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Helena's Many Daughters: More Mitogenome Diversity behind the Most Common West Eurasian mtDNA Control Region Haplotype in an Extended Italian Population Sample. Int J Mol Sci 2022; 23:ijms23126725. [PMID: 35743173 PMCID: PMC9223851 DOI: 10.3390/ijms23126725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel sequencing a large number of mitogenomes that share the most common West Eurasian mtDNA control region (CR) haplotype motif (263G 315.1C 16519C). We augmented a pilot study on 29 to a total of 216 Italian mitogenomes that represents the largest set of the most common CR haplotype compiled from a single country. The extended population sample confirmed and extended the huge coding region diversity behind the most common CR motif. Complete mitogenome sequencing allowed for the detection of 163 distinct haplotypes, raising the power of discrimination from 0 (CR) to 99.6% (mitogenome). The mtDNAs were clustered into 61 named clades of haplogroup H and did not reveal phylogeographic trends within Italy. Rapid individualization approaches for investigative purposes are limited to the most frequent H clades of the dataset, viz. H1, H3, and H7.
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Bioarchaeological and palaeogenomic portrait of two Pompeians that died during the eruption of Vesuvius in 79 AD. Sci Rep 2022; 12:6468. [PMID: 35618734 PMCID: PMC9135728 DOI: 10.1038/s41598-022-10899-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/08/2022] [Indexed: 12/12/2022] Open
Abstract
The archaeological site of Pompeii is one of the 54 UNESCO World Heritage sites in Italy, thanks to its uniqueness: the town was completely destroyed and buried by a Vesuvius’ eruption in 79 AD. In this work, we present a multidisciplinary approach with bioarchaeological and palaeogenomic analyses of two Pompeian human remains from the Casa del Fabbro. We have been able to characterize the genetic profile of the first Pompeian’ genome, which has strong affinities with the surrounding central Italian population from the Roman Imperial Age. Our findings suggest that, despite the extensive connection between Rome and other Mediterranean populations, a noticeable degree of genetic homogeneity exists in the Italian peninsula at that time. Moreover, palaeopathological analyses identified the presence of spinal tuberculosis and we further investigated the presence of ancient DNA from Mycobacterium tuberculosis. In conclusion, our study demonstrates the power of a combined approach to investigate ancient humans and confirms the possibility to retrieve ancient DNA from Pompeii human remains. Our initial findings provide a foundation to promote an intensive and extensive paleogenetic analysis in order to reconstruct the genetic history of population from Pompeii, a unique archaeological site.
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Malyarchuk B, Skonieczna K, Duleba A, Derenko M, Malyarchuk A, Grzybowski T. Mitogenomic diversity in Czechs and Slovaks. Forensic Sci Int Genet 2022; 59:102714. [PMID: 35468348 DOI: 10.1016/j.fsigen.2022.102714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/17/2022] [Accepted: 04/18/2022] [Indexed: 11/19/2022]
Affiliation(s)
- Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan 685000, Russian Federation.
| | - Katarzyna Skonieczna
- Department of Forensic Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz 85-094, Poland
| | - Anna Duleba
- Department of Forensic Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz 85-094, Poland
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan 685000, Russian Federation
| | - Alexandra Malyarchuk
- Center for Genetics and Genetic Technologies, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234, Russian Federation
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz 85-094, Poland
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Calò CM, Vona G, Robledo R, Francalacci P. From old markers to next generation: reconstructing the history of the peopling of Sardinia. Ann Hum Biol 2021; 48:203-212. [PMID: 34459339 DOI: 10.1080/03014460.2021.1944312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
CONTEXT For many years the Sardinian population has been the object of numerous studies because of its unique genetic structure. Despite the extreme abundance of papers, various aspects of the peopling and genetic structure of Sardinia still remain uncertain and sometimes controversial. OBJECTIVE We reviewed what has emerged from different studies, focussing on some still open questions, such as the origin of Sardinians, their relationship with the Corsican population, and the intra-regional genetic heterogeneity. METHODS The various issues have been addressed through the analysis of classical markers, molecular markers and, finally, genomic data through next generation sequencing. RESULTS AND CONCLUSIONS Although the most ancient human remains date back to the end of the Palaeolithic, Mesolithic populations brought founding lineages that left evident traces in the modern population. Then, with the Neolithic, the island underwent an important demographic expansion. Subsequently, isolation and genetic drift contributed to maintain a significant genetic heterogeneity, but preserving the overall homogeneity on a regional scale. At the same time, isolation and genetic drift contributed to differentiate Sardinia from Corsica, which saw an important gene flow from the mainland. However, the isolation did not prevent gene flow from the neighbouring populations whose contribution are still recognisable in the genome of Sardinians.
