DOCSLIB.ORG

Mtdna Variation in the South African Kung and Khwe—And Their Genetic Relationships to Other African Populations Yu-Sheng Chen,1,* Antonel Olckers,4 Theodore G

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mtdna Variation in the South African Kung and Khwe—And Their Genetic Relationships to Other African Populations Yu-Sheng Chen,1,* Antonel Olckers,4 Theodore G View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Am. J. Hum. Genet. 66:1362–1383, 2000 mtDNA Variation in the South African Kung and Khwe—and Their Genetic Relationships to Other African Populations Yu-Sheng Chen,1,* Antonel Olckers,4 Theodore G. Schurr,1,2,† Andreas M. Kogelnik,1,3 Kirsi Huoponen,1,‡ and Douglas C. Wallace1,2 1Center for Molecular Medicine and 2Department of Anthropology, Emory University, and 3Program in Biomedical Engineering, College of Computing, Georgia Institute of Technology, Atlanta; and 4Department of Human Genetics, University of Pretoria, Pretoria The mtDNA variation of 74 Khoisan-speaking individuals (Kung and Khwe) from Schmidtsdrift, in the Northern Cape Province of South Africa, was examined by high-resolution RFLP analysis and control region (CR) sequencing. The resulting data were combined with published RFLP haplotype and CR sequence data from sub-Saharan African populations and then were subjected to phylogenetic analysis to deduce the evolutionary relationships among them. More than 77% of the Kung and Khwe mtDNA samples were found to belong to the major mtDNA lineage, macrohaplogroup L* (defined by a HpaI site at nucleotide position 3592), which is prevalent in sub-Saharan African populations. Additional sets of RFLPs subdivided macrohaplogroup L* into two extended haplogroups—L1 and L2—both of which appeared in the Kung and Khwe. Besides revealing the significant substructure of macrohap- logroup L* in African populations, these data showed that the Biaka Pygmies have one of the most ancient RFLP sublineages observed in African mtDNA and, thus, that they could represent one of the oldest human populations. In addition, the Kung exhibited a set of related haplotypes that were positioned closest to the root of the human mtDNA phylogeny, suggesting that they, too, represent one of the most ancient African populations. Comparison of Kung and Khwe CR sequences with those from other African populations confirmed the genetic association of the Kung with other Khoisan-speaking peoples, whereas the Khwe were more closely linked to non–Khoisan- speaking (Bantu) populations. Finally, the overall sequence divergence of 214 African RFLP haplotypes defined in both this and an earlier study was 0.364%, giving an estimated age, for all African mtDNAs, of 125,500–165,500 years before the present, a date that is concordant with all previous estimates derived from mtDNA and other genetic data, for the time of origin of modern humans in Africa. Introduction 95% of the Kung mtDNAs were characterized by a HpaI site gain at nucleotide position (np) 3592. This marker The South African Kung San were among the first human was subsequently found at very high frequencies in groups in which mtDNA variation was analyzed by re- mtDNAs of other sub-Saharan African populations striction analysis (Denaro et al. 1981; Johnson et al. (Scozzari et al. 1988, 1994; Soodyall and Jenkins 1992, 1983). In these studies, the mtDNA sequences of the 1993; Chen et al. 1995) but was not observed in pop- Kung were surveyed for variation, by means of six rare- ulations of non-African origin, with a few exceptions cutting restriction endonucleases (AvaII, BamHI, HaeII, (Cann et al. 1987; Soodyall 1993). Furthermore, the HincII, HpaI, and MspI) and Southern blotting. Al- African mtDNAs defined by the HpaI np-3592 site gain though this procedure screened only 2%–3% of the formed a group of related mtDNA haplotypes (originally ∼ mtDNA sequence for variation, it revealed that 90%– defined as haplogroup “L” and here redefined as “L*”), which was found to be the most divergent of those iden- Received May 19, 1999; accepted for publication