] Open
Abstract
High-resolution Y-chromosome haplogroup analyses coupled with Y-short tandem repeat (STR) haplotypes were used to (1) investigate the genetic affinities of three populations from Nepal--including Newar, Tamang, and people from cosmopolitan Kathmandu (referred to as "Kathmandu" subsequently)--as well as a collection from Tibet and (2) evaluate whether the Himalayan mountain range represents a geographic barrier for gene flow between the Tibetan plateau and the South Asian subcontinent. The results suggest that the Tibetans and Nepalese are in part descendants of Tibeto-Burman-speaking groups originating from Northeast Asia. All four populations are represented predominantly by haplogroup O3a5-M134-derived chromosomes, whose Y-STR-based age (+/-SE) was estimated at 8.1+/-2.9 thousand years ago (KYA), more recent than its Southeast Asian counterpart. The most pronounced difference between the two regions is reflected in the opposing high-frequency distributions of haplogroups D in Tibet and R in Nepal. With the exception of Tamang, both Newar and Kathmandu exhibit considerable similarities to the Indian Y-haplogroup distribution, particularly in their haplogroup R and H composition. These results indicate gene flow from the Indian subcontinent and, in the case of haplogroup R, from Eurasia as well, a conclusion that is also supported by the admixture analysis. In contrast, whereas haplogroup D is completely absent in Nepal, it accounts for 50.6% of the Tibetan Y-chromosome gene pool. Coalescent analyses suggest that the expansion of haplogroup D derivatives--namely, D1-M15 and D3-P47 in Tibet--involved two different demographic events (5.1+/-1.8 and 11.3+/-3.7 KYA, respectively) that are more recent than those of D2-M55 representatives common in Japan. Low frequencies, relative to Nepal, of haplogroup J and R lineages in Tibet are also consistent with restricted gene flow from the subcontinent. Yet the presence of haplogroup O3a5-M134 representatives in Nepal indicates that the Himalayas have been permeable to dispersals from the east. These genetic patterns suggest that this cordillera has been a biased bidirectional barrier.
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Affiliation(s)
- Tenzin Gayden
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
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Thangaraj K, Chaubey G, Reddy AG, Singh VK, Singh L. Unique origin of Andaman Islanders: insight from autosomal loci. J Hum Genet 2006; 51:800-804. [PMID: 16924390 DOI: 10.1007/s10038-006-0026-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2006] [Accepted: 06/01/2006] [Indexed: 10/24/2022]
Abstract
Our mtDNA and Y chromosome studies lead to the conclusion that the Andamanese "Negrito" mtDNA lineages have survived in the Andaman Islands in complete genetic isolation from other South and Southeast Asian populations since the initial settlement of the region by the out-of-Africa migration. In order to obtain a robust reconstruction of the evolutionary history of the Andamanese, we carried out a study on the three aboriginal populations, namely, the Great Andamanese, Onge and Nicobarese, using autosomal microsatellite markers. The range of alleles (7-31.2) observed in the studied population and heterozygosity values (0.392-0.857) indicate that the selected STR markers are highly polymorphic in all the three populations, and genetic variability within the populations is significantly high, with a mean gene diversity of 77%. The Andaman "Negrito" populations do not show particular affinities either with the African populations or with the Indian populations, confirming their unique origin. In contrast, Nicobarese show close affinities with the Southeast Asian populations, suggesting their recent entry in the Islands.
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Affiliation(s)
- K Thangaraj
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India
| | - G Chaubey
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India
- Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, 51010, Estonia
| | - A G Reddy
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India
| | - V K Singh
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India
| | - L Singh
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India.
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Adeyemo AA, Chen G, Chen Y, Rotimi C. Genetic structure in four West African population groups. BMC Genet 2005; 6:38. [PMID: 15978124 PMCID: PMC1180433 DOI: 10.1186/1471-2156-6-38] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Accepted: 06/24/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Africa contains the most genetically divergent group of continental populations and several studies have reported that African populations show a high degree of population stratification. In this regard, it is important to investigate the potential for population genetic structure or stratification in genetic epidemiology studies involving multiple African populations. The presences of genetic sub-structure, if not properly accounted for, have been reported to lead to spurious association between a putative risk allele and a disease. Within the context of the Africa America Diabetes Mellitus (AADM) Study (a genetic epidemiologic study of type 2 diabetes mellitus in West Africa), we have investigated population structure or stratification in four ethnic groups in two countries (Akan and Gaa-Adangbe from Ghana, Yoruba and Igbo from Nigeria) using data from 372 autosomal microsatellite loci typed in 493 unrelated persons (986 chromosomes). RESULTS There was no significant population genetic structure in the overall sample. The smallest probability is associated with an inferred cluster of 1 and little of the posterior probability is associated with a higher number of inferred clusters. The distribution of members of the sample to inferred clusters is consistent with this finding; roughly the same proportion of individuals from each group is assigned to each cluster with little variation between the ethnic groups. Analysis of molecular variance (AMOVA) showed that the between-population component of genetic variance is less than 0.1% in contrast to 99.91% for the within population component. Pair-wise genetic distances between the four ethnic groups were also very similar. Nonetheless, the small between-population genetic variance was sufficient to distinguish the two Ghanaian groups from the two Nigerian groups. CONCLUSION There was little evidence for significant population substructure in the four major West African ethnic groups represented in the AADM study sample. Ethnicity apparently did not introduce differential allele frequencies that may affect analysis and interpretation of linkage and association studies. These findings, although not entirely surprising given the geographical proximity of these groups, provide important insights into the genetic relationships between the ethnic groups studied and confirm previous results that showed close genetic relationship between most studied West African groups.
