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Schurr TG, Shengelia R, Shamoon-Pour M, Chitanava D, Laliashvili S, Laliashvili I, Kibret R, Kume-Kangkolo Y, Akhvlediani I, Bitadze L, Mathieson I, Yardumian A. Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus). Genome Biol Evol 2023; 15:evad198. [PMID: 37935112 PMCID: PMC10665041 DOI: 10.1093/gbe/evad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/09/2023] Open
Abstract
To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian speaking. From these DNA samples, we generated mitochondrial DNA (mtDNA) control region sequences for all 485 participants (female and male), Y-short tandem repeat haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal single nucleotide polymorphisms (SNPs) plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, and W. X2) and low frequencies of East Eurasian haplogroups (A, C, D, F, and G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared with ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community.
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Affiliation(s)
- Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ramaz Shengelia
- Department of the History of Medicine, Tbilisi State Medical University, Tbilisi, Georgia
| | - Michel Shamoon-Pour
- First-year Research Immersion, Binghamton University, Binghamton, New York, USA
| | - David Chitanava
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Shorena Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Irma Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Redate Kibret
- Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA
| | - Yanu Kume-Kangkolo
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Lia Bitadze
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Aram Yardumian
- Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA
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2
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Kralick AE, O'Connell CA, Bastian ML, Hoke MK, Zemel BS, Schurr TG, Tocheri MW. Beyond Dimorphism: Body Size Variation Among Adult Orangutans Is Not Dichotomous by Sex. Integr Comp Biol 2023; 63:907-921. [PMID: 37061788 PMCID: PMC10563650 DOI: 10.1093/icb/icad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 04/17/2023] Open
Abstract
Among extant great apes, orangutans are considered the most sexually dimorphic in body size. However, the expression of sexual dimorphism in orangutans is more complex than simply males being larger than females. At sexual maturity, some male orangutans develop cheek pads (flanges), while other males remain unflanged even after becoming reproductively capable. Sometimes flange development is delayed in otherwise sexually mature males for a few years. In other cases, flange development is delayed for many years or decades, with some males even spending their entire lifespan as unflanged adults. Thus, unflanged males of various chronological ages can be mistakenly identified as "subadults." Unflanged adult males are typically described as "female-sized," but this may simply reflect the fact that unflanged male body size has only ever been measured in peri-pubescent individuals. In this study, we measured the skeletons of 111 wild adult orangutans (Pongo spp.), including 20 unflanged males, 45 flanged males, and 46 females, resulting in the largest skeletal sample of unflanged males yet studied. We assessed long bone lengths (as a proxy for stature) for all 111 individuals and recorded weights-at-death, femoral head diameters, bi-iliac breadths, and long bone cross-sectional areas (CSA) (as proxies for mass) for 27 of these individuals, including seven flanged males, three adult confirmed-unflanged males, and three young adult likely-unflanged males. ANOVA and Kruskal-Wallis tests with Tukey and Dunn post-hoc pairwise comparisons, respectively, showed that body sizes for young adult unflanged males are similar to those of the adult females in the sample (all P ≥ 0.09 except bi-iliac breadth), whereas body sizes for adult unflanged males ranged between those of adult flanged males and adult females for several measurements (all P < 0.001). Thus, sexually mature male orangutans exhibit body sizes that range from the female end of the spectrum to the flanged male end of the spectrum. These results exemplify that the term "sexual dimorphism" fails to capture the full range of variation in adult orangutan body size. By including adult unflanged males in analyses of body size and other aspects of morphology, not as aberrations but as an expected part of orangutan variation, we may begin to shift the way that we think about features typically considered dichotomous according to biological sex.
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Affiliation(s)
- Alexandra E Kralick
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Caitlin A O'Connell
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Anthropology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Meredith L Bastian
- Proceedings of the National Academy of Sciences, Washington, DC 20001, USA
| | - Morgan K Hoke
- Department of Anthropology & Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Babette S Zemel
- Division of Gastroenterology, Hepatology and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- , Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew W Tocheri
- Department of Anthropology, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
- Human Origins Program, Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong NSW 2522, Australia
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Pereson MJ, Sanabria DJ, Torres C, Liotta DJ, Campos RH, Schurr TG, Di Lello FA, Badano I. Evolutionary analysis of JC polyomavirus in Misiones' population yields insight into the population dynamics of the early human dispersal in the Americas. Virology 2023; 585:100-108. [PMID: 37327595 DOI: 10.1016/j.virol.2023.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND JC polyomavirus (JCV) has an ethno-geographical distribution across human populations. OBJECTIVE Study the origins of the population of Misiones (Argentina) by using JCV as genetic marker. METHODS Viral detection and characterization was conducted by PCR amplification and evolutionary analysis of the intergenic region sequences. RESULTS 22 out of 121 samples were positive for JCV, including 5 viral lineages: MY (n = 8), Eu-a (n = 7), B1-c (n = 4), B1-b (n = 2) and Af2 (n = 1). MY sequences clustered within a branch of Native American origin that diverged from its Asian counterpart about 21,914 years ago (HPD 95% interval 15,383-30,177), followed by a sustained demographic expansion around 5000 years ago. CONCLUSIONS JCV in Misiones reflects the multiethnic origin of the current population, with an important Amerindian contribution. Analysis of the MY viral lineage shows a pattern consistent with the arrival of early human migrations to the Americas and a population expansion by the pre-Columbian native societies.
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Affiliation(s)
- Matias J Pereson
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Daiana J Sanabria
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina
| | - Carolina Torres
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Domingo J Liotta
- Instituto Nacional de Medicina Tropical-ANLIS ''Dr. Malbrán'', Neuquén y Jujuy S/n, N3370, Puerto Iguazú, Misiones, Argentina
| | - Rodolfo H Campos
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania. Philadelphia, PA 19104-6398, USA
| | - Federico A Di Lello
- Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM). Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina
| | - Inés Badano
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Ciudad Autónoma de Buenos Aires, Argentina; Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales. Laboratorio de Biología Molecular Aplicada (LaBiMAp). Posadas, Misiones, Argentina; Universidad Nacional de Misiones. Red de Laboratorios. Laboratorio de Antropología Biológica y Bioinformática Aplicada (LABBA). Misiones, Argentina.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Kristjansson D, Schurr TG, Bohlin J, Jugessur A. Phylogeographic history of mitochondrial haplogroup J in Scandinavia. Am J Biol Anthropol 2023; 180:298-315. [PMID: 36790764 PMCID: PMC10100211 DOI: 10.1002/ajpa.24666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/10/2022] [Accepted: 11/13/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Mitochondrial DNA haplogroup J is the third most frequent haplogroup in modern-day Scandinavia, although it did not originate there. To infer the genetic history of haplogroup J in Scandinavia, we examined worldwide mitogenome sequences using a maximum-likelihood phylogenetic approach. METHODS Haplogroup J mitogenome sequences were gathered from GenBank (n = 2245) and aligned against the ancestral Reconstructed Sapiens Reference Sequence. We also analyzed haplogroup J Viking Age sequences from the European Nucleotide Archive (n = 54). Genetic distances were estimated from these data and projected onto a maximum likelihood rooted phylogenetic tree to analyze clustering and branching dates. RESULTS Haplogroup J originated approximately 42.6 kya (95% CI: 30.0-64.7), with several of its earliest branches being found within the Arabian Peninsula and Northern Africa. J1b was found most frequently in the Near East and Arabian Peninsula, while J1c occurred most frequently in Europe. Based on phylogenetic dating, subhaplogroup J1c has its early roots in the Mediterranean and Western Balkans. Otherwise, the majority of the branches found in Scandinavia are younger than those seen elsewhere, indicating that haplogroup J dispersed relatively recently into Northern Europe, most plausibly with Neolithic farmers. CONCLUSIONS Haplogroup J appeared when Scandinavia was transitioning to agriculture over 6 kya, with J1c being the most common lineage there today. Changes in the distribution of haplogroup J mtDNAs were likely driven by the expansion of farming from West Asia into Southern Europe, followed by a later expansion into Scandinavia, with other J subhaplogroups appearing among Scandinavian groups as early as the Viking Age.
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Affiliation(s)
- Dana Kristjansson
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jon Bohlin
- Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
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Fleskes RE, Cabana GS, Gilmore JK, Juarez C, Karcher E, Oubré L, Mishoe G, Ofunniyin AA, Schurr TG. Community-engaged ancient DNA project reveals diverse origins of 18th-century African descendants in Charleston, South Carolina. Proc Natl Acad Sci U S A 2023; 120:e2201620120. [PMID: 36623185 PMCID: PMC9934026 DOI: 10.1073/pnas.2201620120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 11/18/2022] [Indexed: 01/11/2023] Open
Abstract
In this study, we present the results of community-engaged ancient DNA research initiated after the remains of 36 African-descended individuals dating to the late 18th century were unearthed in the port city of Charleston, South Carolina. The Gullah Society of Charleston, along with other Charleston community members, initiated a collaborative genomic study of these ancestors of presumed enslaved status, in an effort to visibilize their histories. We generated 18 low-coverage genomes and 31 uniparental haplotypes to assess their genetic origins and interrelatedness. Our results indicate that they have predominantly West and West-Central African genomic ancestry, with one individual exhibiting some genomic affiliation with populations in the Americas. Most were assessed as genetic males, and no autosomal kin were identified among them. Overall, this study expands our understanding of the colonial histories of African descendant populations in the US South.
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Affiliation(s)
- Raquel E. Fleskes
- Department of Anthropology, University of Connecticut, Storrs, CT06269
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
| | | | - Joanna K. Gilmore
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
- Department of Sociology and Anthropology, The College of Charleston, Charleston, SC29424
| | - Chelsey Juarez
- Department of Anthropology, California State University, Fresno, CA93740
| | - Emilee Karcher
- Department of Anthropology, University of California, Davis, CA95616
| | - La’Sheia Oubré
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
| | - Grant Mishoe
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
| | - Ade A. Ofunniyin
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
- Department of Sociology and Anthropology, The College of Charleston, Charleston, SC29424
| | - Theodore G. Schurr
- The Anson Street African Burial Ground Project, Mount Pleasant, SC29492
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA19104
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Askapuli A, Vilar M, Garcia-Ortiz H, Zhabagin M, Sabitov Z, Akilzhanova A, Ramanculov E, Schamiloglu U, Martinez-Hernandez A, Contreras-Cubas C, Barajas-Olmos F, Schurr TG, Zhumadilov Z, Flores-Huacuja M, Orozco L, Hawks J, Saitou N. Kazak mitochondrial genomes provide insights into the human population history of Central Eurasia. PLoS One 2022; 17:e0277771. [PMID: 36445929 PMCID: PMC9707748 DOI: 10.1371/journal.pone.0277771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
As a historical nomadic group in Central Asia, Kazaks have mainly inhabited the steppe zone from the Altay Mountains in the East to the Caspian Sea in the West. Fine scale characterization of the genetic profile and population structure of Kazaks would be invaluable for understanding their population history and modeling prehistoric human expansions across the Eurasian steppes. With this mind, we characterized the maternal lineages of 200 Kazaks from Jetisuu at mitochondrial genome level. Our results reveal that Jetisuu Kazaks have unique mtDNA haplotypes including those belonging to the basal branches of both West Eurasian (R0, H, HV) and East Eurasian (A, B, C, D) lineages. The great diversity observed in their maternal lineages may reflect pivotal geographic location of Kazaks in Eurasia and implies a complex history for this population. Comparative analyses of mitochondrial genomes of human populations in Central Eurasia reveal a common maternal genetic ancestry for Turko-Mongolian speakers and their expansion being responsible for the presence of East Eurasian maternal lineages in Central Eurasia. Our analyses further indicate maternal genetic affinity between the Sherpas from the Tibetan Plateau with the Turko-Mongolian speakers.
