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Ying Z, Zheng J, Cai Z, Liu L, Dai Y, Yao J, Wang H, Gao Y, Zheng B, Tang X, Zhu Y, Guan MX, Chen Y. Mitochondrial haplogroup B increases the risk for hearing loss among the Eastern Asian pedigrees carrying 12S rRNA 1555A>G mutation. Protein Cell 2016; 6:844-8. [PMID: 26361786 PMCID: PMC4624676 DOI: 10.1007/s13238-015-0203-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Zhengbiao Ying
- Department of Otolaryngology, Wenling People's Hospital, Wenzhou Medical University, Wenling, 317500, China
| | - Jing Zheng
- Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Zhaoyang Cai
- Department of Otolaryngology, Wenling People's Hospital, Wenzhou Medical University, Wenling, 317500, China
| | - Li Liu
- Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Yu Dai
- Department of Clinical Laboratory, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Juan Yao
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Hui Wang
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yinglong Gao
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Binjiao Zheng
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Xiaowen Tang
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yi Zhu
- Department of Otolaryngology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, China
| | - Min-Xin Guan
- Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, 310058, China
| | - Ye Chen
- Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou, 310058, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, 310058, China.
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Heidari MM, Khatami M, Danafar A, Dianat T, Farahmand G, Talebi AR. Mitochondrial Genetic Variation in Iranian Infertile Men with Varicocele. INTERNATIONAL JOURNAL OF FERTILITY & STERILITY 2016; 10:303-309. [PMID: 27695613 PMCID: PMC5023041 DOI: 10.22074/ijfs.2016.5047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 02/23/2016] [Indexed: 12/05/2022]
Abstract
Background: Several recent studies have shown that mitochondrial DNA mutations lead
to major disabilities and premature death in carriers. More than 150 mutations in
human mitochondrial DNA (mtDNA) genes have been associated with a wide spectrum of
disorders. Varicocele, one of the causes of infertility in men wherein abnormal inflexion
and distension of veins of the pampiniform plexus is observed within spermatic cord, can
increase reactive oxygen species (ROS) production in semen and cause oxidative stress
and sperm dysfunction in patients. Given that mitochondria are the source of ROS
production in cells, the aim of this study was to scan nine mitochondrial genes (MT-COX2,
MT-tRNALys , MT-ATP8, MT-ATP6, MT-COX3, MT-tRNAGly , MT-ND3, MT-tRNAArg and MT-ND4L) for mutations in infertile patients with varicocele. Materials and Methods: In this cross-sectional study, polymerase chain reaction-single strand
conformation polymorphism (PCR-SSCP) and DNA sequencing were used to detect and
identify point mutations respectively in 9 mitochondrial genes in 72 infertile men with varicocele
and 159 fertile men. In brief, the samples showing altered electrophoretic patterns of DNA in the
SSCP gel were sent for DNA sequencing to identify the exact nucleotide variation. Results: Ten type nucleotide variants were detected exclusively in mitochondrial DNA
of infertile men. These include six novel nucleotide changes and four variants previously
reported for other disorders. Conclusion: Mutations in mitochondrial genes may affect respiratory complexes in
combination with environmental risk factors. Therefore these nucleotide variants probably
lead to impaired ATP synthesis and mitochondrial function ultimately interfering with
sperm motility and infertility.
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Affiliation(s)
| | - Mehri Khatami
- Department of Biology, Faculty of Science, Yazd University, Yazd, Iran
| | - Amirhossein Danafar
- Department of Biology, Ashkezar Islamic Azad University, Ashkezar, Yazd, Iran
| | - Tahere Dianat
- Department of Biology, Faculty of Science, Yazd University, Yazd, Iran
| | - Ghazaleh Farahmand
- Department of Biology, Faculty of Science, Islamic Azad University Shahrekord, Shahrekord, Iran
| | - Ali Reza Talebi
- Research and Clinical Center for Infertility and Department of Anatomy, Shahid Sadughi University of Medical Sciences, Yazd, Iran
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Turchi C, Stanciu F, Paselli G, Buscemi L, Parson W, Tagliabracci A. The mitochondrial DNA makeup of Romanians: A forensic mtDNA control region database and phylogenetic characterization. Forensic Sci Int Genet 2016; 24:136-142. [DOI: 10.1016/j.fsigen.2016.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/26/2016] [Accepted: 06/18/2016] [Indexed: 01/13/2023]
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Barral-Arca R, Pischedda S, Gómez-Carballa A, Pastoriza A, Mosquera-Miguel A, López-Soto M, Martinón-Torres F, Álvarez-Iglesias V, Salas A. Meta-Analysis of Mitochondrial DNA Variation in the Iberian Peninsula. PLoS One 2016; 11:e0159735. [PMID: 27441366 PMCID: PMC4956223 DOI: 10.1371/journal.pone.0159735] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 07/07/2016] [Indexed: 12/14/2022] Open
Abstract
The Iberian Peninsula has been the focus of attention of numerous studies dealing with mitochondrial DNA (mtDNA) variation, most of them targeting the control region segment. In the present study we sequenced the control region of 3,024 Spanish individuals from areas where available data were still limited. We also compiled mtDNA haplotypes from the literature involving 4,588 sequences and 28 population groups or small regions. We meta-analyzed all these data in order to shed further light on patterns of geographic variation, taking advantage of the large sample size and geographic coverage, in contrast with the atomized sampling strategy of previous work. The results indicate that the main mtDNA haplogroups show primarily clinal geographic patterns across the Iberian geography, roughly along a North-South axis. Haplogroup HV0 (where haplogroup U is nested) is more prevalent in the Franco Cantabrian region, in good agreement with previous findings that identified this area as a climate refuge during the Last Glacial Maximum (LGM), prior to a subsequent demographic re-expansion towards Central Europe and the Mediterranean. Typical sub-Saharan and North African lineages are slightly more prevalent in South Iberia, although at low frequencies; this pattern has been shaped mainly by the transatlantic slave trade and the Arab invasion of the Iberian Peninsula. The results also indicate that summary statistics that aim to measure molecular variation, or AMOVA, have limited sensitivity to detect population substructure, in contrast to patterns revealed by phylogeographic analysis. Overall, the results suggest that mtDNA variation in Iberia is substantially stratified. These patterns might be relevant in biomedical studies given that stratification is a common cause of false positives in case-control mtDNA association studies, and should be also considered when weighting the DNA evidence in forensic casework, which is strongly dependent on haplotype frequencies.
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Affiliation(s)
- Ruth Barral-Arca
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- GenPop Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Sara Pischedda
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- GenPop Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- GenPop Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
| | - Ana Pastoriza
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Ana Mosquera-Miguel
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Manuel López-Soto
- Servicio de Biología, Instituto Nacional de Toxicología y Ciencias Forenses, Departamento de Sevilla, Sevilla, Spain
| | - Federico Martinón-Torres
- Grupo de Investigación en Genética, Vacunas, Infecciones y Pediatría (GENVIP), Hospital Clínico Universitario and Universidade de Santiago de Compostela (USC), Galicia, Spain
- Pediatric Emergency and Critical Care Division, Department of Pediatrics, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Galicia, Spain
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- GenPop Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
- * E-mail:
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55
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Núñez C, Baeta M, Cardoso S, Palencia-Madrid L, García-Romero N, Llanos A, M. de Pancorbo M. Mitochondrial DNA Reveals the Trace of the Ancient Settlers of a Violently Devastated Late Bronze and Iron Ages Village. PLoS One 2016; 11:e0155342. [PMID: 27176817 PMCID: PMC4866787 DOI: 10.1371/journal.pone.0155342] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 04/27/2016] [Indexed: 11/19/2022] Open
Abstract
La Hoya (Alava, Basque Country) was one of the most important villages of the Late Bronze and Iron Ages of the north of the Iberian Peninsula, until it was violently devastated around the 4th century and abandoned in the 3rd century B.C. Archaeological evidences suggest that descendants from La Hoya placed their new settlement in a nearby hill, which gave rise to the current village of Laguardia. In this study, we have traced the genetic imprints of the extinct inhabitants of La Hoya through the analysis of maternal lineages. In particular, we have analyzed the mitochondrial DNA (mtDNA) control region of 41 human remains recovered from the archaeological site for comparison with a sample of 51 individuals from the geographically close present-day population of Laguardia, as well as 56 individuals of the general population of the province of Alava, where the archaeological site and Laguardia village are located. MtDNA haplotypes were successfully obtained in 25 out of 41 ancient samples, and 14 different haplotypes were identified. The major mtDNA subhaplogroups observed in La Hoya were H1, H3, J1 and U5, which show a distinctive frequency pattern in the autochthonous populations of the north of the Iberian Peninsula. Approximate Bayesian Computation analysis was performed to test the most likely model for the local demographic history. The results did not sustain a genealogical continuity between Laguardia and La Hoya at the haplotype level, although factors such as sampling effects, recent admixture events, and genetic bottlenecks need to be considered. Likewise, the highly similar subhaplogroup composition detected between La Hoya and Laguardia and Alava populations do not allow us to reject a maternal genetic continuity in the human groups of the area since at least the Iron Age to present times. Broader analyses, based on a larger collection of samples and genetic markers, would be required to study fine-scale population events in these human groups.
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Affiliation(s)
- Carolina Núñez
- BIOMICs Research Group, Centro de Investigación “Lascaray” Ikergunea, Universidad del País Vasco (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Centro de Investigación “Lascaray” Ikergunea, Universidad del País Vasco (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Sergio Cardoso
- BIOMICs Research Group, Centro de Investigación “Lascaray” Ikergunea, Universidad del País Vasco (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Leire Palencia-Madrid
- BIOMICs Research Group, Centro de Investigación “Lascaray” Ikergunea, Universidad del País Vasco (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Noemí García-Romero
- BIOMICs Research Group, Centro de Investigación “Lascaray” Ikergunea, Universidad del País Vasco (UPV/EHU), Vitoria-Gasteiz, Spain
| | | | - Marian M. de Pancorbo
- BIOMICs Research Group, Centro de Investigación “Lascaray” Ikergunea, Universidad del País Vasco (UPV/EHU), Vitoria-Gasteiz, Spain
- * E-mail:
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56
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Waldman YY, Biddanda A, Davidson NR, Billing-Ross P, Dubrovsky M, Campbell CL, Oddoux C, Friedman E, Atzmon G, Halperin E, Ostrer H, Keinan A. The Genetics of Bene Israel from India Reveals Both Substantial Jewish and Indian Ancestry. PLoS One 2016; 11:e0152056. [PMID: 27010569 PMCID: PMC4806850 DOI: 10.1371/journal.pone.0152056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 03/08/2016] [Indexed: 12/01/2022] Open
Abstract
The Bene Israel Jewish community from West India is a unique population whose history before the 18th century remains largely unknown. Bene Israel members consider themselves as descendants of Jews, yet the identity of Jewish ancestors and their arrival time to India are unknown, with speculations on arrival time varying between the 8th century BCE and the 6th century CE. Here, we characterize the genetic history of Bene Israel by collecting and genotyping 18 Bene Israel individuals. Combining with 486 individuals from 41 other Jewish, Indian and Pakistani populations, and additional individuals from worldwide populations, we conducted comprehensive genome-wide analyses based on FST, principal component analysis, ADMIXTURE, identity-by-descent sharing, admixture linkage disequilibrium decay, haplotype sharing and allele sharing autocorrelation decay, as well as contrasted patterns between the X chromosome and the autosomes. The genetics of Bene Israel individuals resemble local Indian populations, while at the same time constituting a clearly separated and unique population in India. They are unique among Indian and Pakistani populations we analyzed in sharing considerable genetic ancestry with other Jewish populations. Putting together the results from all analyses point to Bene Israel being an admixed population with both Jewish and Indian ancestry, with the genetic contribution of each of these ancestral populations being substantial. The admixture took place in the last millennium, about 19–33 generations ago. It involved Middle-Eastern Jews and was sex-biased, with more male Jewish and local female contribution. It was followed by a population bottleneck and high endogamy, which can lead to increased prevalence of recessive diseases in this population. This study provides an example of how genetic analysis advances our knowledge of human history in cases where other disciplines lack the relevant data to do so.