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Affiliation(s)
- Adebowale A Adeyemo
- College of Medicine, University of Ibadan, Ibadan. Nigeria
- National Human Genome Center, Howard University, Washington DC, USA
| | - Guanjie Chen
- National Human Genome Center, Howard University, Washington DC, USA
| | - Yuanxiu Chen
- National Human Genome Center, Howard University, Washington DC, USA
| | - Charles Rotimi
- National Human Genome Center, Howard University, Washington DC, USA
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Kwak KD, Jin HJ, Shin DJ, Kim JM, Roewer L, Krawczak M, Tyler-Smith C, Kim W. Y-chromosomal STR haplotypes and their applications to forensic and population studies in east Asia. Int J Legal Med 2005; 119:195-201. [PMID: 15856270 DOI: 10.1007/s00414-004-0518-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Accepted: 12/08/2004] [Indexed: 11/26/2022]
Abstract
We have analyzed 11 Y-STR loci (DYS19, the two DYS385 loci, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DXYS156Y) in 700 males from ten ethnic groups in east Asia in order to evaluate their usefulness for forensic and population genetic studies. A total of 644 different haplotypes were identified, among which 603 (86.14%) were individual-specific. The haplotype diversity averaged over all populations was 0.9997; using only the nine Y-STRs comprising the "minimal haplotype" (excluding DYS388 and DXYS156Y) it was 0.9996, a value similar to that found in 1924 samples from other Asian populations (0.9996; Lessig et al. Legal Medicine 5(2003) 160-163), and slightly higher than in European populations (0.9976; n=11,610; Roewer et al. For Sci International (2001) 118:103-111). All of the individual east Asian populations examined here had high haplotype diversity (> or =0.997), except for the Mongolians (0.992) and Manchurians (0.960). The most frequent haplotype identified by the nine markers was present at only 1% (7/700). Population comparisons based on Phi(ST) or rho genetic distance measures revealed clustering according to the traditional northeast-southeast distinction, but with exceptions. For example, the Yunnan population from southern China lay among the northern populations, possibly reflecting recent migration, while the Korean population, traditionally considered northern, lay at the boundary between northern and southern populations. An admixture estimate suggested 55(51-59)% northern, 45(41-49)% southern contribution to the Koreans, illustrating the complexity of the genetic history of this region.
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Affiliation(s)
- Kyoung Don Kwak
- Department of Biological Sciences, Dankook University, Cheonan, 330-714, South Korea
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Jin HJ, Kwak KD, Hammer MF, Nakahori Y, Shinka T, Lee JW, Jin F, Jia X, Tyler-Smith C, Kim W. Y-chromosomal DNA haplogroups and their implications for the dual origins of the Koreans. Hum Genet 2003; 114:27-35. [PMID: 14505036 DOI: 10.1007/s00439-003-1019-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2003] [Accepted: 07/31/2003] [Indexed: 10/26/2022]
Abstract
We have analyzed eight Y-chromosomal binary markers (YAP, RPS4Y(711), M9, M175, LINE1, SRY(+465), 47z, and M95) and three Y-STR markers (DYS390, DYS391, and DYS393) in 738 males from 11 ethnic groups in east Asia in order to study the male lineage history of Korea. Haplogroup DE-YAP was found at a high frequency only in Japan but was also present at low frequencies in northeast Asia, including 2.5% in Korea, suggesting a northern origin for these chromosomes. Haplogroup C-RPS4Y(711) was present in Korea and Manchuria at moderate frequencies: higher than in populations from southeast Asia, but lower than those in the northeast, which may imply a northern Asian expansion of these lineages, perhaps from Mongolia or Siberia. The major Y-chromosomal expansions in east Asia were those of haplogroup O-M175 (and its sublineages). This haplogroup is likely to have originated in southern east Asia and subsequently expanded to all of east Asia. The moderate frequency of one sublineage in the Koreans, haplogroup O-LINE1 (12.5%), could be a result of interaction with Chinese populations. The age of another sublineage, haplogroup O-SRY(+465), and Y-STR haplotype diversity provide evidence for relatively recent male migration, originally from China, through Korea into Japan. In conclusion, the distribution pattern of Y-chromosomal haplogroups reveals the complex origin of the Koreans, resulting from genetic contributions involving the northern Asian settlement and range expansions mostly from southern-to-northern China.