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Affiliation(s)
- Carla Maria Calò
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Giuseppe Vona
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Renato Robledo
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Paolo Francalacci
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
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Davidovic S, Malyarchuk B, Grzybowski T, Aleksic JM, Derenko M, Litvinov A, Rogalla-Ładniak U, Stevanovic M, Kovacevic-Grujicic N. Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases. Int J Legal Med 2020; 134:1581-1590. [PMID: 32504149 DOI: 10.1007/s00414-020-02324-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 05/28/2020] [Indexed: 11/24/2022]
Abstract
Mitochondrial genome (mtDNA) is a valuable resource in resolving various human forensic casework. The usage of variability of complete mtDNA genomes increases their discriminatory power to the maximum and enables ultimate resolution of distinct maternal lineages. However, their wider employment in forensic casework is nowadays limited by the lack of appropriate reference database. In order to fill in the gap in the reference data, which, considering Slavic-speaking populations, currently comprises only mitogenomes of East and West Slavs, we present mitogenome data for 226 Serbians, representatives of South Slavs from the Balkan Peninsula. We found 143 (sub)haplogroups among which West Eurasian ones were dominant. The percentage of unique haplotypes was 85%, and the random match probability was as low as 0.53%. We support previous findings on both high levels of genetic diversity in the Serbian population and patterns of genetic differentiation among this and ten studied European populations. However, our high-resolution data supported more pronounced genetic differentiation among Serbians and two Slavic populations (Russians and Poles) as well as expansion of the Serbian population after the Last Glacial Maximum and during the Migration period (fourth to ninth century A.D.), as inferred from the Bayesian skyline analysis. Phylogenetic analysis of haplotypes found in Serbians contributed towards the improvement of the worldwide mtDNA phylogeny, which is essential for the interpretation of the mtDNA casework.
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Affiliation(s)
- Slobodan Davidovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.,Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, 11060, Serbia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine, Nicolaus Copernicus University, Marii-Sklodowskiej-Curie Str. 9, 85-094, Bydgoszcz, Poland
| | - Jelena M Aleksic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Andrey Litvinov
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Urszula Rogalla-Ładniak
- Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine, Nicolaus Copernicus University, Marii-Sklodowskiej-Curie Str. 9, 85-094, Bydgoszcz, Poland
| | - Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.,Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia.,Serbian Academy of Sciences and Arts, Kneza Mihaila 35, Belgrade, 11000, Serbia
| | - Natasa Kovacevic-Grujicic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.
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Insights into matrilineal genetic structure, differentiation and ancestry of Armenians based on complete mitogenome data. Mol Genet Genomics 2019; 294:1547-1559. [DOI: 10.1007/s00438-019-01596-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/22/2019] [Indexed: 01/01/2023]
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Malyarchuk B, Derenko M, Denisova G, Litvinov A, Rogalla U, Skonieczna K, Grzybowski T, Pentelényi K, Guba Z, Zeke T, Molnár MJ. Whole mitochondrial genome diversity in two Hungarian populations. Mol Genet Genomics 2018; 293:1255-1263. [PMID: 29948329 DOI: 10.1007/s00438-018-1458-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/06/2018] [Indexed: 11/28/2022]
Abstract
Complete mitochondrial genomics is an effective tool for studying the demographic history of human populations, but there is still a deficit of mitogenomic data in European populations. In this paper, we present results of study of variability of 80 complete mitochondrial genomes in two Hungarian populations from eastern part of Hungary (Szeged and Debrecen areas). The genetic diversity of Hungarian mitogenomes is remarkably high, reaching 99.9% in a combined sample. According to the analysis of molecular variance (AMOVA), European populations showed a low, but statistically significant level of between-population differentiation (Fst = 0.61%, p = 0), and two Hungarian populations demonstrate lack of between-population differences. Phylogeographic analysis allowed us to identify 71 different mtDNA sub-clades in Hungarians, sixteen of which are novel. Analysis of ancestry-informative mtDNA sub-clades revealed a complex genetic structure associated with the genetic impact of populations from different parts of Eurasia, though the contribution from European populations is the most pronounced. At least 8% of ancestry-informative haplotypes found in Hungarians demonstrate similarity with East and West Slavic populations (sub-clades H1c23a, H2a1c1, J2b1a6, T2b25a1, U4a2e, K1c1j, and I1a1c), while the influence of Siberian populations is not so noticeable (sub-clades A12a, C4a1a, and probably U4b1a4).
