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Fähnrich A, Stephan I, Hirose M, Haarich F, Awadelkareem MA, Ibrahim S, Busch H, Wohlers I. North and East African mitochondrial genetic variation needs further characterization towards precision medicine. J Adv Res 2023; 54:59-76. [PMID: 36736695 DOI: 10.1016/j.jare.2023.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION Mitochondria are maternally inherited cell organelles with their own genome, and perform various functions in eukaryotic cells such as energy production and cellular homeostasis. Due to their inheritance and manifold biological roles in health and disease, mitochondrial genetics serves a dual purpose of tracing the history as well as disease susceptibility of human populations across the globe. This work requires a comprehensive catalogue of commonly observed genetic variations in the mitochondrial DNAs for all regions throughout the world. So far, however, certain regions, such as North and East Africa have been understudied. OBJECTIVES To address this shortcoming, we have created the most comprehensive quality-controlled North and East African mitochondrial data set to date and use it for characterizing mitochondrial genetic variation in this region. METHODS We compiled 11 published cohorts with novel data for mitochondrial genomes from 159 Sudanese individuals. We combined these 641 mitochondrial sequences with sequences from the 1000 Genomes (n = 2504) and the Human Genome Diversity Project (n = 828) and used the tool haplocheck for extensive quality control and detection of in-sample contamination, as well as Nanopore long read sequencing for haplogroup validation of 18 samples. RESULTS Using a subset of high-coverage mitochondrial sequences, we predict 15 potentially novel haplogroups in North and East African subjects and observe likely phylogenetic deviations from the established PhyloTree reference for haplogroups L0a1 and L2a1. CONCLUSION Our findings demonstrate common hitherto unexplored variants in mitochondrial genomes of North and East Africa that lead to novel phylogenetic relationships between haplogroups present in these regions. These observations call for further in-depth population genetic studies in that region to enable the prospective use of mitochondrial genetic variation for precision medicine.
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Affiliation(s)
- Anke Fähnrich
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Isabel Stephan
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Misa Hirose
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Franziska Haarich
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research), Partner Site Hamburg/Lübeck/Kiel, and University Heart Center, Lübeck, Lübeck, Germany
| | - Mosab Ali Awadelkareem
- Faculty of Medical Laboratory Sciences, Al-Neelain University, Khartoum, Sudan; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Saleh Ibrahim
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; Khalifa University, Abu Dhabi, United Arab Emirates
| | - Hauke Busch
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538 Lübeck, Germany
| | - Inken Wohlers
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; Biomedical Data Science, Research Center Borstel, 23845 Borstel, Germany.
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Havaš Auguštin D, Šarac J, Reidla M, Tamm E, Grahovac B, Kapović M, Novokmet N, Rudan P, Missoni S, Marjanović D, Korolija M. Refining the Global Phylogeny of Mitochondrial N1a, X, and HV2 Haplogroups Based on Rare Mitogenomes from Croatian Isolates. Genes (Basel) 2023; 14:1614. [PMID: 37628665 PMCID: PMC10454736 DOI: 10.3390/genes14081614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) has been used for decades as a predominant tool in population genetics and as a valuable addition to forensic genetic research, owing to its unique maternal inheritance pattern that enables the tracing of individuals along the maternal lineage across numerous generations. The dynamic interplay between evolutionary forces, primarily genetic drift, bottlenecks, and the founder effect, can exert significant influence on genetic profiles. Consequently, the Adriatic islands have accumulated a subset of lineages that exhibits remarkable absence or rarity within other European populations. This distinctive genetic composition underscores the islands' potential as a significant resource in phylogenetic research, with implications reaching beyond regional boundaries to contribute to a global understanding. In the initial attempt to expand the mitochondrial forensic database of the Croatian population with haplotypes from small isolated communities, we sequenced mitogenomes of rare haplogroups from different Croatian island and mainland populations using next-generation sequencing (NGS). In the next step and based on the obtained results, we refined the global phylogeny of haplogroup N1a, HV2, and X by analyzing rare haplotypes, which are absent from the current phylogenetic tree. The trees were based on 16 novel and 52 previously published samples, revealing completely novel branches in the X and HV2 haplogroups and a new European cluster in the ancestral N1a variant, previously believed to be an exclusively African-Asian haplogroup. The research emphasizes the importance of investigating geographically isolated populations and their unique characteristics within a global context.
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Affiliation(s)
- Dubravka Havaš Auguštin
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Jelena Šarac
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Maere Reidla
- Institute of Genomics, University of Tartu, 50090 Tartu, Estonia
| | - Erika Tamm
- Institute of Genomics, University of Tartu, 50090 Tartu, Estonia
| | | | | | | | - Pavao Rudan
- Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Saša Missoni
- Institute for Anthropological Research, 10000 Zagreb, Croatia
- Faculty of Dental Medicine and Health, J. J. Strossmayer University, 31000 Osijek, Croatia
| | - Damir Marjanović
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
- Genetics and Bioengineering Department, International Burch University, 71000 Sarajevo, Bosnia and Herzegovina
| | - Marina Korolija
- Forensic Science Centre “Ivan Vučetić”, Ministry of the Interior, 10000 Zagreb, Croatia
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Fleskes RE, Owsley DW, Bruwelheide KS, Barca KG, Griffith DR, Cabana GS, Schurr TG. Historical genomes elucidate European settlement and the African diaspora in Delaware. Curr Biol 2023:S0960-9822(23)00551-1. [PMID: 37207647 DOI: 10.1016/j.cub.2023.04.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 02/01/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
The 17th-century colonization of North America brought thousands of Europeans to Indigenous lands in the Delaware region, which comprises the eastern boundary of the Chesapeake Bay in what is now the Mid-Atlantic region of the United States.1 The demographic features of these initial colonial migrations are not uniformly characterized, with Europeans and European-Americans migrating to the Delaware area from other countries and neighboring colonies as single persons or in family units of free persons, indentured servants, or tenant farmers.2 European colonizers also instituted a system of racialized slavery through which they forcibly transported thousands of Africans to the Chesapeake region. Historical information about African-descended individuals in the Delaware region is limited, with a population estimate of less than 500 persons by 1700 CE.3,4 To shed light on the population histories of this period, we analyzed low-coverage genomes of 11 individuals from the Avery's Rest archaeological site (circa 1675-1725 CE), located in Delaware. Previous osteological and mitochondrial DNA (mtDNA) sequence analyses showed a southern group of eight individuals of European maternal descent, buried 15-20 feet from a northern group of three individuals of African maternal descent.5 Autosomal results further illuminate genomic similarities to Northwestern European reference populations or West and West-Central African reference populations, respectively. We also identify three generations of maternal kin of European ancestry and a paternal parent-offspring relationship between an adult and child of African ancestry. These findings expand our understanding of the origins and familial relationships in late 17th and early 18th century North America.
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Affiliation(s)
- Raquel E Fleskes
- Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA; Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Douglas W Owsley
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
| | - Karin S Bruwelheide
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Kathryn G Barca
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | | | - Graciela S Cabana
- Department of Anthropology, University of Tennessee, Knoxville, TN 37996, USA; Molecular Anthropology Laboratories, University of Tennessee, Knoxville, TN 37996, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Barbarić L, Horjan-Zanki I. Challenges in the recovery of the genetic data from human remains found on the Western Balkan migration route. Int J Legal Med 2023; 137:181-193. [PMID: 35449468 DOI: 10.1007/s00414-022-02829-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 04/13/2022] [Indexed: 01/11/2023]
Abstract
Traditional DNA-based identification of human remains relies on the system of matching STR profile of the deceased with the family references or antemortem samples. In forensic cases without any available samples for the comparison, the body remains unidentified. The aim of this study was to assess the applicability of massively parallel sequencing (MPS) approach in the forensic cases of five drowned individuals recovered on the Western Balkan migration route. Besides capillary electrophoresis (CE)-based genetic profiling (aSTR, Y STR, and mitochondrial control region sequencing) of postmortem samples, we applied ForenSeq DNA Signature Prep Kit/Primer Mix B on MiSeqFGx platform and concomitant ForenSeq Universal Analysis (UAS) software. The assay showed high reproducibility and complete concordance with CE-based data except in locus DYF387S1. Allele and locus drop was evident in 2.9% of total SNPs that slightly reduced the completeness of the data. We endeavored to predict the phenotype of the tested samples and accurate biogeographical ancestry of European individual. UAS was less informative for the remaining samples assigned to Admixed American cluster. Nevertheless, the application of FROG-kb and Snipper tools along with admixture analysis in STRUCTURE and lineage markers revealed likely Middle Eastern and North African ancestry. We conclude that the combination of the phenotype and biogeographical ancestry predictions, including paternal and maternal genetic ancestry, represent a promising tool for humanitarian identification of dead migrants. Nevertheless, the data interpretation remains a challenging task.
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Affiliation(s)
- Lucija Barbarić
- Forensic Science Centre "Ivan Vučetić, " Ministry of the Interior, Ilica 335, 10000, Zagreb, Croatia.
| | - Ivana Horjan-Zanki
- Forensic Science Centre "Ivan Vučetić, " Ministry of the Interior, Ilica 335, 10000, Zagreb, Croatia
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Martini R, Delpe P, Chu TR, Arora K, Lord B, Verma A, Bedi D, Karanam B, Elhussin I, Chen Y, Gebregzabher E, Oppong JK, Adjei EK, Jibril Suleiman A, Awuah B, Muleta MB, Abebe E, Kyei I, Aitpillah FS, Adinku MO, Ankomah K, Osei-Bonsu EB, Chitale DA, Bensenhaver JM, Nathanson DS, Jackson L, Petersen LF, Proctor E, Stonaker B, Gyan KK, Gibbs LD, Monojlovic Z, Kittles RA, White J, Yates CC, Manne U, Gardner K, Mongan N, Cheng E, Ginter P, Hoda S, Elemento O, Robine N, Sboner A, Carpten JD, Newman L, Davis MB. African Ancestry-Associated Gene Expression Profiles in Triple-Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome in Women of African Descent. Cancer Discov 2022; 12:2530-2551. [PMID: 36121736 PMCID: PMC9627137 DOI: 10.1158/2159-8290.cd-22-0138] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/17/2022] [Accepted: 08/23/2022] [Indexed: 01/12/2023]
Abstract
Women of sub-Saharan African descent have disproportionately higher incidence of triple-negative breast cancer (TNBC) and TNBC-specific mortality across all populations. Population studies show racial differences in TNBC biology, including higher prevalence of basal-like and quadruple-negative subtypes in African Americans (AA). However, previous investigations relied on self-reported race (SRR) of primarily U.S. populations. Due to heterogeneous genetic admixture and biological consequences of social determinants, the true association of African ancestry with TNBC biology is unclear. To address this, we conducted RNA sequencing on an international cohort of AAs, as well as West and East Africans with TNBC. Using comprehensive genetic ancestry estimation in this African-enriched cohort, we found expression of 613 genes associated with African ancestry and 2,000+ associated with regional African ancestry. A subset of African-associated genes also showed differences in normal breast tissue. Pathway enrichment and deconvolution of tumor cellular composition revealed that tumor-associated immunologic profiles are distinct in patients of African descent. SIGNIFICANCE Our comprehensive ancestry quantification process revealed that ancestry-associated gene expression profiles in TNBC include population-level distinctions in immunologic landscapes. These differences may explain some differences in race-group clinical outcomes. This study shows the first definitive link between African ancestry and the TNBC immunologic landscape, from an African-enriched international multiethnic cohort. See related commentary by Hamilton et al., p. 2496. This article is highlighted in the In This Issue feature, p. 2483.