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Affiliation(s)
- Han-Jun Jin
- Department of Biological Sciences, Dankook University, 330-714 Cheonan, Korea
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Zhivotovsky LA, Rosenberg NA, Feldman MW. Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers. Am J Hum Genet 2003; 72:1171-86. [PMID: 12690579 PMCID: PMC1180270 DOI: 10.1086/375120] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2002] [Accepted: 02/20/2003] [Indexed: 11/03/2022] Open
Abstract
We study data on variation in 52 worldwide populations at 377 autosomal short tandem repeat loci, to infer a demographic history of human populations. Variation at di-, tri-, and tetranucleotide repeat loci is distributed differently, although each class of markers exhibits a decrease of within-population genetic variation in the following order: sub-Saharan Africa, Eurasia, East Asia, Oceania, and America. There is a similar decrease in the frequency of private alleles. With multidimensional scaling, populations belonging to the same major geographic region cluster together, and some regions permit a finer resolution of populations. When a stepwise mutation model is used, a population tree based on TD estimates of divergence time suggests that the branches leading to the present sub-Saharan African populations of hunter-gatherers were the first to diverge from a common ancestral population (approximately 71-142 thousand years ago). The branches corresponding to sub-Saharan African farming populations and those that left Africa diverge next, with subsequent splits of branches for Eurasia, Oceania, East Asia, and America. African hunter-gatherer populations and populations of Oceania and America exhibit no statistically significant signature of growth. The features of population subdivision and growth are discussed in the context of the ancient expansion of modern humans.
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Affiliation(s)
- Lev A. Zhivotovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Program in Molecular and Computational Biology, University of Southern California, Los Angeles; and Department of Biological Sciences, Stanford University, Stanford, CA
| | - Noah A. Rosenberg
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Program in Molecular and Computational Biology, University of Southern California, Los Angeles; and Department of Biological Sciences, Stanford University, Stanford, CA
| | - Marcus W. Feldman
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Program in Molecular and Computational Biology, University of Southern California, Los Angeles; and Department of Biological Sciences, Stanford University, Stanford, CA
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Kivisild T, Rootsi S, Metspalu M, Mastana S, Kaldma K, Parik J, Metspalu E, Adojaan M, Tolk HV, Stepanov V, Gölge M, Usanga E, Papiha SS, Cinnioğlu C, King R, Cavalli-Sforza L, Underhill PA, Villems R. The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. Am J Hum Genet 2003; 72:313-32. [PMID: 12536373 PMCID: PMC379225 DOI: 10.1086/346068] [Citation(s) in RCA: 299] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2002] [Accepted: 10/29/2002] [Indexed: 11/04/2022] Open
Abstract
Two tribal groups from southern India--the Chenchus and Koyas--were analyzed for variation in mitochondrial DNA (mtDNA), the Y chromosome, and one autosomal locus and were compared with six caste groups from different parts of India, as well as with western and central Asians. In mtDNA phylogenetic analyses, the Chenchus and Koyas coalesce at Indian-specific branches of haplogroups M and N that cover populations of different social rank from all over the subcontinent. Coalescence times suggest early late Pleistocene settlement of southern Asia and suggest that there has not been total replacement of these settlers by later migrations. H, L, and R2 are the major Indian Y-chromosomal haplogroups that occur both in castes and in tribal populations and are rarely found outside the subcontinent. Haplogroup R1a, previously associated with the putative Indo-Aryan invasion, was found at its highest frequency in Punjab but also at a relatively high frequency (26%) in the Chenchu tribe. This finding, together with the higher R1a-associated short tandem repeat diversity in India and Iran compared with Europe and central Asia, suggests that southern and western Asia might be the source of this haplogroup. Haplotype frequencies of the MX1 locus of chromosome 21 distinguish Koyas and Chenchus, along with Indian caste groups, from European and eastern Asian populations. Taken together, these results show that Indian tribal and caste populations derive largely from the same genetic heritage of Pleistocene southern and western Asians and have received limited gene flow from external regions since the Holocene. The phylogeography of the primal mtDNA and Y-chromosome founders suggests that these southern Asian Pleistocene coastal settlers from Africa would have provided the inocula for the subsequent differentiation of the distinctive eastern and western Eurasian gene pools.
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MESH Headings
- Asia, Central/ethnology
- Asia, Western/ethnology
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Y/genetics
- DNA, Mitochondrial/analysis
- DNA, Mitochondrial/genetics
- Ethnicity/genetics
- Europe
- Gene Frequency
- Genetic Variation
- Genetics, Population
- Haplotypes
- Humans
- India
- Male
- Phylogeny
- Polymorphism, Single Nucleotide
- Social Class
- Tandem Repeat Sequences
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Affiliation(s)
- T Kivisild
- Institute of Molecular and Cell Biology, Tartu University, Tartu, Estonia.
