349 results match your criteria african haplogroups

Impact of modular mitochondrial epistatic interactions on the evolution of human subpopulations.

Mitochondrion 2021 Feb 20;58:111-122. Epub 2021 Feb 20.

Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore 453552, India; Complex Systems Lab, Department of Physics, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore 453552, India; Center for Theoretical Physics of Complex Systems, Institute for Basic Science(IBS), Daejeon 34126, Korea. Electronic address:

Investigation of human mitochondrial (mt) genome variation has been shown to provide insights to the human history and natural selection. By analyzing 24,167 human mt-genome samples, collected for five continents, we have developed a co-mutation network model to investigate characteristic human evolutionary patterns. The analysis highlighted richer co-mutating regions of the mt-genome, suggesting the presence of epistasis. Read More

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February 2021

Mitochondrial DNA haplogroups and weight gain following switch to integrase strand transfer inhibitor-based antiretroviral therapy.

AIDS 2021 03;35(3):439-445

Vanderbilt University Medical Center, Nashville, Tennessee.

Background: Integrase strand transfer inhibitor (INSTI)-based antiretroviral therapy (ART) has been associated with excess weight gain in some adults, which may be influenced by genetic factors. We assessed mitochondrial DNA (mtDNA) haplogroups and weight gain following switch to INSTI-based ART.

Methods: All AIDS Clinical Trials Group A5001 and A5322 participants with mtDNA genotyping who switched to INSTI were included. Read More

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Differential effects of cisplatin on cybrid cells with varying mitochondrial DNA haplogroups.

PeerJ 2020 1;8:e9908. Epub 2020 Oct 1.

Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, United States of America.

Background: Drug therapy yields different results depending on its recipient population. Cisplatin, a commonly used chemotherapeutic agent, causes different levels of resistance and side effects for different patients, but the mechanism(s) are presently unknown. It has been assumed that this variation is a consequence of differences in nuclear (n) DNA, epigenetics, or some external factor(s). Read More

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October 2020

Ancestry, health, and lived experiences of enslaved Africans in 18th century Charleston: An osteobiographical analysis.

Am J Phys Anthropol 2020 Oct 6. Epub 2020 Oct 6.

Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

Objectives: In 2013, the burials of 36 individuals of putative African ancestry were discovered during renovation of the Gaillard Center in downtown Charleston, South Carolina. The Charleston community facilitated a bioarchaeological and mitogenomic study to gain insights into the lives of these unknown persons, referred to as the Anson Street Ancestors, including their ancestry, health, and lived experiences in the 18th century.

Methods: Metric and morphological assessments of skeletal and dental characteristics were recorded, and enamel and cortical bone strontium stable isotope values generated. Read More

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October 2020

"Distribution of paternal lineages in Mestizo populations throughout Mexico: an in silico study based on Y-STR haplotypes".

J Hum Genet 2021 Mar 12;66(3):327-332. Epub 2020 Sep 12.

Instituto de Investigación en Genética Molecular, Universidad de Guadalajara (CUCiénega-UdeG), Ocotlán, Jalisco, México.

The Mexican-Mestizo population arose following European contact with the Americas due to the admixture of principally Spaniards, Native Americans, and Africans around 500 years ago. Because the paternal lineage distribution of the Mexican population has been poorly investigated, this study inferred the haplogroups of ten populations based on 1859 haplotypes (Y-STR data) using two haplogroup predictor programs. In the Mexican population sample, we found predominantly European ancestry (50. Read More

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Maternal origin and genetic diversity of Algerian domestic chicken () from North-Western Africa based on mitochondrial DNA analysis.

Anim Biotechnol 2020 Aug 13:1-11. Epub 2020 Aug 13.

Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Université des Sciences et de la Technologie d'Oran Mohamed Boudiaf, USTO-MB, BP 1505, El M'naouer, Oran Algérie.