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Affiliation(s)
- Ayken Askapuli
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Miguel Vilar
- The Genographic Project, National Geographic Society, Washington, DC, United States of America
- Department of Anthropology, University of Maryland, College Park, Maryland, United States of America
| | - Humberto Garcia-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Maxat Zhabagin
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | | | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Erlan Ramanculov
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
- National Center for Biotechnology, Astana, Kazakhstan
| | - Uli Schamiloglu
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Angelica Martinez-Hernandez
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Zhaxybay Zhumadilov
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
- School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Marlen Flores-Huacuja
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - John Hawks
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Anthropology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Okinawa Ken, Japan
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Kaneva K, Schurr TG, Tatarinova TV, Buckley J, Merkurjev D, Triska P, Liu X, Done J, Maglinte DT, Deapen D, Hwang A, Schiffman JD, Triche TJ, Biegel JA, Gai X. Mitochondrial DNA haplogroup, genetic ancestry, and susceptibility to Ewing sarcoma. Mitochondrion 2022; 67:6-14. [PMID: 36115539 PMCID: PMC9997094 DOI: 10.1016/j.mito.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/30/2022] [Accepted: 09/09/2022] [Indexed: 01/11/2023]
Abstract
Based on current studies, the incidence of Ewing sarcoma (ES) varies significantly by race and ethnicity, with the disease being most common in patients of European ancestry. However, race/ethnicity has generally been self-reported rather than formally evaluated at a population level using DNA evidence. Additionally, mitochondrial dysfunction is a hallmark of ES, yet there have been no reported studies of mitochondrial genetics in ES. Thus, we evaluated both the mitochondrial and nuclear ancestries of 420 pediatric ES patients in the United States using whole-genome sequencing. We found that the mitochondrial DNA (mtDNA) genomes of only six (1.4 %) patients belonged to African L haplogroups, while those of 90 % of the patients belonged to macrohaplogroup R, which includes haplogroup H, the most common maternal lineage in Europe. Compared to the general US population, European haplogroups were significantly enriched in ES patients (p < 2.2e-16) and the African haplogroups are significantly impoverished (p < 4.6e-16). Using the ancestry informative markers defined in a National Genographic study, the vast majority of patients exhibited significant nuclear ancestry originating from the Mediterranean, Northern Europe, and Southwest Asia, including all six patients with African L mtDNAs. Very few had primarily African nuclear ancestry. This is the first genomic epidemiology study to simultaneously interrogate the mitochondrial and nuclear ancestries of ES patients. While supporting previous findings of enriched European ancestry in ES patients, these results also suggest alternative hypotheses for the significant contribution of mitochondrial ancestry in ES patients, as well as the protective role of African ancestry.
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Affiliation(s)
- Kristiyana Kaneva
- Division of Hematology, Oncology, and Blood and Marrow Transplant Program, Children's Center for Cancer and Blood Diseases, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jonathan Buckley
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Daria Merkurjev
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Petr Triska
- Department of Pediatric Hematology and Oncology, Charles University, Prague, Czech Republic
| | - Xiyu Liu
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - James Done
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Dennis T Maglinte
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Dennis Deapen
- Cancer Surveillance Program, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Amie Hwang
- Cancer Surveillance Program, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joshua D Schiffman
- Department of Pediatrics and Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA; PEEL Therapeutics, Inc., Salt Lake City, UT, USA
| | - Timothy J Triche
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jaclyn A Biegel
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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9
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Liu YC, Hunter-Anderson R, Cheronet O, Eakin J, Camacho F, Pietrusewsky M, Rohland N, Ioannidis A, Athens JS, Douglas MT, Ikehara-Quebral RM, Bernardos R, Culleton BJ, Mah M, Adamski N, Broomandkhoshbacht N, Callan K, Lawson AM, Mandl K, Michel M, Oppenheimer J, Stewardson K, Zalzala F, Kidd K, Kidd J, Schurr TG, Auckland K, Hill AVS, Mentzer AJ, Quinto-Cortés CD, Robson K, Kennett DJ, Patterson N, Bustamante CD, Moreno-Estrada A, Spriggs M, Vilar M, Lipson M, Pinhasi R, Reich D. Ancient DNA reveals five streams of migration into Micronesia and matrilocality in early Pacific seafarers. Science 2022; 377:72-79. [PMID: 35771911 PMCID: PMC9983687 DOI: 10.1126/science.abm6536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Micronesia began to be peopled earlier than other parts of Remote Oceania, but the origins of its inhabitants remain unclear. We generated genome-wide data from 164 ancient and 112 modern individuals. Analysis reveals five migratory streams into Micronesia. Three are East Asian related, one is Polynesian, and a fifth is a Papuan source related to mainland New Guineans that is different from the New Britain-related Papuan source for southwest Pacific populations but is similarly derived from male migrants ~2500 to 2000 years ago. People of the Mariana Archipelago may derive all of their precolonial ancestry from East Asian sources, making them the only Remote Oceanians without Papuan ancestry. Female-inherited mitochondrial DNA was highly differentiated across early Remote Oceanian communities but homogeneous within, implying matrilocal practices whereby women almost never raised their children in communities different from the ones in which they grew up.
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Affiliation(s)
- Yue-Chen Liu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria
| | - Joanne Eakin
- Independent Researcher, Albuquerque, NM 87107, USA
| | - Frank Camacho
- Department of Biology, University of Guam, Mangilao 96923, Guam
| | - Michael Pietrusewsky
- Department of Anthropology, University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - J. Stephen Athens
- International Archaeological Research Institute, Inc., Honolulu, HI 96826, USA
| | | | | | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan J. Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kenneth Kidd
- Department of Genetics, Yale Medical School, New Haven, CT 06520, USA
| | - Judith Kidd
- Department of Genetics, Yale Medical School, New Haven, CT 06520, USA
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Adrian V. S. Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK,The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK
| | - Consuelo D. Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato 36821, Mexico
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Douglas J. Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carlos D. Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.,Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA 94305, USA,Current Address: Galatea Bio, Inc. 975 W 22nd St. Hialeah, FL 33010, USA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato 36821, Mexico
| | - Matthew Spriggs
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT 2601, Australia,Vanuatu National Museum, Vanuatu Culture Centre, P.O. Box 184, Port Vila, Vanuatu
| | - Miguel Vilar
- Department of Anthropology, University of Maryland, College Park, MD 20742, USA
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria,Human Evolution and Archaeological Sciences, University of Vienna, Vienna 1030, Austria
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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10
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Kristjansson D, Bohlin J, Nguyen TT, Jugessur A, Schurr TG. Correction: Evolution and dispersal of mitochondrial DNA haplogroup U5 in Northern Europe: insights from an unsupervised learning approach to phylogeography. BMC Genomics 2022; 23:459. [PMID: 35729533 PMCID: PMC9210683 DOI: 10.1186/s12864-022-08696-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Dana Kristjansson
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway. .,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.
| | - Jon Bohlin
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Truc Trung Nguyen
- IT Systems Bergen, Norwegian Institute of Public Health, Bergen, Norway
| | - Astanand Jugessur
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA, USA
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11
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Kristjansson D, Bohlin J, Nguyen TT, Jugessur A, Schurr TG. Evolution and dispersal of mitochondrial DNA haplogroup U5 in Northern Europe: insights from an unsupervised learning approach to phylogeography. BMC Genomics 2022; 23:354. [PMID: 35525961 PMCID: PMC9080151 DOI: 10.1186/s12864-022-08572-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/20/2022] [Indexed: 12/28/2022] Open
Abstract
Background We combined an unsupervised learning methodology for analyzing mitogenome sequences with maximum likelihood (ML) phylogenetics to make detailed inferences about the evolution and diversification of mitochondrial DNA (mtDNA) haplogroup U5, which appears at high frequencies in northern Europe. Methods Haplogroup U5 mitogenome sequences were gathered from GenBank. The hierarchal Bayesian Analysis of Population Structure (hierBAPS) method was used to generate groups of sequences that were then projected onto a rooted maximum likelihood (ML) phylogenetic tree to visualize the pattern of clustering. The haplogroup statuses of the individual sequences were assessed using Haplogrep2. Results A total of 23 hierBAPS groups were identified, all of which corresponded to subclades defined in Phylotree, v.17. The hierBAPS groups projected onto the ML phylogeny accurately clustered all haplotypes belonging to a specific haplogroup in accordance with Haplogrep2. By incorporating the geographic source of each sequence and subclade age estimates into this framework, inferences about the diversification of U5 mtDNAs were made. Haplogroup U5 has been present in northern Europe since the Mesolithic, and spread in both eastern and western directions, undergoing significant diversification within Scandinavia. A review of historical and archeological evidence attests to some of the population interactions contributing to this pattern. Conclusions The hierBAPS algorithm accurately grouped mitogenome sequences into subclades in a phylogenetically robust manner. This analysis provided new insights into the phylogeographic structure of haplogroup U5 diversity in northern Europe, revealing a detailed perspective on the diversity of subclades in this region and their distribution in Scandinavian populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08572-y.
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Affiliation(s)
- Dana Kristjansson
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway. .,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.
| | - Jon Bohlin
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Truc Trung Nguyen
- IT Systems Bergen, Norwegian Institute of Public Health, Bergen, Norway
| | - Astanand Jugessur
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA, USA
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12
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Sanchez-Fernandez C, Bolatti EM, Culasso ACA, Chouhy D, Kowalewski MM, Stella EJ, Schurr TG, Rinas MA, Liotta DJ, Campos RH, Giri AA, Badano I. Identification and evolutionary analysis of papillomavirus sequences in New World monkeys (genera Sapajus and Alouatta) from Argentina. Arch Virol 2022; 167:1257-1268. [PMID: 35353206 DOI: 10.1007/s00705-022-05420-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/03/2022] [Indexed: 12/23/2022]
Abstract
OBJECTIVE In this study, we investigated the occurrence of papillomavirus (PV) infection in non-human primates (NHPs) in northeastern Argentina. We also explored their evolutionary history and evaluated the co-speciation hypothesis in the context of primate evolution. METHODS We obtained DNA samples from 57 individuals belonging to wild and captive populations of Alouatta caraya, Sapajus nigritus, and Sapajus cay. We assessed PV infection by PCR amplification with the CUT primer system and sequencing of 337 bp (112 amino acids) of the L1 gene. The viral sequences were analyzed by phylogenetic and Bayesian coalescence methods to estimate the time to the most common recent ancestor (tMRCA) using BEAST, v1.4.8 software. We evaluated viral/host tree congruence with TreeMap v3.0. RESULTS We identified two novel putative PV sequences of the genus Gammapapillomavirus in Sapajus spp. and Alouatta caraya (SPV1 and AcPV1, respectively). The tMRCA of SPV1 was estimated to be 11,941,682 years before present (ybp), and that of AcPV1 was 46,638,071 ybp, both before the coalescence times of their hosts (6.4 million years ago [MYA] and 6.8 MYA, respectively). Based on the comparison of primate and viral phylogenies, we found that the PV tree was no more congruent with the host tree than a random tree would be (P > 0.05), thus allowing us to reject the model of virus-host coevolution. CONCLUSION This study presents the first evidence of PV infection in platyrrhine species from Argentina, expands the range of described hosts for these viruses, and suggests new scenarios for their origin and dispersal.