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Affiliation(s)
- Rachel Martini
- Department of Surgery, Weill Cornell Medical College, New York, New York.,Department of Genetics, University of Georgia, Athens, Georgia
| | - Princesca Delpe
- Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, New York
| | | | | | - Brittany Lord
- Department of Surgery, Weill Cornell Medical College, New York, New York.,Department of Genetics, University of Georgia, Athens, Georgia
| | - Akanksha Verma
- Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, New York
| | - Deepa Bedi
- Department of Biomedical Sciences, Tuskegee University, Tuskegee, Alabama
| | | | - Isra Elhussin
- Center for Cancer Research, Tuskegee University, Tuskegee, Alabama
| | - Yalei Chen
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | - Endale Gebregzabher
- Department of Biochemistry, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Joseph K Oppong
- Department of Surgery, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Ernest K Adjei
- Department of Pathology, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Aisha Jibril Suleiman
- Department of Pathology, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Baffour Awuah
- Directorate of Oncology, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Mahteme Bekele Muleta
- Department of Surgery, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Engida Abebe
- Department of Surgery, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Ishmael Kyei
- Department of Surgery, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Frances S Aitpillah
- Department of Surgery, Komfo Anokye Teaching Hospital, Kumasi, Ghana.,Department of Surgery, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael O Adinku
- Department of Surgery, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Kwasi Ankomah
- Directorate of Radiology, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | | | | | | | | | - LaToya Jackson
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
| | | | - Erica Proctor
- Department of Surgery, Henry Ford Health System, Detroit, Michigan
| | - Brian Stonaker
- Department of Surgery, Weill Cornell Medical College, New York, New York
| | - Kofi K Gyan
- Department of Surgery, Weill Cornell Medical College, New York, New York
| | - Lee D Gibbs
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Zarko Monojlovic
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Rick A Kittles
- Department of Population Sciences, City of Hope, Duarte, California
| | - Jason White
- Department of Biology, Tuskegee University, Tuskegee, Alabama
| | - Clayton C Yates
- Center for Cancer Research, Tuskegee University, Tuskegee, Alabama
| | - Upender Manne
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kevin Gardner
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Nigel Mongan
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom.,Department of Pharmacology, Weill Cornell Medical College, New York, New York
| | - Esther Cheng
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Paula Ginter
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Syed Hoda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, New York.,Institute of Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | | | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - John D Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Lisa Newman
- Department of Surgery, Weill Cornell Medical College, New York, New York
| | - Melissa B Davis
- Department of Surgery, Weill Cornell Medical College, New York, New York.,Department of Genetics, University of Georgia, Athens, Georgia.,Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, New York.,New York Genome Center, New York, New York.,Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan
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African mitochondrial haplogroup L7: a 100,000-year-old maternal human lineage discovered through reassessment and new sequencing. Sci Rep 2022; 12:10747. [PMID: 35750688 PMCID: PMC9232647 DOI: 10.1038/s41598-022-13856-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Archaeological and genomic evidence suggest that modern Homo sapiens have roamed the planet for some 300–500 thousand years. In contrast, global human mitochondrial (mtDNA) diversity coalesces to one African female ancestor (“Mitochondrial Eve”) some 145 thousand years ago, owing to the ¼ gene pool size of our matrilineally inherited haploid genome. Therefore, most of human prehistory was spent in Africa where early ancestors of Southern African Khoisan and Central African rainforest hunter-gatherers (RFHGs) segregated into smaller groups. Their subdivisions followed climatic oscillations, new modes of subsistence, local adaptations, and cultural-linguistic differences, all prior to their exodus out of Africa. Seven African mtDNA haplogroups (L0–L6) traditionally captured this ancient structure—these L haplogroups have formed the backbone of the mtDNA tree for nearly two decades. Here we describe L7, an eighth haplogroup that we estimate to be ~ 100 thousand years old and which has been previously misclassified in the literature. In addition, L7 has a phylogenetic sublineage L7a*, the oldest singleton branch in the human mtDNA tree (~ 80 thousand years). We found that L7 and its sister group L5 are both low-frequency relics centered around East Africa, but in different populations (L7: Sandawe; L5: Mbuti). Although three small subclades of African foragers hint at the population origins of L5'7, the majority of subclades are divided into Afro-Asiatic and eastern Bantu groups, indicative of more recent admixture. A regular re-estimation of the entire mtDNA haplotype tree is needed to ensure correct cladistic placement of new samples in the future.
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7
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Razali RM, Rodriguez-Flores J, Ghorbani M, Naeem H, Aamer W, Aliyev E, Jubran A, Clark AG, Fakhro KA, Mokrab Y. Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes. Nat Commun 2021; 12:5929. [PMID: 34642339 PMCID: PMC8511259 DOI: 10.1038/s41467-021-25287-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/02/2021] [Indexed: 12/15/2022] Open
Abstract
Arab populations are largely understudied, notably their genetic structure and history. Here we present an in-depth analysis of 6,218 whole genomes from Qatar, revealing extensive diversity as well as genetic ancestries representing the main founding Arab genealogical lineages of Qahtanite (Peninsular Arabs) and Adnanite (General Arabs and West Eurasian Arabs). We find that Peninsular Arabs are the closest relatives of ancient hunter-gatherers and Neolithic farmers from the Levant, and that founder Arab populations experienced multiple splitting events 12–20 kya, consistent with the aridification of Arabia and farming in the Levant, giving rise to settler and nomadic communities. In terms of recent genetic flow, we show that these ancestries contributed significantly to European, South Asian as well as South American populations, likely as a result of Islamic expansion over the past 1400 years. Notably, we characterize a large cohort of men with the ChrY J1a2b haplogroup (n = 1,491), identifying 29 unique sub-haplogroups. Finally, we leverage genotype novelty to build a reference panel of 12,432 haplotypes, demonstrating improved genotype imputation for both rare and common alleles in Arabs and the wider Middle East. Arab populations are relatively understudied, especially their genetic architecture and historical relationship with early founders of the ancient Near East. Here, the authors examine 6,218 Qatari whole genomes, revealing insights on migration, population history and genetic structure of populations across the Middle Eastern region.
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Affiliation(s)
| | | | | | - Haroon Naeem
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Waleed Aamer
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Ali Jubran
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, New York, NY, USA
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar. .,Weill Cornell Medicine-Qatar, Doha, Qatar. .,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
| | - Younes Mokrab
- Department of Human Genetics, Sidra Medicine, Doha, Qatar. .,Weill Cornell Medicine-Qatar, Doha, Qatar. .,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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8
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Maternal Phylogenetic Relationships and Genetic Variation among Rare, Phenotypically Similar Donkey Breeds. Genes (Basel) 2021; 12:genes12081109. [PMID: 34440283 PMCID: PMC8392470 DOI: 10.3390/genes12081109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/02/2021] [Accepted: 07/13/2021] [Indexed: 11/17/2022] Open
Abstract
The mitochondrial DNA (mtDNA) D-loop of endangered and critically endangered breeds has been studied to identify maternal lineages, characterize genetic inheritance, reconstruct phylogenetic relations among breeds, and develop biodiversity conservation and breeding programs. The aim of the study was to determine the variability remaining and the phylogenetic relationship of Martina Franca (MF, with total population of 160 females and 36 males), Ragusano (RG, 344 females and 30 males), Pantesco (PT, 47 females and 15 males), and Catalonian (CT) donkeys by collecting genetic data from maternal lineages. Genetic material was collected from saliva, and a 350 bp fragment of D-loop mtDNA was amplified and sequenced. Sequences were aligned and evaluated using standard bioinformatics software. A total of 56 haplotypes including 33 polymorphic sites were found in 77 samples (27 MF, 22 RG, 8 PT, 19 CT, 1 crossbred). The breed nucleotide diversity value (π) for all the breeds was 0.128 (MF: 0.162, RG: 0.132, PT: 0.025, CT: 0.038). Principal components analysis grouped most of the haplogroups into two different clusters, I (including all haplotypes from PT and CT, together with haplotypes from MF and RG) and II (including haplotypes from MF and RG only). In conclusion, we found that the primeval haplotypes, haplogroup variability, and a large number of maternal lineages were preserved in MF and RG; thus, these breeds play putative pivotal roles in the phyletic relationships of donkey breeds. Maternal inheritance is indispensable genetic information required to evaluate inheritance, variability, and breeding programs.
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López S, Tarekegn A, Band G, van Dorp L, Bird N, Morris S, Oljira T, Mekonnen E, Bekele E, Blench R, Thomas MG, Bradman N, Hellenthal G. Evidence of the interplay of genetics and culture in Ethiopia. Nat Commun 2021; 12:3581. [PMID: 34117245 PMCID: PMC8196081 DOI: 10.1038/s41467-021-23712-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/13/2021] [Indexed: 11/13/2022] Open
Abstract
The rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with-and shape-genetic structure in human populations. Using primarily new genetic variation data covering 1,214 Ethiopians representing 68 different ethnic groups, together with information on individuals' birthplaces, linguistic/religious practices and 31 cultural practices, we disentangle the effects of geographic distance, elevation, and social factors on the genetic structure of Ethiopians today. We provide evidence of associations between social behaviours and genetic differences among present-day peoples. We show that genetic similarity is broadly associated with linguistic affiliation, but also identify pronounced genetic similarity among groups from disparate language classifications that may in part be attributable to recent intermixing. We also illustrate how groups reporting the same culture traits are more genetically similar on average and show evidence of recent intermixing, suggesting that shared cultural traits may promote admixture. In addition to providing insights into the genetic structure and history of Ethiopia, we identify the most important cultural and geographic predictors of genetic differentiation and provide a resource for designing sampling protocols for future genetic studies involving Ethiopians.