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Affiliation(s)
- Yedael Y. Waldman
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Arjun Biddanda
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
| | - Natalie R. Davidson
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
| | - Paul Billing-Ross
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
| | - Maya Dubrovsky
- Danek Gertner Institute of Human Genetics, Chaim Sheba Medical Center, Tel-Hashomer, Israel
- Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Christopher L. Campbell
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Carole Oddoux
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Eitan Friedman
- Danek Gertner Institute of Human Genetics, Chaim Sheba Medical Center, Tel-Hashomer, Israel
- Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
| | - Gil Atzmon
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, United States of America
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Eran Halperin
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
- The Blavatnik School of Computer Science, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
- International Computer Science Institute, Berkeley, California, United States of America
| | - Harry Ostrer
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States of America
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Alon Keinan
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
- * E-mail:
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57
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Different Evolutionary History for Basque Diaspora Populations in USA and Argentina Unveiled by Mitochondrial DNA Analysis. PLoS One 2015; 10:e0144919. [PMID: 26659590 PMCID: PMC4679185 DOI: 10.1371/journal.pone.0144919] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/25/2015] [Indexed: 11/23/2022] Open
Abstract
The Basque Diaspora in Western USA and Argentina represents two populations which have maintained strong Basque cultural and social roots in a completely different geographic context. Hence, they provide an exceptional opportunity to study the maternal genetic legacy from the ancestral Basque population and assess the degree of genetic introgression from the host populations in two of the largest Basque communities outside the Basque Country. For this purpose, we analyzed the complete mitochondrial DNA control region of Basque descendants living in Western USA (n = 175) and in Argentina (n = 194). The Diaspora populations studied here displayed a genetic diversity in their European maternal input which was similar to that of the Basque source populations, indicating that not important founder effects would have occurred. Actually, the genetic legacy of the Basque population still prevailed in their present-day maternal pools, by means of a haplogroup distribution similar to the source population characterized by the presence of autochthonous Basque lineages, such as U5b1f1a and J1c5c1. However, introgression of non-Basque lineages, mostly Native American, has been observed in the Diaspora populations, particularly in Argentina, where the quick assimilation of the newcomers would have favored a wider admixture with host populations. In contrast, a longer isolation of the Diaspora groups in USA, because of language and cultural differences, would have limited the introgression of local lineages. This study reveals important differences in the maternal evolutionary histories of these Basque Diaspora populations, which have to be taken into consideration in forensic and medical genetic studies.
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De Fanti S, Barbieri C, Sarno S, Sevini F, Vianello D, Tamm E, Metspalu E, van Oven M, Hübner A, Sazzini M, Franceschi C, Pettener D, Luiselli D. Fine Dissection of Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia. PLoS One 2015; 10:e0144391. [PMID: 26640946 PMCID: PMC4671665 DOI: 10.1371/journal.pone.0144391] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 11/17/2015] [Indexed: 02/08/2023] Open
Abstract
Genetic signatures from the Paleolithic inhabitants of Eurasia can be traced from the early divergent mitochondrial DNA lineages still present in contemporary human populations. Previous studies already suggested a pre-Neolithic diffusion of mitochondrial haplogroup HV*(xH,V) lineages, a relatively rare class of mtDNA types that includes parallel branches mainly distributed across Europe and West Asia with a certain degree of structure. Up till now, variation within haplogroup HV was addressed mainly by analyzing sequence data from the mtDNA control region, except for specific sub-branches, such as HV4 or the widely distributed haplogroups H and V. In this study, we present a revised HV topology based on full mtDNA genome data, and we include a comprehensive dataset consisting of 316 complete mtDNA sequences including 60 new samples from the Italian peninsula, a previously underrepresented geographic area. We highlight points of instability in the particular topology of this haplogroup, reconstructed with BEAST-generated trees and networks. We also confirm a major lineage expansion that probably followed the Late Glacial Maximum and preceded Neolithic population movements. We finally observe that Italy harbors a reservoir of mtDNA diversity, with deep-rooting HV lineages often related to sequences present in the Caucasus and the Middle East. The resulting hypothesis of a glacial refugium in Southern Italy has implications for the understanding of late Paleolithic population movements and is discussed within the archaeological cultural shifts occurred over the entire continent.
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Affiliation(s)
- Sara De Fanti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Chiara Barbieri
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- * E-mail: (CB); (DL)
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Federica Sevini
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- C.I.G. Interdepartmental Centre L. Galvani for Integrated Studies on Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy
| | - Dario Vianello
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- C.I.G. Interdepartmental Centre L. Galvani for Integrated Studies on Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy
| | - Erika Tamm
- Estonian Biocentre, Evolutionary Biology group, Tartu, Estonia
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Evolutionary Biology group, Tartu, Estonia
- Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Mannis van Oven
- Estonian Biocentre, Evolutionary Biology group, Tartu, Estonia
- Department of Forensic Molecular Biology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marco Sazzini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- C.I.G. Interdepartmental Centre L. Galvani for Integrated Studies on Bioinformatics, Biophysics and Biocomplexity, University of Bologna, Bologna, Italy
- IRCCS, Institute of Neurological Sciences of Bologna, Ospedale Bellaria, Bologna, Italy
- CNR, Institute of Organic Synthesis and Photoreactivity (ISOF), Bologna, Italy
| | - Davide Pettener
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- * E-mail: (CB); (DL)
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Grugni V, Battaglia V, Perego UA, Raveane A, Lancioni H, Olivieri A, Ferretti L, Woodward SR, Pascale JM, Cooke R, Myres N, Motta J, Torroni A, Achilli A, Semino O. Exploring the Y Chromosomal Ancestry of Modern Panamanians. PLoS One 2015; 10:e0144223. [PMID: 26636572 PMCID: PMC4670172 DOI: 10.1371/journal.pone.0144223] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 11/16/2015] [Indexed: 01/07/2023] Open
Abstract
Geologically, Panama belongs to the Central American land-bridge between North and South America crossed by Homo sapiens >14 ka ago. Archaeologically, it belongs to a wider Isthmo-Colombian Area. Today, seven indigenous ethnic groups account for 12.3% of Panama’s population. Five speak Chibchan languages and are characterized by low genetic diversity and a high level of differentiation. In addition, no evidence of differential structuring between maternally and paternally inherited genes has been reported in isthmian Chibchan cultural groups. Recent data have shown that 83% of the Panamanian general population harbour mitochondrial DNAs (mtDNAs) of Native American ancestry. Considering differential male/female mortality at European contact and multiple degrees of geographical and genetic isolation over the subsequent five centuries, the Y-chromosome Native American component is expected to vary across different geographic regions and communities in Panama. To address this issue, we investigated Y-chromosome variation in 408 modern males from the nine provinces of Panama and one indigenous territory (the comarca of Kuna Yala). In contrast to mtDNA data, the Y-chromosome Native American component (haplogroup Q) exceeds 50% only in three populations facing the Caribbean Sea: the comarca of Kuna Yala and Bocas del Toro province where Chibchan languages are spoken by the majority, and the province of Colón where many Kuna and people of mixed indigenous-African-and-European descent live. Elsewhere the Old World component is dominant and mostly represented by western Eurasian haplogroups, which signal the strong male genetic impact of invaders. Sub-Saharan African input accounts for 5.9% of male haplotypes. This reflects the consequences of the colonial Atlantic slave trade and more recent influxes of West Indians of African heritage. Overall, our findings reveal a local evolution of the male Native American ancestral gene pool, and a strong but geographically differentiated unidirectional sex bias in the formation of local modern Panamanian populations.
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Affiliation(s)
- Viola Grugni
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Vincenza Battaglia
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Ugo Alessandro Perego
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Alessandro Raveane
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Luca Ferretti
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Scott R. Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | | | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Natalie Myres
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- Ancestry, Provo, Utah, United States of America
| | - Jorge Motta
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | - Antonio Torroni
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- * E-mail:
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Chaitanya L, Ralf A, van Oven M, Kupiec T, Chang J, Lagacé R, Kayser M. Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine. Hum Mutat 2015; 36:1236-47. [PMID: 26387877 PMCID: PMC5057296 DOI: 10.1002/humu.22905] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/01/2015] [Indexed: 11/13/2022]
Abstract
Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long-range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications.
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Affiliation(s)
- Lakshmi Chaitanya
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Arwin Ralf
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Mannis van Oven
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
| | - Tomasz Kupiec
- Institute of Forensic ResearchSection of Forensic GeneticsKrakówPoland
| | - Joseph Chang
- Thermo Fisher ScientificSouth San FranciscoCalifornia, USA
| | - Robert Lagacé
- Thermo Fisher ScientificSouth San FranciscoCalifornia, USA
| | - Manfred Kayser
- Department of Genetic IdentificationErasmus MC University Medical CenterRotterdamThe Netherlands
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Carr SM, Duggan AT, Stenson GB, Marshall HD. Quantitative Phylogenomics of Within-Species Mitogenome Variation: Monte Carlo and Non-Parametric Analysis of Phylogeographic Structure among Discrete Transatlantic Breeding Areas of Harp Seals (Pagophilus groenlandicus). PLoS One 2015; 10:e0134207. [PMID: 26301872 PMCID: PMC4547794 DOI: 10.1371/journal.pone.0134207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 07/07/2015] [Indexed: 11/18/2022] Open
Abstract
Phylogenomic analysis of highly-resolved intraspecific phylogenies obtained from complete mitochondrial DNA genomes has had great success in clarifying relationships within and among human populations, but has found limited application in other wild species. Analytical challenges include assessment of random versus non-random phylogeographic distributions, and quantification of differences in tree topologies among populations. Harp Seals (Pagophilus groenlandicus Erxleben, 1777) have a biogeographic distribution based on four discrete trans-Atlantic breeding and whelping populations located on "fast ice" attached to land in the White Sea, Greenland Sea, the Labrador ice Front, and Southern Gulf of St Lawrence. This East to West distribution provides a set of a priori phylogeographic hypotheses. Outstanding biogeographic questions include the degree of genetic distinctiveness among these populations, in particular between the Greenland Sea and White Sea grounds. We obtained complete coding-region DNA sequences (15,825 bp) for 53 seals. Each seal has a unique mtDNA genome sequence, which differ by 6 ~ 107 substitutions. Six major clades / groups are detectable by parsimony, neighbor-joining, and Bayesian methods, all of which are found in breeding populations on either side of the Atlantic. The species coalescent is at 180 KYA; the most recent clade, which accounts for 66% of the diversity, reflects an expansion during the mid-Wisconsinan glaciation 40~60 KYA. FST is significant only between the White Sea and Greenland Sea or Ice Front populations. Hierarchal AMOVA of 2-, 3-, or 4-island models identifies small but significant ΦSC among populations within groups, but not among groups. A novel Monte-Carlo simulation indicates that the observed distribution of individuals within breeding populations over the phylogenetic tree requires significantly fewer dispersal events than random expectation, consistent with island or a priori East to West 2- or 3-stepping-stone biogeographic models, but not a simple 1-step trans-Atlantic model. Plots of the cumulative pairwise sequence difference curves among seals in each of the four populations provide continuous proxies for phylogenetic diversification within each. Non-parametric Kolmogorov-Smirnov (K-S) tests of maximum pairwise differences between these curves indicates that the Greenland Sea population has a markedly younger phylogenetic structure than either the White Sea population or the two Northwest Atlantic populations, which are of intermediate age and homogeneous structure. The Monte Carlo and K-S assessments provide sensitive quantitative tests of within-species mitogenomic phylogeography. This is the first study to indicate that the White Sea and Greenland Sea populations have different population genetic histories. The analysis supports the hypothesis that Harp Seals comprises three genetically distinguishable breeding populations, in the White Sea, Greenland Sea, and Northwest Atlantic. Implications for an ice-dependent species during ongoing climate change are discussed.