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Affiliation(s)
- C Sanchez-Fernandez
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - E M Bolatti
- Laboratorio de Virología Humana, Instituto de Biología Molecular y Celular de Rosario, CONICET/UNR, Rosario, Argentina.,Área Virología, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - A C A Culasso
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - D Chouhy
- Laboratorio de Virología Humana, Instituto de Biología Molecular y Celular de Rosario, CONICET/UNR, Rosario, Argentina.,Área Virología, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - M M Kowalewski
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Estación Biológica Corrientes (EBCo-MACN-CONICET), Corrientes, Argentina
| | - E J Stella
- Laboratorio de Virología Humana, Instituto de Biología Molecular y Celular de Rosario, CONICET/UNR, Rosario, Argentina
| | - T G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania, Philadelphia, 19104, USA
| | - M A Rinas
- Ministerio de Ecología y Recursos Naturales Renovables, Posadas, Misiones, Argentina
| | - D J Liotta
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina.,Instituto Nacional de Medicina Tropical, ANLIS, Pto. Iguazú, Misiones, Argentina
| | - R H Campos
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - A A Giri
- Laboratorio de Virología Humana, Instituto de Biología Molecular y Celular de Rosario, CONICET/UNR, Rosario, Argentina.,Área Virología, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - I Badano
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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13
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Totaro ME, Gili JA, Liotta DJ, Schurr TG, Picconi MA, Badano I. Genetic variation in the E6 and E7 genes of human papillomavirus type 16 in northeastern Argentina. J Med Virol 2021; 94:745-751. [PMID: 34569642 DOI: 10.1002/jmv.27359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/10/2021] [Accepted: 09/22/2021] [Indexed: 11/09/2022]
Abstract
The province of Misiones is considered a region with a high mortality rate due to cervical cancer (CC). To gain insight into this problem, we explored the association between genetic variation in the E6 and E7 oncogenes of HPV16 and the risk of CC. We studied 160 women with cytological diagnoses of negative for intraepithelial lesion or malignity, low-grade squamous intraepithelial lesion, and high-grade squamous intraepithelial lesion/CC and a positive test for HPV16 infection. The genetic characterization of E6 and E7 genes was undertaken through PCR amplification and direct Sanger sequencing. Phylogenetic classification was conducted using Bayesian methods. To estimate the odds ratio (OR) for an association between genetic variants in the E6 and E7 genes and the risk of CC, we used ordinal logistic regression adjusted by age. The final data set comprised 112 samples. Diagnostic single-nucleotide polymorphisms (SNPs) and phylogenetic trees confirmed the presence of Lineage A (95.5%) and D (4.5%) in the samples. For the E6 gene, we identified eleven different sequences, with the most common ones being Lineage A E6 350G (58.9%) and E6 350T (37.5%). The E6 350G was associated with progression to HSIL/CC, with an OR of 19.41 (4.95-76.10). The E7 gene was more conserved than E6, probably due to the functional constraints of this small protein. Our results confirmed the association of the E6 350G SNP with a higher risk of developing CC. These data will contribute to understanding the biological bases of CC incidence in this region.
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Affiliation(s)
- M Elina Totaro
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Juan A Gili
- Laboratorio de Epidemiología Genética, Dirección de Investigación CEMIC-CONICET, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - D Javier Liotta
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Posadas, Misiones, Argentina.,Instituto Nacional de Medicina Tropical-ANLIS "Dr. Malbrán", Puerto Iguazú, Misiones, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maria A Picconi
- Servicio de Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS ''Dr. Malbrán'', Buenos Aires, Buenos Aires, Argentina
| | - Inés Badano
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Posadas, Misiones, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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14
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Zimmerman KD, Schurr TG, Chen W, Nayak U, Mychaleckyj JC, Quet Q, Moultrie LH, Divers J, Keene KL, Kamen DL, Gilkeson GS, Hunt KJ, Spruill IJ, Fernandes JK, Aldrich MC, Reich D, Garvey WT, Langefeld CD, Sale MM, Ramos PS. Genetic landscape of Gullah African Americans. Am J Phys Anthropol 2021; 175:905-919. [PMID: 34008864 PMCID: PMC8286328 DOI: 10.1002/ajpa.24333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 03/30/2021] [Accepted: 04/17/2021] [Indexed: 01/20/2023]
Abstract
OBJECTIVES Gullah African Americans are descendants of formerly enslaved Africans living in the Sea Islands along the coast of the southeastern U.S., from North Carolina to Florida. Their relatively high numbers and geographic isolation were conducive to the development and preservation of a unique culture that retains deep African features. Although historical evidence supports a West-Central African ancestry for the Gullah, linguistic and cultural evidence of a connection to Sierra Leone has led to the suggestion of this country/region as their ancestral home. This study sought to elucidate the genetic structure and ancestry of the Gullah. MATERIALS AND METHODS We leveraged whole-genome genotype data from Gullah, African Americans from Jackson, Mississippi, African populations from Sierra Leone, and population reference panels from Africa and Europe to infer population structure, ancestry proportions, and global estimates of admixture. RESULTS Relative to non-Gullah African Americans from the Southeast US, the Gullah exhibited higher mean African ancestry, lower European admixture, a similarly small Native American contribution, and increased male-biased European admixture. A slightly tighter bottleneck in the Gullah 13 generations ago suggests a largely shared demographic history with non-Gullah African Americans. Despite a slightly higher relatedness to populations from Sierra Leone, our data demonstrate that the Gullah are genetically related to many West African populations. DISCUSSION This study confirms that subtle differences in African American population structure exist at finer regional levels. Such observations can help to inform medical genetics research in African Americans, and guide the interpretation of genetic data used by African Americans seeking to explore ancestral identities.
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Affiliation(s)
- Kip D. Zimmerman
- Center for Precision MedicineWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Theodore G. Schurr
- Department of AnthropologyUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Wei‐Min Chen
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Public Health SciencesUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Uma Nayak
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Josyf C. Mychaleckyj
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Public Health SciencesUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Queen Quet
- Gullah/Geechee NationSt. Helena IslandSouth CarolinaUSA
| | - Lee H. Moultrie
- Lee H. Moultrie & AssociatesNorth CharlestonSouth CarolinaUSA
| | - Jasmin Divers
- Department of Health Services ResearchNew York University Winthrop HospitalMineolaNew YorkUSA
| | - Keith L. Keene
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
- Center for Health DisparitiesEast Carolina University Brody School of MedicineGreenvilleNorth CarolinaUSA
| | - Diane L. Kamen
- Department of MedicineMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Gary S. Gilkeson
- Department of MedicineMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Kelly J. Hunt
- Department of Public Health SciencesMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Ida J. Spruill
- College of NursingMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Jyotika K. Fernandes
- Department of MedicineMedical University of South CarolinaCharlestonSouth CarolinaUSA
| | - Melinda C. Aldrich
- Department of Thoracic SurgeryVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Vanderbilt Genetics InstituteVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - David Reich
- Department of GeneticsHarvard Medical SchoolBostonMassachusettsUSA
- Howard Hughes Medical InstituteHarvard Medical SchoolBostonMassachusettsUSA
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Department of Human Evolutionary BiologyHarvard UniversityCambridgeMassachusettsUSA
| | - W. Timothy Garvey
- Department of Nutrition ScienceUniversity of Alabama at BirminghamBirminghamAlabamaUSA
| | - Carl D. Langefeld
- Center for Precision MedicineWake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Michèle M. Sale
- Center for Public Health GenomicsUniversity of VirginiaCharlottesvilleVirginiaUSA
- Department of Public Health SciencesUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Paula S. Ramos
- Department of MedicineMedical University of South CarolinaCharlestonSouth CarolinaUSA
- Department of Public Health SciencesMedical University of South CarolinaCharlestonSouth CarolinaUSA
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15
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Friedrich VK, Rubel MA, Schurr TG. Mitochondrial genetic variation in human bioenergetics, adaptation, and adult disease. Am J Hum Biol 2021; 34:e23629. [PMID: 34146380 DOI: 10.1002/ajhb.23629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES Mitochondria are critical for the survival of eukaryotic organisms due to their ability to produce cellular energy, which drives virtually all aspects of host biology. However, the effects of mitochondrial DNA (mtDNA) variation in relation to disease etiology and adaptation within contemporary global human populations remains incompletely understood. METHODS To develop a more holistic understanding of the role of mtDNA diversity in human adaptation, health, and disease, we investigated mitochondrial biology and bioenergetics. More specifically, we synthesized details from studies of mitochondrial function and variation in the context of haplogroup background, climatic adaptation, and oxidative disease. RESULTS The majority of studies show that mtDNA variation arose during modern human dispersal around the world. Some of these variants appear to have been positively selected for their adaptiveness in colder climates, with these sequence changes having implications for tissue-specific function and thermogenic capacity. In addition, many variants modulating energy production are also associated with damaging metabolic byproducts and mitochondrial dysfunction, which, in turn, are implicated in the onset and severity of several different adult mitochondrial diseases. Thus, mtDNA variation that governs bioenergetics, metabolism, and thermoregulation may potentially have adverse consequences for human health, depending on the genetic background and context in which it occurs. CONCLUSIONS Our review suggests that the mitochondrial research field would benefit from independently replicating mtDNA haplogroup-phenotype associations across global populations, incorporating potentially confounding environmental, demographic, and disease covariates into studies of mtDNA variation, and extending association-based studies to include analyses of complete mitogenomes and assays of mitochondrial function.
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Affiliation(s)
- Volney K Friedrich
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Meagan A Rubel
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Center for Translational Imaging and Precision Medicine, University of California - San Diego, La Jolla, California, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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16
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Kristjansson D, Bohlin J, Jugessur A, Schurr TG. Matrilineal diversity and population history of Norwegians. Am J Phys Anthropol 2021; 176:120-133. [PMID: 34110627 DOI: 10.1002/ajpa.24345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/19/2021] [Accepted: 05/23/2021] [Indexed: 11/06/2022]
Abstract
BACKGROUND While well known for its Viking past, Norway's population history and the influences that have shaped its genetic diversity are less well understood. This is particularly true with respect to its demography, migration patterns, and dialectal regions, despite there being curated historical records for the past several centuries. In this study, we undertook an analysis of mitochondrial DNA (mtDNA) diversity within the country to elaborate this history from a matrilineal genetic perspective. METHODS We aggregated 1174 partial modern Norwegian mtDNA sequences from the published literature and subjected them to detailed statistical and phylogenetic analysis by dialectal regions and localities. We further contextualized the matrilineal ancestry of modern Norwegians with data from Mesolithic, Iron Age, and historic period populations. RESULTS Modern Norwegian mtDNAs fell into eight West Eurasian (N, HV, JT, I, U, K, X, W), five East Eurasian (A, F, G, N11, Z), and one African (L2) haplogroups. Pairwise analysis of molecular variance (AMOVA) estimates for all Norwegians indicated they were differentiated from each other at 1.68% (p < 0.001). Norwegians within the same dialectal region also showed genetic similarities to each other, although differences between subpopulations within dialectal regions were also observed. In addition, certain mtDNA lineages in modern Norwegians were also found among prehistoric and historic period populations, suggesting some level of genetic continuity over hundreds to many thousands of years. CONCLUSIONS This analysis of mtDNA diversity provides a detailed picture of the genetic variation within Norway in light of its topography, settlement history, and historical migrations over the past several centuries.