Local chicken populations are a major source of food in the rural areas of Algeria. However, their origin has not been well characterized. The objectives of this study were to assess genetic diversity and maternal origin of domestic chicken from five agro-ecological regions of western Algeria: coastal (CT), inland plains (IP), highlands (HL), mountains (MT) and sahara (SH, including Oasis, Req and Erg regions). Read More

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Genomic Landscape of the Mitochondrial Genome in the United Arab Emirates Native Population.

Genes (Basel) 2020 08 1;11(8). Epub 2020 Aug 1.

Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE.

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. Read More

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Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences.

Genome Biol Evol 2020 07;12(7):1031-1039

Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden.

Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, however, has removed this bias and allowed for the discovery of thousands of new variants for use in improving the Y-chromosome phylogeny and computing estimates that are more accurate. Here, we describe the high-coverage sequencing of the whole Y chromosome in a data set of 19 male Khoe-San individuals in comparison with existing whole Y-chromosome sequence data. Read More

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The Y-chromosome of the Soliga, an ancient forest-dwelling tribe of South India.

Gene X 2020 Dec 13;5:100026. Epub 2020 Jan 13.

Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA.

A previous autosomal STR study provided evidence of a connection between the ancient Soliga tribe at the southern tip of the Indian subcontinent and Australian aboriginal populations, possibly reflecting an eastbound coastal migration circa (15 Kya). The Soliga are considered to be among India's earliest inhabitants. In this investigation, we focus on the Y chromosomal characteristics shared between the Soliga population and other Indian tribes as well as western Eurasia and Sub-Saharan Africa groups. Read More

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December 2020

The maternal origin of indigenous domestic chicken from the Middle East, the north and the horn of Africa.

BMC Genet 2020 03 14;21(1):30. Epub 2020 Mar 14.

School of Life Sciences, the University of Nottingham, University Park, Nottingham, NG7 2RD, UK.

Background: Indigenous domestic chicken represents a major source of protein for agricultural communities around the world. In the Middle East and Africa, they are adapted to hot dry and semi-dry areas, in contrast to their wild ancestor, the Red junglefowl, which lives in humid and sub-humid tropical areas. Indigenous populations are declining following increased demand for poultry meat and eggs, favouring the more productive exotic commercial breeds. Read More

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Phylogenetic Studies on Red Junglefowl () and Native Chicken () in Samar Island, Philippines using the Mitochondrial DNA D-Loop Region.

J Poult Sci 2019 Oct;56(4):237-244

Department of Animal Science, Visayas State University, Visca, Baybay City, Leyte, Philippines.

A study was conducted to provide genetic information on the matrilineal phylogeny and genetic diversity of Red junglefowl (RJF) and native chickens in Samar Island, Philippines and to identify the genetic distance between Philippine junglefowls and other RJF species in Southeast Asia using complete mitochondrial DNA D-loop sequences. A total of 5 RJFs and 43 native chickens from Samar Island were included in this study. The results showed that Samar RJFs had a nucleotide diversity of 0. Read More

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October 2019

New insights on intercontinental origins of paternal lineages in Northeast Brazil.

BMC Evol Biol 2020 01 29;20(1):15. Epub 2020 Jan 29.

Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil.

Background: The current Brazilian population is the product of centuries of admixture between intercontinental founding groups. Although previous results have revealed a heterogeneous distribution of mitochondrial lineages in the Northeast region, the most targeted by foreign settlers during the sixteenth century, little is known about the paternal ancestry of this particular population. Considering historical records have documented a series of territorial invasions in the Northeast by various European populations, we aimed to characterize the male lineages found in Brazilian individuals in order to discover to what extent these migrations have influenced the present-day gene pool. Read More

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January 2020

African Mitochondrial DNA Haplogroup L2 Is Associated With Slower Decline of β-cell Function and Lower Incidence of Diabetes Mellitus in Non-Hispanic, Black Women Living With Human Immunodeficiency Virus.

Clin Infect Dis 2020 Nov;71(8):e218-e225

Tennessee Valley Healthcare System-Veterans Affairs Hospital, Nashville, Tennessee, USA.