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Affiliation(s)
- Steven M. Carr
- Genetics, Evolution, and Molecular Systematics Laboratory, Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
- * E-mail:
| | - Ana T. Duggan
- Genetics, Evolution, and Molecular Systematics Laboratory, Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Garry B. Stenson
- Wildlife Genetics and Genomics Laboratory, Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - H. Dawn Marshall
- Marine Mammals Section, Science Branch, Dept. of Fisheries and Oceans, PO Box 5667, St. John's, Nfld., A1C 5X1, Canada
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Whole mitochondrial genome genetic diversity in an Estonian population sample. Int J Legal Med 2015; 130:67-71. [PMID: 26289416 DOI: 10.1007/s00414-015-1249-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/12/2015] [Indexed: 10/23/2022]
Abstract
Mitochondrial DNA is a useful marker for population studies, human identification, and forensic analysis. Commonly used hypervariable regions I and II (HVI/HVII) were reported to contain as little as 25% of mitochondrial DNA variants and therefore the majority of power of discrimination of mitochondrial DNA resides in the coding region. Massively parallel sequencing technology enables entire mitochondrial genome sequencing. In this study, buccal swabs were collected from 114 unrelated Estonians and whole mitochondrial genome sequences were generated using the Illumina MiSeq system. The results are concordant with previous mtDNA control region reports of high haplogroup HV and U frequencies (47.4 and 23.7% in this study, respectively) in the Estonian population. One sample with the Northern Asian haplogroup D was detected. The genetic diversity of the Estonian population sample was estimated to be 99.67 and 95.85%, for mtGenome and HVI/HVII data, respectively. The random match probability for mtGenome data was 1.20 versus 4.99% for HVI/HVII. The nucleotide mean pairwise difference was 27 ± 11 for mtGenome and 7 ± 3 for HVI/HVII data. These data describe the genetic diversity of the Estonian population sample and emphasize the power of discrimination of the entire mitochondrial genome over the hypervariable regions.
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Zhen X, Wu B, Wang J, Lu C, Gao H, Qiao J. Increased Incidence of Mitochondrial Cytochrome C Oxidase 1 Gene Mutations in Patients with Primary Ovarian Insufficiency. PLoS One 2015. [PMID: 26225554 PMCID: PMC4520565 DOI: 10.1371/journal.pone.0132610] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Primary ovarian insufficiency (POI), also known as premature ovarian failure (POF), is defined as more than six months of cessation of menses before the age of 40 years, with two serum follicle stimulating hormone (FSH) levels (at least 1 month apart) falling in the menopause range. The cause of POI remains undetermined in the majority of cases, although some studies have reported increased levels of reactive oxygen species (ROS) in idiopathic POF. The role of mitochondrial DNA in the pathogenesis of POI has not been studied extensively. This aim of this study was to uncover underlying mitochondrial genetic defects in patients with POI. The entire region of the mitochondrial genome was amplified in subjects with idiopathic POI (n=63) and age-matched healthy female controls (n=63) using nine pair sets of primers, followed by screening of the mitochondrial genome using an Illumina MiSeq. We identified a total of 96 non-synonymous mitochondrial variations in POI patients and 93 non-synonymous variations in control subjects. Of these, 21 (9 in POI and 12 in control) non-synonymous variations had not been reported previously. Eight mitochondrial cytochrome coxidase 1 (MT-CO1) missense variants were identified in POI patients, whereas only four missense mutations were observed in controls. A high incidence of MT-CO1 missense variants were identified in POI patients compared with controls, and the difference between the groups was statistically significant (13/63 vs. 5/63, p=0.042). Our results show that patients with primary ovarian insufficiency exhibit an increased incidence of mitochondrial cytochrome c oxidase 1 gene mutations, suggesting that MT-CO1 gene mutation may be causal in POI.
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Affiliation(s)
- Xiumei Zhen
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- Genetic Diagnosis Lab Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Bailin Wu
- Genetic Diagnosis Lab Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Jian Wang
- Genetic Diagnosis Lab Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, 02115, United States of America
- Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Cuiling Lu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
| | - Huafang Gao
- Genetic Diagnosis Lab Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, 02115, United States of America
- Human Genetic Resource Center, National Research Institute for Health and Family Planning, Beijing, 100081, China
- * E-mail: (HG); (JQ)
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- * E-mail: (HG); (JQ)
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Li W, Wen C, Li W, Wang H, Guan X, Zhang W, Ye W, Lu J. The tRNA(Gly) T10003C mutation in mitochondrial haplogroup M11b in a Chinese family with diabetes decreases the steady-state level of tRNA(Gly), increases aberrant reactive oxygen species production, and reduces mitochondrial membrane potential. Mol Cell Biochem 2015; 408:171-9. [PMID: 26134044 DOI: 10.1007/s11010-015-2493-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 06/18/2015] [Indexed: 11/28/2022]
Abstract
Mitochondrial diabetes originates mainly from mutations located in maternally transmitted, mitochondrial tRNA-coding genes. In a genetic screening program of type 2 diabetes conducted with a Chinese Han population, we found one family with suggestive maternally transmitted diabetes. The proband's mitochondrial genome was analyzed using DNA sequencing. Total 42 known nucleoside changes and 1 novel variant were identified, and the entire mitochondrial DNA sequence was assigned to haplogroup M11b. Phylogenetic analysis showed that a homoplasmic mutation, 10003T>C transition, occurred at the highly conserved site in the gene encoding tRNA(Gly). Using a transmitochondrial cybrid cell line harboring this mutation, we observed that the steady-state level of tRNA(Gly) significantly affected and the amount of tRNA(Gly) decreased by 97%, production of reactive oxygen species was enhanced, and mitochondrial membrane potential, mtDNA copy number and cellular oxygen consumption rate were remarkably decreased compared with wild-type cybrid cells. The homoplasmic 10003T>C mutation in the mitochondrial tRNA(Gly) gene suggested to be as a pathogenesis-related mutation which might contribute to the maternal inherited diabetes in the Han Chinese family.
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Affiliation(s)
- Wei Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, 325035, Zhejiang, People's Republic of China.,Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou, 325035, Zhejiang, People's Republic of China.,Wenzhou Medical University School of Laboratory Medicine and Life Sciences, Higher Education Park, Chashan Town, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Chaowei Wen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Weixing Li
- Department of Laboratory Medicine, Zhejiang Provincial People's Hospital, Hangzhou, 310014, Zhejiang, People's Republic of China
| | - Hailing Wang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Xiaomin Guan
- Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Wanlin Zhang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Wei Ye
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Jianxin Lu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, 325035, Zhejiang, People's Republic of China. .,Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou, 325035, Zhejiang, People's Republic of China. .,Wenzhou Medical University School of Laboratory Medicine and Life Sciences, Higher Education Park, Chashan Town, Wenzhou, 325035, Zhejiang, People's Republic of China.
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65
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Vestiges of an Ancient Border in the Contemporary Genetic Diversity of North-Eastern Europe. PLoS One 2015; 10:e0130331. [PMID: 26132657 PMCID: PMC4488853 DOI: 10.1371/journal.pone.0130331] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 05/19/2015] [Indexed: 11/25/2022] Open
Abstract
It has previously been demonstrated that the advance of the Neolithic Revolution from the Near East through Europe was decelerated in the northernmost confines of the continent, possibly as a result of space and resource competition with lingering Mesolithic populations. Finland was among the last domains to adopt a farming lifestyle, and is characterized by substructuring in the form of a distinct genetic border dividing the northeastern and southwestern regions of the country. To explore the origins of this divergence, the geographical patterns of mitochondrial and Y-chromosomal haplogroups of Neolithic and Mesolithic ancestry were assessed in Finnish populations. The distribution of these uniparental markers revealed a northeastern bias for hunter-gatherer haplogroups, while haplogroups associated with the farming lifestyle clustered in the southwest. In addition, a correlation could be observed between more ancient mitochondrial haplogroup age and eastern concentration. These results coupled with prior archeological evidence suggest the genetic northeast/southwest division observed in contemporary Finland represents an ancient vestigial border between Mesolithic and Neolithic populations undetectable in most other regions of Europe.
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66
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Zupan A, Hauptman N, Glavač D. The maternal perspective for five Slovenian regions: The importance of regional sampling. Ann Hum Biol 2015; 43:57-66. [PMID: 26065896 DOI: 10.3109/03014460.2015.1006678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND The Slovenian territory is geographically positioned between the Alps, Adriatic Sea, Pannonian basin and the Dinaric Mountains and, as such, has served as a passageway for various populations in different periods of time. Turbulent historic events and diverse geography of the region have produced a diverse contemporary population whose genetic analysis could provide insight into past demographic events. AIM The aims of this study were to characterize the Slovenian mitochondrial gene pool at the micro-geographic level and to compare it with surrounding populations. SUBJECTS AND METHODS A total of 402 individuals from five Slovenian regions were analysed in this study by typing HVR I, HVR II and coding region polymorphisms of mtDNA. RESULTS Analysis revealed 47 haplogroups and sub-haplogroups, the most common of which were H*, H1, J1c, T2 and U5a. Intra-population comparisons revealed a sharp gradient of the J1c haplogroup between Slovenian regions, with a peak frequency of 24.5% being observed in the population of the Littoral Region. CONCLUSION The sharp gradient of the J1c haplogroup between Slovenian regions is in line with the archaeological horizon known as Impressed Ware culture and could, therefore, represent a genetic trace of the early Neolithic expansion route along the East Adriatic coastal region.
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Affiliation(s)
- Andrej Zupan
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
| | - Nina Hauptman
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
| | - Damjan Glavač
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
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Palanichamy MG, Mitra B, Zhang CL, Debnath M, Li GM, Wang HW, Agrawal S, Chaudhuri TK, Zhang YP. West Eurasian mtDNA lineages in India: an insight into the spread of the Dravidian language and the origins of the caste system. Hum Genet 2015; 134:637-47. [PMID: 25832481 DOI: 10.1007/s00439-015-1547-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/25/2015] [Indexed: 11/28/2022]
Abstract
There is no indication from the previous mtDNA studies that west Eurasian-specific subclades have evolved within India and played a role in the spread of languages and the origins of the caste system. To address these issues, we have screened 14,198 individuals (4208 from this study) and analyzed 112 mitogenomes (41 new sequences) to trace west Eurasian maternal ancestry. This has led to the identification of two autochthonous subhaplogroups--HV14a1 and U1a1a4, which are likely to have originated in the Dravidian-speaking populations approximately 10.5-17.9 thousand years ago (kya). The carriers of these maternal lineages might have settled in South India during the time of the spread of the Dravidian language. In addition to this, we have identified several subsets of autochthonous U7 lineages, including U7a1, U7a2b, U7a3, U7a6, U7a7, and U7c, which seem to have originated particularly in the higher-ranked caste populations in relatively recent times (2.6-8.0 kya with an average of 5.7 kya). These lineages have provided crucial clues to the differentiation of the caste system that has occurred during the recent past and possibly, this might have been influenced by the Indo-Aryan migration. The remaining west Eurasian lineages observed in the higher-ranked caste groups, like the Brahmins, were found to cluster with populations who possibly arrived from west Asia during more recent times.