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Affiliation(s)
- Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia.
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Galina Denisova
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Andrey Litvinov
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya Street, 18, Magadan, 685000, Russia
| | - Urszula Rogalla
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 85-094, Bydgoszcz, Poland
| | - Katarzyna Skonieczna
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 85-094, Bydgoszcz, Poland
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 85-094, Bydgoszcz, Poland
| | - Klára Pentelényi
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, 1085, Hungary
| | - Zsuzsanna Guba
- Hungarian Molecular Anthropological Research Group, Debrecen, 4030, Hungary
| | - Tamás Zeke
- Hungarian Molecular Anthropological Research Group, Debrecen, 4030, Hungary
| | - Mária Judit Molnár
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, 1085, Hungary
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Malyarchuk B, Litvinov A, Derenko M, Skonieczna K, Grzybowski T, Grosheva A, Shneider Y, Rychkov S, Zhukova O. Mitogenomic diversity in Russians and Poles. Forensic Sci Int Genet 2017. [PMID: 28633069 DOI: 10.1016/j.fsigen.2017.06.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Complete mtDNA genome sequencing improves molecular resolution for distinguishing variation between individuals and populations, but there is still deficiency of mitogenomic population data. To overcome this limitation, we used Sanger-based protocol to generate complete mtDNA sequences of 376 Russian individuals from six populations of European part of Russia and 100 Polish individuals from northern Poland. Nearly complete resolution of mtDNA haplotypes was achieved - about 97% of haplotypes were unique both in Russians and Poles, and no haplotypes overlapped between them when indels were considered. While European populations showed a low, but statistically significant level of between-population differentiation (Fst=0.66%, p=0), Russians demonstrate lack of between-population differences (Fst=0.22%, p=0.15). Results of the Bayesian skyline analysis of Russian mitogenomes demonstrate not only post-Last Glacial Maximum expansion, but also rapid population growth starting from about 4.3kya (95% CI: 2.9-5.8kya), i.e. in the Bronze Age. This expansion strongly correlates with the Kurgan model established by archaeologists and confirmed by paleogeneticists.
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Affiliation(s)
- Boris Malyarchuk
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia.
| | - Andrey Litvinov
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Far-East Branch of the Russian Academy of Sciences, Portovaya Street 18, Magadan 685000, Russia
| | - Katarzyna Skonieczna
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University,Sklodowskiej-Curie Street 9, Bydgoszcz 85-094, Poland
| | - Tomasz Grzybowski
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University,Sklodowskiej-Curie Street 9, Bydgoszcz 85-094, Poland
| | - Aleksandra Grosheva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences,Gubkin Street 3, Moscow 119991, Russia, Russia
| | - Yuri Shneider
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences,Gubkin Street 3, Moscow 119991, Russia, Russia
| | - Sergei Rychkov
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences,Gubkin Street 3, Moscow 119991, Russia, Russia
| | - Olga Zhukova
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences,Gubkin Street 3, Moscow 119991, Russia, Russia
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Zarei F, Rajabi-Maham H. Phylogeography, genetic diversity and demographic history of the Iranian Kurdish groups based on mtDNA sequences. J Genet 2017; 95:767-776. [PMID: 27994175 DOI: 10.1007/s12041-016-0692-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Throughout the history of modern humans, the current Kurdish-inhabited area has served as part of a tricontinental crossroad for major human migrations. Also, a significant body of archaeological evidence points to this area as the site of Neolithic transition. To investigate the phylogeography, origins and demographic history, mtDNA D-loop region of individuals representing four Kurdish groups from Iran were analysed. Our data indicated that most of the Kurds mtDNA lineages belong to branches of the haplogroups with the Western Eurasian origin; with small fractions of the Eastern Eurasian and sub-Saharan African lineages. The low level of mtDNA diversity observed in the Havrami group presented a bias towards isolation or increased drift due to small population size; while in the Kurmanji group it indicated a bias towards drift or mass migration events during the 5-18th century AD. The Mantel test showed strong isolation by distance, and AMOVA results for global and regional scales confirmed that the geography had acted as the main driving force in shaping the current pattern of mtDNA diversity, rather than linguistic similarity. The results of demographic analyses, in agreement with archaeological data, revealed a recent expansion of the Kurds (~9,500 years before present) related to the Neolithic transition from hunting and gathering, to farming and cattle breeding in the Near East. Further, the high frequencies of typical haplogroups for early farmers (H; 37.1%) and hunter-gatherers (U; 13.8%) in the Kurds may testify the earlier hunter-gatherers in the Kurdish-inhabited area that adopted and admixed the Kurds ancestors following the Neolithic transition.