October 17, 1999; tified in human populations from around the world electronically published March 30, 2000. Address for correspondence and reprints: Dr. Douglas C. Wallace, (Chen et al. 1995). These findings contributed to the Director, Center for Molecular Medicine, Emory University School of hypothesis of an African origin of modern human Medicine, 1462 Clifton Road, N.E., Atlanta, GA 30322. E-mail: mtDNAs (Johnson et al. 1983; Cann et al. 1987; Chen [email protected] et al. 1995), although other interpretations of these data * Present affiliation: Department of Psychiatry, University of Chi- cago Medical School, Chicago. have also been put forward (Excoffier and Langaney † Present affiliation: Southwest Foundation for Biomedical Re- 1989; Templeton 1992). search, Department of Genetics, San Antonio. Since 1981, relatively limited data have been collected ‡ Present affiliation: Laboratory of Genetics, Department of Biology, on the RFLP variation in Kung or related Khoisan- University of Turku, Turku, Finland. ᭧ 2000 by The American Society of Human Genetics. All rights reserved. speaking populations. Those studies that were con- 0002-9297/2000/6604-0019$02.00 ducted on Khoisan-speaking populations continued to 1362 Chen et al.: mtDNA Variation in South African Populations 1363 use low-resolution (LR)–RFLP analysis with only the their phylogenetic relationships to other African and six rare-cutting restriction endonucleases listed above non-African mtDNAs. (Soodyall and Jenkins 1992, 1993). As a consequence, Similarly, until very recently, only a limited num- these data provided additional information about Khoi- ber of Kung mtDNAs had been surveyed for control san groups but could not be entirely integrated with region (CR) sequence variation. In earlier studies (Vig- those obtained, on other populations, by high-resolu- ilant et al. 1989, 1991), mtDNAs from Kung individuals tion (HR)–RFLP analysis (Cann et al. 1987; Torroni et consistently clustered at the deepest nodes of the phy- al. 1992). logenies constructed from CR sequences, a result that The value of using HR-RFLP analysis with African indicated that they are some of the most diver- mtDNAs, for phylogenetic reconstructions of human gent—hence, oldest—mtDNAs present in human pop- mtDNA, has been shown primarily by two studies of ulations. Soodyall et al. (1996) also studied CR se- African populations (Cann et al. 1987; Chen et al. quence variation in southern-African populations and Lys 1995). In the first study, Cann et al. (1987) conducted found that the COII/tRNA intergenic 9-bp deletion genomic digestions of mtDNAs, by 12 enzymes (AluI, had occurred multiple times in African populations, in- AvaII, DdeI, FnuDII, HaeIII, HhaI, HinfI, HpaI, HpaII, dependent of those appearing in Asian mtDNAs, a trend MboI, RsaI, and TaqI), with the resulting restriction first noted by Vigilant (1990). Interestingly, deletion fragments being resolved by PAGE. In the later study, mtDNAs were not observed in Khoisan-speaking pop- the entire genome of African mtDNAs was PCR am- ulations and were rare in western- and southwestern- plified in nine overlapping fragments, which were then African groups, whereas they occurred frequently in subjected to digestion by 14 enzymes (AluI, AvaII, Pygmy and so-called Negroid populations from central BamHI, DdeI, HaeII, HaeIII, HhaI, HincII, HinfI, HpaI, Africa and in Bantu-speaking peoples of southern Africa HpaII, MboI, RsaI, and TaqI), with the resulting re- (Soodyall et al. 1996). This distribution suggested that striction fragments being resolved by agarose gel elec- deletion mtDNAs arose in central Africa and were dis- trophoresis. Both of these studies revealed that African seminated into southern Africa via the recent Bantu haplotypes form the deepest branches of the human expansion. mtDNA phylogeny and that African groups are the most Although studies using HR-RFLP methods of analysis have provided new insights into the mtDNA variation divergent of all world populations. of African populations, there has been almost