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Affiliation(s)
- Saioa López
- Research Department of Genetics, Evolution & Environment, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
| | - Ayele Tarekegn
- Department of Archaeology and Heritage Management, College of Social Sciences, Addis Ababa University, New Classrooms (NCR) Building, Second Floor, Office No. 214, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lucy van Dorp
- Research Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Nancy Bird
- Research Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Sam Morris
- Research Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Tamiru Oljira
- Genomics & Bioinformatics Research Directorate (GBRD), Ethiopian Biotechnology Institute (EBTi), Addis Ababa, Ethiopia
| | - Ephrem Mekonnen
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Endashaw Bekele
- College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Roger Blench
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of History, University of Jos, Jos, Nigeria
| | - Mark G Thomas
- Research Department of Genetics, Evolution & Environment, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | | | - Garrett Hellenthal
- Research Department of Genetics, Evolution & Environment, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
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10
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Mkaouar-Rebai E, Ammar M, Sfaihi L, Alila-Fersi O, Maalej M, Felhi R, Hachicha M, Fakhfakh F. Mitochondrial disease patients with novel ND4 12058A > C and ND1 m.3911A > G variations: implications for a role in the phenotype following a bioinformatic investigation. Mol Biol Rep 2021; 48:4373-4382. [PMID: 34089464 DOI: 10.1007/s11033-021-06452-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Mitochondrial diseases include a wide group of clinically heterogeneous disorders caused by a dysfunction of the mitochondrial respiratory chain and can be related to mutations in nuclear or mitochondrial DNA genes. In the present report, we performed a whole mitochondrial genome screening in two patients with clinical features of mitochondrial diseases. Mutational analysis revealed the presence of two undescribed heteroplasmic mitochondrial variations, the m.3911A > G (E202G) variant in the MT-ND1 gene found in two patients (P1 and P2) and the m.12058A > C (E433D) pathogenic variant in the MT-ND4 gene present only in patient P2 who had a more severe phenotype. These two substitutions were predicted to be damaging by several bioinformatics tools and lead to amino acid changes in two conserved residues localized in two important functional domains of the mitochondrial subunits of complex I. Furthermore, the 3D modeling suggested that the two amino acid changes could therefore alter the structure of the two subunits and may decrease the stability and the function of complex I. The two described pathogenic variants found in patient P2 could act synergically and alter the complex I function by affecting the proton pumping processes and the energy production and then could explain the severe phenotype compared to patient P1 presenting only the E202G substitution in ND1.
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Affiliation(s)
- Emna Mkaouar-Rebai
- Molecular and Functional Genetics Laboratory, Department of Life Science, Faculty of Sciences of Sfax, The University of Sfax, Sfax, Tunisia.
| | - Marwa Ammar
- Molecular and Functional Genetics Laboratory, Department of Life Science, Faculty of Sciences of Sfax, The University of Sfax, Sfax, Tunisia
| | - Lamia Sfaihi
- Department of Pediatrics, C.H.U. Hedi Chaker, Sfax, Tunisia
| | - Olfa Alila-Fersi
- Molecular and Functional Genetics Laboratory, Department of Life Science, Faculty of Sciences of Sfax, The University of Sfax, Sfax, Tunisia
| | - Marwa Maalej
- Molecular and Functional Genetics Laboratory, Department of Life Science, Faculty of Sciences of Sfax, The University of Sfax, Sfax, Tunisia
| | - Rahma Felhi
- Molecular and Functional Genetics Laboratory, Department of Life Science, Faculty of Sciences of Sfax, The University of Sfax, Sfax, Tunisia
| | | | - Faiza Fakhfakh
- Molecular and Functional Genetics Laboratory, Department of Life Science, Faculty of Sciences of Sfax, The University of Sfax, Sfax, Tunisia
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11
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Mostafa BE, El Sawi MA, Sabry SM, Hassan DM, Rezk Shafik M. Genetic Screening for 35delG Mutation in Egyptian Patients with Profound Sensorineural Hearing Loss Scheduled for Cochlear Implantation: A Population-Based Study. ORL J Otorhinolaryngol Relat Spec 2021; 83:181-186. [PMID: 33756453 DOI: 10.1159/000513752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/14/2020] [Indexed: 11/19/2022]
Abstract
OBJECTIVES The aim of this work was to assess the type and site of the 35delG gene mutation in patients presenting with profound SNHL and scheduled for cochlear implantation. The secondary objectives were to determine their geographical distribution throughout Egypt, screening of the parents for the mutation, and to correlate the type of mutation with clinical severity and outcomes after surgery. METHODS The study was carried out on 100 consecutive patients scheduled for cochlear implantation. Patients with syndromic hearing loss or noncongenital hearing loss (trauma, infections, and ototoxicity) were excluded. All patients were subjected to detailed history taking including geographic tagging for their origins in Egypt, imaging (CT and MRI cochlear implantation protocols), full audiological evaluation (PTA, ABR, and TEOAE), and genetic screening for GJB2 mutation using Invitrogen PCR mix and ApaI restriction enzyme (North America, CA, 10572-014). The parents of mutation-positive patients were also subjected to audiological and genetic analysis. All patients were subjected to postimplantation evaluation of hearing after 6 and 12 months. RESULTS There were 64 males and 36 females from 98 families. Ages ranged between 1.9 and 7 years (mean 3.72 years). They originated from all over Egypt but the majority came from the Giza and Cairo areas. The 35delG mutations were found in exon 2 in 31% of the cases and all were heterozygous. In the parents, 18 mothers and 13 fathers were positive but only 8 had mild to moderate SNHL. Hearing evaluation by pure tone and speech discrimination scores at 6 and 12 months showed that the 35delG children had a statistically better result compared to the children without this mutation. CONCLUSION The prevalence of the 35delG mutation in nonsyndromic children in this sample was 31% which is different from previous studies in the Egyptian population but close to the values found in other populations in the Mediterranean basin.
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Affiliation(s)
- Badr Eldin Mostafa
- Department of Otorhinolaryngology Head and Neck Surgery, Faculty of Medicine, Ain-Shams University, Cairo, Egypt,
| | - Mohammed Abdel El Sawi
- Department of Pediatrics and Medical Genetics, Faculty of Medicine, Ain-Shams University, Cairo, Egypt
| | - Sabry Magdi Sabry
- Department of Otorhinolaryngology Head and Neck Surgery, Faculty of Medicine, Ain-Shams University, Cairo, Egypt
| | - Dalia Mohammed Hassan
- Department of Otorhinolaryngology Head and Neck Surgery, Faculty of Medicine, Ain-Shams University, Cairo, Egypt
| | - Michael Rezk Shafik
- Department of Otorhinolaryngology Head and Neck Surgery, Faculty of Medicine, Ain-Shams University, Cairo, Egypt
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12
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Osman MM, Hassan HY, Elnour MA, Makkan H, Gebremeskel EI, Gais T, Koko ME, Soodyall H, Ibrahim ME. Mitochondrial HVRI and whole mitogenome sequence variations portray similar scenarios on the genetic structure and ancestry of northeast Africans. Meta Gene 2021. [DOI: 10.1016/j.mgene.2020.100837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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13
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Aljasmi FA, Vijayan R, Sudalaimuthuasari N, Souid AK, Karuvantevida N, Almaskari R, Mohammed Abdul Kader H, Kundu B, Michel Hazzouri K, Amiri KMA. Genomic Landscape of the Mitochondrial Genome in the United Arab Emirates Native Population. Genes (Basel) 2020; 11:genes11080876. [PMID: 32752197 PMCID: PMC7464197 DOI: 10.3390/genes11080876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 11/19/2022] Open
Abstract
In order to assess the genomic landscape of the United Arab Emirates (UAE) mitogenome, we sequenced and analyzed the complete genomes of 232 Emirate females mitochondrial DNA (mtDNA) within and compared those to Africa. We investigated the prevalence of haplogroups, genetic variation, heteroplasmy, and demography among the UAE native population with diverse ethnicity and relatively high degree of consanguinity. We identified 968 mtDNA variants and high-resolution 15 haplogroups. Our results show that the UAE population received enough gene flow from Africa represented by the haplogroups L, U6, and M1, and that 16.8% of the population has an eastern provenance, depicted by the U haplogroup and the M Indian haplogroup (12%), whereas western Eurasian and Asian haplogroups (R, J, and K) represent 11 to 15%. Interestingly, we found an ancient migration present through the descendant of L (N1 and X) and other sub-haplogroups (L2a1d and L4) and (L3x1b), which is one of the oldest evolutionary histories outside of Africa. Our demographic analysis shows no population structure among populations, with low diversity and no population differentiation. In addition, we show that the transmission of mtDNA in the UAE population is under purifying selection with hints of diversifying selection on ATP8 gene. Last, our results show a population bottleneck, which coincides with the Western European contact (1400 ybp). Our study of the UAE mitogenomes suggest that several maternal lineage migratory episodes liking African–Asian corridors occurred since the first modern human emerges out of Africa.
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Affiliation(s)
- Fatma A Aljasmi
- Pediatric Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Ranjit Vijayan
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Abdul-Kader Souid
- Pediatric Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Raja Almaskari
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Biduth Kundu
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Khaled Michel Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Khaled M A Amiri
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
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14
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Fendt L, Fazzini F, Weissensteiner H, Bruckmoser E, Schönherr S, Schäfer G, Losso JL, Streiter GA, Lamina C, Rasse M, Klocker H, Kofler B, Kloss-Brandstätter A, Huck CW, Kronenberg F, Laimer J. Profiling of Mitochondrial DNA Heteroplasmy in a Prospective Oral Squamous Cell Carcinoma Study. Cancers (Basel) 2020; 12:E1933. [PMID: 32708892 PMCID: PMC7409097 DOI: 10.3390/cancers12071933] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/25/2023] Open
Abstract
While a shift in energy metabolism is essential to cancers, the knowledge about the involvement of the mitochondrial genome in tumorigenesis and progression in oral squamous cell carcinoma (OSCC) is still very limited. In this study, we evaluated 37 OSCC tumors and the corresponding benign mucosa tissue pairs by deep sequencing of the complete mitochondrial DNA (mtDNA). After extensive quality control, we identified 287 variants, 137 in tumor and 150 in benign samples exceeding the 1% threshold. Variant heteroplasmy levels were significantly increased in cancer compared to benign tissues (p = 0.0002). Furthermore, pairwise high heteroplasmy frequency difference variants (∆HF% > 20) with potential functional impact were increased in the cancer tissues (p = 0.024). Fourteen mutations were identified in the protein-coding region, out of which thirteen were detected in cancer and only one in benign tissue. After eight years of follow-up, the risk of mortality was higher for patients who harbored at least one ∆HF% > 20 variant in mtDNA protein-coding regions relative to those with no mutations (HR = 4.6, (95%CI = 1.3-17); p = 0.019 in primary tumor carriers). Haplogroup affiliation showed an impact on survival time, which however needs confirmation in a larger study. In conclusion, we observed a significantly higher accumulation of somatic mutations in the cancer tissues associated with a worse prognosis.