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Affiliation(s)
- Fatah Zarei
- Faculty of Biological Sciences, Department of Animal Sciences, Shahid Beheshti University (GC), Tehran 1983963113, Iran.
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Caldararo N. Denisovans, Melanesians, Europeans, and Neandertals: The Confusion of DNA Assumptions and the Biological Species Concept. J Mol Evol 2016; 83:78-87. [DOI: 10.1007/s00239-016-9755-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/30/2016] [Indexed: 10/21/2022]
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Messina F, Scano G, Contini I, Martínez-Labarga C, De Stefano GF, Rickards O. Linking between genetic structure and geographical distance: Study of the maternal gene pool in the Ethiopian population. Ann Hum Biol 2016; 44:53-69. [PMID: 26883569 DOI: 10.3109/03014460.2016.1155646] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background The correlation between genetics and geographical distance has already been examined through the study of the dispersion of human populations, especially in terms of uniparental genetic markers. Aim The present work characterises, at the level of the mitochondrial DNA (mtDNA), two new samples of Amhara and Oromo populations from Ethiopia to evaluate the possible pattern of distribution for mtDNA variation and to test the hypothesis of the Isolation-by-Distance (IBD) model among African, European and Middle-Eastern populations. Subjects and methods This study analysed 173 individuals belonging to two ethnic groups of Ethiopia, Amhara and Oromo, by assaying HVS-I and HVS-II of mtDNA D-loop and informative coding region SNPs of mtDNA. Results The analysis suggests a relationship between genetic and geographic distances, affirming that the mtDNA pool of Africa, Europe and the Middle East might be coherent with the IBD model. Moreover, the mtDNA gene pools of the Sub-Saharan African and Mediterranean populations were very different. Conclusion In this study the pattern of mtDNA distribution, beginning with the Ethiopian plateau, was tested in the IBD model. It could be affirmed that, on a continent scale, the mtDNA pool of Africa, Europe and the Middle East might fall under the IBD model.
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Affiliation(s)
- Francesco Messina
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Giuseppina Scano
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Irene Contini
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Cristina Martínez-Labarga
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Gian Franco De Stefano
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Olga Rickards
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
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Biino G, Concas MP, Cena H, Parracciani D, Vaccargiu S, Cosso M, Marras F, D'Esposito V, Beguinot F, Pirastu M. Dissecting metabolic syndrome components: data from an epidemiologic survey in a genetic isolate. SPRINGERPLUS 2015; 4:324. [PMID: 26180744 PMCID: PMC4493262 DOI: 10.1186/s40064-015-1049-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/19/2015] [Indexed: 01/18/2023]
Abstract
The metabolic syndrome (MetS) is a large-scale and expanding public-health and clinical threat worldwide. We investigated the determinants of MetS, assessed its prevalence and components and, estimated their genetic contribution, taking advantage of the special characteristics of Sardinian isolated populations. Inhabitants of 10 villages in Ogliastra region participated in a cross-sectional survey in 2002–2008 (n = 9,647). Blood samples, blood pressure (BP), anthropometry and, data from a standardized interview were collected. Prevalence of MetS was estimated by the direct method of standardization. Variables associated with the MetS were identified using multilevel logistic regression. Heritability was determined using variance component models. MetS Prevalence was 19.6% (95% CI 18.9–20.4%) according to NCEP-ATPIII, 24.8% (95% CI 24.0–25.6%) according to IDF and, 29% (95% CI 28.1–29.8%) according to AHA/NHLBI harmonized criteria, ranging from 9 to 26% among villages. The most prevalent combination was BP + HDL-cholesterol (HDL) + triglycerides (TRIG) (19%), followed by BP + HDL + waist circumference (WAIST) (17%) and, BP + HDL + TRIG + WAIST (13.6%). Heritability of MetS was 48% (p = 1.62 × 10−25), as the two most common combinations (BP + HDL + TRIG and BP + HDL + WAIST) showed heritability of 53 and 52%, respectively. The larger genetic components of the two most frequent combinations determining MetS deserve greater investigation in order to understand the underlying mechanisms. Besides, further studies are warranted to confirm these findings both in isolated and outbred populations.