no effort Several additional aspects of mtDNA variation in Af- to relate the data sets generated by RFLP to those gen- rican populations were shown in the Chen et al. (1995) erated by a CR sequence analyses. To date, only the study. First, two types of length polymorphisms were western-African Mandelaku (Mandenka) have been observed in some of the central-African mtDNAs subjected to both LR-RFLP and CR sequencing analyses (Mbuti [eastern] and Biaka [western] Pygmies), one of (Graven et al. 1995), whereas the linkage between the which was the COII/tRNALys intergenic 9-bp deletion HR-RFLP data and the CR sequence data for the Af- that formerly had been thought to occur only in Asian rican samples analyzed by Cann et al. (1987) and Vig- populations. This length polymorphism had previously ilant et al. (1989, 1991) has not been made explicitly been noted in African individuals but had not been as- clear. Thus, the relationship between HR-RFLP hap- signed to a particular haplogroup or mtDNA lineage lotypes and CR sequences in African populations has (Cann and Wilson 1983). In addition, western-African yet to be adequately addressed. In addition, because of populations from Senegal were found to have haplo- the different methods of RFLP haplotyping used in the types that lacked the HpaI np-3592 site gain and, thus, Cann et al. (1987) and Chen et al. (1995) studies, there appeared not to belong to haplogroup L*. Because were some inconsistencies in the positioning of certain nearly all of these “non-L” haplotypes had the DdeI polymorphisms that were critical for phylogenetic re- np-10394 site gain, a polymorphism that was also pre- constructions of the haplotypes defined in each study. sent in almost every haplogroup L* mtDNA, the data Consequently, a more complete characterization of the suggested that the former haplotypes derived from the distribution of genetic variation in coding (i.e., RFLP) latter, although the exact subhaplogroup (L1 or L2) versus noncoding (i.e., CR) regions of the mtDNA ge- from which these non-L haplotypes originated was not nome was needed. clear. Alternatively, non-L mtDNAs could have evolved Both to increase our knowledge of the genetic rela- from haplotypes observed in Europeans, such as those tionships between Khoisan (Kung San and Khoi) pop- belonging to haplogroups I–K (Torroni et al.
Load more

Recommended publications
  • Analysis of Y-Chromosome Polymorphisms in Pakistani
    ANALYSIS OF Y-CHROMOSOME POLYMORPHISMS IN PAKISTANI POPULATIONS Thesis submitted to the Sindh Institute of Medical Sciences for the degree of Doctor of Philosophy. BY Sadaf Firasat Centre of Human Genetics and Molecular Medicine Sindh Institute of Medical Sciences Sindh Institute of Urology and Transplantation (SIUT) Karachi, Pakistan 2010 TABLE OF CONTENTS Title page Acknowledgements ii List of Tables iii List of Figures iv Summary vi Introduction 1 Literature Review 19 Materials and Methods 34 Results Phylogeography of Pakistani ethnic groups. 51 Comparison between the Pakistani and Greek populations 73 Discussion 86 Comparison within Pakistan 88 Comparison between the Pakistani and Greek population 94 Comparison with world populations 98 Insight in to populations origins 111 Conclusions 121 References 122 Appendix a i ACKNOWLEDGEMENT I thank Prof. Dr. Syed Qasim Mehdi H.I. S.I., for his support, encouragement and for providing all the facilities for doing scientific work in his laboratory. The work presented in this thesis was done under the supervision of Dr. Qasim Ayub T.I. It is great pleasure for me to acknowledge the keen interest, advice, patient guidance and kindness that I have received from him during the course of this work. I would like to thank Dr. Shagufta Khaliq, (PoP), for teaching all the molecular genetics lab techniques and also to Dr Aiysha Abid for comments on this manuscript and suggestion for its improvement. I am also grateful to Mrs. Ambreen Ayub for her help in making the contour map. I thank my colleague Ms. Sadia Ajaz for her help and cooperation in proof reading the thesis.