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Affiliation(s)
- Malliya Gounder Palanichamy
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, 650 091, Yunnan, China,
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68
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Rothe J, Melisch C, Powers N, Geppert M, Zander J, Purps J, Spors B, Nagy M. Genetic research at a fivefold children's burial from medieval Berlin. Forensic Sci Int Genet 2015; 15:90-7. [DOI: 10.1016/j.fsigen.2014.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/20/2014] [Accepted: 10/24/2014] [Indexed: 10/24/2022]
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69
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Bonilla C, Bertoni B, Hidalgo PC, Artagaveytia N, Ackermann E, Barreto I, Cancela P, Cappetta M, Egaña A, Figueiro G, Heinzen S, Hooker S, Román E, Sans M, Kittles RA. Breast cancer risk and genetic ancestry: a case-control study in Uruguay. BMC WOMENS HEALTH 2015; 15:11. [PMID: 25783644 PMCID: PMC4341228 DOI: 10.1186/s12905-015-0171-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 01/27/2015] [Indexed: 01/26/2023]
Abstract
Background Uruguay exhibits one of the highest rates of breast cancer in Latin America, similar to those of developed nations, the reasons for which are not completely understood. In this study we investigated the effect that ancestral background has on breast cancer susceptibility among Uruguayan women. Methods We carried out a case–control study of 328 (164 cases, 164 controls) women enrolled in public hospitals and private clinics across the country. We estimated ancestral proportions using a panel of nuclear and mitochondrial ancestry informative markers (AIMs) and tested their association with breast cancer risk. Results Nuclear individual ancestry in cases was (mean ± SD) 9.8 ± 7.6% African, 13.2 ± 10.2% Native American and 77.1 ± 13.1% European, and in controls 9.1 ± 7.5% African, 14.7 ± 11.2% Native American and 76.2 ± 14.2% European. There was no evidence of a difference in nuclear or mitochondrial ancestry between cases and controls. However, European mitochondrial haplogroup H was associated with breast cancer (OR = 2.0; 95% CI 1.1, 3.5). Conclusions We have not found evidence that overall genetic ancestry differs between breast cancer patients and controls in Uruguay but we detected an association of the disease with a European mitochondrial lineage, which warrants further investigation. Electronic supplementary material The online version of this article (doi:10.1186/s12905-015-0171-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carolina Bonilla
- School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK,
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Sans M, Mones P, Figueiro G, Barreto I, Motti JM, Coble MD, Bravi CM, Hidalgo PC. The mitochondrial DNA history of a former native American village in northern Uruguay. Am J Hum Biol 2014; 27:407-16. [DOI: 10.1002/ajhb.22667] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 10/24/2014] [Accepted: 11/11/2014] [Indexed: 12/20/2022] Open
Affiliation(s)
- Mónica Sans
- Departamento de Antropología Biológica; Facultad de Humanidades y Ciencias de la Educación, Universidad de la República; Montevideo Uruguay
| | - Pablo Mones
- Departamento de Antropología Biológica; Facultad de Humanidades y Ciencias de la Educación, Universidad de la República; Montevideo Uruguay
| | - Gonzalo Figueiro
- Departamento de Antropología Biológica; Facultad de Humanidades y Ciencias de la Educación, Universidad de la República; Montevideo Uruguay
| | - Isabel Barreto
- Departamento de Antropología Biológica; Facultad de Humanidades y Ciencias de la Educación, Universidad de la República; Montevideo Uruguay
| | - Josefina M.B. Motti
- Laboratorio de Ecología Evolutiva Humana; Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires; Quequén Argentina
- Facultad de Ciencias Naturales y Museo; Universidad Nacional de La Plata; La Plata Argentina
| | - Michael D. Coble
- National Institute of Standards and Technology; Gaithersburg Maryland
| | - Claudio M. Bravi
- Facultad de Ciencias Naturales y Museo; Universidad Nacional de La Plata; La Plata Argentina
- Instituto Multidisciplinario de Biología Celular (IMBICE); CCT La Plata CONICET-CICPBA; La Plata Argentina
| | - Pedro C. Hidalgo
- Departamento de Antropología Biológica; Facultad de Humanidades y Ciencias de la Educación, Universidad de la República; Montevideo Uruguay
- Centro Universitario de Tacuarembó; Universidad de la República; Tacuarembó Uruguay
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Brandt G, Szécsényi-Nagy A, Roth C, Alt KW, Haak W. Human paleogenetics of Europe--the known knowns and the known unknowns. J Hum Evol 2014; 79:73-92. [PMID: 25467114 DOI: 10.1016/j.jhevol.2014.06.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/25/2014] [Accepted: 06/19/2014] [Indexed: 12/01/2022]
Abstract
The number of ancient human DNA studies has drastically increased in recent years. This results in a substantial record of mitochondrial sequences available from many prehistoric sites across Western Eurasia, but also growing Y-chromosome and autosomal sequence data. We review the current state of research with specific emphasis on the Holocene population events that likely have shaped the present-day genetic variation in Europe. We reconcile observations from the genetic data with hypotheses about the peopling and settlement history from anthropology and archaeology for various key regions, and also discuss the data in light of evidence from related disciplines, such as modern human genetics, climatology and linguistics.
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Affiliation(s)
- Guido Brandt
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany
| | - Anna Szécsényi-Nagy
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany; Archaeological Institute, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1014 Budapest, Hungary
| | - Christina Roth
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany
| | - Kurt Werner Alt
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Heritage Museum, Richard-Wagner-Straße 9, D-06114 Halle, Germany; Institute for Prehistory and Archaeological Science, Basel University, Petersplatz 1, 4003 Basel, Switzerland; Danube Private University, Faculty of Medicine and Dentistry, Doktor-Karl-Dorrek-Straße 23, 3500 Krems an der Donau, Austria
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, The University of Adelaide, North Terrace Campus, SA-5005 Adelaide, Australia.
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Alt KW, Knipper C, Peters D, Müller W, Maurer AF, Kollig I, Nicklisch N, Müller C, Karimnia S, Brandt G, Roth C, Rosner M, Mende B, Schöne BR, Vida T, von Freeden U. Lombards on the move--an integrative study of the migration period cemetery at Szólád, Hungary. PLoS One 2014; 9:e110793. [PMID: 25369022 PMCID: PMC4219681 DOI: 10.1371/journal.pone.0110793] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 09/11/2014] [Indexed: 12/01/2022] Open
Abstract
In 2005 to 2007 45 skeletons of adults and subadults were excavated at the Lombard period cemetery at Szólád (6th century A.D.), Hungary. Embedded into the well-recorded historical context, the article presents the results obtained by an integrative investigation including anthropological, molecular genetic and isotopic (δ(15)N, δ(13)C, (87)Sr/(86)Sr) analyses. Skeletal stress markers as well as traces of interpersonal violence were found to occur frequently. The mitochondrial DNA profiles revealed a heterogeneous spectrum of lineages that belong to the haplogroups H, U, J, HV, T2, I, and K, which are common in present-day Europe and in the Near East, while N1a and N1b are today quite rare. Evidence of possible direct maternal kinship was identified in only three pairs of individuals. According to enamel strontium isotope ratios, at least 31% of the individuals died at a location other than their birthplace and/or had moved during childhood. Based on the peculiar 87 Sr/86 Sr ratio distribution between females, males, and subadults in comparison to local vegetation and soil samples, we propose a three-phase model of group movement. An initial patrilocal group with narrower male but wider female Sr isotope distribution settled at Szólád, whilst the majority of subadults represented in the cemetery yielded a distinct Sr isotope signature. Owing to the virtual absence of Szólád-born adults in the cemetery, we may conclude that the settlement was abandoned after approx. one generation. Population heterogeneity is furthermore supported by the carbon and nitrogen isotope data. They indicate that a group of high-ranking men had access to larger shares of animal-derived food whilst a few individuals consumed remarkable amounts of millet. The inferred dynamics of the burial community are in agreement with hypotheses of a highly mobile lifestyle during the Migration Period and a short-term occupation of Pannonia by Lombard settlers as conveyed by written sources.
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Affiliation(s)
- Kurt W. Alt
- Center for Natural and Cultural History of the Teeth, Danube Private University, Krems, Austria
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
- Institute for Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | - Corina Knipper
- Curt Engelhorn Centre Archaeometry gGmbH, Mannheim, Germany
| | - Daniel Peters
- Institut für Prähistorische Archäologie, Freie Universität Berlin, Berlin, Germany
| | - Wolfgang Müller
- Department of Earth Sciences, Royal Holloway University of London, London, United Kingdom
| | | | - Isabelle Kollig
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
| | - Nicole Nicklisch
- Center for Natural and Cultural History of the Teeth, Danube Private University, Krems, Austria
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
- Institute for Prehistory and Archaeological Science, Basel University, Basel, Switzerland
| | | | - Sarah Karimnia
- Institute of Anthropology, University of Mainz, Mainz, Germany
| | - Guido Brandt
- Institute of Anthropology, University of Mainz, Mainz, Germany
| | - Christina Roth
- Institute of Anthropology, University of Mainz, Mainz, Germany
| | | | - Balász Mende
- Archaeological Institute, Research Centre for Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Bernd R. Schöne
- Institute of Geosciences, University of Mainz, Mainz, Germany
| | - Tivadar Vida
- Department of Prehistory and Protohistory, Eötvös Loránd University of Budapest, Budapest, Hungary
| | - Uta von Freeden
- German Archaeological Institute, Roman Germanic Commission, Frankfurt a. M., Germany
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73
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Marques SL, Goios A, Rocha AM, Prata MJ, Amorim A, Gusmão L, Alves C, Alvarez L. Portuguese mitochondrial DNA genetic diversity-An update and a phylogenetic revision. Forensic Sci Int Genet 2014; 15:27-32. [PMID: 25457629 DOI: 10.1016/j.fsigen.2014.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/22/2014] [Accepted: 10/03/2014] [Indexed: 10/24/2022]
Abstract
In recent years a large amount of mitochondrial population data for forensic purposes has been produced. Current efforts are focused at increasing the number of studied populations while generating updated genetic information of forensic quality. However, complete mitochondrial control region sequences are still scarce for most populations and even more so for complete mitochondrial genomes. In the case of Portugal, previous population genetics studies have already revealed the general portrait of HVS-I and HVS-II mitochondrial diversity, becoming now important to update and expand the mitochondrial region analysed. Accordingly, a total of 292 complete control region sequences from continental Portugal were obtained, under a stringent experimental design to ensure the quality of data through double sequencing of each target region. Furthermore, H-specific coding region SNPs were examined to detail haplogroup classification and complete mitogenomes were obtained for all sequences belonging to haplogroups U4 and U5. In general, a typical Western European haplogroup composition was found in mainland Portugal, associated to high level of mitochondrial genetic diversity. Within the country, no signs of substructure were detected. The typing of extra coding region SNPs has provided the refinement or confirmation of the previous classification obtained with EMMA tool in 96% of the cases. Finally, it was also possible to enlarge haplogroup U phylogeny with 28 new U4 and U5 mitogenomes.