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Affiliation(s)
- Dana Kristjansson
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Jon Bohlin
- Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Infection Epidemiology and Modelling, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Gómez R, Vilar MG, Meraz-Ríos MA, Véliz D, Zúñiga G, Hernández-Tobías EA, Figueroa-Corona MDP, Owings AC, Gaieski JB, Schurr TG. Y chromosome diversity in Aztlan descendants and its implications for the history of Central Mexico. iScience 2021; 24:102487. [PMID: 34036249 PMCID: PMC8138773 DOI: 10.1016/j.isci.2021.102487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/08/2020] [Accepted: 04/27/2021] [Indexed: 11/16/2022] Open
Abstract
Native Mexican populations are crucial for understanding the genetic ancestry of Aztec descendants and coexisting ethnolinguistic groups in the Valley of Mexico and elucidating the population dynamics of the prehistoric colonization of the Americas. Mesoamerican societies were multicultural in nature and also experienced significant admixture during Spanish colonization of the region. Despite these facts, Native Mexican Y chromosome diversity has been greatly understudied. To further elucidate their genetic history, we conducted a high-resolution Y chromosome analysis with Chichimecas, Nahuas, Otomies, Popolocas, Tepehuas, and Totonacas using 19 Y-short tandem repeat and 21 single nucleotide polymorphism loci. We detected enormous paternal genetic diversity in these groups, with haplogroups Q-MEH2, Q-M3, Q-Z768, Q-L663, Q-Z780, and Q-PV3 being identified. These data affirmed the southward colonization of the Americas via Beringia and connected Native Mexicans with indigenous populations from South-Central Siberia and Canada. They also suggested that multiple population dispersals gave rise to Y chromosome diversity in these populations. Enormous Y chromosome diversity observed in Native Mexican populations. Haplogroups Q-MEH2, Q-M3, Q-Z768, Q-L663, Q-Z780, and Q-PV3 were identified. Patterns of Y chromosome diversity not shaped by ethnicity, geography, or language. Multiple population dispersals contributed to Y chromosome diversity in Mexico.
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Affiliation(s)
- Rocío Gómez
- Departamento de Toxicología, CINVESTAV-IPN, Mexico City 07360, Mexico
| | - Miguel G Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA.,National Geographic Society, Washington, DC 20005, USA
| | | | - David Véliz
- Departamento de Ciencias Ecológicas, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile.,Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas, Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo 1781421, Chile
| | - Gerardo Zúñiga
- Departamento de Zoología, Laboratorio de Variación Biológica y Evolución, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | | | | | - Amanda C Owings
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
| | - Jill B Gaieski
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
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18
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Fleskes RE, Ofunniyin AA, Gilmore JK, Poplin E, Abel SM, Bueschgen WD, Juarez C, Butler N, Mishoe G, Oubré L, Cabana GS, Schurr TG. Ancestry, health, and lived experiences of enslaved Africans in 18th century Charleston: An osteobiographical analysis. Am J Phys Anthropol 2020; 175:3-24. [PMID: 33022107 DOI: 10.1002/ajpa.24149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/30/2020] [Accepted: 09/13/2020] [Indexed: 01/20/2023]
Abstract
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. Whole mitochondrial genomes were sequenced and analyzed. RESULTS Osteological analysis identified adults, both females and males, and subadults at the site, and estimated African ancestry for most individuals. Skeletal trauma and pathology were infrequent, but many individuals exhibited dental decay and abscesses. Strontium isotope data suggested these individuals mostly originated in Charleston or sub-Saharan Africa, with many being long-term residents of Charleston. Nearly all had mitochondrial lineages belonging to African haplogroups (L0-L3, H1cb1a), with two individuals sharing the same L3e2a haplotype, while one had a Native American A2 mtDNA. DISCUSSION This study generated detailed osteobiographies of the Anson Street Ancestors, who were likely of enslaved status. Our results indicate that the Ancestors have diverse maternal African ancestries and are largely unrelated, with most being born locally. These details reveal the demographic impact of the trans-Atlantic slave trade. Our analysis further illuminates the lived experiences of individuals buried at Anson Street, and expands our understanding of 18th century African history in Charleston.
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Affiliation(s)
- Raquel E Fleskes
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ade A Ofunniyin
- The Gullah Society, Inc., Mount Pleasant, South Carolina, USA.,Department of Sociology and Anthropology, The College of Charleston, Charleston, South Carolina, USA
| | - Joanna K Gilmore
- The Gullah Society, Inc., Mount Pleasant, South Carolina, USA.,Department of Sociology and Anthropology, The College of Charleston, Charleston, South Carolina, USA
| | - Eric Poplin
- Brockington and Associates, Inc., Mount Pleasant, South Carolina, USA
| | - Suzanne M Abel
- Charleston County Coroner's Office, North Charleston, South Carolina, USA
| | - Wolf D Bueschgen
- Charleston County Coroner's Office, North Charleston, South Carolina, USA
| | - Chelsey Juarez
- Department of Anthropology, California State University, Fresno, California, USA
| | - Nic Butler
- Charleston County Public Library, Charleston, South Carolina, USA
| | - Grant Mishoe
- The Gullah Society, Inc., Mount Pleasant, South Carolina, USA
| | - La'Sheia Oubré
- The Gullah Society, Inc., Mount Pleasant, South Carolina, USA
| | - Graciela S Cabana
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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19
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Schurr TG. Host genetic factors and susceptibility toSARS‐CoV‐2 infection. Am J Hum Biol 2020; 32:e23497. [DOI: 10.1002/ajhb.23497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 01/08/2023] Open
Affiliation(s)
- Theodore G. Schurr
- Department of Anthropology University of Pennsylvania Philadelphia Pennsylvania USA
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20
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Zubair M, Hemphill BE, Schurr TG, Tariq M, Ilyas M, Ahmad H. Mitochondrial DNA diversity in the Khattak and Kheshgi of the Peshawar Valley, Pakistan. Genetica 2020; 148:195-206. [PMID: 32607672 DOI: 10.1007/s10709-020-00095-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/12/2020] [Indexed: 11/29/2022]
Abstract
The strategic location of Pakistan and its presence at the crossroads of Asia has resulted in it playing a central role in both prehistoric and historic human migratory events, thereby linking and facilitating contacts between the inhabitants of the Middle East, Central Asia, China and South Asia. Despite the importance of this region and its inhabitants for our understanding of modern human origins and population dispersals, the nature of mitochondrial DNA (mtDNA) variation among members of the myriad populations of this area has largely been unexplored. Here, we report mtDNA control region sequences in 58 individuals from the Khattak and the Kheshgi, two major Pakhtun tribes residing within the Peshawar Valley of northwestern Pakistan. The results reveal that these ethnic groups are genetically heterogeneous, having 55.7% West Eurasian, 33.9% South Asian and 10.2% East Asian haplogroups. The genetic diversity observed for the Kheshgi was somewhat higher than that of the Khattak. A multidimensional scaling plot based on haplogroup frequencies for the Khattak, Kheshgi and neighboring populations indicates that the Khattak have close affinities with Baluch, Uzbek and Kazak populations but are only distantly related to the Kheshgi and other Pakistani populations. By contrast, the Kheshgi cluster closely with other Pakhtun or Pathan populations of Pakistan, suggesting a possible common maternal gene pool shared amongst them. These mtDNA data allow us to begin reconstructing the origins of the Khattak and Kheshgi and describe their complex interactions with populations from the surrounding regions.
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Affiliation(s)
- Muhammad Zubair
- Department of Zoology, Hazara University Mansehra, Mansehra, 21120, Pakistan.,Department of Genetics, Hazara University Mansehra, Mansehra, 21120, Pakistan
| | - Brian E Hemphill
- Department of Anthropology, University of Alaska, Fairbanks, AK, 99775, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Muhammad Tariq
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan
| | - Muhammad Ilyas
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan
| | - Habib Ahmad
- Department of Genetics, Hazara University Mansehra, Mansehra, 21120, Pakistan. .,Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan.
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21
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Sanabria DJ, Mojsiejczuk LN, Torres C, Meyer AG, Mbayed VA, Liotta DJ, Campos RH, Schurr TG, Badano I. Genetic diversity of the JC polyomavirus (JCPyV) and mitochondrial DNA ancestry in Misiones, Argentina. Infect Genet Evol 2019; 75:104011. [PMID: 31446138 DOI: 10.1016/j.meegid.2019.104011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/01/2019] [Accepted: 08/19/2019] [Indexed: 11/16/2022]
Abstract
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. STUDY DESIGN 68 individuals were analyzed for JCPyV and mtDNA diversity. JCPyV detection and typing was conducted in urine samples by PCR amplification, sequencing and phylogenetic analysis of the VP1 gene. mtDNA ancestry was assessed through HVS1 sequencing, with the resulting haplotypes being classified into haplogroups of Amerindian, European and African origin. The distribution of JCPyV diversity and mtDNA ancestry in the population was statistically evaluated by Fisher exact test and the level of agreement of both markers at the individual level was evaluated by Cohen's kappa coefficient. RESULTS Our analysis showed that 57.4% of the samples were positive for JCPyV. Of these, the 47.6% were Asian-American Type 2, 33.3% European Type 1 and 19.1% African Type 3 in origin. The mtDNA ancestry of the study participants was 33.3% Amerindian and 66.7% European. There was a significant difference among the distribution of JCPyV diversity and mtDNA ancestry (p = 0.009) and at the individual level there was no correlation between the distribution of the both markers (κ = 0.154, p = 0.297). CONCLUSION The apparent incongruence between JCPyV diversity and mtDNA ancestry may reflect the original settlement process and more recent migration to 25 de Mayo, the latter involving viral spread through migrants from Brazil. Some potential limitations to our interpretations are also discussed.
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Affiliation(s)
- Daiana J Sanabria
- 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.
| | - Laura N Mojsiejczuk
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Carolina Torres
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Alejandro G Meyer
- Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Viviana A Mbayed
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Domingo J Liotta
- Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Rodolfo H Campos
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
| | - Ines Badano
- 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
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22
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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. Am J Phys Anthropol 2019; 170:232-245. [DOI: 10.1002/ajpa.23887] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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24
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Benn Torres J, Martucci V, Aldrich MC, Vilar MG, MacKinney T, Tariq M, Gaieski JB, Bharath Hernandez R, Browne ZE, Stevenson M, Walters W, Schurr TG. Analysis of biogeographic ancestry reveals complex genetic histories for indigenous communities of St. Vincent and Trinidad. Am J Phys Anthropol 2019; 169:482-497. [PMID: 31125126 DOI: 10.1002/ajpa.23859] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 11/07/2022]
Abstract
OBJECTIVES From a genetic perspective, relatively little is known about how mass emigrations of African, European, and Asian peoples beginning in the 16th century affected Indigenous Caribbean populations. Therefore, we explored the impact of serial colonization on the genetic variation of the first Caribbean islanders. MATERIALS AND METHODS Sixty-four members of St. Vincent's Garifuna Community and 36 members of Trinidad's Santa Rosa First People's Community (FPC) of Arima were characterized for mitochondrial DNA and Y-chromosome diversity via direct sequencing and targeted SNP and STR genotyping. A subset of 32 Garifuna and 18 FPC participants were genotyped using the GenoChip 2.0 microarray. The resulting data were used to examine genetic diversity, admixture, and sex biased gene flow in the study communities. RESULTS The Garifuna were most genetically comparable to African descendant populations, whereas the FPC were more similar to admixed American groups. Both communities also exhibited moderate frequencies of Indigenous American matrilines and patrilines. Autosomal SNP analysis indicated modest Indigenous American ancestry in these populations, while both showed varying degrees of African, European, South Asian, and East Asian ancestry, with patterns of sex-biased gene flow differing between the island communities. DISCUSSION These patterns of genetic variation are consistent with historical records of migration, forced, or voluntary, and suggest that different migration events shaped the genetic make-up of each island community. This genomic study is the highest resolution analysis yet conducted with these communities, and provides a fuller understanding of the complex bio-histories of Indigenous Caribbean peoples in the Lesser Antilles.