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Affiliation(s)
- Ginevra Biino
- Institute of Molecular Genetics-CNR, National Research Council of Italy, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Maria Pina Concas
- Institute of Population Genetics, National Research Council of Italy, Sassari, Italy
| | - Hellas Cena
- Unit of Human Nutrition, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | | | - Simona Vaccargiu
- Institute of Population Genetics, National Research Council of Italy, Sassari, Italy
| | - Massimiliano Cosso
- Institute of Population Genetics, National Research Council of Italy, Sassari, Italy
| | - Francesca Marras
- Institute of Population Genetics, National Research Council of Italy, Sassari, Italy
| | - Vittoria D'Esposito
- Dipartimento di Scienze Mediche Traslazionali, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Francesco Beguinot
- Dipartimento di Scienze Mediche Traslazionali, Università degli Studi di Napoli "Federico II", Naples, Italy ; Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS-CNR), Naples, Italy
| | - Mario Pirastu
- Institute of Population Genetics, National Research Council of Italy, Sassari, Italy
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Capra GF, Ganga A, Buondonno A, Grilli E, Gaviano C, Vacca S. Ethnopedology in the study of toponyms connected to the indigenous knowledge on soil resource. PLoS One 2015; 10:e0120240. [PMID: 25789985 PMCID: PMC4366272 DOI: 10.1371/journal.pone.0120240] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/20/2015] [Indexed: 11/18/2022] Open
Abstract
In taking an integrated ethnopedological approach, this study aims to investigate the meaning of the distribution of the toponyms used in traditional and recent cartography of Sardinia (southern Italy). It is particularly, but not only, focused on those related to soil resources. Sardinia is particularly interesting in this respect, as its unique history, geography, and linguistic position makes it one of the Italian and Mediterranean regions with the greatest number of toponyms. This research investigated the toponyms belonging to an important sub-region of Sardinia, called Ogliastra (central-eastern Sardinia). The research was conducted through the following integrated approach: i) toponymy research and collection from different sources; ii) database creation and translation of toponyms from the Sardinian language (SL); iii) categorization of toponyms; and iv) graphical, statistical, and cartographic data processing. Distribution and diversity of toponyms were assessed using the compiled database, coupled with a geographical information system (GIS). Of around 7700 toponyms collected, 79% had already been reported in SL, while just 21% were in Italian. Of the toponyms in SL, 77% are of known meaning and 54% of these toponyms were characterized by a meaning directly and/or indirectly connected to specific environmental features. On the whole, morphology would appear to be the primary environmental factor able to explain the complex, articulated presence, distribution, and typology of the investigated toponyms. A least squares regression analysis of pedodiversity vs. topodiversity shows a very closed distribution, with an impressive high correlation index (R2 = 0.824). The principal factor analysis (PFA) shows that such a connection may be morphologically based, thereby confirming that pedodiversity and topodiversity are strongly linked each other. Overall, the research shows that an integrated ethnopedological approach, combining indigenous and scientific knowledge may be of great interest in order to mitigate the impressive phenomena of the indigenous knowledge lost.