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Affiliation(s)
- Sofia L Marques
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Ana Goios
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Ana M Rocha
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Maria João Prata
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Department of Biology, Faculty of Sciences of the University of Porto, Porto, Portugal
| | - António Amorim
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Department of Biology, Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Leonor Gusmão
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Cíntia Alves
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Luis Alvarez
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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74
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Bodner M, Iuvaro A, Strobl C, Nagl S, Huber G, Pelotti S, Pettener D, Luiselli D, Parson W. Helena, the hidden beauty: Resolving the most common West Eurasian mtDNA control region haplotype by massively parallel sequencing an Italian population sample. Forensic Sci Int Genet 2014; 15:21-6. [PMID: 25303789 DOI: 10.1016/j.fsigen.2014.09.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/16/2014] [Indexed: 01/24/2023]
Abstract
The analysis of mitochondrial (mt)DNA is a powerful tool in forensic genetics when nuclear markers fail to give results or maternal relatedness is investigated. The mtDNA control region (CR) contains highly condensed variation and is therefore routinely typed. Some samples exhibit an identical haplotype in this restricted range. Thus, they convey only weak evidence in forensic queries and limited phylogenetic information. However, a CR match does not imply that also the mtDNA coding regions are identical or samples belong to the same phylogenetic lineage. This is especially the case for the most frequent West Eurasian CR haplotype 263G 315.1C 16519C, which is observed in various clades within haplogroup H and occurs at a frequency of 3-4% in many European populations. In this study, we investigated the power of massively parallel complete mtGenome sequencing in 29 Italian samples displaying the most common West Eurasian CR haplotype - and found an unexpected high diversity. Twenty-eight different haplotypes falling into 19 described sub-clades of haplogroup H were revealed in the samples with identical CR sequences. This study demonstrates the benefit of complete mtGenome sequencing for forensic applications to enforce maximum discrimination, more comprehensive heteroplasmy detection, as well as highest phylogenetic resolution.
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Affiliation(s)
- Martin Bodner
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Alessandra Iuvaro
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Department of Medical and Surgical Sciences, Institute of Legal Medicine, University of Bologna, Bologna, Italy
| | - Christina Strobl
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Simone Nagl
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Susi Pelotti
- Department of Medical and Surgical Sciences, Institute of Legal Medicine, University of Bologna, Bologna, Italy
| | - Davide Pettener
- Department of Biological, Geological and Environmental Science, Laboratory of Molecular Anthropology, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- Department of Biological, Geological and Environmental Science, Laboratory of Molecular Anthropology, University of Bologna, Bologna, Italy.
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, USA.
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75
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Veeramah KR, Novembre J. Demographic events and evolutionary forces shaping European genetic diversity. Cold Spring Harb Perspect Biol 2014; 6:a008516. [PMID: 25059709 PMCID: PMC4142961 DOI: 10.1101/cshperspect.a008516] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Europeans have been the focus of some of the largest studies of genetic diversity in any species to date. Recent genome-wide data have reinforced the hypothesis that present-day European genetic diversity is strongly correlated with geography. The remaining challenge now is to understand more precisely how patterns of diversity in Europe reflect ancient demographic events such as postglacial expansions or the spread of farming. It is likely that recent advances in paleogenetics will give us some of these answers. There has also been progress in identifying specific segments of European genomes that reflect adaptations to selective pressures from the physical environment, disease, and dietary shifts. A growing understanding of how modern European genetic diversity has been shaped by demographic and evolutionary forces is not only of basic historical and anthropological interest but also aids genetic studies of disease.
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Affiliation(s)
- Krishna R Veeramah
- Arizona Research Laboratories Division of Biotechnology, University of Arizona, Tucson, Arizona 85721
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637
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76
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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. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 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] [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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77
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Craniometric analysis of European Upper Palaeolithic and Mesolithic samples supports discontinuity at the Last Glacial Maximum. Nat Commun 2014; 5:4094. [PMID: 24912847 PMCID: PMC5010115 DOI: 10.1038/ncomms5094] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/12/2014] [Indexed: 11/08/2022] Open
Abstract
The Last Glacial Maximum (LGM) represents the most significant climatic event since the emergence of anatomically modern humans (AMH). In Europe, the LGM may have played a role in changing morphological features as a result of adaptive and stochastic processes. We use craniometric data to examine morphological diversity in pre- and post-LGM specimens. Craniometric variation is assessed across four periods--pre-LGM, late glacial, Early Holocene and Middle Holocene--using a large, well-dated, data set. Our results show significant differences across the four periods, using a MANOVA on size-adjusted cranial measurements. A discriminant function analysis shows separation between pre-LGM and later groups. Analyses repeated on a subsample, controlled for time and location, yield similar results. The results are largely influenced by facial measurements and are most consistent with neutral demographic processes. These findings suggest that the LGM had a major impact on AMH populations in Europe prior to the Neolithic.
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78
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An ancient Mediterranean melting pot: investigating the uniparental genetic structure and population history of sicily and southern Italy. PLoS One 2014; 9:e96074. [PMID: 24788788 PMCID: PMC4005757 DOI: 10.1371/journal.pone.0096074] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/03/2014] [Indexed: 11/19/2022] Open
Abstract
Due to their strategic geographic location between three different continents, Sicily and Southern Italy have long represented a major Mediterranean crossroad where different peoples and cultures came together over time. However, its multi-layered history of migration pathways and cultural exchanges, has made the reconstruction of its genetic history and population structure extremely controversial and widely debated. To address this debate, we surveyed the genetic variability of 326 accurately selected individuals from 8 different provinces of Sicily and Southern Italy, through a comprehensive evaluation of both Y-chromosome and mtDNA genomes. The main goal was to investigate the structuring of maternal and paternal genetic pools within Sicily and Southern Italy, and to examine their degrees of interaction with other Mediterranean populations. Our findings show high levels of within-population variability, coupled with the lack of significant genetic sub-structures both within Sicily, as well as between Sicily and Southern Italy. When Sicilian and Southern Italian populations were contextualized within the Euro-Mediterranean genetic space, we observed different historical dynamics for maternal and paternal inheritances. Y-chromosome results highlight a significant genetic differentiation between the North-Western and South-Eastern part of the Mediterranean, the Italian Peninsula occupying an intermediate position therein. In particular, Sicily and Southern Italy reveal a shared paternal genetic background with the Balkan Peninsula and the time estimates of main Y-chromosome lineages signal paternal genetic traces of Neolithic and post-Neolithic migration events. On the contrary, despite showing some correspondence with its paternal counterpart, mtDNA reveals a substantially homogeneous genetic landscape, which may reflect older population events or different demographic dynamics between males and females. Overall, both uniparental genetic structures and TMRCA estimates confirm the role of Sicily and Southern Italy as an ancient Mediterranean melting pot for genes and cultures.
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79
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Subathra M, Selvakumari M, Ramesh A, Ramakrishnan R, Karan KR, Kaur M, Manikandan M, Srikumari Srisailapathy CR. Complete mitochondrial genome analysis and clinical documentation of a five-generational Indian family with mitochondrial 1555A>G mutation and postlingual hearing loss. Ann Hum Genet 2014; 78:217-34. [PMID: 24660976 DOI: 10.1111/ahg.12061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 02/11/2014] [Indexed: 11/26/2022]
Abstract
Hearing loss is the most common sensory disorder and is genetically heterogeneous. Apart from nuclear gene mutations, a number of inherited mitochondrial mutations have also been implicated. The m.1555A>G mutation in the mitochondrial MT-RNR1 gene is reported as the most common mutation causing nonsyndromic hearing loss in various ethnic populations. We report here for the first time the clinical, genetic and molecular characterisation of a single large five-generational Tamil-speaking South Indian family with maternally inherited nonsyndromic postlingual hearing loss. Molecular analysis led to identification of m.1555A>G in 28 maternal relatives with variable degree of phenotypic expression. The penetrance of hearing loss among the maternal relatives in this family was 55%. Sequence analysis of the complete mitochondrial genome in 36 members of this pedigree identified 25 known variants and one novel variant co-transmitted along with m.1555A>G mutation. The mtDNA haplotype analysis revealed that the maternal relatives carry the R*T2 haplotype similar to Europeans and South Asians. Sequencing of the coding exon of GJB2 nuclear gene did not show any pathogenic mutations. The results suggest that other nuclear or environmental modifying factors could have played a role in the differential expression of mutation m.1555A>G in postlingual hearing loss in this family.
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Affiliation(s)
- Mahalingam Subathra
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, India
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80
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Sarac J, Sarić T, Auguštin DH, Jeran N, Kovačević L, Cvjetan S, Lewis AP, Metspalu E, Reidla M, Novokmet N, Vidovič M, Nevajda B, Glasnović A, Marjanović D, Missoni S, Villems R, Rudan P. Maternal genetic heritage of Southeastern Europe reveals a new Croatian isolate and a novel, local sub-branching in the x2 haplogroup. Ann Hum Genet 2014; 78:178-94. [PMID: 24621318 DOI: 10.1111/ahg.12056] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/30/2013] [Indexed: 11/29/2022]
Abstract
High mtDNA variation in Southeastern Europe (SEE) is a reflection of the turbulent and complex demographic history of this area, influenced by gene flow from various parts of Eurasia and a long history of intermixing. Our results of 1035 samples (488 from Croatia, 239 from Bosnia and 130 from Herzegovina, reported earlier, and 97 Slovenians and 81 individuals from Žumberak, reported here for the first time) show that the SEE maternal genetic diversity fits within a broader European maternal genetic landscape. The study also shows that the population of Žumberak, located in the continental part of Croatia, developed some unique mtDNA haplotypes and elevated haplogroup frequencies due to distinctive demographic history and can be considered a moderate genetic isolate. We also report seven samples from the Bosnian population and one Herzegovinian sample designated as X2* individuals that could not be assigned to any of its sublineages (X2a'o) according to the existing X2 phylogeny. In an attempt to clarify the phylogeny of our X2 samples, their mitochondrial DNA has been completely sequenced. We suppose that these lineages are signs of local microdifferentiation processes that occurred in the recent demographic past in this area and could possibly be marked as SEE-specific X2 sublineages.
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Affiliation(s)
- Jelena Sarac
- Institute for Anthropological Research, 10000 Zagreb, Croatia
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81
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Der Sarkissian C, Brotherton P, Balanovsky O, Templeton JEL, Llamas B, Soubrier J, Moiseyev V, Khartanovich V, Cooper A, Haak W. Mitochondrial genome sequencing in Mesolithic North East Europe Unearths a new sub-clade within the broadly distributed human haplogroup C1. PLoS One 2014; 9:e87612. [PMID: 24503968 PMCID: PMC3913659 DOI: 10.1371/journal.pone.0087612] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 12/23/2013] [Indexed: 11/19/2022] Open
Abstract
The human mitochondrial haplogroup C1 has a broad global distribution but is extremely rare in Europe today. Recent ancient DNA evidence has demonstrated its presence in European Mesolithic individuals. Three individuals from the 7,500 year old Mesolithic site of Yuzhnyy Oleni Ostrov, Western Russia, could be assigned to haplogroup C1 based on mitochondrial hypervariable region I sequences. However, hypervariable region I data alone could not provide enough resolution to establish the phylogenetic relationship of these Mesolithic haplotypes with haplogroup C1 mitochondrial DNA sequences found today in populations of Europe, Asia and the Americas. In order to obtain high-resolution data and shed light on the origin of this European Mesolithic C1 haplotype, we target-enriched and sequenced the complete mitochondrial genome of one Yuzhnyy Oleni Ostrov C1 individual. The updated phylogeny of C1 haplogroups indicated that the Yuzhnyy Oleni Ostrov haplotype represents a new distinct clade, provisionally coined “C1f”. We show that all three C1 carriers of Yuzhnyy Oleni Ostrov belong to this clade. No haplotype closely related to the C1f sequence could be found in the large current database of ancient and present-day mitochondrial genomes. Hence, we have discovered past human mitochondrial diversity that has not been observed in modern-day populations so far. The lack of positive matches in modern populations may be explained by under-sampling of rare modern C1 carriers or by demographic processes, population extinction or replacement, that may have impacted on populations of Northeast Europe since prehistoric times.