    [Show full text]
  • A War-Prone Tribe Migrated out of Africa to Populate the World
    A war-prone tribe migrated out of Africa to populate the world. Eduardo Moreno1. 1 CNIO, Melchor Fernández Almagro, 3. Madrid 28029, Spain. Of the tribal hunter gatherers still in existence today, some lead lives of great violence, whereas other groups live in societies with no warfare and very little murder1,2,3,4,5. Here I find that hunter gatherers that belong to mitochondrial haplotypes L0, L1 and L2 do not have a culture of ritualized fights. In contrast to this, almost all L3 derived hunter gatherers have a more belligerent culture that includes ritualized fights such as wrestling, stick fights or headhunting expeditions. This appears to be independent of their environment, because ritualized fights occur in all climates, from the tropics to the arctic. There is also a correlation between mitochondrial haplotypes and warfare propensity or the use of murder and suicide to resolve conflicts. This, in the light of the “recent out of Africa” hypothesis”6,7, suggests that the tribe that left Africa 80.000 years ago performed ritualized fights. In contrast to the more pacific tradition of non-L3 foragers, it may also have had a tendency towards combat. The data implicate that the entire human population outside Africa is descended from only two closely related sub-branches of L3 that practiced ritual fighting and probably had a higher propensity towards warfare and the use of murder for conflict resolution. This may have crucially influenced the subsequent history of the world. There is little evidence for the practice of war before the late Paleolithic3,4.
    [Show full text]
  • Maximizing Mtdna Testing Potential with the Generation of High-Quality Mtgenome Reference Data Author(S): Rebecca S
    The author(s) shown below used Federal funding provided by the U.S. Department of Justice to prepare the following resource: Document Title: Maximizing mtDNA Testing Potential with the Generation of High-Quality mtGenome Reference Data Author(s): Rebecca S. Just, Walther Parson, Jodi A. Irwin Document Number: 253077 Date Received: July 2019 Award Number: 2011-MU-MU-K402 This resource has not been published by the U.S. Department of Justice. This resource is being made publically available through the Office of Justice Programs’ National Criminal Justice Reference Service. Opinions or points of view expressed are those of the author(s) and do not necessarily reflect the official position or policies of the U.S. Department of Justice. Final Technical Report to the National Institute of Justice on Award Number 2011-MU-MU-K402 Maximizing mtDNA Testing Potential with the Generation of High-Quality mtGenome Reference Data Authors: a,b c,d a,b,e Rebecca S. Just , Walther Parson and Jodi A. Irwin aArmed Forces DNA Identification Laboratory, 115 Purple Heart Dr., Dover AFB, DE, 19902 bAmerican Registry of Pathology, 9210 Corporate Blvd., Suite 120, Rockville, MD, 20850 cInstitute of Legal Medicine, Innsbruck Medical University, Mllerstrasse 44, Innsbruck, Austria dPenn State Eberly College of Science, 517 Thomas Building, University Park, PA, 16802 eFederal Bureau of Investigation, 2501 Investigation Parkway, Quantico, VA 22135 Recipient Organization: American Registry of Pathology 9210 Corporate Blvd., Suite 120 Rockville, MD 20850 Project Period: April 1, 2011 - March 31, 2015 This resource was prepared by the author(s) using Federal funds provided by the U.S.