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Affiliation(s)
- Liane Fendt
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Federica Fazzini
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Emanuel Bruckmoser
- Oral and Maxillofacial Surgeon, Private Practice, A-5020 Salzburg, Austria;
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Georg Schäfer
- Institute for Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, A-6020 Innsbruck, Austria;
| | - Jamie Lee Losso
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Gertraud A. Streiter
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Claudia Lamina
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Michael Rasse
- University Hospital for Craniomaxillofacial and Oral Surgery, Medical University of Innsbruck, A-6020 Innsbruck, Austria;
- Clinic for Maxillofacial Surgery, Sechenov University, Trubetskaya Str. 8 b.2, 119992 Moscow, Russia
| | - Helmut Klocker
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, A-6020 Innsbruck, Austria;
| | - Barbara Kofler
- Department of Otorhinolaryngology, Medical University of Innsbruck, Anichstrasse 35, A-6020 Innsbruck, Austria;
| | - Anita Kloss-Brandstätter
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
- Carinthia University of Applied Sciences, A-9524 Villach, Austria
| | - Christian W. Huck
- Institute of Analytical Chemistry and Radiochemistry, CCB-Center for Chemistry and Biomedicine, Leopold Franzens University Innsbruck, A-6020 Innsbruck, Austria;
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (L.F.); (F.F.); (H.W.); (S.S.); (J.L.L.); (G.A.S.); (C.L.); (A.K.-B.); (F.K.)
| | - Johannes Laimer
- University Hospital for Craniomaxillofacial and Oral Surgery, Medical University of Innsbruck, A-6020 Innsbruck, Austria;
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15
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Al-Eitan L, Saadeh H, Alnaamneh A, Darabseh S, Al-Sarhan N, Alzihlif M, Hakooz N, Ivanova E, Kelsey G, Dajani R. The genetic landscape of Arab Population, Chechens and Circassians subpopulations from Jordan through HV1 and HV2 regions of mtDNA. Gene 2019; 729:144314. [PMID: 31884104 DOI: 10.1016/j.gene.2019.144314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 11/29/2022]
Abstract
Mitochondrial DNA (mtDNA) is widely used in several fields including medical genetics, forensic science, genetic genealogy, and evolutionary anthropology. In this study, mtDNA haplotype diversity was determined for 293 unrelated subjects from Jordanian population (Circassians, Chechens, and the original inhabitants of Jordan). A total of 102 haplotypes were identified and analyzed among the populations to describe the maternal lineage landscape. Our results revealed that the distribution of mtDNA haplotype frequencies among the three populations showed disparity and significant differences when compared to each other. We also constructed mitochondrial haplotype classification trees for the three populations to determine the phylogenetic relationship of mtDNA haplotype variants, and we observed clear differences in the distribution of maternal genetic ancestries, especially between Arab and the minority ethnic populations. To our knowledge, this study is the first, to date, to characterize mitochondrial haplotypes and haplotype distributions in a population-based sample from the Jordanian population. It provides a powerful reference for future studies investigating the contribution of mtDNA variation to human health and disease and studying population history and evolution by comparing the mtDNA haplotypes to other populations.
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Affiliation(s)
- Laith Al-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan; Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Heba Saadeh
- Computer Science Department, The University of Jordan, Amman 11942, Jordan
| | - Adan Alnaamneh
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Salma Darabseh
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Na'meh Al-Sarhan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Malek Alzihlif
- Department of Pharmacology, Faculty of Medicine, The University of Jordan, Amman 11942, Jordan
| | - Nancy Hakooz
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Elena Ivanova
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK; The Centre for Trophoblast Research, University of Cambridge, CB2 3EG, UK
| | - Rana Dajani
- Department of Biology and Biotechnology, The Hashemite University, Zarqa 13133, Jordan; Radcliffe Institute for Advanced Studies, Harvard University, Cambridge, MA 02138, USA; Jepson School of Leadership, Richmond University, 221 Richmond Way, Richmond, VA 23173, USA
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16
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Zimmermann B, Sturk-Andreaggi K, Huber N, Xavier C, Saunier J, Tahir M, Chouery E, Jalkh N, Megarbane A, Bodner M, Coble M, Irwin J, Parsons T, Parson W. Mitochondrial DNA control region variation in Lebanon, Jordan, and Bahrain. Forensic Sci Int Genet 2019; 42:99-102. [DOI: 10.1016/j.fsigen.2019.06.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/06/2019] [Accepted: 06/25/2019] [Indexed: 10/26/2022]
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17
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Fleskes RE, Bruwelheide KS, West FL, Owsley DW, Griffith DR, Barca KG, Cabana GS, Schurr TG. Ancient DNA and bioarchaeological perspectives on European and African diversity and relationships on the colonial Delaware frontier. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 170:232-245. [DOI: 10.1002/ajpa.23887] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/07/2019] [Accepted: 06/13/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Raquel E. Fleskes
- Department of AnthropologyUniversity of Pennsylvania Philadelphia Pennsylvania
| | - Karin S. Bruwelheide
- Department of AnthropologySmithsonian Institution, National Museum of Natural History Washington D.C
| | - Frankie L. West
- Department of AnthropologyUniversity of Tennessee Knoxville Tennessee
| | - Douglas W. Owsley
- Department of AnthropologySmithsonian Institution, National Museum of Natural History Washington D.C
| | | | - Kathryn G. Barca
- Department of AnthropologySmithsonian Institution, National Museum of Natural History Washington D.C
| | | | - Theodore G. Schurr
- Department of AnthropologyUniversity of Pennsylvania Philadelphia Pennsylvania
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18
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Fernandes V, Brucato N, Ferreira JC, Pedro N, Cavadas B, Ricaut FX, Alshamali F, Pereira L. Genome-Wide Characterization of Arabian Peninsula Populations: Shedding Light on the History of a Fundamental Bridge between Continents. Mol Biol Evol 2019; 36:575-586. [PMID: 30649405 DOI: 10.1093/molbev/msz005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Arabian Peninsula (AP) was an important crossroad between Africa, Asia, and Europe, being the cradle of the structure defining these main human population groups, and a continuing path for their admixture. The screening of 741,000 variants in 420 Arabians and 80 Iranians allowed us to quantify the dominant sub-Saharan African admixture in the west of the peninsula, whereas South Asian and Levantine/European influence was stronger in the east, leading to a rift between western and eastern sides of the Peninsula. Dating of the admixture events indicated that Indian Ocean slave trade and Islamization periods were important moments in the genetic makeup of the region. The western-eastern axis was also observable in terms of positive selection of diversity conferring lactose tolerance, with the West AP developing local adaptation and the East AP acquiring the derived allele selected in European populations and existing in South Asia. African selected malaria resistance through the DARC gene was enriched in all Arabian genomes, especially in the western part. Clear European influences associated with skin and eye color were equally frequent across the Peninsula.
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Affiliation(s)
- Veronica Fernandes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Nicolas Brucato
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Joana C Ferreira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Nicole Pedro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Bruno Cavadas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - François-Xavier Ricaut
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
| | - Farida Alshamali
- Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates
| | - Luisa Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.,Faculdade de Medicina da Universidade do Porto, Porto, Portugal
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19
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Is mitochondrial DNA profiling predictive for athletic performance? Mitochondrion 2019; 47:125-138. [PMID: 31228565 DOI: 10.1016/j.mito.2019.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 06/03/2019] [Accepted: 06/17/2019] [Indexed: 11/20/2022]
Abstract
Mitochondrial DNA encodes some proteins of the oxidative phosphorylation enzymatic complex, playing an important role in aerobic ATP production; therefore, it can contribute to the ability to respond to endurance exercise training. The accumulation of mitochondrial mutations and the migratory processes of populations have given a great contribution to the development of haplogroups with a different distribution in the world. Several studies have shown the important role of gene polymorphisms in aerobic performance. In this review, some mitochondrial haplogroups and multiple rare alleles were taken into consideration and could be linked to the athlete's physical performance of different ethnic groups.
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20
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Baisvar VS, Singh M, Kumar R. Population structuring of Channa striata from Indian waters using control region of mtDNA. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:414-423. [PMID: 30905237 DOI: 10.1080/24701394.2018.1532416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Striped snakehead (Channa striata) is a freshwater species of early Miocene period belonging to family Channidae. The genetic variability of the snakehead populations in India was not well known. Present study was undertaken using 149 sequences of control region of mitochondrial DNA from seven geographically distinct populations of Indian water, which resulted in 46 haplotypes with 137 variable nucleotide sites (60 singletons and 77 parsimony informative) and the nucleotide frequencies was: A = 33.0, T = 28.1, G = 15.4, and C = 23.5%. The presence of low-frequency of younger haplotypes with a large number of singletons indicates the absence of dominant haplotype. Hierarchical AMOVA showed highly significant genetic differentiation (FST = 0.56, p < .00) among the populations. The pattern of genetic differentiation was not consistent with geographical distributions. AMOVA identified three genetically heterogeneous clades. The significant finding of Imphal and Chaliyar was that they were found genetically close to each other, but geographically much isolated from each other. The inference of the study suggests that the hypothesis of the single panmictic population of C. striata in Indian waters is rejected.
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Affiliation(s)
- Vishwamitra Singh Baisvar
- a Molecular Biology and Biotechnology Division , ICAR-National Bureau of Fish Genetic Resources , Lucknow , India
| | - Mahender Singh
- a Molecular Biology and Biotechnology Division , ICAR-National Bureau of Fish Genetic Resources , Lucknow , India
| | - Ravindra Kumar
- a Molecular Biology and Biotechnology Division , ICAR-National Bureau of Fish Genetic Resources , Lucknow , India
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21
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Vai S, Sarno S, Lari M, Luiselli D, Manzi G, Gallinaro M, Mataich S, Hübner A, Modi A, Pilli E, Tafuri MA, Caramelli D, di Lernia S. Ancestral mitochondrial N lineage from the Neolithic 'green' Sahara. Sci Rep 2019; 9:3530. [PMID: 30837540 PMCID: PMC6401177 DOI: 10.1038/s41598-019-39802-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 01/30/2019] [Indexed: 11/16/2022] Open
Abstract
Because Africa’s climate hampers DNA preservation, knowledge of its genetic variability is mainly restricted to modern samples, even though population genetics dynamics and back-migrations from Eurasia may have modified haplotype frequencies, masking ancient genetic scenarios. Thanks to improved methodologies, ancient genetic data for the African continent are now increasingly available, starting to fill in the gap. Here we present newly obtained mitochondrial genomes from two ~7000-year-old individuals from Takarkori rockshelter, Libya, representing the earliest and first genetic data for the Sahara region. These individuals carry a novel mutation motif linked to the haplogroup N root. Our result demonstrates the presence of an ancestral lineage of the N haplogroup in the Holocene “Green Sahara”, associated to a Middle Pastoral (Neolithic) context.
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Affiliation(s)
- Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Martina Lari
- Department of Biology, University of Florence, Florence, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Giorgio Manzi
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Marina Gallinaro
- Department of Ancient World Studies, Sapienza University of Rome, Rome, Italy
| | - Safaa Mataich
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Alexander Hübner
- Max-Planck-Institute for Evolutionary Anthropology, Department Evolutionary Genetics, Leipzig, Germany
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence, Italy
| | - Elena Pilli
- Department of Biology, University of Florence, Florence, Italy
| | - Mary Anne Tafuri
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy.
| | - Savino di Lernia
- Department of Ancient World Studies, Sapienza University of Rome, Rome, Italy. .,School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa.