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Affiliation(s)
- Clio Der Sarkissian
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
- * E-mail: (CDS); (WH)
| | - Paul Brotherton
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Oleg Balanovsky
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Jennifer E. L. Templeton
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Julien Soubrier
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St Petersburg, Russia
| | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St Petersburg, Russia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
- * E-mail: (CDS); (WH)
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Hernández CL, Reales G, Dugoujon JM, Novelletto A, Rodríguez JN, Cuesta P, Calderón R. Human maternal heritage in Andalusia (Spain): its composition reveals high internal complexity and distinctive influences of mtDNA haplogroups U6 and L in the western and eastern side of region. BMC Genet 2014; 15:11. [PMID: 24460736 PMCID: PMC3905667 DOI: 10.1186/1471-2156-15-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 01/17/2014] [Indexed: 12/03/2022] Open
Abstract
Background The archeology and history of the ancient Mediterranean have shown that this sea has been a permeable obstacle to human migration. Multiple cultural exchanges around the Mediterranean have taken place with presumably population admixtures. A gravitational territory of those migrations has been the Iberian Peninsula. Here we present a comprehensive analysis of the maternal gene pool, by means of control region sequencing and PCR-RFLP typing, of autochthonous Andalusians originating from the coastal provinces of Huelva and Granada, located respectively in the west and the east of the region. Results The mtDNA haplogroup composition of these two southern Spanish populations has revealed a wide spectrum of haplogroups from different geographical origins. The registered frequencies of Eurasian markers, together with the high incidence and diversification of African maternal lineages (15% of the total mitochondrial variability) among Huelva Andalusians when compared to its eastwards relatives of Granada and other Iberian populations, constitute relevant findings unknown up-to-date on the characteristics of mtDNA within Andalusia that testifies a female population substructure. Therefore, Andalusia must not be considered a single, unique population. Conclusions The maternal legacy among Andalusians reflects distinctive local histories, pointing out the role of the westernmost territory of Peninsular Spain as a noticeable recipient of multiple and diverse human migrations. The obtained results underline the necessity of further research on genetic relationships in both sides of the western Mediterranean, using carefully collected samples from autochthonous individuals. Many studies have focused on recent North African gene flow towards Iberia, yet scientific attention should be now directed to thoroughly study the introduction of European genes in northwest Africa across the sea, in order to determine its magnitude, timescale and methods, and to compare them to those terrestrial movements from eastern Africa and southwestern Asia.
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Affiliation(s)
| | | | | | | | | | | | - Rosario Calderón
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain.
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Nedoluzhko AV, Boulygina ES, Sokolov AS, Tsygankova SV, Gruzdeva NM, Rezepkin AD, Prokhortchouk EB. Analysis of the Mitochondrial Genome of a Novosvobodnaya Culture Representative using Next-Generation Sequencing and Its Relation to the Funnel Beaker Culture. Acta Naturae 2014; 6:31-5. [PMID: 25093108 PMCID: PMC4115223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Novosvobodnaya culture is known as a Bronze Age archaeological culture in the North Caucasus region of Southern Russia. It dates back to the middle of the 4th millennium B.C. and seems to have occurred during the time of the Maikop culture. There are now two hypotheses about the emergence of the Novosvobodnaya culture. One hypothesis suggests that the Novosvobodnaya culture was a phase of the Maikop culture, whereas the other one classifies it as an independent event based on the material culture items found in graves. Comparison between Novosvobodnaya pottery and Funnelbeaker (TRB) pottery from Germany has allowed researchers to suggest that the Novosvobodnaya culture developed under the influence of Indo-European culture. Nevertheless, the origin of the Novosvobodnaya culture remains a matter of debate. We applied next-generation sequencing to study ~5000-year-old human remains from the Klady kurgan grave in Novosvobodnaya stanitsa (now the Republic of Adygea, Russia). A total of 58,771,105 reads were generated using Illumina GAIIx with a coverage depth of 13.4x over the mitochondrial (mt) DNA genome. The mtDNA haplogroup affiliation was determined as V7, suggesting a role of the TRB culture in the development of the Novosvobodnaya culture and supporting the model of sharing between Novosvobodnaya and early Indo-European cultures.
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Affiliation(s)
- A. V. Nedoluzhko
- National Research Center “Kurchatov Institute”, Kurchatov sq. 1, 123182, Moscow, Russia
| | - E. S. Boulygina
- National Research Center “Kurchatov Institute”, Kurchatov sq. 1, 123182, Moscow, Russia
| | - A. S. Sokolov
- National Research Center “Kurchatov Institute”, Kurchatov sq. 1, 123182, Moscow, Russia
| | - S. V. Tsygankova
- National Research Center “Kurchatov Institute”, Kurchatov sq. 1, 123182, Moscow, Russia
| | - N. M. Gruzdeva
- National Research Center “Kurchatov Institute”, Kurchatov sq. 1, 123182, Moscow, Russia
| | - A. D. Rezepkin
- Institute for the History of Material Culture, Russian Academy of Sciences, Dvortsovaya Naberezhnaya, 18, 191186, St. Petersburg, Russia
| | - E. B. Prokhortchouk
- National Research Center “Kurchatov Institute”, Kurchatov sq. 1, 123182, Moscow, Russia,Center of Bioengineering, Russian Academy of Sciences, 60-letiya Oktyabrya Av., 7-1, 117312, Moscow, Russia
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84
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Ramos-Luis E, Blanco-Verea A, Brión M, Van Huffel V, Sánchez-Diz P, Carracedo A. Y-chromosomal DNA analysis in French male lineages. Forensic Sci Int Genet 2013; 9:162-8. [PMID: 24528594 DOI: 10.1016/j.fsigen.2013.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 12/16/2013] [Accepted: 12/18/2013] [Indexed: 10/25/2022]
Abstract
French population, despite of its crucial geographic location for repopulation movements of Europe across time, it has been insufficiently characterized at the genetic level, especially for Y-chromosomal DNA variation. In order to make a genetic structure characterization, we have analyzed the Y-chromosome diversity of 558 male individuals, scattered along 7 different French regions: Alsace (Strasbourg), Auvergne (Clermont-Ferrand), Bretagne (Rennes), Île-de-France (Paris), Midi-Pyrénées (Toulouse), Nord-Pas-de-Calais (Lille) and Provence-Alpes-Côte d'Azur (Marseille). A total of 17 Y-chromosome STRs and 27 Y-chromosome SNPs were genotyped for each individual. Even though we find that most of the individual populations in France were not differentiated from each other, Bretagne population shows population substructure, an important fact to be considered when establishing general population databases.
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Affiliation(s)
- E Ramos-Luis
- Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain.
| | - A Blanco-Verea
- Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - M Brión
- Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - V Van Huffel
- Institut National de la Transfusion Sanguine, Paris, France
| | - P Sánchez-Diz
- Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - A Carracedo
- Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
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85
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Santos C, Fregel R, Cabrera VM, Álvarez L, Larruga JM, Ramos A, López MA, Pilar Aluja M, González AM. Mitochondrial DNA and Y-chromosome structure at the mediterranean and atlantic façades of the iberian peninsula. Am J Hum Biol 2013; 26:130-41. [DOI: 10.1002/ajhb.22497] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/31/2013] [Accepted: 12/07/2013] [Indexed: 01/24/2023] Open
Affiliation(s)
- Cristina Santos
- Unitat Antropologia Biològica; Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
| | - Rosa Fregel
- Department of Genetics; University of La Laguna; 38271 Tenerife Canary Islands Spain
| | - Vicente M. Cabrera
- Department of Genetics; University of La Laguna; 38271 Tenerife Canary Islands Spain
| | - Luis Álvarez
- Unitat Antropologia Biològica; Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
- IPATIMUP; Institute of Molecular Pathology and Immunology of the University of Porto; 4200-465 Porto Portugal
| | - Jose M. Larruga
- Department of Genetics; University of La Laguna; 38271 Tenerife Canary Islands Spain
| | - Amanda Ramos
- Unitat Antropologia Biològica; Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
- Centre of Research in Natural Resources (CIRN), Department of Biology; University of the Azores; 9500-321 Ponta Delgada Portugal
- Molecular and Cellular Biology Institute (IBMC); University of Porto; 4150-180 Porto Portugal
| | - Miguel A. López
- Clinical Management and Biotechnology Unit; Torre Cárdena Hospital; 04008 Almería Spain
| | - María Pilar Aluja
- Unitat Antropologia Biològica; Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona; 08193 Bellaterra Barcelona Spain
| | - Ana M. González
- Department of Genetics; University of La Laguna; 38271 Tenerife Canary Islands Spain
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86
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Horan MP, Cooper DN. The emergence of the mitochondrial genome as a partial regulator of nuclear function is providing new insights into the genetic mechanisms underlying age-related complex disease. Hum Genet 2013; 133:435-58. [DOI: 10.1007/s00439-013-1402-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 11/23/2013] [Indexed: 12/17/2022]
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87
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Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, Jane Adler C, Richards SM, Der Sarkissian C, Ganslmeier R, Friederich S, Dresely V, van Oven M, Kenyon R, Van der Hoek MB, Korlach J, Luong K, Ho SYW, Quintana-Murci L, Behar DM, Meller H, Alt KW, Cooper A. Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nat Commun 2013; 4:1764. [PMID: 23612305 DOI: 10.1038/ncomms2656] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 02/27/2013] [Indexed: 11/09/2022] Open
Abstract
Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this 'real-time' genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.
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Affiliation(s)
- Paul Brotherton
- The Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia 5005, Australia.,Archaeogenetics Research Group, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
| | - Wolfgang Haak
- The Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jennifer Templeton
- The Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Guido Brandt
- Institute of Anthropology, Colonel-Kleinmann Weg 2, Johannes Gutenberg University, Mainz, D-55128 Mainz, Germany
| | - Julien Soubrier
- The Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Christina Jane Adler
- The Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephen M Richards
- The Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Clio Der Sarkissian
- The Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Robert Ganslmeier
- State Office for Heritage Management and Archaeology Saxony-Anhalt / State Museum for Prehistory Halle, Richard-Wagner-Straße 9, D-06114 Halle/Saale, Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt / State Museum for Prehistory Halle, Richard-Wagner-Straße 9, D-06114 Halle/Saale, Germany
| | - Veit Dresely
- State Office for Heritage Management and Archaeology Saxony-Anhalt / State Museum for Prehistory Halle, Richard-Wagner-Straße 9, D-06114 Halle/Saale, Germany
| | - Mannis van Oven
- Department of Forensic Molecular Biology, Erasmus MC, University Medical Centre, Rotterdam, 3000 CA Rotterdam, The Netherlands
| | | | | | | | | | - Simon Y W Ho
- School of Biological Sciences, The University of Sydney, New South Wales 2006, Australia
| | | | | | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt / State Museum for Prehistory Halle, Richard-Wagner-Straße 9, D-06114 Halle/Saale, Germany
| | - Kurt W Alt
- Institute of Anthropology, Colonel-Kleinmann Weg 2, Johannes Gutenberg University, Mainz, D-55128 Mainz, Germany
| | - Alan Cooper
- Institute of Anthropology, Colonel-Kleinmann Weg 2, Johannes Gutenberg University, Mainz, D-55128 Mainz, Germany
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88
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Brandt G, Haak W, Adler CJ, Roth C, Szécsényi-Nagy A, Karimnia S, Möller-Rieker S, Meller H, Ganslmeier R, Friederich S, Dresely V, Nicklisch N, Pickrell JK, Sirocko F, Reich D, Cooper A, Alt KW. Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity. Science 2013; 342:257-61. [PMID: 24115443 DOI: 10.1126/science.1241844] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The processes that shaped modern European mitochondrial DNA (mtDNA) variation remain unclear. The initial peopling by Palaeolithic hunter-gatherers ~42,000 years ago and the immigration of Neolithic farmers into Europe ~8000 years ago appear to have played important roles but do not explain present-day mtDNA diversity. We generated mtDNA profiles of 364 individuals from prehistoric cultures in Central Europe to perform a chronological study, spanning the Early Neolithic to the Early Bronze Age (5500 to 1550 calibrated years before the common era). We used this transect through time to identify four marked shifts in genetic composition during the Neolithic period, revealing a key role for Late Neolithic cultures in shaping modern Central European genetic diversity.