    [Show full text]
  • Africa from MIS 6–2: Population Dynamics and Paleoenvironments Sacha C
    Africa from MIS 6–2: Population Dynamics and Paleoenvironments Sacha C. Jones and Brian A. Stewart (eds.) Vertebrate Paleobiology and Paleoanthropology Series, Dordrecht: Springer, 2016, 424 pp. (hardback), £103.99. ISBN-13: 9789401775205. Reviewed by DEBORAH I. OLSZEWSKI Department of Anthropology, Penn Museum, 3260 South Street, University of Pennsylvania, Philadelphia, PA 19104, USA; [email protected] his volume includes papers from a conference held at ests, they ask if such contexts were biogeographical corri- Tthe McDonald Institute for Archaeological Research in dors or instead might have operated as barriers to move- 2010. The aim of the conference was to examine the his- ment. In particular, rainforests were patchy spots across tories of populations on the African continent through the the landscape during arid periods, and likely not refugia, use of a variety of data sets—archaeology, genetics, pa- partly due to significant deficiencies in food resources for leoenvironments, and paleontology—to reach a more nu- hominins. anced understanding of hominin skeletal and behavioral Part I: The first three chapters in Part I (Coasts) are evolution, how populations were spatially distributed studies from the coastlines of southern Africa. Chapter 2, across Africa, and the impact of climatic factors on group by A.S. Carr, B.M. Chase, and A. Mackay, focuses on the size and movement. The conference participants sought to Middle Stone Age (MSA) in the southern part of South position data from Africa to aid in the construction of theo- Africa. It is an overview of the archaeology in the period retical frameworks and to benefit from frameworks devel- from 170–55 kya, which is derived primarily from cave and oped elsewhere.
    [Show full text]
  • Whole Mitochondrial Genome Sequencing Highlights Mitochondrial Impact in Gastric Cancer Giovanna Chaves Cavalcante1,2, Anderson N
    www.nature.com/scientificreports OPEN Whole mitochondrial genome sequencing highlights mitochondrial impact in gastric cancer Giovanna Chaves Cavalcante1,2, Anderson N. R. Marinho1, Ana Karyssa Anaissi2, Tatiana Vinasco-Sandoval 1, André Ribeiro-dos-Santos1,2, Amanda Ferreira Vidal1, Gilderlanio S. de Araújo1, Samia Demachki2 & Ândrea Ribeiro-dos-Santos 1,2* Mitochondria are organelles that perform major roles in cellular operation. Thus, alterations in mitochondrial genome (mtGenome) may lead to mitochondrial dysfunction and cellular deregulation, infuencing carcinogenesis. Gastric cancer (GC) is one of the most incident and mortal types of cancer in Brazil, particularly in the Amazon region. Here, we sequenced and compared the whole mtGenome extracted from FFPE tissue samples of GC patients (tumor and internal control – IC) and cancer-free individuals (external control – EC) from this region. We found 3-fold more variants and up to 9-fold more heteroplasmic regions in tumor when compared to paired IC samples. Moreover, tumor presented more heteroplasmic variants when compared to EC, while IC and EC showed no signifcant diference when compared to each other. Tumor also presented substantially more variants in the following regions: MT-RNR1, MT-ND5, MT-ND4, MT-ND2, MT-DLOOP1 and MT-CO1. In addition, our haplogroup results indicate an association of Native American ancestry (particularly haplogroup C) to gastric cancer development. To the best of our knowledge, this is the frst study to sequence the whole mtGenome from FFPE samples and to apply mtGenome analysis in association to GC in Brazil. Mitochondria are cytoplasmic organelles that perform major roles in cell operation, including energy generation through oxidative phosphorylation (OXPHOS), cell death, calcium levels control, lipid homeostasis and meta- bolic cell signaling1.