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Affiliation(s)
- Gian Franco Capra
- Dipartimento di Architettura, Design e Urbanistica, Università degli Studi di Sassari, Via Colombo n° 1, Nuoro, Italy
- * E-mail:
| | - Antonio Ganga
- Dipartimento di Architettura, Design e Urbanistica, Università degli Studi di Sassari, Via Colombo n° 1, Nuoro, Italy
| | - Andrea Buondonno
- Dipartimento di Architettura e Disegno Industriale “Luigi Vanvitelli”, Seconda Università degli Studi di Napoli, Abazia San Lorenzo ad Septimum, Borgo San Lorenzo, Aversa (Caserta), Italy
| | - Eleonora Grilli
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università degli Studi di Napoli, Via Vivaldi n° 43, Caserta, Italy
| | - Carla Gaviano
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Via Trentino n° 51, Cagliari, Italy
| | - Sergio Vacca
- Dipartimento di Architettura, Design e Urbanistica, Università degli Studi di Sassari, Via Colombo n° 1, Nuoro, Italy
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Messina F, Finocchio A, Rolfo MF, De Angelis F, Rapone C, Coletta M, Martínez-Labarga C, Biondi G, Berti A, Rickards O. Traces of forgotten historical events in mountain communities in Central Italy: A genetic insight. Am J Hum Biol 2015; 27:508-19. [PMID: 25728801 DOI: 10.1002/ajhb.22677] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 11/20/2014] [Accepted: 12/20/2014] [Indexed: 01/16/2023] Open
Abstract
OBJECTIVES Analysis of human genetic variation in mountain communities can shed light on the peopling of mountainous regions, perhaps revealing whether the remote geographic location spared them from outside invasion and preserved their gene pool from admixture. In this study, we created a model to assess genetic traces of historical events by reconstructing the paternal and maternal genetic history of seven small mountain villages in inland valleys of Central Italy. METHODS The communities were selected for their geographic isolation, attested biodemographic stability, and documented history prior to the Roman conquest. We studied the genetic structure by analyzing two hypervariable segments (HVS-I and HVS-II) of the mtDNA D-loop and several informative single nucleotide polymorphisms (SNPs) of the mtDNA coding region in 346 individuals, in addition to 17 short tandem repeats (STRs) and Y-chromosome SNPs in 237 male individuals. RESULTS For both uniparental markers, most of the haplogroups originated in Western Europe while some Near Eastern haplogroups were identified at low frequencies. However, there was an evident genetic similarity between the Central Italian samples and Near Eastern populations mainly in the male genetic pool. CONCLUSIONS The samples highlight an overall European genetic pattern both for mtDNA and Y chromosome. Notwithstanding this scenario, Y chromosome haplogroup Q, a common paternal lineage in Central/Western Asia but almost Europe-wide absent, was found, suggesting that Central Italy could have hosted a settlement from Anatolia that might be supported by cultural, topographic and genetic evidence.
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Affiliation(s)
- Francesco Messina
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Andrea Finocchio
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Mario Federico Rolfo
- Department of Historical, Philosophical and Social Sciences, Cultural and Territory Heritage, University of Rome 'Tor Vergata', Via Columbia n. 1, 00173, Rome, Italy
| | - Flavio De Angelis
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Cesare Rapone
- Carabinieri, Scientific Investigation Department, Viale di Tor di Quinto 151, 00191, Rome, Italy
| | - Martina Coletta
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Cristina Martínez-Labarga
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Gianfranco Biondi
- Department of Environmental Sciences, University of L'Aquila, Via Vetoio, 67010, L'Aquila, Italy
| | - Andrea Berti
- Carabinieri, Scientific Investigation Department, Viale di Tor di Quinto 151, 00191, Rome, Italy
| | - Olga Rickards
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
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15
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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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16
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Elhassan N, Gebremeskel EI, Elnour MA, Isabirye D, Okello J, Hussien A, Kwiatksowski D, Hirbo J, Tishkoff S, Ibrahim ME. The episode of genetic drift defining the migration of humans out of Africa is derived from a large east African population size. PLoS One 2014; 9:e97674. [PMID: 24845801 PMCID: PMC4028218 DOI: 10.1371/journal.pone.0097674] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 04/23/2014] [Indexed: 01/01/2023] Open
Abstract
Human genetic variation particularly in Africa is still poorly understood. This is despite a consensus on the large African effective population size compared to populations from other continents. Based on sequencing of the mitochondrial Cytochrome C Oxidase subunit II (MT-CO2), and genome wide microsatellite data we observe evidence suggesting the effective size (Ne) of humans to be larger than the current estimates, with a foci of increased genetic diversity in east Africa, and a population size of east Africans being at least 2-6 fold larger than other populations. Both phylogenetic and network analysis indicate that east Africans possess more ancestral lineages in comparison to various continental populations placing them at the root of the human evolutionary tree. Our results also affirm east Africa as the likely spot from which migration towards Asia has taken place. The study reflects the spectacular level of sequence variation within east Africans in comparison to the global sample, and appeals for further studies that may contribute towards filling the existing gaps in the database. The implication of these data to current genomic research, as well as the need to carry out defined studies of human genetic variation that includes more African populations; particularly east Africans is paramount.