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Molinaro L, Pagani L. Human evolutionary history of Eastern Africa. Curr Opin Genet Dev 2018; 53:134-139. [DOI: 10.1016/j.gde.2018.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/31/2018] [Accepted: 10/08/2018] [Indexed: 01/16/2023]
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ElHefnawi M, Jeon S, Bhak Y, ElFiky A, Horaiz A, Jun J, Kim H, Bhak J. Whole genome sequencing and bioinformatics analysis of two Egyptian genomes. Gene 2018; 668:129-134. [DOI: 10.1016/j.gene.2018.05.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/13/2018] [Indexed: 12/27/2022]
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Cabrera VM, Marrero P, Abu-Amero KK, Larruga JM. Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago. BMC Evol Biol 2018; 18:98. [PMID: 29921229 PMCID: PMC6009813 DOI: 10.1186/s12862-018-1211-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/05/2018] [Indexed: 11/15/2022] Open
Abstract
Background The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya. Results The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis. Electronic supplementary material The online version of this article (10.1186/s12862-018-1211-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
| | - Patricia Marrero
- Research Support General Service, E-38271, La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
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25
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Mekonnen E, Bekele E, Stein CM. Novel polymorphisms in TICAM2 and NOD1 associated with tuberculosis progression phenotypes in Ethiopian populations. Glob Health Epidemiol Genom 2018; 3:e1. [PMID: 29868226 PMCID: PMC5870410 DOI: 10.1017/gheg.2017.17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 12/04/2017] [Accepted: 12/08/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Infection by Mycobacterium tuberculosis (Mtb) is a necessary but not sufficient cause for tuberculosis (TB). Although numerous studies suggest human genetic variation may influence TB pathogenesis, there is a conspicuous lack of replication, likely due to imprecise phenotype definition. We aimed to replicate novel findings from a Ugandan cohort in Ethiopian populations. METHOD We ascertained TB cases and household controls (n = 292) from three different ethnic groups. Latent Mtb infection was determined using Quantiferon to develop reliable TB progression phenotypes. We sequenced exonic regions of TICAM2 and NOD1. RESULT Significant novel associations were observed between two variants in NOD1 and TB: rs751770147 [unadjusted p = 7.28 × 10-5] and chr7:30477156(T), a novel variant, [unadjusted p = 1.04 × 10-4]. Two SNPs in TICAM2 were nominally associated with TB, including rs2288384 [unadjusted p = 0.003]. Haplotype-based association tests supported the SNP-based results. CONCLUSION We replicated the association of TICAM2 and NOD1 with TB and identified novel genetic associations with TB in Ethiopian populations.
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Affiliation(s)
- E. Mekonnen
- Microbial, Cellular, Molecular Biology Department, Addis Ababa University, P.O.Box:17087, Addis Ababa, Ethiopia
- Health Biotechnology Department, Institute of Biotechnology, Addis Ababa University, P.O.Box:17087, Addis Ababa, Ethiopia
| | - E. Bekele
- Microbial, Cellular, Molecular Biology Department, Addis Ababa University, Ethiopia
| | - C. M. Stein
- Department of Population & Quantitative Health Sciences, Center for Proteomics & Bioinformatics, and Tuberculosis Research Unit, Case Western Reserve University, USA
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Elkamel S, Boussetta S, Khodjet-El-Khil H, Benammar Elgaaied A, Cherni L. Ancient and recent Middle Eastern maternal genetic contribution to North Africa as viewed by mtDNA diversity in Tunisian Arab populations. Am J Hum Biol 2018; 30:e23100. [PMID: 29359455 DOI: 10.1002/ajhb.23100] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/06/2017] [Accepted: 12/29/2017] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES Through previous mitochondrial DNA studies, the Middle Eastern maternal genetic contribution to Tunisian populations appears limited. In fact, most of the studied communities were cosmopolitan, or of Berber or Andalusian origin. To provide genetic evidence for the actual contribution of Middle Eastern mtDNA lineages to Tunisia, we focused on two Arab speaking populations from Kairouan and Wesletia known to belong to an Arab genealogical lineage. MATERIALS AND METHODS A total of 114 samples were sequenced for the mtDNA HVS-I and HVS-II regions. Using these data, we evaluated the distribution of Middle Eastern haplogroups in the study populations, constructed interpolation maps, and established phylogenetic networks allowing estimation of the coalescence time for three specific Middle Eastern subclades (R0a, J1b, and T1). RESULTS Both studied populations displayed North African genetic structure and Middle Eastern lineages with a frequency of 12% and 28.12% in Kairouan and Wesletia, respectively. TMRCA estimates for haplogroups T1a, R0a, and J1b in Tunisian Arabian samples were around 15 000 YBP, 9000 to 5000 YBP, and 960 to 600 YBP, respectively. CONCLUSIONS The Middle Eastern maternal genetic contribution to Tunisian populations, as to other North African populations, occurred mostly in deep prehistory. They were brought in different migration waves during the Upper Paleolithic, probably with the expansion of Iberomaurusian culture, and during Epipaleolithic and Early Neolithic periods, which are concomitant with the Capsian civilization. Middle Eastern lineages also came to Tunisia during the recent Islamic expansion of the 7th CE and the subsequent massive Bedouin migration during the 11th CE.
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Affiliation(s)
- Sarra Elkamel
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Sami Boussetta
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Houssein Khodjet-El-Khil
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Amel Benammar Elgaaied
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, 2092, Tunisia.,High Institute of Biotechnology, University of Monastir, Monastir, 5000, Tunisia
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28
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Vyas DN, Al‐Meeri A, Mulligan CJ. Testing support for the northern and southern dispersal routes out of Africa: an analysis of Levantine and southern Arabian populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:736-749. [DOI: 10.1002/ajpa.23312] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Deven N. Vyas
- Department of AnthropologyUniversity of Florida, 1112 Turlington Hall, PO Box 117305Gainesville Florida 32611‐7305
- Genetics InstituteUniversity of Florida, Cancer & Genetics Research Complex, PO Box 103610Gainesville Florida 32610‐3610
| | - Ali Al‐Meeri
- Department of Clinical Biochemistry, Faculty of Medicine and Health SciencesUniversity of Sana'aSana'a Yemen
| | - Connie J. Mulligan
- Department of AnthropologyUniversity of Florida, 1112 Turlington Hall, PO Box 117305Gainesville Florida 32611‐7305
- Genetics InstituteUniversity of Florida, Cancer & Genetics Research Complex, PO Box 103610Gainesville Florida 32610‐3610
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Primativo G, Ottoni C, Biondi G, Serafino S, Martínez-Labarga C, Larmuseau MHD, Scardi M, Decorte R, Rickards O. Bight of Benin: a Maternal Perspective of Four Beninese Populations and their Genetic Implications on the American Populations of African Ancestry. Ann Hum Genet 2017; 81:78-90. [PMID: 28205221 DOI: 10.1111/ahg.12186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/03/2017] [Indexed: 12/01/2022]
Abstract
The understanding of the first movements of the ancestral populations within the African continent is still unclear, particularly in West Africa, due to several factors that have shaped the African genetic pool across time. To improve the genetic representativeness of the Beninese population and to better understand the patterns of human settlement inside West Africa and the dynamics of peopling of the Democratic Republic of Benin, we analyzed the maternal genetic variation of 193 Beninese individuals belonging to Bariba, Berba, Dendi, and Fon populations. Results support the oral traditions indicating that the western neighbouring populations have been the ancestors of the first Beninese populations, and the extant genetic structure of the Beninese populations is most likely the result of admixture between populations from neighbouring countries and native people. The present findings highlight how the Beninese populations contributed to the gene pool of the extant populations of some American populations of African ancestry. This strengthens the hypothesis that the Bight of Benin was not only an assembly point for the slave trade during the Trans-Atlantic Slave Trade but also an important slave trapping area.
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Affiliation(s)
| | - Claudio Ottoni
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium
| | - Gianfranco Biondi
- Department of Clinical Medicine, Public Health, Life and Environment, University of L'Aquila, L'Aquila, Italy
| | - Sara Serafino
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.,Department of Public Health and Infectious Diseases, University of Rome Sapienza, Rome, Italy
| | | | - Maarten H D Larmuseau
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven - University of Leuven, Leuven, Belgium
| | - Michele Scardi
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Ronny Decorte
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium
| | - Olga Rickards
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
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30
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Larruga JM, Marrero P, Abu-Amero KK, Golubenko MV, Cabrera VM. Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area. BMC Evol Biol 2017; 17:115. [PMID: 28535779 PMCID: PMC5442693 DOI: 10.1186/s12862-017-0964-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia. Here, we assess as the Eurasian macrohaplogroup R fits in the northern path. RESULTS Haplogroup U, with a founder age around 50 kya, is one of the oldest clades of macrohaplogroup R in western Asia. The main branches of U expanded in successive waves across West, Central and South Asia before the Last Glacial Maximum. All these dispersions had rather overlapping ranges. Some of them, as those of U6 and U3, reached North Africa. At the other end of Asia, in Wallacea, another branch of macrohaplogroup R, haplogroup P, also independently expanded in the area around 52 kya, in this case as isolated bursts geographically well structured, with autochthonous branches in Australia, New Guinea, and the Philippines. CONCLUSIONS Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.
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Affiliation(s)
- Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Patricia Marrero
- Research Support General Service, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
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Lindberg MR, Schmedes SE, Hewitt FC, Haas JL, Ternus KL, Kadavy DR, Budowle B. A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes. PLoS One 2016; 11:e0167600. [PMID: 27936026 PMCID: PMC5147911 DOI: 10.1371/journal.pone.0167600] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/16/2016] [Indexed: 12/17/2022] Open
Abstract
Single source and multiple donor (mixed) samples of human mitochondrial DNA were analyzed and compared using the MinION and the MiSeq platforms. A generalized variant detection strategy was employed to provide a cursory framework for evaluating the reliability and accuracy of mitochondrial sequences produced by the MinION. The feasibility of long-read phasing was investigated to establish its efficacy in quantitatively distinguishing and deconvolving individuals in a mixture. Finally, a proof-of-concept was demonstrated by integrating both platforms in a hybrid assembly that leverages solely mixture data to accurately reconstruct full mitochondrial genomes.
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Affiliation(s)
| | - Sarah E. Schmedes
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | | | - Jamie L. Haas
- Signature Science, LLC, Austin, Texas, United States of America
| | | | - Dana R. Kadavy
- Signature Science, LLC, Austin, Texas, United States of America
| | - Bruce Budowle
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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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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Gandini F, Achilli A, Pala M, Bodner M, Brandini S, Huber G, Egyed B, Ferretti L, Gómez-Carballa A, Salas A, Scozzari R, Cruciani F, Coppa A, Parson W, Semino O, Soares P, Torroni A, Richards MB, Olivieri A. Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes. Sci Rep 2016; 6:25472. [PMID: 27146119 PMCID: PMC4857117 DOI: 10.1038/srep25472] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/18/2016] [Indexed: 01/29/2023] Open
Abstract
Rare mitochondrial lineages with relict distributions can sometimes be disproportionately informative about deep events in human prehistory. We have studied one such lineage, haplogroup R0a, which uniquely is most frequent in Arabia and the Horn of Africa, but is distributed much more widely, from Europe to India. We conclude that: (1) the lineage ancestral to R0a is more ancient than previously thought, with a relict distribution across the Mediterranean/Southwest Asia; (2) R0a has a much deeper presence in Arabia than previously thought, highlighting the role of at least one Pleistocene glacial refugium, perhaps on the Red Sea plains; (3) the main episode of dispersal into Eastern Africa, at least concerning maternal lineages, was at the end of the Late Glacial, due to major expansions from one or more refugia in Arabia; (4) there was likely a minor Late Glacial/early postglacial dispersal from Arabia through the Levant and into Europe, possibly alongside other lineages from a Levantine refugium; and (5) the presence of R0a in Southwest Arabia in the Holocene at the nexus of a trading network that developed after ~3 ka between Africa and the Indian Ocean led to some gene flow even further afield, into Iran, Pakistan and India.