    [Show full text]
  • Reduced-Median-Network Analysis of Complete Mitochondrial DNA
    Am. J. Hum. Genet. 70:1152–1171, 2002 Reduced-Median-Network Analysis of Complete Mitochondrial DNA Coding-Region Sequences for the Major African, Asian, and European Haplogroups Corinna Herrnstadt,1 Joanna L. Elson,3 Eoin Fahy,1 Gwen Preston,1 Douglass M. Turnbull,3 Christen Anderson,1 Soumitra S. Ghosh,1 Jerrold M. Olefsky,2 M. Flint Beal,4,* Robert E. Davis,1,† and Neil Howell1,5 1MitoKor and 2Veterans Administration Medical Center, San Diego; 3Department of Neurology, University of Newcastle upon Tyne, Newcastle upon Tyne; 4Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and 5Department of Radiation Oncology, University of Texas Medical Branch, Galveston The evolution of the human mitochondrial genome is characterized by the emergence of ethnically distinct lineages or haplogroups. Nine European, seven Asian (including Native American), and three African mitochondrial DNA (mtDNA) haplogroups have been identified previously on the basis of the presence or absence of a relatively small number of restriction-enzyme recognition sites or on the basis of nucleotide sequences of the D-loop region. We have used reduced-median-network approaches to analyze 560 complete European, Asian, and African mtDNA coding-region sequences from unrelated individuals to develop a more complete understanding of sequence diversity both within and between haplogroups. A total of 497 haplogroup-associated polymorphisms were identified, 323 (65%) of which were associated with one haplogroup and 174 (35%) of which were associated with two or more haplogroups. Approximately one-half of these polymorphisms are reported for the first time here. Our results confirm and substantially extend the phylogenetic relationships among mitochondrial genomes described elsewhere from the major human ethnic groups.
    [Show full text]
  • Extensive Female-Mediated Gene Flow from Sub-Saharan Africa Into Near Eastern Arab Populations
    Edinburgh Research Explorer Extensive female-mediated gene flow from sub-Saharan Africa into near eastern Arab populations Citation for published version: Richards, M, Rengo, C, Cruciani, F, Gratrix, F, Wilson, JF, Scozzari, R, Macaulay, V & Torroni, A 2003, 'Extensive female-mediated gene flow from sub-Saharan Africa into near eastern Arab populations', American Journal of Human Genetics, vol. 72, no. 4, pp. 1058-64. https://doi.org/10.1086/374384 Digital Object Identifier (DOI): 10.1086/374384 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: American Journal of Human Genetics Publisher Rights Statement: Copyright © 2003 by The American Society of Human Genetics. All rights reserved. General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 29. Sep. 2021 Am. J. Hum. Genet. 72:1058–1064, 2003 Report Extensive Female-Mediated Gene Flow from Sub-Saharan Africa into Near Eastern Arab Populations Martin Richards,1 Chiara Rengo,2,3 Fulvio Cruciani,2 Fiona Gratrix,4 James F.
    [Show full text]
  • Health and Genetic Ancestry Testing: Time to Bridge the Gap Andrew Smart1* , Deborah A
    Smart et al. BMC Medical Genomics (2017) 10:3 DOI 10.1186/s12920-016-0240-3 DEBATE Open Access Health and genetic ancestry testing: time to bridge the gap Andrew Smart1* , Deborah A. Bolnick2 and Richard Tutton3 Abstract Background: It is becoming increasingly difficult to keep information about genetic ancestry separate from information about health, and consumers of genetic ancestry tests are becoming more aware of the potential health risks associated with particular ancestral lineages. Because some of the proposed associations have received little attention from oversight agencies and professional genetic associations, scientific developments are currently outpacing governance regimes for consumer genetic testing. Main text: We highlight the recent and unremarked upon emergence of biomedical studies linking markers of genetic ancestry to disease risks, and show that this body of scientific research is becoming part of public discourse connecting ancestry and health. For instance, data on genome-wide ancestry informative markers are being used to assess health risks, and we document over 100 biomedical research articles that propose associations between mitochondrial DNA and Y chromosome markers of genetic ancestry and a wide variety of disease risks. Taking as an example an association between coronary heart disease and British men belonging to Y chromosome haplogroup I, we show how this science was translated into mainstream and online media, and how it circulates among consumers of genetic tests for ancestry. We find wide variations in how the science is interpreted, which suggests the potential for confusion or misunderstanding. Conclusion: We recommend that stakeholders involved in creating and using estimates of genetic ancestry reconsider their policies for communicating with each other and with the public about the health implications of ancestry information.