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Affiliation(s)
- Nuha Elhassan
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Eyoab Iyasu Gebremeskel
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
- Department of Biology, Eritrea Institute of Technology, Mai-Nefhi, Eritrea
| | - Mohamed Ali Elnour
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Dan Isabirye
- Department of Biochemistry, Makerere University, Kampala, Uganda
| | - John Okello
- Department of Biochemistry, Makerere University, Kampala, Uganda
| | - Ayman Hussien
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Dominic Kwiatksowski
- Welcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Jibril Hirbo
- Department of Genetics and Biology, School of Medicine and School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sara Tishkoff
- Department of Genetics and Biology, School of Medicine and School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Muntaser E. Ibrahim
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
- * E-mail:
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17
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Sardinians genetic background explained by runs of homozygosity and genomic regions under positive selection. PLoS One 2014; 9:e91237. [PMID: 24651212 PMCID: PMC3961211 DOI: 10.1371/journal.pone.0091237] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 02/10/2014] [Indexed: 11/19/2022] Open
Abstract
The peculiar position of Sardinia in the Mediterranean sea has rendered its population an interesting biogeographical isolate. The aim of this study was to investigate the genetic population structure, as well as to estimate Runs of Homozygosity and regions under positive selection, using about 1.2 million single nucleotide polymorphisms genotyped in 1077 Sardinian individuals. Using four different methods--fixation index, inflation factor, principal component analysis and ancestry estimation--we were able to highlight, as expected for a genetic isolate, the high internal homogeneity of the island. Sardinians showed a higher percentage of genome covered by RoHs>0.5 Mb (F(RoH%0.5)) when compared to peninsular Italians, with the only exception of the area surrounding Alghero. We furthermore identified 9 genomic regions showing signs of positive selection and, we re-captured many previously inferred signals. Other regions harbor novel candidate genes for positive selection, like TMEM252, or regions containing long non coding RNA. With the present study we confirmed the high genetic homogeneity of Sardinia that may be explained by the shared ancestry combined with the action of evolutionary forces.
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18
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Bachis V, Calò CM, Vona G, Corrias L, Carreras-Torres R, Moral P. Analysis of 16 STRs of NOS gene regions and around in six sardinian populations (Italy). Am J Hum Biol 2014; 26:401-6. [DOI: 10.1002/ajhb.22533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/12/2014] [Accepted: 02/14/2014] [Indexed: 01/09/2023] Open
Affiliation(s)
- Valeria Bachis
- Department of Science of Life and Environment; University of Cagliari; Monserrato 09042 Italy
| | - Carla Maria Calò
- Department of Science of Life and Environment; University of Cagliari; Monserrato 09042 Italy
| | - Giuseppe Vona
- Department of Science of Life and Environment; University of Cagliari; Monserrato 09042 Italy
| | - Laura Corrias
- Department of Science of Life and Environment; University of Cagliari; Monserrato 09042 Italy
| | - Robert Carreras-Torres
- Department of Animal Biology and Anthropology; Institute of Biodiversity; University of Barcelona; Barcelona 08028 Spain
| | - Pedro Moral
- Department of Animal Biology and Anthropology; Institute of Biodiversity; University of Barcelona; Barcelona 08028 Spain
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19
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Coia V, Capocasa M, Anagnostou P, Pascali V, Scarnicci F, Boschi I, Battaggia C, Crivellaro F, Ferri G, Alù M, Brisighelli F, Busby GBJ, Capelli C, Maixner F, Cipollini G, Viazzo PP, Zink A, Destro Bisol G. Demographic histories, isolation and social factors as determinants of the genetic structure of Alpine linguistic groups. PLoS One 2013; 8:e81704. [PMID: 24312576 PMCID: PMC3847036 DOI: 10.1371/journal.pone.0081704] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 10/15/2013] [Indexed: 11/25/2022] Open
Abstract
Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of “local ethnicity” on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet to be understood aspects of the genetic structure of European populations.