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Vioarsdóttir US, O'Higgins P, Stringer C. A geometric morphometric study of regional differences in the ontogeny of the modern human facial skeleton. J Anat 2002; 201:211-29. [PMID: 12363273 PMCID: PMC1570912 DOI: 10.1046/j.1469-7580.2002.00092.x] [Citation(s) in RCA: 187] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2002] [Indexed: 11/20/2022] Open
Abstract
This study examines interpopulation variations in the facial skeleton of 10 modern human populations and places these in an ontogenetic perspective. It aims to establish the extent to which the distinctive features of adult representatives of these populations are present in the early post natal period and to what extent population differences in ontogenetic scaling and allometric trajectories contribute to distinct facial forms. The analyses utilize configurations of facial landmarks and are carried out using geometric morphometric methods. The results of this study show that modern human populations can be distinguished based on facial shape alone, irrespective of age or sex, indicating the early presence of differences. Additionally, some populations have statistically distinct facial ontogenetic trajectories that lead to the development of further differences later in ontogeny. We conclude that population-specific facial morphologies develop principally through distinctions in facial shape probably already present at birth and further accentuated and modified to variable degrees during growth. These findings raise interesting questions regarding the plasticity of facial growth patterns in modern humans. Further, they have important implications in relation to the study of growth in the face of fossil hominins and in relation to the possibility of developing effective discriminant functions for the identification of population affinities of immature facial skeletal material. Such tools would be of value in archaeological, forensic and anthropological applications. The findings of this study underline the need to examine more deeply, and in more detail, the ontogenetic basis of other causes of craniometric variation, such as sexual dimorphism and hominin species differentiation.
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Kurzban R, Tooby J, Cosmides L. Can race be erased? Coalitional computation and social categorization. Proc Natl Acad Sci U S A 2001; 98:15387-92. [PMID: 11742078 PMCID: PMC65039 DOI: 10.1073/pnas.251541498] [Citation(s) in RCA: 299] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Previous studies have established that people encode the race of each individual they encounter, and do so via computational processes that appear to be both automatic and mandatory. If true, this conclusion would be important, because categorizing others by their race is a precondition for treating them differently according to race. Here we report experiments, using unobtrusive measures, showing that categorizing individuals by race is not inevitable, and supporting an alternative hypothesis: that encoding by race is instead a reversible byproduct of cognitive machinery that evolved to detect coalitional alliances. The results show that subjects encode coalitional affiliations as a normal part of person representation. More importantly, when cues of coalitional affiliation no longer track or correspond to race, subjects markedly reduce the extent to which they categorize others by race, and indeed may cease doing so entirely. Despite a lifetime's experience of race as a predictor of social alliance, less than 4 min of exposure to an alternate social world was enough to deflate the tendency to categorize by race. These results suggest that racism may be a volatile and eradicable construct that persists only so long as it is actively maintained through being linked to parallel systems of social alliance.
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Affiliation(s)
- R Kurzban
- Center for Evolutionary Psychology, University of California, Santa Barbara, CA 93106-2070, USA.
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Karafet T, Xu L, Du R, Wang W, Feng S, Wells RS, Redd AJ, Zegura SL, Hammer MF. Paternal population history of East Asia: sources, patterns, and microevolutionary processes. Am J Hum Genet 2001; 69:615-28. [PMID: 11481588 PMCID: PMC1235490 DOI: 10.1086/323299] [Citation(s) in RCA: 173] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2001] [Accepted: 07/12/2001] [Indexed: 11/03/2022] Open
Abstract
Asia has served as a focal point for human migration during much of the Late Pleistocene and Holocene. Clarification of East Asia's role as a source and/or transit point for human dispersals requires that this region's own settlement history be understood. To this end, we examined variation at 52 polymorphic sites on the nonrecombining portion of the Y chromosome (NRY) in 1,383 unrelated males, representing 25 populations from southern East Asia (SEAS), northern East Asia (NEAS), and central Asia (CAS). The polymorphisms defined 45 global haplogroups, 28 of which were present in these three regions. Although heterozygosity levels were similar in all three regions, the average pairwise difference among haplogroups was noticeably smaller in SEAS. Multidimensional scaling analysis indicated a general separation of SEAS versus NEAS and CAS populations, and analysis of molecular variance produced very different values of Phi(ST) in NEAS and SEAS populations. In spatial autocorrelation analyses, the overall correlogram exhibited a clinal pattern; however, the NEAS populations showed evidence of both isolation by distance and ancient clines, whereas there was no evidence of structure in SEAS populations. Nested cladistic analysis demonstrated that population history events and ongoing demographic processes both contributed to the contrasting patterns of NRY variation in NEAS and SEAS. We conclude that the peopling of East Asia was more complex than earlier models had proposed-that is, a multilayered, multidirectional, and multidisciplinary framework is necessary. For instance, in addition to the previously recognized genetic and dental dispersal signals from SEAS to NEAS populations, CAS has made a significant contribution to the contemporary gene pool of NEAS, and the Sino-Tibetan expansion has left traces of a genetic trail from northern to southern China.