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Affiliation(s)
- Francesca Gandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.,School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.,Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Maria Pala
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefania Brandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Balazs Egyed
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Galicia, Spain
| | - Rosaria Scozzari
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Pedro Soares
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Martin B Richards
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
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Messina F, Scano G, Contini I, Martínez-Labarga C, De Stefano GF, Rickards O. Linking between genetic structure and geographical distance: Study of the maternal gene pool in the Ethiopian population. Ann Hum Biol 2016; 44:53-69. [PMID: 26883569 DOI: 10.3109/03014460.2016.1155646] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background The correlation between genetics and geographical distance has already been examined through the study of the dispersion of human populations, especially in terms of uniparental genetic markers. Aim The present work characterises, at the level of the mitochondrial DNA (mtDNA), two new samples of Amhara and Oromo populations from Ethiopia to evaluate the possible pattern of distribution for mtDNA variation and to test the hypothesis of the Isolation-by-Distance (IBD) model among African, European and Middle-Eastern populations. Subjects and methods This study analysed 173 individuals belonging to two ethnic groups of Ethiopia, Amhara and Oromo, by assaying HVS-I and HVS-II of mtDNA D-loop and informative coding region SNPs of mtDNA. Results The analysis suggests a relationship between genetic and geographic distances, affirming that the mtDNA pool of Africa, Europe and the Middle East might be coherent with the IBD model. Moreover, the mtDNA gene pools of the Sub-Saharan African and Mediterranean populations were very different. Conclusion In this study the pattern of mtDNA distribution, beginning with the Ethiopian plateau, was tested in the IBD model. It could be affirmed that, on a continent scale, the mtDNA pool of Africa, Europe and the Middle East might fall under the IBD model.
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Affiliation(s)
- Francesco Messina
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Giuseppina Scano
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Irene Contini
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Cristina Martínez-Labarga
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Gian Franco De Stefano
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Olga Rickards
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
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Fanosie A, Gelaw B, Tessema B, Tesfay W, Admasu A, Yitayew G. Mycobacterium tuberculosis Complex and HIV Co-Infection among Extrapulmonary Tuberculosis Suspected Cases at the University of Gondar Hospital, Northwestern Ethiopia. PLoS One 2016; 11:e0150646. [PMID: 26950547 PMCID: PMC4780813 DOI: 10.1371/journal.pone.0150646] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/16/2016] [Indexed: 11/25/2022] Open
Abstract
Background Extrapulmonary Tuberculosis (EPTB) and Human Immunodeficiency Virus (HIV) infection are interrelated as a result of immune depression. The aim of this study was to determine the prevalence of Mycobacterium tuberculosis complex isolates and the burden of HIV co-infection among EPTB suspected patients. Method An institution based cross-sectional study was conducted among EPTB suspected patients at the University of Gondar Hospital. Socio-demographic characteristics and other clinical data were collected using a pretested questionnaire. GeneXpert MTB/RIF assay was performed to diagnosis Mycobacterium tuberculosis complex and Rifampicin resistance. All samples were also investigated by cytology and culture. The HIV statuses of all patients were screened initially by KHB, and all positive cases were further re-tested by STAT-pack. Data was analyzed using SPSS version 20 computer software and a P-value of < 0.05 was taken as statistically significant. Results A total of 141 extrapulmonary suspected patients were enrolled in this study. The overall prevalence of culture confirmed extrapulmonary tuberculosis infection was 29.8%, but the GeneXpert result showed a 26.2% prevalence of Mycobacterium tuberculosis complex infection. The 78.4% prevalence of extrapulmonary tuberculosis infection was found to be higher among the adult population. The prevalence of HIV infection among EPTB suspected patients was 14.1%, while it was 32.4% among GeneXpert-confirmed extrapulmonary TB cases (12/37). Tuberculosis lymphadenitis was the predominant (78.4%) type of EPTB infection followed by tuberculosis cold abscess (10.7%). Adult hood, previous history of contact with known pulmonary tuberculosis patients, and HIV co-infection showed a statistically significant association with extrapulmonary tuberculosis infection (P<0.013). Conclusion The prevalence of culture confirmed-EPTB infection was high, and a higher EPTB-HIV co-infection was also observed.
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Affiliation(s)
- Alemu Fanosie
- School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences (CMHS), The University of Gondar (UOG), P.O. box 196, Gondar, Ethiopia
| | - Baye Gelaw
- School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences (CMHS), The University of Gondar (UOG), P.O. box 196, Gondar, Ethiopia
- * E-mail:
| | - Belay Tessema
- School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences (CMHS), The University of Gondar (UOG), P.O. box 196, Gondar, Ethiopia
| | - Wogahta Tesfay
- School of Medicine, College of Medicine and Health Sciences (CMHS), The University of Gondar (UOG), P.O. box 196, Gondar, Ethiopia
| | - Aschalew Admasu
- Bahir Dar Regional Health and Research Laboratory Center, Bahir Dar, Ethiopia
| | - Gashaw Yitayew
- Bahir Dar Regional Health and Research Laboratory Center, Bahir Dar, Ethiopia
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Černý V, Čížková M, Poloni ES, Al‐Meeri A, Mulligan CJ. Comprehensive view of the population history of
A
rabia as inferred by mt
DNA
variation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:607-16. [DOI: 10.1002/ajpa.22920] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 11/06/2015] [Accepted: 11/23/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Viktor Černý
- Archaeogenetics LaboratoryInstitute of Archaeology of the Academy of Sciences of the Czech Republic Czech Republic
| | - Martina Čížková
- Department of Anthropology and Human GeneticsFaculty of Science, Charles University in Prague Czech Republic
| | - Estella S. Poloni
- Department of Genetics and EvolutionAnthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of GenevaGeneva Switzerland
| | - Ali Al‐Meeri
- Department of Clinical BiochemistryFaculty of Medicine and Health Sciences, University of Sana'aSana'a Yemen
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Comas I, Hailu E, Kiros T, Bekele S, Mekonnen W, Gumi B, Tschopp R, Ameni G, Hewinson RG, Robertson BD, Goig GA, Stucki D, Gagneux S, Aseffa A, Young D, Berg S. Population Genomics of Mycobacterium tuberculosis in Ethiopia Contradicts the Virgin Soil Hypothesis for Human Tuberculosis in Sub-Saharan Africa. Curr Biol 2015; 25:3260-6. [PMID: 26687624 PMCID: PMC4691238 DOI: 10.1016/j.cub.2015.10.061] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 02/06/2023]
Abstract
Colonial medical reports claimed that tuberculosis (TB) was largely unknown in Africa prior to European contact, providing a "virgin soil" for spread of TB in highly susceptible populations previously unexposed to the disease [1, 2]. This is in direct contrast to recent phylogenetic models which support an African origin for TB [3-6]. To address this apparent contradiction, we performed a broad genomic sampling of Mycobacterium tuberculosis in Ethiopia. All members of the M. tuberculosis complex (MTBC) arose from clonal expansion of a single common ancestor [7] with a proposed origin in East Africa [3, 4, 8]. Consistent with this proposal, MTBC lineage 7 is almost exclusively found in that region [9-11]. Although a detailed medical history of Ethiopia supports the view that TB was rare until the 20(th) century [12], over the last century Ethiopia has become a high-burden TB country [13]. Our results provide further support for an African origin for TB, with some genotypes already present on the continent well before European contact. Phylogenetic analyses reveal a pattern of serial introductions of multiple genotypes into Ethiopia in association with human migration and trade. In place of a "virgin soil" fostering the spread of TB in a previously naive population, we propose that increased TB mortality in Africa was driven by the introduction of European strains of M. tuberculosis alongside expansion of selected indigenous strains having biological characteristics that carry a fitness benefit in the urbanized settings of post-colonial Africa.
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Affiliation(s)
- Iñaki Comas
- Genomics and Health Unit, FISABIO Public Health, Valencia 46020, Spain; CIBER (Centros de Investigación Biomédica en Red) in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid 28029, Spain.
| | - Elena Hailu
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Teklu Kiros
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Shiferaw Bekele
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Wondale Mekonnen
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Balako Gumi
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Rea Tschopp
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia; Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel 4002, and University of Basel, Basel 4003, Switzerland
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - R Glyn Hewinson
- Bovine TB Research Group, Animal and Plant Health Agency, Surrey KT15 3NB, UK
| | - Brian D Robertson
- Center for Molecular Bacteriology and Infection, Department of Medicine, Flowers Building, South Kensington, Imperial College London, London SW7 2AZ, UK
| | - Galo A Goig
- Genomics and Health Unit, FISABIO Public Health, Valencia 46020, Spain
| | - David Stucki
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel 4002, and University of Basel, Basel 4003, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel 4002, and University of Basel, Basel 4003, Switzerland
| | - Abraham Aseffa
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Douglas Young
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Stefan Berg
- Bovine TB Research Group, Animal and Plant Health Agency, Surrey KT15 3NB, UK.
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The First Mitogenome of the Cyprus Mouflon (Ovis gmelini ophion): New Insights into the Phylogeny of the Genus Ovis. PLoS One 2015; 10:e0144257. [PMID: 26636977 PMCID: PMC4670089 DOI: 10.1371/journal.pone.0144257] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/16/2015] [Indexed: 01/06/2023] Open
Abstract
Sheep are thought to have been one of the first livestock to be domesticated in the Near East, thus playing an important role in human history. The current whole mitochondrial genome phylogeny for the genus Ovis is based on: the five main domestic haplogroups occurring among sheep (O. aries), along with molecular data from two wild European mouflons, three urials, and one argali. With the aim to shed some further light on the phylogenetic relationship within this genus, the first complete mitochondrial genome sequence of a Cypriot mouflon (O. gmelini ophion) is here reported. Phylogenetic analyses were performed using a dataset of whole Ovis mitogenomes as well as D-loop sequences. The concatenated sequence of 28 mitochondrial genes of one Cypriot mouflon, and the D-loop sequence of three Cypriot mouflons were compared to sequences obtained from samples representatives of the five domestic sheep haplogroups along with samples of the extant wild and feral sheep. The sample included also individuals from the Mediterranean islands of Sardinia and Corsica hosting remnants of the first wave of domestication that likely went then back to feral life. The divergence time between branches in the phylogenetic tree has been calculated using seven different calibration points by means of Bayesian and Maximum Likelihood inferences. Results suggest that urial (O. vignei) and argali (O. ammon) diverged from domestic sheep about 0.89 and 1.11 million years ago (MYA), respectively; and dates the earliest radiation of domestic sheep common ancestor at around 0.3 MYA. Additionally, our data suggest that the rise of the modern sheep haplogroups happened in the span of time between six and 32 thousand years ago (KYA). A close phylogenetic relationship between the Cypriot and the Anatolian mouflon carrying the X haplotype was detected. The genetic distance between this group and the other ovine haplogroups supports the hypothesis that it may be a new haplogroup never described before. Furthermore, the updated phylogenetic tree presented in this study determines a finer classification of ovine species and may help to classify more accurately new mitogenomes within the established haplogroups so far identified.