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Affiliation(s)
- Jada Benn Torres
- Department of Anthropology, Vanderbilt University, Nashville, Tennessee.,Department of Anthropology, University of Notre Dame, Notre Dame, Indiana
| | - Victoria Martucci
- Department of Thoracic Surgery and Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Melinda C Aldrich
- Department of Thoracic Surgery and Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Miguel G Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania.,Science and Exploration, National Geographic Society, Washington, District of Columbia
| | - Taryn MacKinney
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Muhammad Tariq
- Department of Anthropology, Vanderbilt University, Nashville, Tennessee.,Department of Genetics, Hazara University, Mansehra, KP, Pakistan
| | - Jill B Gaieski
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Zoila E Browne
- The Garifuna Heritage Foundation Inc., Kingstown, St. Vincent
| | | | - Wendell Walters
- The Garifuna Heritage Foundation Inc., Kingstown, St. Vincent.,Sandy Bay Village, St. Vincent
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania
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25
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Badano I, Sanabria DJ, Totaro ME, Rubinstein S, Gili JA, Liotta DJ, Picconi MA, Campos RH, Schurr TG. Mitochondrial DNA ancestry, HPV infection and the risk of cervical cancer in a multiethnic population of northeastern Argentina. PLoS One 2018; 13:e0190966. [PMID: 29329337 PMCID: PMC5766133 DOI: 10.1371/journal.pone.0190966] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 12/22/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Misiones Province in northeastern Argentina is considered to be a region with a high prevalence of HPV infection and a high mortality rate due to cervical cancer. The reasons for this epidemiological trend are not completely understood. To gain insight into this problem, we explored the relationship between mitochondrial DNA (mtDNA) ancestry, HPV infection, and development of cervical lesions/cancer in women from the city of Posadas in Misiones Province. METHODS Two hundred and sixty-one women, including 92 cases of patients diagnosed with cervical lesions and 169 controls, were analyzed. mtDNA ancestry was assessed through HVS1 sequencing, while the detection and typing of HPV infection was conducted through nested multiplex PCR analysis. Multivariate logistic regression was conducted with the resulting data to estimate the odds ratios (ORs) adjusted by socio-demographic variables. RESULTS The study participants showed 68.6% Amerindian, 26.1% European and 5.3% African mtDNA ancestry, respectively. Multiple regression analysis showed that women with African mtDNAs were three times more likely to develop a cervical lesion than those with Native American or European mtDNAs [OR of 3.8 (1.2-11.5) for ancestry and OR of 3.5 (1.0-12.0) for L haplogroups], although the associated p values were not significant when tested under more complex multivariate models. HPV infection and the development of cervical lesions/cancer were significant for all tested models, with the highest OR values for HPV16 [OR of 24.2 (9.3-62.7)] and HPV-58 [OR of 19.0 (2.4-147.7)]. CONCLUSION HPV infection remains a central risk factor for cervical cancer in the Posadas population. The potential role of African mtDNA ancestry opens a new avenue for future medical association studies in multiethnic populations, and will require further confirmation in large-scale studies.
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Affiliation(s)
- Ines Badano
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- * E-mail:
| | - Daiana J. Sanabria
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Maria E. Totaro
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina
| | - Samara Rubinstein
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania, Philadelphia, United States of America
| | - Juan A. Gili
- Laboratorio de Epidemiología Genética, Dirección de Investigación CEMIC-CONICET, Buenos Aires, Argentina
| | - Domingo J. Liotta
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina
| | - Maria A. Picconi
- Servicio de Virus Oncogénicos, Departamento de Virología, INEI-ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Rodolfo H. Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Theodore G. Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania, Philadelphia, United States of America
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Yardumian A, Shengelia R, Chitanava D, Laliashvili S, Bitadze L, Laliashvili I, Villanea F, Sanders A, Azzam A, Groner V, Edleson K, Vilar MG, Schurr TG. Genetic diversity in Svaneti and its implications for the human settlement of the Highland Caucasus. Am J Phys Anthropol 2017; 164:837-852. [PMID: 29076141 DOI: 10.1002/ajpa.23324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 07/19/2017] [Accepted: 09/10/2017] [Indexed: 11/11/2022]
Abstract
OBJECTIVES In this study, we characterized genetic diversity in the Svans from northwestern Georgia to better understand the phylogeography of their genetic lineages, determine whether genetic diversity in the highland South Caucasus has been shaped by language or geography, and assess whether Svan genetic diversity was structured by regional residence patterns. MATERIALS AND METHODS We analyzed mtDNA and Y-chromosome variation in 184 individuals from 13 village districts and townlets located throughout the region. For all individuals, we analyzed mtDNA diversity through control region sequencing, and, for males, we analyzed Y-chromosome diversity through SNP and STR genotyping. The resulting data were compared with those for populations from the Caucasus and Middle East. RESULTS We observed significant mtDNA heterogeneity in Svans, with haplogroups U1-U7, H, K, and W6 being common there. By contrast, ∼78% of Svan males belonged to haplogroup G2a, with the remainder falling into four other haplogroups (J2a1, I2, N, and R1a). While showing a distinct genetic profile, Svans also clustered with Caucasus populations speaking languages from different families, suggesting a deep common ancestry for all of them. The mtDNA data were not structured by geography or linguistic affiliation, whereas the NRY data were influenced only by geography. DISCUSSION These patterns of genetic variation confirm a complex set of geographic sources and settlement phases for the Caucasus highlands. Such patterns may also reflect social and cultural practices in the region. The high frequency and antiquity of Y-chromosome haplogroup G2a in this region further points to its emergence there.
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Affiliation(s)
- Aram Yardumian
- Department of History and Social Sciences, Bryn Athyn College, Pennsylvania 19009.,Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ramaz Shengelia
- Department of the History of Medicine and Bioethics, Tbilisi State Medical University, Tbilisi 01747, Georgia
| | - David Chitanava
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Shorena Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Lia Bitadze
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Irma Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Fernando Villanea
- Grant Programs, Science and Exploration, National Geographic Society, Washington, DC 20036
| | - Akiva Sanders
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Andrew Azzam
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Victoria Groner
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Kristi Edleson
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Miguel G Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104.,Grant Programs, Science and Exploration, National Geographic Society, Washington, DC 20036
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Elhaik E, Tatarinova T, Chebotarev D, Piras IS, Calò CM, De Montis A, Atzori M, Marini M, Tofanelli S, Francalacci P, Pagani L, Tyler-Smith C, Xue Y, Cucca F, Schurr TG, Gaieski JB, Melendez C, Vilar MG, Owings AC, Gómez R, Fujita R, Santos FR, Comas D, Balanovsky O, Balanovska E, Zalloua P, Soodyall H, Pitchappan R, GaneshPrasad A, Hammer M, Matisoo-Smith L, Wells RS. Corrigendum: Geographic population structure analysis of worldwide human populations infers their biogeographical origins. Nat Commun 2016; 7:13468. [PMID: 27796289 PMCID: PMC5095557 DOI: 10.1038/ncomms13468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Krzywanski DM, Moellering DR, Westbrook DG, Dunham-Snary KJ, Brown J, Bray AW, Feeley KP, Sammy MJ, Smith MR, Schurr TG, Vita JA, Ambalavanan N, Calhoun D, Dell'Italia L, Ballinger SW. Endothelial Cell Bioenergetics and Mitochondrial DNA Damage Differ in Humans Having African or West Eurasian Maternal Ancestry. ACTA ACUST UNITED AC 2016; 9:26-36. [PMID: 26787433 DOI: 10.1161/circgenetics.115.001308] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 01/13/2016] [Indexed: 01/09/2023]
Abstract
BACKGROUND We hypothesized that endothelial cells having distinct mitochondrial genetic backgrounds would show variation in mitochondrial function and oxidative stress markers concordant with known differential cardiovascular disease susceptibilities. To test this hypothesis, mitochondrial bioenergetics were determined in endothelial cells from healthy individuals with African versus European maternal ancestries. METHODS AND RESULTS Bioenergetics and mitochondrial DNA (mtDNA) damage were assessed in single-donor human umbilical vein endothelial cells belonging to mtDNA haplogroups H and L, representing West Eurasian and African maternal ancestries, respectively. Human umbilical vein endothelial cells from haplogroup L used less oxygen for ATP production and had increased levels of mtDNA damage compared with those in haplogroup H. Differences in bioenergetic capacity were also observed in that human umbilical vein endothelial cells belonging to haplogroup L had decreased maximal bioenergetic capacities compared with haplogroup H. Analysis of peripheral blood mononuclear cells from age-matched healthy controls with West Eurasian or African maternal ancestries showed that haplogroups sharing an A to G mtDNA mutation at nucleotide pair 10398 had increased mtDNA damage compared with those lacking this mutation. Further study of angiographically proven patients with coronary artery disease and age-matched healthy controls revealed that mtDNA damage was associated with vascular function and remodeling and that age of disease onset was later in individuals from haplogroups lacking the A to G mutation at nucleotide pair 10398. CONCLUSIONS Differences in mitochondrial bioenergetics and mtDNA damage associated with maternal ancestry may contribute to endothelial dysfunction and vascular disease.
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Affiliation(s)
- David M Krzywanski
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Douglas R Moellering
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - David G Westbrook
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Kimberly J Dunham-Snary
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Jamelle Brown
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Alexander W Bray
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Kyle P Feeley
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Melissa J Sammy
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Matthew R Smith
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Theodore G Schurr
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Joseph A Vita
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Namasivayam Ambalavanan
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - David Calhoun
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Louis Dell'Italia
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.)
| | - Scott W Ballinger
- From the Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport (D.M.K.); Department of Nutrition Sciences (D.R.M.), Center for Free Radical Biology and Medicine (D.R.M., D.G.W., K.J.D.-S., J.B., A.W.B., K.P.F., M.J.S., M.R.S., L.D., S.W.B.), Division of Molecular and Cellular Pathology, Department of Pathology (D.G.W., J.B., A.W.B., K.P.F., M.J.S., M.R.S., S.W.B.), Department of Pediatrics (N.A.), Department of Medicine (D.C., L.D.), University of Alabama at Birmingham; Department of Medicine, Queen's University, Kingston, Ontario, Canada (K.J.D.-S.); Department of Anthropology, University of Pennsylvania, Philadelphia (T.G.S.); and Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, MA (J.A.V.).
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Benn Torres J, Vilar MG, Torres GA, Gaieski JB, Bharath Hernandez R, Browne ZE, Stevenson M, Walters W, Schurr TG. Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin. PLoS One 2015; 10:e0139192. [PMID: 26447794 PMCID: PMC4598113 DOI: 10.1371/journal.pone.0139192] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 09/10/2015] [Indexed: 11/18/2022] Open
Abstract
Historical discourses about the Caribbean often chronicle West African and European influence to the general neglect of indigenous people's contributions to the contemporary region. Consequently, demographic histories of Caribbean people prior to and after European contact are not well understood. Although archeological evidence suggests that the Lesser Antilles were populated in a series of northward and eastern migratory waves, many questions remain regarding the relationship of the Caribbean migrants to other indigenous people of South and Central America and changes to the demography of indigenous communities post-European contact. To explore these issues, we analyzed mitochondrial DNA and Y-chromosome diversity in 12 unrelated individuals from the First Peoples Community in Arima, Trinidad, and 43 unrelated Garifuna individuals residing in St. Vincent. In this community-sanctioned research, we detected maternal indigenous ancestry in 42% of the participants, with the remainder having haplotypes indicative of African and South Asian maternal ancestry. Analysis of Y-chromosome variation revealed paternal indigenous American ancestry indicated by the presence of haplogroup Q-M3 in 28% of the male participants from both communities, with the remainder possessing either African or European haplogroups. This finding is the first report of indigenous American paternal ancestry among indigenous populations in this region of the Caribbean. Overall, this study illustrates the role of the region's first peoples in shaping the genetic diversity seen in contemporary Caribbean populations.