Background: Susceptibility to metabolic diseases may be influenced by mitochondrial genetic variability among people living with human immunodeficiency virus (HIV; PLWH), but remains unexplored in populations with African ancestry. We investigated the association between mitochondrial DNA (mtDNA) haplogroups and the homeostatic model assessments of β-cell function (HOMA-B) and insulin resistance (HOMA-IR), as well as incident diabetes mellitus (DM), among Black women living with or at risk for HIV.

Methods: Women without DM who had fasting glucose (FG) and insulin (FI) data for ≥2 visits were included. Read More

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November 2020

African and Asian Mitochondrial DNA Haplogroups Confer Resistance Against Diabetic Stresses on Retinal Pigment Epithelial Cybrid Cells In Vitro.

Mol Neurobiol 2020 Mar 6;57(3):1636-1655. Epub 2019 Dec 6.

Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA, 92697, USA.

Diabetic retinopathy (DR) is the most common cause of blindness for individuals under the age of 65. This loss of vision can be due to ischemia, neovascularization, and/or diabetic macular edema, which are caused by breakdown of the blood-retina barrier at the level of the retinal pigment epithelium (RPE) and inner retinal vasculature. The prevalence of diabetes and its complications differ between Caucasian-Americans and certain minority populations, such as African-Americans and Asian-Americans. Read More

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Population genetic structure of the thick-tailed bushbaby () from the Soutpansberg Mountain range, Northern South Africa, based on four mitochondrial DNA regions.

Mitochondrial DNA A DNA Mapp Seq Anal 2020 01 25;31(1):1-10. Epub 2019 Nov 25.

South African National Biodiversity Institute, Pretoria, South Africa.

Greater bushbabies, strepsirrhine primates, that are distributed across central, eastern and southern Africa, with northern and eastern South Africa representing the species' most southerly distribution. Greater bushbabies are habitat specialists whose naturally fragmented habitats are getting even more fragmented due to anthropogenic activities. Currently, there is no population genetic data or study published on the species. Read More

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January 2020

A Comprehensive Haplotype-Targeting Strategy for Allele-Specific HTT Suppression in Huntington Disease.

Am J Hum Genet 2019 12 7;105(6):1112-1125. Epub 2019 Nov 7.

Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z4H4, Canada. Electronic address:

Huntington disease (HD) is a fatal neurodegenerative disorder caused by a gain-of-function mutation in HTT. Suppression of mutant HTT has emerged as a leading therapeutic strategy for HD, with allele-selective approaches targeting HTT SNPs now in clinical trials. Haplotypes associated with the HD mutation (A1, A2, A3a) represent panels of allele-specific gene silencing targets for efficient treatment of individuals with HD of Northern European and indigenous South American ancestry. Read More

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December 2019

Paternal lineages and forensic parameters based on 23 Y-STRs (Powerplex® Y23) in Mestizo males from Mexico City.

Int J Legal Med 2020 Jan 9;134(1):199-202. Epub 2019 Nov 9.

Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara (CUCiénega-UdeG), Av. Universidad #1115, Col. Paso Blanco, CP 47810, Ocotlán, Jalisco, México.

We analyzed 307 Mexican-Mestizo (admixed) males from Mexico City with the Powerplex® Y23 system. The complete list of Y-STR haplotypes was uploaded into the YHRD database (accession number YA004275). The discriminatory capacity (98. Read More

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January 2020

Male lineages in Brazilian populations and performance of haplogroup prediction tools.

Forensic Sci Int Genet 2020 01 15;44:102163. Epub 2019 Oct 15.

DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil.

The use of Y-chromosomal genetic markers in forensic investigations demands the establishment of reliable and representative DNA databases of different reference populations. The genetic characterization of the Y chromosome variation in human populations requires the analyses of haplotype frequencies allied to haplogroup determination. The present study aimed to contribute to the Brazilian database by providing 1,382 Yfiler Plus individual profiles, from 11 Brazilian states. Read More

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January 2020

What can a comparative genomics approach tell us about the pathogenicity of mtDNA mutations in human populations?