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Affiliation(s)
- T Karafet
- Laboratory of Molecular Systematics and Evolution, University of Arizona, Tucson, AZ 85721, USA
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Kayser M, Brauer S, Weiss G, Schiefenhövel W, Underhill PA, Stoneking M. Independent histories of human Y chromosomes from Melanesia and Australia. Am J Hum Genet 2001; 68:173-190. [PMID: 11115381 PMCID: PMC1234911 DOI: 10.1086/316949] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2000] [Accepted: 11/14/2000] [Indexed: 01/08/2023] Open
Abstract
To investigate the origins and relationships of Australian and Melanesian populations, 611 males from 18 populations from Australia, Melanesia, and eastern/southeastern Asia were typed for eight single-nucleotide polymorphism (SNP) loci and seven short tandem-repeat loci on the Y chromosome. A unique haplotype, DYS390.1del/RPS4Y711T, was found at a frequency of 53%-69% in Australian populations, whereas the major haplotypes found in Melanesian populations (M4G/M5T/M9G and DYS390.3del/RPS4Y711T) are absent from the Australian populations. The Y-chromosome data thus indicate independent histories for Australians and Melanesians, a finding that is in agreement with evidence from mtDNA but that contradicts some analyses of autosomal loci, which show a close relationship between Australian and Melanesian (specifically, highland Papua New Guinean) populations. Since the Australian and New Guinean landmasses were connected when first colonized by humans > or =50,000 years ago but separated some 8,000 years ago, a possible way to reconcile all the genetic data is to infer that the Y-chromosome and mtDNA results reflect the past 8,000 years of independent history for Australia and New Guinea, whereas the autosomal loci reflect the long preceding period of common origin and shared history. Two Y-chromosome haplotypes (M119C/M9G and M122C/M9G) that originated in eastern/southeastern Asia are present in coastal and island Melanesia but are rare or absent in both Australia and highland Papua New Guinea. This distribution, along with demographic analyses indicating that population expansions for both haplotypes began approximately 4,000-6,000 years ago, suggests that these haplotypes were brought to Melanesia by the Austronesian expansion. Most of the populations in this study were previously typed for mtDNA SNPs; population differentiation is greater for the Y chromosome than for mtDNA and is significantly correlated with geographic distance, a finding in agreement with results of similar analyses of European populations.
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Affiliation(s)
- M Kayser
- Max Planck Institute for Evolutionary Anthropology, Department for Evolutionary Genetics, D-04103 Leipzig, Germany.
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Tishkoff SA, Pakstis AJ, Stoneking M, Kidd JR, Destro-Bisol G, Sanjantila A, Lu RB, Deinard AS, Sirugo G, Jenkins T, Kidd KK, Clark AG. Short tandem-repeat polymorphism/alu haplotype variation at the PLAT locus: implications for modern human origins. Am J Hum Genet 2000; 67:901-25. [PMID: 10986042 PMCID: PMC1287905 DOI: 10.1086/303068] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2000] [Accepted: 07/18/2000] [Indexed: 01/10/2023] Open
Abstract
Two dinucleotide short tandem-repeat polymorphisms (STRPs) and a polymorphic Alu element spanning a 22-kb region of the PLAT locus on chromosome 8p12-q11.2 were typed in 1,287-1,420 individuals originating from 30 geographically diverse human populations, as well as in 29 great apes. These data were analyzed as haplotypes consisting of each of the dinucleotide repeats and the flanking Alu insertion/deletion polymorphism. The global pattern of STRP/Alu haplotype variation and linkage disequilibrium (LD) is informative for the reconstruction of human evolutionary history. Sub-Saharan African populations have high levels of haplotype diversity within and between populations, relative to non-Africans, and have highly divergent patterns of LD. Non-African populations have both a subset of the haplotype diversity present in Africa and a distinct pattern of LD. The pattern of haplotype variation and LD observed at the PLAT locus suggests a recent common ancestry of non-African populations, from a small population originating in eastern Africa. These data indicate that, throughout much of modern human history, sub-Saharan Africa has maintained both a large effective population size and a high level of population substructure. Additionally, Papua New Guinean and Micronesian populations have rare haplotypes observed otherwise only in African populations, suggesting ancient gene flow from Africa into Papua New Guinea, as well as gene flow between Melanesian and Micronesian populations.
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Affiliation(s)
- S A Tishkoff
- University of Maryland, Department of Biology, University of Maryland, College Park, MD 20742, USA.