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Affiliation(s)
- Jada Benn Torres
- Department of Anthropology, University of Notre Dame, Notre Dame, Indiana, United States of America
- * E-mail:
| | - Miguel G. Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Missions Programs, National Geographic Society, Washington, D.C., United States of America
| | - Gabriel A. Torres
- Department of Anthropology, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Jill B. Gaieski
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Zoila E. Browne
- The Garifuna Heritage Foundation Inc., Kingston, St. Vincent and the Grenadines
| | - Marlon Stevenson
- The Garifuna Heritage Foundation Inc., Kingston, St. Vincent and the Grenadines
| | - Wendell Walters
- The Garifuna Heritage Foundation Inc., Kingston, St. Vincent and the Grenadines
- Sandy Bay Village, St. Vincent and the Grenadines
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Badano I, Totaro ME, Culasso ACA, Sanabria DJ, Schurr TG, Balette IC, Roisman A, Basiletti J, Picconi MA, Campos RH, Liotta DJ. Genetic characterization and clinical implications of human papillomavirus type 16 (HPV16) variants from northeastern Argentina. Infect Genet Evol 2014; 29:103-9. [PMID: 25461847 DOI: 10.1016/j.meegid.2014.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 11/27/2022]
Abstract
BACKGROUND Human papillomavirus type 16 (HPV16) plays a central role in the development of cervical cancer. Worldwide studies indicate the existence of HPV16 variants that show different geographic distributions and oncogenic potential. OBJECTIVE Our goal was to describe the genetic variation of HPV16 isolates identified in urban women with different grades of cervical lesions living in northeastern Argentina. STUDY DESIGN We analyzed 116 HPV16-positive cervical samples (16 NLIM, 62 L-SIL, 16 H-SIL and 22 cervical cancer) from patients attending health centers in Misiones (Argentina) during 2006-13. HPV16 isolates were genetically characterized through PCR amplification and direct sequencing of 364 bp within the long control region, and the resulting sequences classified into variants based on phylogenetic analysis (lineages A, B, C and D). A potential association between HPV16 variants and lesion grade was evaluated through an odds ratio (OR) test. A temporal framework for the origin of HPV16 variants was assessed through coalescence analysis (BEAST v 1.7.5). RESULTS Phylogenetic analysis of HPV16 sequences showed that 92.1% of the samples clustered with lineage A, and 6.9% to lineage D. HPV16 variants from lineage D were more frequently associated with high-grade lesions and cancer (HSIL+) than lineage A variants at an OR of 13.8 (1.6-117.0). The time to most common recent ancestor (tMCRA) of all variants was 119,103 years before present (HPD 95%=48,486-197,239), a date consistent with the time frame for modern human evolution. CONCLUSION Our results suggest that HPV16 variants from lineage D may represent an additional risk factor for the development of cervical cancer in women living in northeastern Argentina. This study provides new information about viral isolates present in Argentina that will contribute to the monitoring of HPV16 infection in the vaccine era.
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Affiliation(s)
- Inés Badano
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas 3300, Misiones, Argentina.
| | - Maria Elina Totaro
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas 3300, Misiones, Argentina
| | - Andrés Carlos Alberto Culasso
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junin 954, 4to piso, Capital Federal (C1113AAD), Buenos Aires, Argentina
| | - Daiana Jimena Sanabria
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas 3300, Misiones, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania, 3260 South Street, Philadelphia, PA 19104-6398, USA
| | - Ileana Cristina Balette
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas 3300, Misiones, Argentina
| | - Alejandro Roisman
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas 3300, Misiones, Argentina
| | - Jorge Basiletti
- Servicio de Virus Oncogénicos, Departamento de Virología, INEI-ANLIS "Dr. Carlos G. Malbrán", Av. Velez Sarsfield 563, Capital Federal (C1282AFF), Buenos Aires, Argentina
| | - María Alejandra Picconi
- Servicio de Virus Oncogénicos, Departamento de Virología, INEI-ANLIS "Dr. Carlos G. Malbrán", Av. Velez Sarsfield 563, Capital Federal (C1282AFF), Buenos Aires, Argentina
| | - Rodolfo Héctor Campos
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junin 954, 4to piso, Capital Federal (C1113AAD), Buenos Aires, Argentina
| | - Domingo Javier Liotta
- Laboratorio de Biología Molecular Aplicada, Facultad de Ciencias Exactas, Quimicas y Naturales, Universidad Nacional de Misiones, Av. Mariano Moreno 1375, Posadas 3300, Misiones, Argentina
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Vilar MG, Melendez C, Sanders AB, Walia A, Gaieski JB, Owings AC, Schurr TG. Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies. Am J Phys Anthropol 2014; 155:352-68. [PMID: 25043798 DOI: 10.1002/ajpa.22569] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 06/30/2014] [Accepted: 07/01/2014] [Indexed: 01/05/2023]
Abstract
Puerto Rico and the surrounding islands rest on the eastern fringe of the Caribbean's Greater Antilles, located less than 100 miles northwest of the Lesser Antilles. Puerto Ricans are genetic descendants of pre-Columbian peoples, as well as peoples of European and African descent through 500 years of migration to the island. To infer these patterns of pre-Columbian and historic peopling of the Caribbean, we characterized genetic diversity in 326 individuals from the southeastern region of Puerto Rico and the island municipality of Vieques. We sequenced the mitochondrial DNA (mtDNA) control region of all of the samples and the complete mitogenomes of 12 of them to infer their putative place of origin. In addition, we genotyped 121 male samples for 25 Y-chromosome single nucleotide polymorphism and 17 STR loci. Approximately 60% of the participants had indigenous mtDNA haplotypes (mostly from haplogroups A2 and C1), while 25% had African and 15% European haplotypes. Three A2 sublineages were unique to the Greater Antilles, one of which was similar to Mesoamerican types, while C1b haplogroups showed links to South America, suggesting that people reached the island from the two distinct continental source areas. However, none of the male participants had indigenous Y-chromosomes, with 85% of them instead being European/Mediterranean and 15% sub-Saharan African in origin. West Eurasian Y-chromosome short tandem repeat haplotypes were quite diverse and showed similarities to those observed in southern Europe, North Africa and the Middle East. These results attest to the distinct, yet equally complex, pasts for the male and female ancestors of modern day Puerto Ricans.
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Affiliation(s)
- Miguel G Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA, 19104-6398
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Dingley SD, Polyak E, Ostrovsky J, Srinivasan S, Lee I, Rosenfeld AB, Tsukikawa M, Xiao R, Selak MA, Coon JJ, Hebert AS, Grimsrud PA, Kwon YJ, Pagliarini DJ, Gai X, Schurr TG, Hüttemann M, Nakamaru-Ogiso E, Falk MJ. Mitochondrial DNA variant in COX1 subunit significantly alters energy metabolism of geographically divergent wild isolates in Caenorhabditis elegans. J Mol Biol 2014; 426:2199-216. [PMID: 24534730 DOI: 10.1016/j.jmb.2014.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 12/12/2022]
Abstract
Mitochondrial DNA (mtDNA) sequence variation can influence the penetrance of complex diseases and climatic adaptation. While studies in geographically defined human populations suggest that mtDNA mutations become fixed when they have conferred metabolic capabilities optimally suited for a specific environment, it has been challenging to definitively assign adaptive functions to specific mtDNA sequence variants in mammals. We investigated whether mtDNA genome variation functionally influences Caenorhabditis elegans wild isolates of distinct mtDNA lineages and geographic origins. We found that, relative to N2 (England) wild-type nematodes, CB4856 wild isolates from a warmer native climate (Hawaii) had a unique p.A12S amino acid substitution in the mtDNA-encoded COX1 core catalytic subunit of mitochondrial complex IV (CIV). Relative to N2, CB4856 worms grown at 20°C had significantly increased CIV enzyme activity, mitochondrial matrix oxidant burden, and sensitivity to oxidative stress but had significantly reduced lifespan and mitochondrial membrane potential. Interestingly, mitochondrial membrane potential was significantly increased in CB4856 grown at its native temperature of 25°C. A transmitochondrial cybrid worm strain, chpIR (M, CB4856>N2), was bred as homoplasmic for the CB4856 mtDNA genome in the N2 nuclear background. The cybrid strain also displayed significantly increased CIV activity, demonstrating that this difference results from the mtDNA-encoded p.A12S variant. However, chpIR (M, CB4856>N2) worms had significantly reduced median and maximal lifespan relative to CB4856, which may relate to their nuclear-mtDNA genome mismatch. Overall, these data suggest that C. elegans wild isolates of varying geographic origins may adapt to environmental challenges through mtDNA variation to modulate critical aspects of mitochondrial energy metabolism.
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Affiliation(s)
- Stephen D Dingley
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Erzsebet Polyak
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Julian Ostrovsky
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Satish Srinivasan
- Department of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Icksoo Lee
- Dankook University College of Medicine, Yongin-si, Gyeonggi-do, South Korea
| | - Amy B Rosenfeld
- Department of Molecular Pharmacology and Therapeutics, Loyola University Health Sciences Division, Maywood, IL, 60153, USA
| | - Mai Tsukikawa
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Rui Xiao
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mary A Selak
- Mitochondria Research Core Facility, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, 19104, USA
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA; Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alexander S Hebert
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA; Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Paul A Grimsrud
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Young Joon Kwon
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
| | - David J Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Xiaowu Gai
- Department of Molecular Pharmacology and Therapeutics, Loyola University Health Sciences Division, Maywood, IL, 60153, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics and Cardiovascular Research Institute, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Eiko Nakamaru-Ogiso
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Marni J Falk
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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Elhaik E, Greenspan E, Staats S, Krahn T, Tyler-Smith C, Xue Y, Tofanelli S, Francalacci P, Cucca F, Pagani L, Jin L, Li H, Schurr TG, Greenspan B, Spencer Wells R. The GenoChip: a new tool for genetic anthropology. Genome Biol Evol 2013; 5:1021-31. [PMID: 23666864 PMCID: PMC3673633 DOI: 10.1093/gbe/evt066] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Genographic Project is an international effort aimed at charting human migratory history. The project is nonprofit and nonmedical, and, through its Legacy Fund, supports locally led efforts to preserve indigenous and traditional cultures. Although the first phase of the project was focused on uniparentally inherited markers on the Y-chromosome and mitochondrial DNA (mtDNA), the current phase focuses on markers from across the entire genome to obtain a more complete understanding of human genetic variation. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism (SNP) genotyping, they were designed for medical genetic studies and contain medically related markers that are inappropriate for global population genetic studies. GenoChip, the Genographic Project’s new genotyping array, was designed to resolve these issues and enable higher resolution research into outstanding questions in genetic anthropology. The GenoChip includes ancestry informative markers obtained for over 450 human populations, an ancient human (Saqqaq), and two archaic hominins (Neanderthal and Denisovan) and was designed to identify all known Y-chromosome and mtDNA haplogroups. The chip was carefully vetted to avoid inclusion of medically relevant markers. To demonstrate its capabilities, we compared the FST distributions of GenoChip SNPs to those of two commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, the GenoChip autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. The chip performances are illustrated in a principal component analysis for 14 worldwide populations. In summary, the GenoChip is a dedicated genotyping platform for genetic anthropology. With an unprecedented number of approximately 12,000 Y-chromosomal and approximately 3,300 mtDNA SNPs and over 130,000 autosomal and X-chromosomal SNPs without any known health, medical, or phenotypic relevance, the GenoChip is a useful tool for genetic anthropology and population genetics.