Evol Appl 2019 Dec 27;12(10):1912-1930. Epub 2019 Aug 27.

Institute of Genetic Medicine Newcastle University Newcastle-upon-Tyne UK.

Mitochondrial disorders are heterogeneous, showing variable presentation and penetrance. Over the last three decades, our ability to recognize mitochondrial patients and diagnose these mutations, linking genotype to phenotype, has greatly improved. However, it has become increasingly clear that these strides in diagnostics have not benefited all population groups. Read More

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December 2019

Comparative study between Helicobacter pylori and host human genetics in the Dominican Republic.

BMC Evol Biol 2019 11 1;19(1):197. Epub 2019 Nov 1.

Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Oita, Japan.

Background: Helicobacter pylori, a bacterium that infects the human stomach, has high genetic diversity. Because its evolution is parallel to human, H. pylori is used as a tool to trace human migration. Read More

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November 2019

Tracing the genetic legacy in the French Caribbean islands: A study of mitochondrial and Y-chromosome lineages in the Guadeloupe archipelago.

Am J Phys Anthropol 2019 12 10;170(4):507-518. Epub 2019 Oct 10.

University of Bordeaux, UMR 5199 PACEA, Allée Geoffroy de St Hilaire, Pessac, France.

Objectives: The history of the Caribbean region is marked by numerous and various successive migration waves that resulted in a global blending of African, European, and Amerindian lineages. As the origin and genetic composition of the current population of French Caribbean islands has not been studied to date, we used both mitochondrial DNA and Y-chromosome markers to complete the characterization of the dynamics of admixture in the Guadeloupe archipelago.

Materials And Methods: We sequenced the mitochondrial hypervariable regions and genotyped mitochondrial and Y-chromosomal single nucleotide polymorphisms (SNPs) of 198 individuals from five localities of the Guadeloupe archipelago. Read More

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December 2019

Assessment of the global paradigms of genetic variability in Strongyloides stercoralis infrapopulations determined by mitochondrial DNA sequences.

Comp Immunol Microbiol Infect Dis 2019 Dec 26;67:101354. Epub 2019 Sep 26.

Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.

Microevolutionary data of Strongyloides stercoralis infrapopulations are regarded as a requirement for determining the global genetic structure and transmission paradigms of this neglected tropical nematode among the neighboring countries of the world. English databases were searched from 2010 to 2019, analyzing a total of 10 publications. The cytochrome c oxidase subunit 1 sequences of S. Read More

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December 2019

Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes.

PLoS Genet 2019 09 16;15(9):e1008369. Epub 2019 Sep 16.

Bioinformatics and Genomics Graduate Program, The Huck Institutes for the Life Sciences, Pennsylvania State University, University Park, PA, United States of America.

The Y chromosome harbors nine multi-copy ampliconic gene families expressed exclusively in testis. The gene copies within each family are >99% identical to each other, which poses a major challenge in evaluating their copy number. Recent studies demonstrated high variation in Y ampliconic gene copy number among humans. Read More

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September 2019

Genomic clues of the evolutionary history of Bos indicus cattle.

Anim Genet 2019 Dec 2;50(6):557-568. Epub 2019 Sep 2.

Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA and BioDNA, Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, Piacenza, 29122, Italy.

Together with their sister subspecies Bos taurus, zebu cattle (Bos indicus) have contributed to important socioeconomic changes that have shaped modern civilizations. Zebu cattle were domesticated in the Indus Valley 8000 years before present (YBP). From the domestication site, they expanded to Africa, East Asia, southwestern Asia and Europe between 4000 and 1300 YBP, intercrossing with B. Read More

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December 2019

Genetic diversity of the JC polyomavirus (JCPyV) and mitochondrial DNA ancestry in Misiones, Argentina.

Infect Genet Evol 2019 11 22;75:104011. Epub 2019 Aug 22.

Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina.