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40
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Ting CT, Tsaur SC, Wu CI. The phylogeny of closely related species as revealed by the genealogy of a speciation gene, Odysseus. Proc Natl Acad Sci U S A 2000; 97:5313-6. [PMID: 10779562 PMCID: PMC25825 DOI: 10.1073/pnas.090541597] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/1999] [Indexed: 11/18/2022] Open
Abstract
Molecular differentiation between races or closely related species is often incongruent with the reproductive divergence of the taxa of interest. Shared ancient polymorphism and/or introgression during secondary contact may be responsible for the incongruence. At loci contributing to speciation, these two complications should be minimized (1, 2); hence, their variation may more faithfully reflect the history of the species' reproductive differentiation. In this study, we analyzed DNA polymorphism at the Odysseus (OdsH) locus of hybrid sterility between Drosophila mauritiana and Drosophila simulans and were able to verify such a prediction. Interestingly, DNA variation only a short distance away (1.8 kb) appears not to be influenced by the forces that shape the recent evolution of the OdsH coding region. This locus thus may represent a test case of inferring phylogeny of very closely related species.
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Affiliation(s)
- C T Ting
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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41
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Green LD, Derr JN, Knight A. mtDNA affinities of the peoples of North-Central Mexico. Am J Hum Genet 2000; 66:989-98. [PMID: 10712213 PMCID: PMC1288179 DOI: 10.1086/302801] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
mtDNA haplotypes of representatives of the cosmopolitan peoples of north-central Mexico were studied. Two hundred twenty-three samples from individuals residing in vicinities of two localities in north-central Mexico were analyzed. A combination of strategies was employed to identify the origin of each haplotype, including length variation analysis of the COII and tRNALYS intergenic region, nucleotide sequence analysis of control region hypervariable segment 1, and RFLP analysis of PCR products spanning diagnostic sites. Analysis of these data revealed that the majority of the mtDNA haplotypes were of Native American origin, belonging to one of four primary Native American haplogroups. Others were of European or African origin, and the frequency of African haplotypes was equivalent to that of haplotypes of European derivation. These results provide diagnostic, discrete character, molecular genetic evidence that, together with results of previous studies of classical genetic systems, is informative with regard to both the magnitude of African admixture and the relative maternal contribution of African, European, and Native American peoples to the genetic heritage of Mexico. Phylogenetic analysis revealed that African sequences formed a basal, paraphyletic group.
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Affiliation(s)
- L D Green
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
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42
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Peterson RJ, Goldman D, Long JC. Effects of worldwide population subdivision on ALDH2 linkage disequilibrium. Genome Res 1999; 9:844-52. [PMID: 10508843 PMCID: PMC310807 DOI: 10.1101/gr.9.9.844] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/1999] [Accepted: 06/29/1999] [Indexed: 11/25/2022]
Abstract
The effect of human population subdivision on linkage disequilibrium has previously been studied for unlinked genes. However, no study has focused on closely linked polymorphisms or formally partitioned linkage disequilibrium within and among worldwide populations. With an emphasis on population subdivision, the goal of this paper is to investigate the causes of linkage disequilibrium in ALDH2, the gene that encodes aldehyde dehydrogenase 2. Haplotypes for 756 people from 17 populations across five continents were estimated by maximum-likelihood from genotypes at six closely linked ALDH2 nucleotide substitutions. Linkage disequilibrium was partitioned into three components: within populations, among populations within continents, and among continents. It was found that population subdivision among continents had a larger and more disparate effect on linkage disequilibrium than subdivision among local populations. Further, linkage disequilibrium did not increase with population divergence as predicted by a simple model. Rather, the patterns of linkage disequilibrium were complicated because of the interplay of a near absence of recombination, the linkage disequilibrium that existed prior to the divergence of modern humans, subsequent mutation, population subdivision, random genetic drift, and perhaps natural selection. These results suggest that simple models may not well predict patterns of linkage disequilibrium in human populations.
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Affiliation(s)
- R J Peterson
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland 20892-8110 USA.
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43
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Redd AJ, Stoneking M. Peopling of Sahul: mtDNA variation in aboriginal Australian and Papua New Guinean populations. Am J Hum Genet 1999; 65:808-28. [PMID: 10441589 PMCID: PMC1377989 DOI: 10.1086/302533] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
We examined genetic affinities of Aboriginal Australian and New Guinean populations by using nucleotide variation in the two hypervariable segments of the mtDNA control region (CR). A total of 318 individuals from highland Papua New Guinea (PNG), coastal PNG, and Aboriginal Australian populations were typed with a panel of 29 sequence-specific oligonucleotide (SSO) probes. The SSO-probe panel included five new probes that were used to type an additional 1,037 individuals from several Asian populations. The SSO-type data guided the selection of 78 individuals from Australia and east Indonesia for CR sequencing. A gene tree of these CR sequences, combined with published sequences from worldwide populations, contains two previously identified highland PNG clusters that do not include any Aboriginal Australians; the highland PNG clusters have coalescent time estimates of approximately 80,000 and 122,000 years ago, suggesting ancient isolation and genetic drift. SSO-type data indicate that 84% of the sample of PNG highlander mtDNA belong to these two clusters. In contrast, the Aboriginal Australian sequences are intermingled throughout the tree and cluster with sequences from multiple populations. Phylogenetic and multidimensional-scaling analyses of CR sequences and SSO types split PNG highland and Aboriginal Australian populations and link Aboriginal Australian populations with populations from the subcontinent of India. These mtDNA results do not support a close relationship between Aboriginal Australian and PNG populations but instead suggest multiple migrations in the peopling of Sahul.