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Affiliation(s)
- Eran Elhaik
- Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, USA
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Schurr TG, Dulik MC, Cafaro TA, Suarez MF, Urrets-Zavalia JA, Serra HM. Genetic background and climatic droplet keratopathy incidence in a Mapuche population from Argentina. PLoS One 2013; 8:e74593. [PMID: 24040292 PMCID: PMC3764023 DOI: 10.1371/journal.pone.0074593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/05/2013] [Indexed: 11/18/2022] Open
Abstract
Purpose To determine whether the incidence of and susceptibility to climatic droplet keratopathy (CDK), an acquired, often bilateral degenerative corneal disease, is influenced by the genetic background of the individuals who exhibit the disorder. Methods To determine whether the disease expression was influenced by the genetic ancestry of CDK cases in native Mapuche of the northwest area of Patagonia in Argentina, we examined mitochondrial DNA and Y-chromosome variation in 53 unrelated individuals. Twenty-nine of them were part of the CDK (patient) population, while 24 were part of the control group. The analysis revealed the maternal and paternal lineages that were present in the two study groups. Results This analysis demonstrated that nearly all persons had a Native American mtDNA background, whereas 50% of the CDK group and 37% of the control group had Native American paternal ancestry, respectively. There was no significant difference in the frequencies of mtDNA haplogroups between the CDK patient and control groups. Although the Y-chromosome data revealed differences in specific haplogroup frequencies between these two groups, there was no statistically significant relationship between individual paternal genetic backgrounds and the incidence or stage of disease. Conclusions These results indicate a lack of correlation between genetic ancestry as represented by haploid genetic systems and the incidence of CDK in Mapuche populations. In addition, the mtDNA appears to play less of a role in CDK expression than for other complex diseases linked to bioenergetic processes. However, further analysis of the mtDNA genome sequence and other genes involved in corneal function may reveal the more precise role that mitochondria play in the expression of CDK.
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Affiliation(s)
- Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew C. Dulik
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Thamara A. Cafaro
- CIBICI (Centro de Investigaciones en Bioquímica Clínica e Inmunología), Faculty of Chemistry, National University of Córdoba, Córdoba, Argentina
| | - María F. Suarez
- CIBICI (Centro de Investigaciones en Bioquímica Clínica e Inmunología), Faculty of Chemistry, National University of Córdoba, Córdoba, Argentina
| | | | - Horacio M. Serra
- CIBICI (Centro de Investigaciones en Bioquímica Clínica e Inmunología), Faculty of Chemistry, National University of Córdoba, Córdoba, Argentina
- * E-mail:
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ArunKumar G, Soria-Hernanz DF, Kavitha VJ, Arun VS, Syama A, Ashokan KS, Gandhirajan KT, Vijayakumar K, Narayanan M, Jayalakshmi M, Ziegle JS, Royyuru AK, Parida L, Wells RS, Renfrew C, Schurr TG, Smith CT, Platt DE, Pitchappan R. Population differentiation of southern Indian male lineages correlates with agricultural expansions predating the caste system. PLoS One 2012; 7:e50269. [PMID: 23209694 PMCID: PMC3508930 DOI: 10.1371/journal.pone.0050269] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 10/22/2012] [Indexed: 02/06/2023] Open
Abstract
Previous studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes of the establishment of the Varna caste system and its genetic impact on the origins and demographic histories of Indian populations. To further investigate these questions we took advantage that both Y chromosome and caste designation are paternally inherited, and genotyped 1,680 Y chromosomes representing 12 tribal and 19 non-tribal (caste) endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India. Tribes and castes were both characterized by an overwhelming proportion of putatively Indian autochthonous Y-chromosomal haplogroups (H-M69, F-M89, R1a1-M17, L1-M27, R2-M124, and C5-M356; 81% combined) with a shared genetic heritage dating back to the late Pleistocene (10–30 Kya), suggesting that more recent Holocene migrations from western Eurasia contributed <20% of the male lineages. We found strong evidence for genetic structure, associated primarily with the current mode of subsistence. Coalescence analysis suggested that the social stratification was established 4–6 Kya and there was little admixture during the last 3 Kya, implying a minimal genetic impact of the Varna (caste) system from the historically-documented Brahmin migrations into the area. In contrast, the overall Y-chromosomal patterns, the time depth of population diversifications and the period of differentiation were best explained by the emergence of agricultural technology in South Asia. These results highlight the utility of detailed local genetic studies within India, without prior assumptions about the importance of Varna rank status for population grouping, to obtain new insights into the relative influences of past demographic events for the population structure of the whole of modern India.
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Affiliation(s)
- GaneshPrasad ArunKumar
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
- Chettinad Academy of Research and Education, Kelampakkam, Chennai, Tamil Nadu, India
| | - David F. Soria-Hernanz
- National Geographic Society, Washington, District of Columbia, United States of America
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Valampuri John Kavitha
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
- Department of Biotechnology, Mother Teresa Women's University, Kodaikanal, Tamil Nadu, India
| | | | - Adhikarla Syama
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Kumaran Samy Ashokan
- Nilgiri Adivasi Welfare Association, Kota Hall Road, Kothagiri, Tamil Nadu, India
| | | | | | | | - Mariakuttikan Jayalakshmi
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Janet S. Ziegle
- Applied Biosystems, Foster City, California, United States of America
| | - Ajay K. Royyuru
- Computational Biology Group, IBM - Thomas J. Watson Research Center, New York, New York, United States of America
| | - Laxmi Parida
- Computational Biology Group, IBM - Thomas J. Watson Research Center, New York, New York, United States of America
| | - R. Spencer Wells
- National Geographic Society, Washington, District of Columbia, United States of America
| | - Colin Renfrew
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Chris Tyler Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Daniel E. Platt
- Computational Biology Group, IBM - Thomas J. Watson Research Center, New York, New York, United States of America
| | - Ramasamy Pitchappan
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
- Chettinad Academy of Research and Education, Kelampakkam, Chennai, Tamil Nadu, India
- * E-mail:
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Schurr TG, Dulik MC, Owings AC, Zhadanov SI, Gaieski JB, Vilar MG, Ramos J, Moss MB, Natkong F. Clan, language, and migration history has shaped genetic diversity in Haida and Tlingit populations from Southeast Alaska. Am J Phys Anthropol 2012; 148:422-35. [PMID: 22549307 DOI: 10.1002/ajpa.22068] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Accepted: 03/06/2012] [Indexed: 11/10/2022]
Abstract
The linguistically distinctive Haida and Tlingit tribes of Southeast Alaska are known for their rich material culture, complex social organization, and elaborate ritual practices. However, much less is known about these tribes from a population genetic perspective. For this reason, we analyzed mtDNA and Y-chromosome variation in Haida and Tlingit populations to elucidate several key issues pertaining to the history of this region. These included the genetic relationships of Haida and Tlingit to other indigenous groups in Alaska and Canada; the relationship between linguistic and genetic data for populations assigned to the Na-Dene linguistic family, specifically, the inclusion of Haida with Athapaskan, Eyak, and Tlingit in the language family; the possible influence of matrilineal clan structure on patterns of genetic variation in Haida and Tlingit populations; and the impact of European entry into the region on the genetic diversity of these indigenous communities. Our analysis indicates that, while sharing a "northern" genetic profile, the Haida and the Tlingit are genetically distinctive from each other. In addition, Tlingit groups themselves differ across their geographic range, in part due to interactions of Tlingit tribes with Athapaskan and Eyak groups to the north. The data also reveal a strong influence of maternal clan identity on mtDNA variation in these groups, as well as the significant influence of non-native males on Y-chromosome diversity. These results yield new details about the histories of the Haida and Tlingit tribes in this region.
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Affiliation(s)
- Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, 19104-6398, USA.
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Babb PL, McIntosh AM, Fernandez-Duque E, Di Fiore A, Schurr TG. An optimized microsatellite genotyping strategy for assessing genetic identity and kinship in Azara's owl monkeys (Aotus azarai). Folia Primatol (Basel) 2011; 82:107-17. [PMID: 21912137 DOI: 10.1159/000330564] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 07/01/2011] [Indexed: 11/19/2022]
Abstract
In this study, we characterize a panel of 20 microsatellite markers that reproducibly amplify in Azara's owl monkeys (Aotus azarai) for use in genetic profiling analyses. A total of 128 individuals from our study site in Formosa, Argentina, were genotyped for 20 markers, 13 of which were found to be polymorphic. The levels of allelic variation at these loci provided paternity exclusion probabilities of 0.852 when neither parent was known, and 0.981 when one parent was known. In addition, our analysis revealed that, although genotypes can be rapidly scored using fluorescence-based fragment analysis, the presence of complex or multiple short tandem repeat (STR) motifs at a microsatellite locus could generate similar fragment patterns from alleles that have different nucleotide sequences and perhaps different evolutionary origins. Even so, this collection of microsatellite loci is suitable for parentage analyses and will allow us to test various hypotheses about the relationship between social behavior and kinship in wild owl monkey populations. Furthermore, given the limited number of platyrrhine-specific microsatellite loci available in the literature, this STR panel represents a valuable tool for population studies of other cebines and callitrichines.
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Affiliation(s)
- Paul L Babb
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
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Gaieski JB, Owings AC, Vilar MG, Dulik MC, Gaieski DF, Gittelman RM, Lindo J, Gau L, Schurr TG. Genetic ancestry and indigenous heritage in a Native American descendant community in Bermuda. Am J Phys Anthropol 2011; 146:392-405. [PMID: 21994016 DOI: 10.1002/ajpa.21588] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 06/17/2011] [Indexed: 11/09/2022]
Abstract
Discovered in the early 16th century by European colonists, Bermuda is an isolated set of islands located in the mid-Atlantic. Shortly after its discovery, Bermuda became the first English colony to forcibly import its labor by trafficking in enslaved Africans, white ethnic minorities, and indigenous Americans. Oral traditions circulating today among contemporary tribes from the northeastern United States recount these same events, while, in Bermuda, St. David's Islanders consider their histories to be linked to a complex Native American, European, and African past. To investigate the influence of historical events on biological ancestry and native cultural identity, we analyzed genetic variation in 111 members of Bermuda's self-proclaimed St. David's Island Native Community. Our results reveal that the majority of mitochondrial DNA (mtDNA) and Y-chromosome haplotypes are of African and West Eurasian origin. However, unlike other English-speaking New World colonies, most African mtDNA haplotypes appear to derive from central and southeast Africa, reflecting the extent of maritime activities in the region. In light of genealogical and oral historical data from the St. David's community, the low frequency of Native American mtDNA and NRY lineages may reflect the influence of genetic drift, the demographic impact of European colonization, and historical admixture with persons of non-native backgrounds, which began with the settlement of the islands. By comparing the genetic data with genealogical and historical information, we are able to reconstruct the complex history of this Bermudian community, which is unique among New World populations.
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Affiliation(s)
- Jill B Gaieski
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
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Babb PL, Fernandez-Duque E, Baiduc CA, Gagneux P, Evans S, Schurr TG. mtDNA diversity in azara's owl monkeys (Aotus azarai azarai) of the Argentinean Chaco. Am J Phys Anthropol 2011; 146:209-24. [DOI: 10.1002/ajpa.21567] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 05/04/2011] [Indexed: 11/05/2022]
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Gokcumen Ö, Gultekin T, Alakoc YD, Tug A, Gulec E, Schurr TG. Biological ancestries, kinship connections, and projected identities in four central Anatolian settlements: insights from culturally contextualized genetic anthropology. Am Anthropol 2011; 113:116-31. [PMID: 21560269 DOI: 10.1111/j.1548-1433.2010.01310.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Previous population genetics studies in Turkey failed to delineate recent historical and social factors that shaped Anatolian cultural and genetic diversity at the local level. To address this shortcoming, we conducted focused ethnohistorical fieldwork and screened biological samples collected from the Yuksekyer region for mitochondrial, Y chromosome, and autosomal markers and then analyzed the data within an ethnohistorical context. Our results revealed that, at the village level, paternal genetic diversity is structured among settlements, whereas maternal genetic diversity is distributed more homogenously, reflecting the strong patrilineal cultural traditions that transcend larger ethnic and religious structures. Local ancestries and origin myths, rather than ethnic or religious affiliations, delineate the social boundaries and projected identities among the villages. Therefore, we conclude that broad, ethnicity-based sampling is inadequate to capture the genetic signatures of recent social and historical dynamics, which have had a profound influence on contemporary genetic and cultural regional diversity.