Background: The use of human and viral genetic markers offers a novel way to study human migration in multiethnic populations of Latin America.

Objectives: Our goal was to characterize the genetic diversity and geographical origins of JC Polyomavirus (JCPyV) and the genetic ancestry of mitochondrial DNA (mtDNA) in inhabitants from 25 de Mayo, Misiones-Argentina, a small village of largely German ancestry located close to the border with Brazil. We also evaluated the extent of agreement between viral and mtDNA markers for the different ancestry components of this population. Read More

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November 2019

Polymorphisms in CAMKK2 associate with susceptibility to sensory neuropathy in HIV patients treated without stavudine.

J Neurovirol 2019 12 15;25(6):814-824. Epub 2019 Jul 15.

School of Pharmacy and Biomedical Science, Curtin University, Bentley, Australia.

HIV-associated sensory neuropathy (HIV-SN) is a debilitating neurological complication of HIV infection potentiated by the antiretroviral drug stavudine. While stavudine is no longer used, HIV-SN now affects around 15% of HIV+ Indonesians. Here, we investigate whether polymorphisms within the P2X-block (P2X4R, P2X7R, CAMKK2) and/or ANAPC5 mark susceptibility to HIV-SN in this setting. Read More

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December 2019

Mitochondrial DNA Haplogroups and Delirium During Sepsis.

Crit Care Med 2019 08;47(8):1065-1071

Clinical Research, Investigation, and Systems Modeling of Acute illness (CRISMA) Center in the Department of Critical Care Medicine, University of Pittsburgh School of Medicine.

Objectives: Studies suggest that mitochondrial dysfunction underlies some forms of sepsis-induced organ failure. We sought to test the hypothesis that variations in mitochondrial DNA haplogroup affect susceptibility to sepsis-associated delirium, a common manifestation of acute brain dysfunction during sepsis.

Design: Retrospective cohort study. Read More

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Mitochondrial haplogroup L1c2 is associated with increased disease severity in African American patients with primary open-angle glaucoma.

J Clin Exp Ophthalmol 2019 18;10(2). Epub 2019 Apr 18.

Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA.

Objective: The purpose of this study is to evaluate the role mitochondrial inheritance plays in primary open-angle glaucoma (POAG) characteristics in African Americans.

Methods: POAG cases from the L1c2 and L1b mitochondrial haplogroups were compared in a retrospective case-case study. Twenty-six pairs of self-identified African American POAG cases from L1c2 and L1b mitochondrial haplogroups matched on age (mean [SD] = 71. Read More

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Rapid ecological specialization despite constant population sizes.

PeerJ 2019 19;7:e6476. Epub 2019 Apr 19.

Department of Zoology, University of Venda, Thohoyandou, Limpopo, Republic of South Africa.

Background: The bushbuck, , is a widespread and ecologically diverse ungulate species complex within the spiral-horned antelopes. This species was recently found to consist of two genetically divergent but monophyletic lineages, which are paraphyletic at mitochondrial (mt)DNA owing to an ancient interspecific hybridization event. The Scriptus lineage () inhabits the north-western half of the African continent while Sylvaticus () is found in the south-eastern half. Read More

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Nomadic pastoralists and sedentary farmers of the Sahel/Savannah Belt of Africa in the light of geometric morphometrics based on facial portraits.

Am J Phys Anthropol 2019 08 29;169(4):632-645. Epub 2019 Apr 29.

Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic.

Objectives: The Sahel/Savannah belt is a region where two sympatric human subsistence strategies-nomadic pastoralism and sedentary farming-have been coexisting for millennia. While earlier studies focused on estimating population differentiation and genetic structure of this ecologically remarkable region's inhabitants, less effort has been expended on understanding the morphological variation among local populations.

Materials And Methods: To fill this gap, we used geometric morphometrics to analyze the facial features of three groups of pastoralists and three groups of sedentary farmers belonging to three language families (Niger-Congo, Nilo-Saharan, and Afro-Asiatic) whose mitochondrial DNA sequences have been published previously. Read More

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