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Vyas DN, Kitchen A, Miró‐Herrans AT, Pearson LN, Al‐Meeri A, Mulligan CJ. Bayesian analyses of Yemeni mitochondrial genomes suggest multiple migration events with Africa and Western Eurasia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:382-93. [DOI: 10.1002/ajpa.22890] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/21/2015] [Accepted: 10/23/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Deven N. Vyas
- Department of AnthropologyUniversity of FloridaGainesville FL32611‐7305
- Genetics Institute, University of FloridaGainesville FL32610‐3610
| | - Andrew Kitchen
- Department of AnthropologyUniversity of IowaIowa City IA52242
| | - Aida T. Miró‐Herrans
- Department of AnthropologyUniversity of FloridaGainesville FL32611‐7305
- Genetics Institute, University of FloridaGainesville FL32610‐3610
| | - Laurel N. Pearson
- Department of AnthropologyUniversity of FloridaGainesville FL32611‐7305
- Genetics Institute, University of FloridaGainesville FL32610‐3610
| | - Ali Al‐Meeri
- Department of Clinical Biochemistry, Faculty of Medicine and Health SciencesUniversity of Sana'aSana'a Yemen
| | - Connie J. Mulligan
- Department of AnthropologyUniversity of FloridaGainesville FL32611‐7305
- Genetics Institute, University of FloridaGainesville FL32610‐3610
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Llorente MG, Jones ER, Eriksson A, Siska V, Arthur KW, Arthur JW, Curtis MC, Stock JT, Coltorti M, Pieruccini P, Stretton S, Brock F, Higham T, Park Y, Hofreiter M, Bradley DG, Bhak J, Pinhasi R, Manica A. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa. Science 2015; 350:820-2. [DOI: 10.1126/science.aad2879] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 09/28/2015] [Indexed: 12/26/2022]
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41
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Cerezo M, Gusmão L, Černý V, Uddin N, Syndercombe-Court D, Gómez-Carballa A, Göbel T, Schneider PM, Salas A. Comprehensive Analysis of Pan-African Mitochondrial DNA Variation Provides New Insights into Continental Variation and Demography. J Genet Genomics 2015; 43:133-43. [PMID: 27020033 DOI: 10.1016/j.jgg.2015.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/30/2015] [Accepted: 09/15/2015] [Indexed: 01/15/2023]
Abstract
Africa is the cradle of all human beings, and although it has been the focus of a number of genetic studies, there are many questions that remain unresolved. We have performed one of the largest and most comprehensive meta-analyses of mitochondrial DNA (mtDNA) lineages carried out in the African continent to date. We generated high-throughput mtDNA single nucleotide polymorphism (SNP) data (230 SNPs) from 2024 Africans, where more than 500 of them were additionally genotyped for the control region. These data were analyzed together with over 12,700 control region profiles collected from the literature, representing more than 300 population samples from Africa. Insights into the African homeland of humans are discussed. Phylogeographic patterns for the African continent are shown at a high phylogeographic resolution as well as at the population and regional levels. The deepest branch of the mtDNA tree, haplogroup L0, shows the highest sub-haplogroup diversity in Southeast and East Africa, suggesting this region as the homeland for modern humans. Several demographic estimates point to the coast as a facilitator of human migration in Africa, but the data indicate complex patterns, perhaps mirroring the effect of recent continental-scaled demographic events in re-shaping African mtDNA variability.
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Affiliation(s)
- María Cerezo
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia 15782, Spain; The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Leonor Gusmão
- DNA Diagnostic Laboratory, Institute of Biology, State University of Rio de Janeiro, Rio de Janeiro 20550-900, Brazil; IPATIMUP Institute of Molecular Pathology and Immunology of the University of Porto, Porto 4200-465, Portugal
| | - Viktor Černý
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague 118-01, Czech Republic
| | - Nabeel Uddin
- Faculty of Life Sciences and Medicine, King's College London, London SE1 9NH, UK
| | | | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia 15782, Spain
| | - Tanja Göbel
- Institute of Legal Medicine, Medical Faculty, University of Cologne, Cologne D-50823, Germany
| | - Peter M Schneider
- Institute of Legal Medicine, Medical Faculty, University of Cologne, Cologne D-50823, Germany
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia 15782, Spain.
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Gomes V, Pala M, Salas A, Álvarez-Iglesias V, Amorim A, Gómez-Carballa A, Carracedo Á, Clarke DJ, Hill C, Mormina M, Shaw MA, Dunne DW, Pereira R, Pereira V, Prata MJ, Sánchez-Diz P, Rito T, Soares P, Gusmão L, Richards MB. Mosaic maternal ancestry in the Great Lakes region of East Africa. Hum Genet 2015; 134:1013-27. [PMID: 26188410 DOI: 10.1007/s00439-015-1583-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 07/04/2015] [Indexed: 01/21/2023]
Abstract
The Great Lakes lie within a region of East Africa with very high human genetic diversity, home of many ethno-linguistic groups usually assumed to be the product of a small number of major dispersals. However, our knowledge of these dispersals relies primarily on the inferences of historical, linguistics and oral traditions, with attempts to match up the archaeological evidence where possible. This is an obvious area to which archaeogenetics can contribute, yet Uganda, at the heart of these developments, has not been studied for mitochondrial DNA (mtDNA) variation. Here, we compare mtDNA lineages at this putative genetic crossroads across 409 representatives of the major language groups: Bantu speakers and Eastern and Western Nilotic speakers. We show that Uganda harbours one of the highest mtDNA diversities within and between linguistic groups, with the various groups significantly differentiated from each other. Despite an inferred linguistic origin in South Sudan, the data from the two Nilotic-speaking groups point to a much more complex history, involving not only possible dispersals from Sudan and the Horn but also large-scale assimilation of autochthonous lineages within East Africa and even Uganda itself. The Eastern Nilotic group also carries signals characteristic of West-Central Africa, primarily due to Bantu influence, whereas a much stronger signal in the Western Nilotic group suggests direct West-Central African ancestry. Bantu speakers share lineages with both Nilotic groups, and also harbour East African lineages not found in Western Nilotic speakers, likely due to assimilating indigenous populations since arriving in the region ~3000 years ago.
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Affiliation(s)
- Verónica Gomes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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Fernandes V, Triska P, Pereira JB, Alshamali F, Rito T, Machado A, Fajkošová Z, Cavadas B, Černý V, Soares P, Richards MB, Pereira L. Genetic stratigraphy of key demographic events in Arabia. PLoS One 2015; 10:e0118625. [PMID: 25738654 PMCID: PMC4349752 DOI: 10.1371/journal.pone.0118625] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 01/21/2015] [Indexed: 01/01/2023] Open
Abstract
At the crossroads between Africa and Eurasia, Arabia is necessarily a melting pot, its peoples enriched by successive gene flow over the generations. Estimating the timing and impact of these multiple migrations are important steps in reconstructing the key demographic events in the human history. However, current methods based on genome-wide information identify admixture events inefficiently, tending to estimate only the more recent ages, as here in the case of admixture events across the Red Sea (∼8–37 generations for African input into Arabia, and 30–90 generations for “back-to-Africa” migrations). An mtDNA-based founder analysis, corroborated by detailed analysis of the whole-mtDNA genome, affords an alternative means by which to identify, date and quantify multiple migration events at greater time depths, across the full range of modern human history, albeit for the maternal line of descent only. In Arabia, this approach enables us to infer several major pulses of dispersal between the Near East and Arabia, most likely via the Gulf corridor. Although some relict lineages survive in Arabia from the time of the out-of-Africa dispersal, 60 ka, the major episodes in the peopling of the Peninsula took place from north to south in the Late Glacial and, to a lesser extent, the immediate post-glacial/Neolithic. Exchanges across the Red Sea were mainly due to the Arab slave trade and maritime dominance (from ∼2.5 ka to very recent times), but had already begun by the early Holocene, fuelled by the establishment of maritime networks since ∼8 ka. The main “back-to-Africa” migrations, again undetected by genome-wide dating analyses, occurred in the Late Glacial period for introductions into eastern Africa, whilst the Neolithic was more significant for migrations towards North Africa.
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Affiliation(s)
- Verónica Fernandes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Petr Triska
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Instituto de Ciências Biomédicas da Universidade do Porto (ICBAS), Porto, Portugal
| | - Joana B. Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Farida Alshamali
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates
| | - Teresa Rito
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Alison Machado
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Zuzana Fajkošová
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Bruno Cavadas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Viktor Černý
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Martin B. Richards
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Luísa Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- * E-mail:
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Berg S, Schelling E, Hailu E, Firdessa R, Gumi B, Erenso G, Gadisa E, Mengistu A, Habtamu M, Hussein J, Kiros T, Bekele S, Mekonnen W, Derese Y, Zinsstag J, Ameni G, Gagneux S, Robertson BD, Tschopp R, Hewinson G, Yamuah L, Gordon SV, Aseffa A. Investigation of the high rates of extrapulmonary tuberculosis in Ethiopia reveals no single driving factor and minimal evidence for zoonotic transmission of Mycobacterium bovis infection. BMC Infect Dis 2015; 15:112. [PMID: 25886866 PMCID: PMC4359574 DOI: 10.1186/s12879-015-0846-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 02/19/2015] [Indexed: 11/14/2022] Open
Abstract
Background Ethiopia, a high tuberculosis (TB) burden country, reports one of the highest incidence rates of extra-pulmonary TB dominated by cervical lymphadenitis (TBLN). Infection with Mycobacterium bovis has previously been excluded as the main reason for the high rate of extrapulmonary TB in Ethiopia. Methods Here we examined demographic and clinical characteristics of 953 pulmonary (PTB) and 1198 TBLN patients visiting 11 health facilities in distinct geographic areas of Ethiopia. Clinical characteristics were also correlated with genotypes of the causative agent, Mycobacterium tuberculosis. Results No major patient or bacterial strain factor could be identified as being responsible for the high rate of TBLN, and there was no association with HIV infection. However, analysis of the demographic data of involved patients showed that having regular and direct contact with live animals was more associated with TBLN than with PTB, although no M. bovis was isolated from patients with TBLN. Among PTB patients, those infected with Lineage 4 reported “contact with other TB patient” more often than patients infected with Lineage 3 did (OR = 1.6, CI 95% 1.0-2.7; p = 0.064). High fever, in contrast to low and moderate fever, was significantly associated with Lineage 4 (OR = 2.3; p = 0.024). On the other hand, TBLN cases infected with Lineage 4 tended to get milder symptoms overall for the constitutional symptoms than those infected with Lineage 3. Conclusions The study suggests a complex role for multiple interacting factors in the epidemiology of extrapulmonary TB in Ethiopia, including factors that can only be derived from population-based studies, which may prove to be significant for TB control in Ethiopia. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-0846-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefan Berg
- Animal and Plant Health Agency, TB Research Group, New Haw, Addlestone, Surrey, KT15 3NB, UK.
| | - Esther Schelling
- Swiss Tropical and Public Health Institute, PO Box CH-4002, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Elena Hailu
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Rebuma Firdessa
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia. .,University of Würzburg, Institute for Molecular Infection Biology, Würzburg, Germany.
| | - Balako Gumi
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Girume Erenso
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Endalamaw Gadisa
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Araya Mengistu
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Meseret Habtamu
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Jemal Hussein
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Teklu Kiros
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Shiferaw Bekele
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Wondale Mekonnen
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Yohannes Derese
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, PO Box CH-4002, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia.