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Affiliation(s)
- Ömer Gokcumen
- Harvard University Medical School and Brigham and Women's Hospital, Boston
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Babb PL, Fernandez-Duque E, Schurr TG. AVPR1A Sequence Variation in Monogamous Owl Monkeys (Aotus azarai) and Its Implications for the Evolution of Platyrrhine Social Behavior. J Mol Evol 2010; 71:279-97. [DOI: 10.1007/s00239-010-9383-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 08/17/2010] [Indexed: 12/31/2022]
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Zhadanov SI, Dulik MC, Markley M, Jennings GW, Gaieski JB, Elias G, Schurr TG. Genetic heritage and native identity of the Seaconke Wampanoag tribe of massachusetts. Am J Phys Anthropol 2010; 142:579-89. [DOI: 10.1002/ajpa.21281] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Alakoc YD, Gokcumen O, Tug A, Gultekin T, Gulec E, Schurr TG. Y-chromosome and autosomal STR diversity in four proximate settlements in Central Anatolia. Forensic Sci Int Genet 2010; 4:e135-7. [PMID: 20457085 DOI: 10.1016/j.fsigen.2010.01.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Revised: 01/26/2010] [Accepted: 01/26/2010] [Indexed: 11/19/2022]
Abstract
Due to the longstanding human presence in the region and the influence of social traditions, the genetic make-up of populations currently inhabiting Turkey (Anatolia) is quite complex. To characterize the patterns of genetic diversity in rural Central Anatolian villages, we analyzed samples collected at four local settlements for variation at 17 Y-chromosome STR and 15 autosomal STR loci. The resulting data reveal considerable diversity within these settlements, as well as some structure in the paternal genetic variation, with a limited number of haplotypes being shared between the communities. These findings have important implications for forensic studies of Turkish populations.
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Affiliation(s)
- Yesim Dogan Alakoc
- Ankara University Medical School, Department of Forensic Medicine, 06100 Cebeci, Ankara, Turkey.
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Stefflova K, Dulik MC, Pai AA, Walker AH, Zeigler-Johnson CM, Gueye SM, Schurr TG, Rebbeck TR. Evaluation of group genetic ancestry of populations from Philadelphia and Dakar in the context of sex-biased admixture in the Americas. PLoS One 2009; 4:e7842. [PMID: 19946364 PMCID: PMC2776971 DOI: 10.1371/journal.pone.0007842] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 10/15/2009] [Indexed: 11/18/2022] Open
Abstract
Background Population history can be reflected in group genetic ancestry, where genomic variation captured by the mitochondrial DNA (mtDNA) and non-recombining portion of the Y chromosome (NRY) can separate female- and male-specific admixture processes. Genetic ancestry may influence genetic association studies due to differences in individual admixture within recently admixed populations like African Americans. Principal Findings We evaluated the genetic ancestry of Senegalese as well as European Americans and African Americans from Philadelphia. Senegalese mtDNA consisted of ∼12% U haplotypes (U6 and U5b1b haplotypes, common in North Africa) while the NRY haplotypes belonged solely to haplogroup E. In Philadelphia, we observed varying degrees of admixture. While African Americans have 9–10% mtDNAs and ∼31% NRYs of European origin, these results are not mirrored in the mtDNA/NRY pools of European Americans: they have less than 7% mtDNAs and less than 2% NRYs from non-European sources. Additionally, there is <2% Native American contribution to Philadelphian African American ancestry and the admixture from combined mtDNA/NRY estimates is consistent with the admixture derived from autosomal genetic data. To further dissect these estimates, we have analyzed our samples in the context of different demographic groups in the Americas. Conclusions We found that sex-biased admixture in African-derived populations is present throughout the Americas, with continual influence of European males, while Native American females contribute mainly to populations of the Caribbean and South America. The high non-European female contribution to the pool of European-derived populations is consistently characteristic of Iberian colonization. These data suggest that genomic data correlate well with historical records of colonization in the Americas.
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Affiliation(s)
- Klara Stefflova
- Department of Biostatistics and Epidemiology, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
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Schroeder KB, Jakobsson M, Crawford MH, Schurr TG, Boca SM, Conrad DF, Tito RY, Osipova LP, Tarskaia LA, Zhadanov SI, Wall JD, Pritchard JK, Malhi RS, Smith DG, Rosenberg NA. Haplotypic background of a private allele at high frequency in the Americas. Mol Biol Evol 2009; 26:995-1016. [PMID: 19221006 DOI: 10.1093/molbev/msp024] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Recently, the observation of a high-frequency private allele, the 9-repeat allele at microsatellite D9S1120, in all sampled Native American and Western Beringian populations has been interpreted as evidence that all modern Native Americans descend primarily from a single founding population. However, this inference assumed that all copies of the 9-repeat allele were identical by descent and that the geographic distribution of this allele had not been influenced by natural selection. To investigate whether these assumptions are satisfied, we genotyped 34 single nucleotide polymorphisms across approximately 500 kilobases (kb) around D9S1120 in 21 Native American and Western Beringian populations and 54 other worldwide populations. All chromosomes with the 9-repeat allele share the same haplotypic background in the vicinity of D9S1120, suggesting that all sampled copies of the 9-repeat allele are identical by descent. Ninety-one percent of these chromosomes share the same 76.26 kb haplotype, which we call the "American Modal Haplotype" (AMH). Three observations lead us to conclude that the high frequency and widespread distribution of the 9-repeat allele are unlikely to be the result of positive selection: 1) aside from its association with the 9-repeat allele, the AMH does not have a high frequency in the Americas, 2) the AMH is not unusually long for its frequency compared with other haplotypes in the Americas, and 3) in Latin American mestizo populations, the proportion of Native American ancestry at D9S1120 is not unusual compared with that observed at other genomewide microsatellites. Using a new method for estimating the time to the most recent common ancestor (MRCA) of all sampled copies of an allele on the basis of an estimate of the length of the genealogy descended from the MRCA, we calculate the mean time to the MRCA of the 9-repeat allele to be between 7,325 and 39,900 years, depending on the demographic model used. The results support the hypothesis that all modern Native Americans and Western Beringians trace a large portion of their ancestry to a single founding population that may have been isolated from other Asian populations prior to expanding into the Americas.
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Affiliation(s)
- Kari B Schroeder
- Department of Anthropology, University of California, Davis, CA, USA.
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Schroeder KB, Schurr TG, Long JC, Rosenberg NA, Crawford MH, Tarskaia LA, Osipova LP, Zhadanov SI, Smith DG. A private allele ubiquitous in the Americas. Biol Lett 2008; 3:218-23. [PMID: 17301009 PMCID: PMC2375964 DOI: 10.1098/rsbl.2006.0609] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The three-wave migration hypothesis of Greenberg et al. has permeated the genetic literature on the peopling of the Americas. Greenberg et al. proposed that Na-Dene, Aleut-Eskimo and Amerind are language phyla which represent separate migrations from Asia to the Americas. We show that a unique allele at autosomal microsatellite locus D9S1120 is present in all sampled North and South American populations, including the Na-Dene and Aleut-Eskimo, and in related Western Beringian groups, at an average frequency of 31.7%. This allele was not observed in any sampled putative Asian source populations or in other worldwide populations. Neither selection nor admixture explains the distribution of this regionally specific marker. The simplest explanation for the ubiquity of this allele across the Americas is that the same founding population contributed a large fraction of ancestry to all modern Native American populations.
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Affiliation(s)
- K B Schroeder
- Department of Anthropology, University of California, Davis, CA 95616, USA.
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Gokcumen O, Dulik MC, Pai AA, Zhadanov SI, Rubinstein S, Osipova LP, Andreenkov OV, Tabikhanova LE, Gubina MA, Labuda D, Schurr TG. Genetic variation in the enigmatic Altaian Kazakhs of South-Central Russia: Insights into Turkic population history. Am J Phys Anthropol 2008; 136:278-93. [DOI: 10.1002/ajpa.20802] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Rubinstein S, Dulik MC, Gokcumen O, Zhadanov S, Osipova L, Cocca M, Mehta N, Gubina M, Posukh O, Schurr TG. Russian Old Believers: Genetic Consequences of Their Persecution and Exile, as Shown by Mitochondrial DNA Evidence. Hum Biol 2008; 80:203-37. [DOI: 10.3378/1534-6617-80.3.203] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Friedlaender JS, Friedlaender FR, Hodgson JA, Stoltz M, Koki G, Horvat G, Zhadanov S, Schurr TG, Merriwether DA. Melanesian mtDNA complexity. PLoS One 2007; 2:e248. [PMID: 17327912 PMCID: PMC1803017 DOI: 10.1371/journal.pone.0000248] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2006] [Accepted: 02/05/2007] [Indexed: 12/02/2022] Open
Abstract
Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA) sequences from hypervariable regions 1 and 2 (HVR1 and HVR2) from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups). Persistent differences between shore and inland groups in effective population sizes and marital migration rates probably cause these differences. We also add 16 whole sequences to the Melanesian mtDNA phylogenies. We identify the likely origins of a number of the haplogroups and ancient branches in specific islands, point to some ancient mtDNA connections between Near Oceania and Australia, and show additional Holocene connections between Island Southeast Asia/Taiwan and Island Melanesia with branches of haplogroup E. Coalescence estimates based on synonymous transitions in the coding region suggest an initial settlement and expansion in the region at ∼30–50,000 years before present (YBP), and a second important expansion from Island Southeast Asia/Taiwan during the interval ∼3,500–8,000 YBP. However, there are some important variance components in molecular dating that have been overlooked, and the specific nature of ancestral (maternal) Austronesian influence in this region remains unresolved.
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Affiliation(s)
- Jonathan S Friedlaender
- Anthropology Department, Temple University, Philadelphia, Pennsylvania, United States of America.
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50
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Zhadanov SI, Grechanina EY, Grechanina YB, Gusar VA, Fedoseeva NP, Lebon S, Münnich A, Schurr TG. Fatal manifestation of a de novo ND5 mutation: Insights into the pathogenetic mechanisms of mtDNA ND5 gene defects. Mitochondrion 2007; 7:260-6. [PMID: 17317336 DOI: 10.1016/j.mito.2007.01.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 01/08/2007] [Accepted: 01/10/2007] [Indexed: 11/23/2022]
Abstract
We report the de novo occurrence of a heteroplasmic 12706T-->C (12705C) ND5 mutation associated with the clinical expression of fatal Leigh syndrome. Phylogenetic analysis of several cases having the 12706C mutation confirmed that this mutation occurred independently in distinctive mtDNA backgrounds. In each of these cases, the low level of heteroplasmy and the association of the mutation with a deleterious phenotype indicated that the 12706C had a primary role in the expression of LS/MELAS in its carriers. Secondary structure analysis of the ND5 protein further supported the deleterious role of the 12706C mutation, as it was found to affect a functionally significant transmembrane domain that is likely responsible for the proton-translocation function of complex I.
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Affiliation(s)
- Sergey I Zhadanov
- Department of Anthropology, University of Pennsylvania, 325 University Museum, 3260 South Street, Philadelphia, PA 19104-6398, USA.
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