    [Show full text]
  • Reduced-Median-Network Analysis of Complete Mitochondrial DNA Coding-Region Sequences for the Major African, Asian, and European Haplogroups
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by DigitalCommons@University of Nebraska University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Public Health Resources Public Health Resources 2002 Reduced-Median-Network Analysis of Complete Mitochondrial DNA Coding-Region Sequences for the Major African, Asian, and European Haplogroups Corinna Herrnstadt MitoKor Joanna L. Elson University of Newcastle upon Tyne Eoin Fahy MitoKor Gwen Preston MitoKor Douglass M. Turnbull University of Newcastle upon Tyne See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/publichealthresources Part of the Public Health Commons Herrnstadt, Corinna; Elson, Joanna L.; Fahy, Eoin; Preston, Gwen; Turnbull, Douglass M.; Anderson, Christen; Ghosh, Soumitra S.; Olefsky, Jerrold M.; Beal, M. Flint; Davis, Robert E.; and Howell, Neil, "Reduced-Median-Network Analysis of Complete Mitochondrial DNA Coding-Region Sequences for the Major African, Asian, and European Haplogroups" (2002). Public Health Resources. 103. https://digitalcommons.unl.edu/publichealthresources/103 This Article is brought to you for free and open access by the Public Health Resources at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Public Health Resources by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Corinna Herrnstadt, Joanna L. Elson, Eoin Fahy, Gwen Preston, Douglass M. Turnbull, Christen Anderson, Soumitra S. Ghosh, Jerrold M. Olefsky, M. Flint Beal, Robert E. Davis, and Neil Howell This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ publichealthresources/103 Am. J. Hum. Genet. 70:1152–1171, 2002 Reduced-Median-Network Analysis of Complete Mitochondrial DNA Coding-Region Sequences for the Major African, Asian, and European Haplogroups Corinna Herrnstadt,1 Joanna L.
    [Show full text]
  • Mtdna Landscape in South African Paediatric Patients Clinically Diagnosed With
    mtDNA landscape in South African paediatric patients clinically diagnosed with suspected mitochondria1 disorders DAN ISABIRYE, M.Sc. Dissertation submitted for the degree Magister Scientiae (M.Sc.) in Biochemistry at the North-West University SUPERVISOR: Professor Antonel Olckers Centre for Genome Research, North-West University (Potchefstroom Campus) CO-SUPERVISOR: Doctor lzelle Smuts Department of Paediatrics, University of Pretoria December 2004 mtDNA landskap in Suid-Afrikaanse pediatriese pasiente klinies gediagnoseer met vermeende mitochondriale siektetoestande DEUR DAN ISABIRYE, M.Sc. Verhandeling voorgele vir die graad Magister Scientiae (M.Sc.) in Biochemie aan die Noordwes-Universiteit STUDIELEIER: Professor Antonel Olckers Sentrum vir Genomiese Navorsing, Noordwes-Universiteit (Potchefstroom Kampus) MEDESTUDIELEIER: Dokter lzelle Smuts Departement Pediatrie, Universiteit van Pretoria Desember 2004 This thesis is dedicated to my Son, Dan ABSTRACT The relevance of haplogroups in rnitochondrial disease was investigated in this study. Twenty-seven paediatric patients with clinically suspected mitochondrial disorders from diverse ethnic origins were investigated via an automated sequencing strategy. Previous studies in a similar population identified only the A3243G reported causative mutation in a single patient, in addition to a number of reported and unreported polymorphisms. It suggested that the aetiology of rnitochondrial disorders in Africa, specifically South Africa, might be different from that of other continents. Comparison between these sequences and the Revised Cambridge Reference Sequence revealed 37 polymorphic sites (7 novel changes, 30 reported alterations). No previously reported causative mutation was detected. The findings support the hypothesis that the aetiology of mitochondrial disorders in Africa is unique. Sixty-three percent of patients in the current study belonged to haplogroup L3 (48% in L3b), 22% to LO, 11% to L2a, and 4% to M.