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Affiliation(s)
- Guido Brandt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany.
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89
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Phylogenetic relationships of three Italian merino-derived sheep breeds evaluated through a complete mitogenome analysis. PLoS One 2013; 8:e73712. [PMID: 24040036 PMCID: PMC3767607 DOI: 10.1371/journal.pone.0073712] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 07/28/2013] [Indexed: 11/19/2022] Open
Abstract
In Italy, the crisis of the wool industry triggered the necessity to reconvert the two traditional Merino-derived breeds, Gentile di Puglia and Sopravissana, to meat production, by creating the Merinizzata Italiana. The aim of the present study was to assess the genetic diversity of these three Italian Merino-derived (IMd) breeds by examining the molecular information encoded in the maternally-inherited mitochondrial DNA (mtDNA). A parallel molecular investigation was performed on the putative paternal and maternal breeds, the Merino from Spain and the Appenninica from Italy, respectively, as well as on three unrelated dairy breeds (Sarda and Comisana from Italy, and Lacaune from France). Firstly, the mtDNA control region of 291 samples was analyzed. When comparing the overall genetic distances among the eight stocks, the three IMd breeds clustered together close to the Appenninica, thus confirming its parental role. Among the 90 IMd samples, 82 different haplotypes were observed, almost all belonging to haplogroup B, and only one to A. For 23 mtDNAs, including nine IMd, the analysis was then brought to the level of entire mitogenomes. Three distinct sub-haplogroups within B were found to encompass the IMd samples, with one clade (B1a2a1) apparently restricted to those sheep. Thus, despite experiencing a drastic reduction in number (mainly due to changes in breeding practices driven by the economy), the IMd breeds still represent a reservoir of distinctive mitochondrial variants, which could potentially contribute to the development of conservation and management programs of Italian sheep breeds.
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90
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Linguistic isolates in Portugal: insights from the mitochondrial DNA pattern. Forensic Sci Int Genet 2013; 7:618-623. [PMID: 24041913 DOI: 10.1016/j.fsigen.2013.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 08/15/2013] [Accepted: 08/21/2013] [Indexed: 11/23/2022]
Abstract
Miranda do Douro, located in the northeastern region of Portugal, has notable characteristics not only from a geographic or naturalistic point of view, but also from a cultural perspective. A remarkable one is the coexistence of two different languages: Portuguese and Mirandese, the second being an Astur-Leonese dialect. The current persistence of the Astur-Leonese dialect in this population falls on the singularity of the region: relative isolation, implying difficulties to communicate with other Portuguese regions, while the same location facilitated the establishment of social and commercial relationships with adjacent Spanish territories, origin of the Astur-Leonese language. The objective of this study was to characterize the population from Miranda through the analysis of maternal lineages in order to evaluate whether its mitochondrial DNA diversity fitted the patterns previously reported for other populations from the Iberian Peninsula. Viewing that, the entire control region of mitochondrial DNA from 121 individuals was examined. Miranda showed a haplogroup composition usual for a Western European population, in the sense that as high as 63.6% of sequences belonged to macro-haplogroup R0. Lineages ascribed to have an African (L2a and L1b) origin, were detected, but reaching an amount commonly found in Portugal. Miranda also presented a few haplogroups typically found in Jewish populations, while rarely observed in other Iberian populations. The finding can be explained by gene flow with crypto-Jew communities that since long are known to be established in the region where Miranda is located. In Miranda, both genetic and nucleotide diversities presented low values (0.9292 ± 0.0180 and 0.01101 ± 0.00614 respectively) when compared to populations from its micro-geographical framework, which constitute a sign of population isolation that certainly provided conditions for the survival of the Astur-Leonese dialect in the region.
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91
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Olivieri A, Pala M, Gandini F, Hooshiar Kashani B, Perego UA, Woodward SR, Grugni V, Battaglia V, Semino O, Achilli A, Richards MB, Torroni A. Mitogenomes from two uncommon haplogroups mark late glacial/postglacial expansions from the near east and neolithic dispersals within Europe. PLoS One 2013; 8:e70492. [PMID: 23936216 PMCID: PMC3729697 DOI: 10.1371/journal.pone.0070492] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 06/20/2013] [Indexed: 11/19/2022] Open
Abstract
The current human mitochondrial (mtDNA) phylogeny does not equally represent all human populations but is biased in favour of representatives originally from north and central Europe. This especially affects the phylogeny of some uncommon West Eurasian haplogroups, including I and W, whose southern European and Near Eastern components are very poorly represented, suggesting that extensive hidden phylogenetic substructure remains to be uncovered. This study expanded and re-analysed the available datasets of I and W complete mtDNA genomes, reaching a comprehensive 419 mitogenomes, and searched for precise correlations between the ages and geographical distributions of their numerous newly identified subclades with events of human dispersal which contributed to the genetic formation of modern Europeans. Our results showed that haplogroups I (within N1a1b) and W originated in the Near East during the Last Glacial Maximum or pre-warming period (the period of gradual warming between the end of the LGM, ∼19 ky ago, and the beginning of the first main warming phase, ∼15 ky ago) and, like the much more common haplogroups J and T, may have been involved in Late Glacial expansions starting from the Near East. Thus our data contribute to a better definition of the Late and postglacial re-peopling of Europe, providing further evidence for the scenario that major population expansions started after the Last Glacial Maximum but before Neolithic times, but also evidencing traces of diffusion events in several I and W subclades dating to the European Neolithic and restricted to Europe.
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Affiliation(s)
- Anna Olivieri
- Dipartimento di Biologia e Biotecnologie L. Spallanzani, Università di Pavia, Pavia, Italy.
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92
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Vankan P. Prevalence gradients of Friedreich's Ataxia and R1b haplotype in Europe co-localize, suggesting a common Palaeolithic origin in the Franco-Cantabrian ice age refuge. J Neurochem 2013; 126 Suppl 1:11-20. [DOI: 10.1111/jnc.12215] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 11/30/2012] [Accepted: 12/17/2012] [Indexed: 11/30/2022]
Affiliation(s)
- Pierre Vankan
- Independent Scientific Consultant; Riehen Switzerland
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93
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Gene flow from North Africa contributes to differential human genetic diversity in southern Europe. Proc Natl Acad Sci U S A 2013; 110:11791-6. [PMID: 23733930 DOI: 10.1073/pnas.1306223110] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Human genetic diversity in southern Europe is higher than in other regions of the continent. This difference has been attributed to postglacial expansions, the demic diffusion of agriculture from the Near East, and gene flow from Africa. Using SNP data from 2,099 individuals in 43 populations, we show that estimates of recent shared ancestry between Europe and Africa are substantially increased when gene flow from North Africans, rather than Sub-Saharan Africans, is considered. The gradient of North African ancestry accounts for previous observations of low levels of sharing with Sub-Saharan Africa and is independent of recent gene flow from the Near East. The source of genetic diversity in southern Europe has important biomedical implications; we find that most disease risk alleles from genome-wide association studies follow expected patterns of divergence between Europe and North Africa, with the principal exception of multiple sclerosis.
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94
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Boattini A, Martinez-Cruz B, Sarno S, Harmant C, Useli A, Sanz P, Yang-Yao D, Manry J, Ciani G, Luiselli D, Quintana-Murci L, Comas D, Pettener D. Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata. PLoS One 2013; 8:e65441. [PMID: 23734255 PMCID: PMC3666984 DOI: 10.1371/journal.pone.0065441] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 04/24/2013] [Indexed: 11/18/2022] Open
Abstract
Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally-inherited markers in ∼900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West–South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe.
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Affiliation(s)
- Alessio Boattini
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Begoña Martinez-Cruz
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Stefania Sarno
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Christine Harmant
- Institut Pasteur, Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Paris, France
- Centre National de la Recherche Scientifique, Paris, France
| | - Antonella Useli
- Dipartimento di Scienze della Natura e del Territorio, Università di Sassari, Sassari, Italy
| | - Paula Sanz
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniele Yang-Yao
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Jeremy Manry
- Institut Pasteur, Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Paris, France
- Centre National de la Recherche Scientifique, Paris, France
| | - Graziella Ciani
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Donata Luiselli
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Lluis Quintana-Murci
- Institut Pasteur, Human Evolutionary Genetics Unit, Department of Genomes and Genetics, Paris, France
- Centre National de la Recherche Scientifique, Paris, France
| | - David Comas
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències de la Salut i de la Vida, Universitat Pompeu Fabra, Barcelona, Spain
- * E-mail: (DC); (DP)
| | - Davide Pettener
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
- * E-mail: (DC); (DP)
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95
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Bekada A, Fregel R, Cabrera VM, Larruga JM, Pestano J, Benhamamouch S, González AM. Introducing the Algerian mitochondrial DNA and Y-chromosome profiles into the North African landscape. PLoS One 2013; 8:e56775. [PMID: 23431392 PMCID: PMC3576335 DOI: 10.1371/journal.pone.0056775] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 01/15/2013] [Indexed: 11/18/2022] Open
Abstract
North Africa is considered a distinct geographic and ethnic entity within Africa. Although modern humans originated in this Continent, studies of mitochondrial DNA (mtDNA) and Y-chromosome genealogical markers provide evidence that the North African gene pool has been shaped by the back-migration of several Eurasian lineages in Paleolithic and Neolithic times. More recent influences from sub-Saharan Africa and Mediterranean Europe are also evident. The presence of East-West and North-South haplogroup frequency gradients strongly reinforces the genetic complexity of this region. However, this genetic scenario is beset with a notable gap, which is the lack of consistent information for Algeria, the largest country in the Maghreb. To fill this gap, we analyzed a sample of 240 unrelated subjects from a northwest Algeria cosmopolitan population using mtDNA sequences and Y-chromosome biallelic polymorphisms, focusing on the fine dissection of haplogroups E and R, which are the most prevalent in North Africa and Europe respectively. The Eurasian component in Algeria reached 80% for mtDNA and 90% for Y-chromosome. However, within them, the North African genetic component for mtDNA (U6 and M1; 20%) is significantly smaller than the paternal (E-M81 and E-V65; 70%). The unexpected presence of the European-derived Y-chromosome lineages R-M412, R-S116, R-U152 and R-M529 in Algeria and the rest of the Maghreb could be the counterparts of the mtDNA H1, H3 and V subgroups, pointing to direct maritime contacts between the European and North African sides of the western Mediterranean. Female influx of sub-Saharan Africans into Algeria (20%) is also significantly greater than the male (10%). In spite of these sexual asymmetries, the Algerian uniparental profiles faithfully correlate between each other and with the geography.