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Affiliation(s)
- A J Redd
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA.
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44
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Nei M, Kumar S, Takahashi K. The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proc Natl Acad Sci U S A 1998; 95:12390-7. [PMID: 9770497 PMCID: PMC22842 DOI: 10.1073/pnas.95.21.12390] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the maximum parsimony (MP) and minimum evolution (ME) methods of phylogenetic inference, evolutionary trees are constructed by searching for the topology that shows the minimum number of mutational changes required (M) and the smallest sum of branch lengths (S), respectively, whereas in the maximum likelihood (ML) method the topology showing the highest maximum likelihood (A) of observing a given data set is chosen. However, the theoretical basis of the optimization principle remains unclear. We therefore examined the relationships of M, S, and A for the MP, ME, and ML trees with those for the true tree by using computer simulation. The results show that M and S are generally greater for the true tree than for the MP and ME trees when the number of nucleotides examined (n) is relatively small, whereas A is generally lower for the true tree than for the ML tree. This finding indicates that the optimization principle tends to give incorrect topologies when n is small. To deal with this disturbing property of the optimization principle, we suggest that more attention should be given to testing the statistical reliability of an estimated tree rather than to finding the optimal tree with excessive efforts. When a reliability test is conducted, simplified MP, ME, and ML algorithms such as the neighbor-joining method generally give conclusions about phylogenetic inference very similar to those obtained by the more extensive tree search algorithms.
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Affiliation(s)
- M Nei
- Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802-5301, USA.
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45
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Suzuki Y, Gojobori T. The origin and evolution of human T-cell lymphotropic virus types I and II. Virus Genes 1998; 16:69-84. [PMID: 9562892 DOI: 10.1023/a:1007953826869] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Studies on human T-cell lymphotropic virus types I (HTLV-I) and II (HTLV-II) are briefly reviewed from the viewpoint of molecular evolution, with special reference to the evolutionary rate and evolutionary relationships among these viruses. In particular, it appears that, in contrast to the low level of variability of HTLV-I among different isolates, individual isolates form quasispecies structures. Elucidating the mechanisms connecting these two phenomena will be one of the future problems in the study of the molecular evolution of HTLV-I and HTLV-II.
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Affiliation(s)
- Y Suzuki
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
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46
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Poloni ES, Semino O, Passarino G, Santachiara-Benerecetti AS, Dupanloup I, Langaney A, Excoffier L. Human genetic affinities for Y-chromosome P49a,f/TaqI haplotypes show strong correspondence with linguistics. Am J Hum Genet 1997; 61:1015-35. [PMID: 9346874 PMCID: PMC1716025 DOI: 10.1086/301602] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Numerous population samples from around the world have been tested for Y chromosome-specific p49a,f/TaqI restriction polymorphisms. Here we review the literature as well as unpublished data on Y-chromosome p49a,f/TaqI haplotypes and provide a new nomenclature unifying the notations used by different laboratories. We use this large data set to study worldwide genetic variability of human populations for this paternally transmitted chromosome segment. We observe, for the Y chromosome, an important level of population genetics structure among human populations (FST = .230, P < .001), mainly due to genetic differences among distinct linguistic groups of populations (FCT = .246, P < .001). A multivariate analysis based on genetic distances between populations shows that human population structure inferred from the Y chromosome corresponds broadly to language families (r = .567, P < .001), in agreement with autosomal and mitochondrial data. Times of divergence of linguistic families, estimated from their internal level of genetic differentiation, are fairly concordant with current archaeological and linguistic hypotheses. Variability of the p49a,f/TaqI polymorphic marker is also significantly correlated with the geographic location of the populations (r = .613, P < .001), reflecting the fact that distinct linguistic groups generally also occupy distinct geographic areas. Comparison of Y-chromosome and mtDNA RFLPs in a restricted set of populations shows a globally high level of congruence, but it also allows identification of unequal maternal and paternal contributions to the gene pool of several populations.
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Affiliation(s)
- E S Poloni
- Département d'Anthropologie et Ecologie, Université de Genève, Carouge, Switzerland.