    [Show full text]
  • Estudo Do ADN Mitocondrial De Uma População De Indivíduos Nativos De Angola Residentes Em Lisboa
    Filipa Isabel Figueira Simão Licenciada em Ciências Forenses e Criminais Estudo do ADN mitocondrial de uma população de indivíduos nativos de Angola residentes em Lisboa Dissertação para obtenção do Grau de Mestre em Bioquímica Orientador: António Amorim, Especialista Superior de Medicina Legal, Instituto Nacional de Medicina Legal e Ciências Forenses, Delegação Sul Co-orientadora: Heloísa Afonso Costa, Especialista Superior de Medicina Legal, Instituto Nacional de Medicina Legal e Ciências Forenses, Delegação Sul Júri: Presidente: Prof. Doutor Pedro António de Brito Tavares Arguente: Prof. Doutora Maria Marise Simões de Almeida Vogal: Mestre Heloísa Afonso Costa Dezembro 2014 Filipa Isabel Figueira Simão Licenciada em Ciências Forenses e Criminais Estudo do ADN mitocondrial de uma população de indivíduos nativos de Angola residentes em Lisboa Dissertação para obtenção do Grau de Mestre em Bioquímica Orientador: António Amorim, Especialista Superior de Medicina Legal, Instituto Nacional de Medicina Legal e Ciências Forenses, Delegação Sul Co-orientadora: Heloísa Afonso Costa, Especialista Superior de Medicina Legal, Instituto Nacional de Medicina Legal e Ciências Forenses, Delegação Sul Monte da Caparica, Faculdade de Ciências e Tecnologia, Universidade de Lisboa Dezembro 2014 Estudo do ADN mitocondrial de uma população de indivíduos nativos de Angola residentes em Lisboa Copyright © Eu, Filipa Isabel Figueira Simão, declaro que a Faculdade de Ciências e Tecnologia e a Universidade Nova de Lisboa têm o direito, perpétuo e sem limites geográficos, de arquivar e publicar esta dissertação através de exemplares impressos reproduzidos em papel ou de forma digital, ou por qualquer outro meio conhecido ou que venha a ser inventado, e de a divulgar através de repositórios científicos e de admitir a sua cópia e distribuição com objetivos educacionais ou de investigação, não comerciais, desde que seja dado crédito ao autor e editor.
    [Show full text]
  • African Human Mtdna Phylogeography At-A-Glance
    doi 10.4436/jass.89006 JASs Invited Reviews Journal of Anthropological Sciences Vol. 89 (2011), pp. 25-58 African human mtDNA phylogeography at-a-glance Alexandra Rosa1,2 & António Brehm2 1) Medical Sciences Unit, Centre of Life Sciences, University of Madeira, Campus of Penteada, 9000-390 Funchal, Portugal e-mail: [email protected] 2) Human Genetics Laboratory, University of Madeira, Campus of Penteada, 9000-390 Funchal, Portugal e-mail: [email protected] Summary - The mitochondrial DNA (mtDNA) genetic system has long proven to be useful for studying the demographic history of our species, since their proposed Southeast/East African origin 200 kya. Despite the weak archaeological and anthropologic records, which render a difficult understanding of early intra- continental migrations, the phylogenetic L0-L1’6 split at about 140-160 kya is thought to represent also an early sub-structuring of small and isolated communities in South and East Africa. Regional variation accumulated over the following millennia, with L2 and L3 lineages arising in Central and East Africa 100-75 kya. Their sub-Saharan dispersal not later than 60 kya, largely overwhelmed the L0’1 distribution, nowadays limited to South African Khoisan and Central African Pygmies. Cyclic expansions and retractions of the equatorial forest between 40 kya and the “Last Glacial Aridity Maximum” were able to reduce the genetic diversity of modern humans. Surviving regional-specific lineages have emerged from the Sahelian refuge areas, repopulating the region and contributing to the overall West African genetic similarity. Particular L1- L3 lineages mirror the substantial population growth made possible by moister and warmer conditions of the Sahara’s Wet Phase and the adoption of agriculture and iron smelting techniques.
    [Show full text]