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Affiliation(s)
- Asmahan Bekada
- Department of Biotechnology, Faculty of Sciences, University of Oran, Oran, Algeria
| | - Rosa Fregel
- Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Tenerife, Spain
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Gran Canaria, Spain
- Forensic Genetics Laboratory, Institute of Legal Medicine of Las Palmas, Las Palmas de Gran Canaria, Gran Canaria, Spain
| | - Vicente M. Cabrera
- Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Tenerife, Spain
| | - José M. Larruga
- Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Tenerife, Spain
| | - José Pestano
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Gran Canaria, Spain
- Forensic Genetics Laboratory, Institute of Legal Medicine of Las Palmas, Las Palmas de Gran Canaria, Gran Canaria, Spain
| | - Soraya Benhamamouch
- Department of Biotechnology, Faculty of Sciences, University of Oran, Oran, Algeria
| | - Ana M. González
- Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Tenerife, Spain
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96
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Der Sarkissian C, Balanovsky O, Brandt G, Khartanovich V, Buzhilova A, Koshel S, Zaporozhchenko V, Gronenborn D, Moiseyev V, Kolpakov E, Shumkin V, Alt KW, Balanovska E, Cooper A, Haak W. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe. PLoS Genet 2013; 9:e1003296. [PMID: 23459685 PMCID: PMC3573127 DOI: 10.1371/journal.pgen.1003296] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 12/18/2012] [Indexed: 11/25/2022] Open
Abstract
North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans. The history of human populations can be retraced by studying the archaeological and anthropological record, but also by examining the current distribution of genetic markers, such as the maternally inherited mitochondrial DNA. Ancient DNA research allows the retrieval of DNA from ancient skeletal remains and contributes to the reconstruction of the human population history through the comparison of ancient and present-day genetic data. Here, we analysed the mitochondrial DNA of prehistoric remains from archaeological sites dated to 7,500 and 3,500 years Before Present. These sites are located in North East Europe, a region that displays a significant cultural and linguistic diversity today but for which no ancient human DNA was available before. We show that prehistoric hunter-gatherers of North East Europe were genetically similar to other European foragers. We also detected a prehistoric genetic input from Siberia, followed by migrations from Western Europe into North East Europe. Our research contributes to the understanding of the origins and past dynamics of human population in Europe.
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Affiliation(s)
- Clio Der Sarkissian
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Guido Brandt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | | | | | - Sergey Koshel
- Faculty of Geography, Moscow State University, Moscow, Russia
| | - Valery Zaporozhchenko
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
| | | | | | - Eugen Kolpakov
- Institute for the History of Material Culture, Russian Academy of Science, St. Petersburg, Russia
| | - Vladimir Shumkin
- Institute for the History of Material Culture, Russian Academy of Science, St. Petersburg, Russia
| | - Kurt W. Alt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
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97
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Mielnik-Sikorska M, Daca P, Malyarchuk B, Derenko M, Skonieczna K, Perkova M, Dobosz T, Grzybowski T. The history of Slavs inferred from complete mitochondrial genome sequences. PLoS One 2013; 8:e54360. [PMID: 23342138 PMCID: PMC3544712 DOI: 10.1371/journal.pone.0054360] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 12/11/2012] [Indexed: 12/28/2022] Open
Abstract
To shed more light on the processes leading to crystallization of a Slavic identity, we investigated variability of complete mitochondrial genomes belonging to haplogroups H5 and H6 (63 mtDNA genomes) from the populations of Eastern and Western Slavs, including new samples of Poles, Ukrainians and Czechs presented here. Molecular dating implies formation of H5 approximately 11.5–16 thousand years ago (kya) in the areas of southern Europe. Within ancient haplogroup H6, dated at around 15–28 kya, there is a subhaplogroup H6c, which probably survived the last glaciation in Europe and has undergone expansion only 3–4 kya, together with the ancestors of some European groups, including the Slavs, because H6c has been detected in Czechs, Poles and Slovaks. Detailed analysis of complete mtDNAs allowed us to identify a number of lineages that seem specific for Central and Eastern Europe (H5a1f, H5a2, H5a1r, H5a1s, H5b4, H5e1a, H5u1, some subbranches of H5a1a and H6a1a9). Some of them could possibly be traced back to at least ∼4 kya, which indicates that some of the ancestors of today's Slavs (Poles, Czechs, Slovaks, Ukrainians and Russians) inhabited areas of Central and Eastern Europe much earlier than it was estimated on the basis of archaeological and historical data. We also sequenced entire mitochondrial genomes of several non-European lineages (A, C, D, G, L) found in contemporary populations of Poland and Ukraine. The analysis of these haplogroups confirms the presence of Siberian (C5c1, A8a1) and Ashkenazi-specific (L2a1l2a) mtDNA lineages in Slavic populations. Moreover, we were able to pinpoint some lineages which could possibly reflect the relatively recent contacts of Slavs with nomadic Altaic peoples (C4a1a, G2a, D5a2a1a1).
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Affiliation(s)
- Marta Mielnik-Sikorska
- Department of Molecular and Forensic Genetics, Bydgoszcz, Institute of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Patrycja Daca
- Department of Molecular and Forensic Genetics, Bydgoszcz, Institute of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Science, Magadan, Russia
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Science, Magadan, Russia
| | - Katarzyna Skonieczna
- Department of Molecular and Forensic Genetics, Bydgoszcz, Institute of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Maria Perkova
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Science, Magadan, Russia
| | - Tadeusz Dobosz
- Department of Forensic Medicine, Wrocław Medical University, Wrocław, Poland
| | - Tomasz Grzybowski
- Department of Molecular and Forensic Genetics, Bydgoszcz, Institute of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
- * E-mail:
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98
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Caporali L, Ghelli AM, Iommarini L, Maresca A, Valentino ML, La Morgia C, Liguori R, Zanna C, Barboni P, De Nardo V, Martinuzzi A, Rizzo G, Tonon C, Lodi R, Calvaruso MA, Cappelletti M, Porcelli AM, Achilli A, Pala M, Torroni A, Carelli V. Cybrid studies establish the causal link between the mtDNA m.3890G>A/MT-ND1 mutation and optic atrophy with bilateral brainstem lesions. Biochim Biophys Acta Mol Basis Dis 2012; 1832:445-52. [PMID: 23246842 PMCID: PMC3778985 DOI: 10.1016/j.bbadis.2012.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 11/29/2012] [Accepted: 12/06/2012] [Indexed: 12/29/2022]
Abstract
Complex I (CI) deficiency is a frequent cause of mitochondrial disorders and, in most cases, is due to mutations in CI subunit genes encoded by mitochondrial DNA (mtDNA). In this study, we establish the pathogenic role of the heteroplasmic mtDNA m.3890G>A/MT-ND1 (p.R195Q) mutation, which affects an extremely conserved amino acid position in ND1 subunit of CI. This mutation was found in a young-adult male with optic atrophy resembling Leber's hereditary optic neuropathy (LHON) and bilateral brainstem lesions. The only previously reported case with this mutation was a girl with fatal infantile Leigh syndrome with bilateral brainstem lesions. Transfer of the mutant mtDNA in the cybrid cell system resulted in a marked reduction of CI activity and CI-dependent ATP synthesis in the presence of a normally assembled enzyme. These findings establish the pathogenicity of the m.3890G>A/MT-ND1 mutation and remark the link between CI mutations affecting the mtDNA-encoded ND subunits and LHON-like optic atrophy, which may be complicated by bilateral and symmetric lesions affecting the central nervous system. Peculiar to this mutation is the distribution of the brainstem lesions, with sparing of the striatum in both patients.
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Arrival of Paleo-Indians to the southern cone of South America: new clues from mitogenomes. PLoS One 2012; 7:e51311. [PMID: 23240014 PMCID: PMC3519775 DOI: 10.1371/journal.pone.0051311] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 10/31/2012] [Indexed: 11/19/2022] Open
Abstract
With analyses of entire mitogenomes, studies of Native American mitochondrial DNA (mtDNA) variation have entered the final phase of phylogenetic refinement: the dissection of the founding haplogroups into clades that arose in America during and after human arrival and spread. Ages and geographic distributions of these clades could provide novel clues on the colonization processes of the different regions of the double continent. As for the Southern Cone of South America, this approach has recently allowed the identification of two local clades (D1g and D1j) whose age estimates agree with the dating of the earliest archaeological sites in South America, indicating that Paleo-Indians might have reached that region from Beringia in less than 2000 years. In this study, we sequenced 46 mitogenomes belonging to two additional clades, termed B2i2 (former B2l) and C1b13, which were recently identified on the basis of mtDNA control-region data and whose geographical distributions appear to be restricted to Chile and Argentina. We confirm that their mutational motifs most likely arose in the Southern Cone region. However, the age estimate for B2i2 and C1b13 (11–13,000 years) appears to be younger than those of other local clades. The difference could reflect the different evolutionary origins of the distinct South American-specific sub-haplogroups, with some being already present, at different times and locations, at the very front of the expansion wave in South America, and others originating later in situ, when the tribalization process had already begun. A delayed origin of a few thousand years in one of the locally derived populations, possibly in the central part of Chile, would have limited the geographical and ethnic diffusion of B2i2 and explain the present-day occurrence that appears to be mainly confined to the Tehuelche and Araucanian-speaking groups.
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Brisighelli F, Álvarez-Iglesias V, Fondevila M, Blanco-Verea A, Carracedo Á, Pascali VL, Capelli C, Salas A. Uniparental markers of contemporary Italian population reveals details on its pre-Roman heritage. PLoS One 2012; 7:e50794. [PMID: 23251386 PMCID: PMC3519480 DOI: 10.1371/journal.pone.0050794] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 10/24/2012] [Indexed: 11/18/2022] Open
Abstract
Background According to archaeological records and historical documentation, Italy has been a melting point for populations of different geographical and ethnic matrices. Although Italy has been a favorite subject for numerous population genetic studies, genetic patterns have never been analyzed comprehensively, including uniparental and autosomal markers throughout the country. Methods/Principal Findings A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities — and from two linguistic isolates (Ladins, Grecani Salentini). All samples were first typed for the mitochondrial DNA (mtDNA) control region and selected coding region SNPs (mtSNPs). This data was pooled for analysis with 3,778 mtDNA control-region profiles collected from the literature. Secondly, a set of Y-chromosome SNPs and STRs were also analyzed in 479 individuals together with a panel of autosomal ancestry informative markers (AIMs) from 441 samples. The resulting genetic record reveals clines of genetic frequencies laid according to the latitude slant along continental Italy – probably generated by demographical events dating back to the Neolithic. The Ladins showed distinctive, if more recent structure. The Neolithic contribution was estimated for the Y-chromosome as 14.5% and for mtDNA as 10.5%. Y-chromosome data showed larger differentiation between North, Center and South than mtDNA. AIMs detected a minor sub-Saharan component; this is however higher than for other European non-Mediterranean populations. The same signal of sub-Saharan heritage was also evident in uniparental markers. Conclusions/Significance Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times.
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Affiliation(s)
- Francesca Brisighelli
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
| | - Manuel Fondevila
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
| | - Alejandro Blanco-Verea
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
- Fundación Pública Galega de Medicina Xenómica (FPGMX-SERGAS), CIBER enfermedades raras, Santiago de Compostela, Galicia, Spain
| | - Vincenzo L. Pascali
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Antonio Salas
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
- * E-mail:
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