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47
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Barbujani G, Magagni A, Minch E, Cavalli-Sforza LL. An apportionment of human DNA diversity. Proc Natl Acad Sci U S A 1997; 94:4516-9. [PMID: 9114021 PMCID: PMC20754 DOI: 10.1073/pnas.94.9.4516] [Citation(s) in RCA: 257] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
It is often taken for granted that the human species is divided in rather homogeneous groups or races, among which biological differences are large. Studies of allele frequencies do not support this view, but they have not been sufficient to rule it out either. We analyzed human molecular diversity at 109 DNA markers, namely 30 microsatellite loci and 79 polymorphic restriction sites (restriction fragment length polymorphism loci) in 16 populations of the world. By partitioning genetic variances at three hierarchical levels of population subdivision, we found that differences between members of the same population account for 84.4% of the total, which is in excellent agreement with estimates based on allele frequencies of classic, protein polymorphisms. Genetic variation remains high even within small population groups. On the average, microsatellite and restriction fragment length polymorphism loci yield identical estimates. Differences among continents represent roughly 1/10 of human molecular diversity, which does not suggest that the racial subdivision of our species reflects any major discontinuity in our genome.
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Affiliation(s)
- G Barbujani
- Department of Biology, University of Ferrara, via Borsari 46, I-44100 Ferrara, Italy
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48
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Jorde LB, Rogers AR, Bamshad M, Watkins WS, Krakowiak P, Sung S, Kere J, Harpending HC. Microsatellite diversity and the demographic history of modern humans. Proc Natl Acad Sci U S A 1997; 94:3100-3. [PMID: 9096352 PMCID: PMC20328 DOI: 10.1073/pnas.94.7.3100] [Citation(s) in RCA: 200] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We have examined differences in diversity at 60 microsatellite loci among human population samples from three major continental groups to evaluate the hypothesis of greater African diversity in this rapidly evolving class of loci. Application of a statistical test that assumes equal mutation rates at all loci fails to demonstrate differences in microsatellite diversity, while a randomization test that does not make this assumption finds that Africans have significantly greater microsatellite diversity (P < 10(-8)) than do Asians and Europeans. Greater African diversity is most apparent at loci with smaller overall variance in allele size, suggesting that the record of population history has been erased at repeat loci with higher mutation rates. A power analysis shows that only 35-40 microsatellites are needed to establish this difference statistically, demonstrating the considerable evolutionary information contained in these systems. On average, African populations have approximately 20% greater microsatellite diversity than do Asian and European populations. A comparison of continental diversity differences in microsatellites and mtDNA sequences suggests earlier demographic expansion of the ancestors of Africans.
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Affiliation(s)
- L B Jorde
- Eccles Institute of Human Genetics, University of Utah Health Sciences Center, Salt Lake City 84112, USA.
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49
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Santos FR, Gerelsaikhan T, Munkhtuja B, Oyunsuren T, Epplen JT, Pena SD. Geographic differences in the allele frequencies of the human Y-linked tetranucleotide polymorphism DYS19. Hum Genet 1996; 97:309-13. [PMID: 8786070 DOI: 10.1007/bf02185760] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have studied the allele frequency distribution of the microsatellite locus DYS19 in several populations with different geographical origins worldwide. Three new alleles were found. In addition, remarkable geographic and ethnic differences were observed in the allele frequency profiles and DNA marker (gene) diversity among populations and major ethnic groups. Amerindians showed an overwhelming predominance of the A allele, while in Caucasians the B allele was modal, and in Greater Asians and Africans allele C became predominant. Even within these geographic regions there were significant gradients, as exemplified by the decreasing frequency profile of the B allele from Great Britain over Germany to Slovakia. Thus, DYS19 emerges as a useful tool for studying the structure and dynamics of human populations.
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Affiliation(s)
- F R Santos
- Departamento de Bioquímica, Instituto de Ciências Biológicas, Belo Horizonte, Brazil
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50
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Batzer MA, Arcot SS, Phinney JW, Alegria-Hartman M, Kass DH, Milligan SM, Kimpton C, Gill P, Hochmeister M, Ioannou PA, Herrera RJ, Boudreau DA, Scheer WD, Keats BJ, Deininger PL, Stoneking M. Genetic variation of recent Alu insertions in human populations. J Mol Evol 1996; 42:22-9. [PMID: 8576959 DOI: 10.1007/bf00163207] [Citation(s) in RCA: 134] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The Alu family of interspersed repeats is comprised of over 500,000 members which may be divided into discrete subfamilies based upon mutations held in common between members. Distinct subfamilies of Alu sequences have amplified within the human genome in recent evolutionary history. Several individual Alu family members have amplified so recently in human evolution that they are variable as to presence and absence at specific loci within different human populations. Here, we report on the distribution of six polymorphic Alu insertions in a survey of 563 individuals from 14 human population groups across several continents. Our results indicate that these polymorphic Alu insertions probably have an African origin and that there is a much smaller amount of genetic variation between European populations than that found between other population groups.
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Affiliation(s)
- M A Batzer
- Human Genome Center, Lawrence Livermore National Laboratory, CA 94551, USA
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