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, PO Box CH-4002, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Brian D Robertson
- Center for Molecular Bacteriology and Infection, Department of Medicine, Flowers building, South Kensington, Imperial College London, London, SW7 2AZ, UK.
| | - Rea Tschopp
- Swiss Tropical and Public Health Institute, PO Box CH-4002, Basel, Switzerland. .,Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia. .,University of Basel, Basel, Switzerland.
| | - Glyn Hewinson
- Animal and Plant Health Agency, TB Research Group, New Haw, Addlestone, Surrey, KT15 3NB, UK.
| | - Lawrence Yamuah
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
| | - Stephen V Gordon
- UCD Schools of Veterinary Medicine, Medicine and Medical Science, Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, Dublin, Republic of Ireland.
| | - Abraham Aseffa
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia.
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45
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John SE, Thareja G, Hebbar P, Behbehani K, Thanaraj TA, Alsmadi O. Kuwaiti population subgroup of nomadic Bedouin ancestry-Whole genome sequence and analysis. GENOMICS DATA 2015; 3:116-27. [PMID: 26484159 PMCID: PMC4535864 DOI: 10.1016/j.gdata.2014.11.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/27/2014] [Accepted: 11/28/2014] [Indexed: 12/21/2022]
Abstract
Kuwaiti native population comprises three distinct genetic subgroups of Persian, "city-dwelling" Saudi Arabian tribe, and nomadic "tent-dwelling" Bedouin ancestry. Bedouin subgroup is characterized by presence of 17% African ancestry; it owes it origin to nomadic tribes of the deserts of Arabian Peninsula and North Africa. By sequencing whole genome of a Kuwaiti male from this subgroup at 41X coverage, we report 3,752,878 SNPs, 411,839 indels, and 8451 structural variations. Neighbor-joining tree, based on shared variant positions carrying disease-risk alleles between the Bedouin and other continental genomes, places Bedouin genome at the nexus of African, Asian, and European genomes in concordance with geographical location of Kuwait and Peninsula. In congruence with participant's medical history for morbid obesity and bronchial asthma, risk alleles are seen at deleterious SNPs associated with obesity and asthma. Many of the observed deleterious 'novel' variants lie in genes associated with autosomal recessive disorders characteristic of the region.
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Affiliation(s)
| | | | | | | | | | - Osama Alsmadi
- Corresponding author. Tel.: + 965 2224 2999x4343(work); fax: + 965 2249 2406.
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46
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Davis C, Peters D, Warshauer D, King J, Budowle B. Sequencing the hypervariable regions of human mitochondrial DNA using massively parallel sequencing: Enhanced data acquisition for DNA samples encountered in forensic testing. Leg Med (Tokyo) 2014; 17:123-7. [PMID: 25459369 DOI: 10.1016/j.legalmed.2014.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 10/03/2014] [Accepted: 10/05/2014] [Indexed: 11/19/2022]
Abstract
Mitochondrial DNA testing is a useful tool in the analysis of forensic biological evidence. In cases where nuclear DNA is damaged or limited in quantity, the higher copy number of mitochondrial genomes available in a sample can provide information about the source of a sample. Currently, Sanger-type sequencing (STS) is the primary method to develop mitochondrial DNA profiles. This method is laborious and time consuming. Massively parallel sequencing (MPS) can increase the amount of information obtained from mitochondrial DNA samples while improving turnaround time by decreasing the numbers of manipulations and more so by exploiting high throughput analyses to obtain interpretable results. In this study 18 buccal swabs, three different tissue samples from five individuals, and four bones samples from casework were sequenced at hypervariable regions I and II using STS and MPS. Sample enrichment for STS and MPS was PCR-based. Library preparation for MPS was performed using Nextera® XT DNA Sample Preparation Kit and sequencing was performed on the MiSeq™ (Illumina, Inc.). MPS yielded full concordance of base calls with STS results, and the newer methodology was able to resolve length heteroplasmy in homopolymeric regions. This study demonstrates short amplicon MPS of mitochondrial DNA is feasible, can provide information not possible with STS, and lays the groundwork for development of a whole genome sequencing strategy for degraded samples.
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Affiliation(s)
- Carey Davis
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - Dixie Peters
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - David Warshauer
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - Jonathan King
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
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47
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Kopp GH, Roos C, Butynski TM, Wildman DE, Alagaili AN, Groeneveld LF, Zinner D. Out of Africa, but how and when? The case of hamadryas baboons (Papio hamadryas). J Hum Evol 2014; 76:154-64. [PMID: 25257698 DOI: 10.1016/j.jhevol.2014.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/07/2014] [Accepted: 08/07/2014] [Indexed: 11/30/2022]
Abstract
Many species of Arabian mammals are considered to be of Afrotropical origin and for most of them the Red Sea has constituted an obstacle for dispersal since the Miocene-Pliocene transition. There are two possible routes, the 'northern' and the 'southern', for terrestrial mammals (including humans) to move between Africa and Arabia. The 'northern route', crossing the Sinai Peninsula, is confirmed for several taxa by an extensive fossil record, especially from northern Egypt and the Levant, whereas the 'southern route', across the Bab-el-Mandab Strait, which links the Red Sea with the Gulf of Aden, is more controversial, although post-Pliocene terrestrial crossings of the Red Sea might have been possible during glacial maxima when sea levels were low. Hamadryas baboons (Papio hamadryas) are the only baboon taxon to disperse out of Africa and still inhabit Arabia. In this study, we investigate the origin of Arabian hamadryas baboons using mitochondrial sequence data from 294 samples collected in Arabia and Northeast Africa. Through the analysis of the geographic distribution of genetic diversity, the timing of population expansions, and divergence time estimates combined with palaeoecological data, we test: (i) if Arabian and African hamadryas baboons are genetically distinct; (ii) if Arabian baboons exhibit population substructure; and (iii) when, and via which route, baboons colonized Arabia. Our results suggest that hamadryas baboons colonized Arabia during the Late Pleistocene (130-12 kya [thousands of years ago]) and also moved back to Africa. We reject the hypothesis that hamadryas baboons were introduced to Arabia by humans, because the initial colonization considerably predates the earliest records of human seafaring in this region. Our results strongly suggest that the 'southern route' from Africa to Arabia could have been used by hamadryas baboons during the same time period as proposed for modern humans.
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Affiliation(s)
- Gisela H Kopp
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.
| | - Thomas M Butynski
- King Khalid Wildlife Research Centre, Saudi Wildlife Authority, P.O. Box 61681, Riyadh 11575, Saudi Arabia; Conservation Programs, Zoological Society of London, Regent's Park, London NW1 4RY, United Kingdom.
| | - Derek E Wildman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 E. Canfield Ave. 3240 Scott Hall, Detroit, MI 48220, USA.
| | - Abdulaziz N Alagaili
- KSU Mammals Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia; Saudi Wildlife Authority, P.O. Box 61681, Riyadh 11575, Saudi Arabia.
| | | | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.
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48
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Marks SJ, Montinaro F, Levy H, Brisighelli F, Ferri G, Bertoncini S, Batini C, Busby GBJ, Arthur C, Mitchell P, Stewart BA, Oosthuizen O, Oosthuizen E, D'Amato ME, Davison S, Pascali V, Capelli C. Static and moving frontiers: the genetic landscape of Southern African Bantu-speaking populations. Mol Biol Evol 2014; 32:29-43. [PMID: 25223418 DOI: 10.1093/molbev/msu263] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A consensus on Bantu-speaking populations being genetically similar has emerged in the last few years, but the demographic scenarios associated with their dispersal are still a matter of debate. The frontier model proposed by archeologists postulates different degrees of interaction among incoming agropastoralist and resident foraging groups in the presence of "static" and "moving" frontiers. By combining mitochondrial DNA and Y chromosome data collected from several southern African populations, we show that Bantu-speaking populations from regions characterized by a moving frontier developing after a long-term static frontier have larger hunter-gatherer contributions than groups from areas where a static frontier was not followed by further spatial expansion. Differences in the female and male components suggest that the process of assimilation of the long-term resident groups into agropastoralist societies was gender biased. Our results show that the diffusion of Bantu languages and culture in Southern Africa was a process more complex than previously described and suggest that the admixture dynamics between farmers and foragers played an important role in shaping the current patterns of genetic diversity.
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Affiliation(s)
- Sarah J Marks
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Francesco Montinaro
- Department of Zoology, University of Oxford, Oxford, United Kingdom Institute of Legal Medicine, Catholic University, Rome, Italy
| | - Hila Levy
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Gianmarco Ferri
- Dipartimento ad Attività Integrata di Laboratori, Anatomia Patologica, Medicina Legale, U.O. Struttura Complessa di Medicina Legale, Azienda Ospedaliero, Universitaria di Modena, Modena, Italy
| | | | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - George B J Busby
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Charles Arthur
- School of Archaeology, University of Oxford, Oxford, United Kingdom
| | - Peter Mitchell
- School of Archaeology, University of Oxford, Oxford, United Kingdom School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | | | - Maria Eugenia D'Amato
- Biotechnology Department, Forensic DNA Laboratory, University of the Western Cape, Bellville, South Africa
| | - Sean Davison
- Biotechnology Department, Forensic DNA Laboratory, University of the Western Cape, Bellville, South Africa
| | | | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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49
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High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq. Forensic Sci Int Genet 2014; 12:128-35. [DOI: 10.1016/j.fsigen.2014.06.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/29/2014] [Accepted: 06/01/2014] [Indexed: 12/21/2022]
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50
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Gomez F, Hirbo J, Tishkoff SA. Genetic variation and adaptation in Africa: implications for human evolution and disease. Cold Spring Harb Perspect Biol 2014; 6:a008524. [PMID: 24984772 DOI: 10.1101/cshperspect.a008524] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Because modern humans originated in Africa and have adapted to diverse environments, African populations have high levels of genetic and phenotypic diversity. Thus, genomic studies of diverse African ethnic groups are essential for understanding human evolutionary history and how this leads to differential disease risk in all humans. Comparative studies of genetic diversity within and between African ethnic groups creates an opportunity to reconstruct some of the earliest events in human population history and are useful for identifying patterns of genetic variation that have been influenced by recent natural selection. Here we describe what is currently known about genetic variation and evolutionary history of diverse African ethnic groups. We also describe examples of recent natural selection in African genomes and how these data are informative for understanding the frequency of many genetic traits, including those that cause disease susceptibility in African populations and populations of recent African descent.
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Affiliation(s)
- Felicia Gomez
- Department of Genetics and Biology, School of Medicine and School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104 Hominid Paleobiology Doctoral Program and The Center for the Advanced Study of Hominid Paleobiology, Department of Anthropology, The George Washington University, Washington, D.C. 20052
| | - Jibril Hirbo
- Department of Genetics and Biology, School of Medicine and School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Sarah A Tishkoff
- Department of Genetics and Biology, School of Medicine and School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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