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MESH Headings
- Chromosomes, Human, Y/genetics
- Demography/history
- Ethnicity/genetics
- Ethnicity/history
- Evolution, Molecular
- Female
- Gene Flow
- Genetic Variation
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- Humans
- Linguistics
- Male
- Mitochondria/genetics
- Polymorphism, Single Nucleotide
- White People/ethnology
- White People/genetics
- White People/history
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Affiliation(s)
- Valentina Coia
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
- * E-mail: (VC); (GDB)
| | - Marco Capocasa
- Dipartimento Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto Italiano di Antropologia, Rome, Italy
| | - Paolo Anagnostou
- Istituto Italiano di Antropologia, Rome, Italy
- Dipartimento Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Vincenzo Pascali
- Istituto di Medicina Legale e delle Assicurazioni, Università Cattolica di Roma, Rome, Italy
| | - Francesca Scarnicci
- Istituto di Medicina Legale e delle Assicurazioni, Università Cattolica di Roma, Rome, Italy
| | - Ilaria Boschi
- Istituto di Medicina Legale e delle Assicurazioni, Università Cattolica di Roma, Rome, Italy
| | - Cinzia Battaggia
- Dipartimento Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Federica Crivellaro
- Sezione di Antropologia, Museo Nazionale Preistorico Etnografico “Luigi Pigorini”, Rome, Italy
| | - Gianmarco Ferri
- Dipartimento Integrato di Servizi Diagnostici e di Laboratorio e di Medicina Legale, Università di Modena e Reggio Emilia, Modena, Italy
| | - Milena Alù
- Dipartimento Integrato di Servizi Diagnostici e di Laboratorio e di Medicina Legale, Università di Modena e Reggio Emilia, Modena, Italy
| | - Francesca Brisighelli
- Istituto di Medicina Legale e delle Assicurazioni, Università Cattolica di Roma, Rome, Italy
| | | | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Frank Maixner
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
| | - Giovanna Cipollini
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
| | - Pier Paolo Viazzo
- Dipartimento Culture, Politica e Società-Sezione Scienze Antropologiche, Università degli Studi di Torino, Turin, Italy
| | - Albert Zink
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
| | - Giovanni Destro Bisol
- Istituto Italiano di Antropologia, Rome, Italy
- Dipartimento Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
- * E-mail: (VC); (GDB)
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20
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Derenko M, Malyarchuk B, Bahmanimehr A, Denisova G, Perkova M, Farjadian S, Yepiskoposyan L. Complete mitochondrial DNA diversity in Iranians. PLoS One 2013; 8:e80673. [PMID: 24244704 PMCID: PMC3828245 DOI: 10.1371/journal.pone.0080673] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 10/07/2013] [Indexed: 11/19/2022] Open
Abstract
Due to its pivotal geographical location and proximity to transcontinental migratory routes, Iran has played a key role in subsequent migrations, both prehistoric and historic, between Africa, Asia and Europe. To shed light on the genetic structure of the Iranian population as well as on the expansion patterns and population movements which affected this region, the complete mitochondrial genomes of 352 Iranians were obtained. All Iranian populations studied here exhibit similarly high diversity values comparable to the other groups from the Caucasus, Anatolia and Europe. The results of AMOVA and MDS analyses did not associate any regional and/or linguistic group of populations in the Anatolia/Caucasus and Iran region pointing to close genetic positions of Persians and Qashqais to each other and to Armenians, and Azeris from Iran to Georgians. By reconstructing the complete mtDNA phylogeny of haplogroups R2, N3, U1, U3, U5a1g, U7, H13, HV2, HV12, M5a and C5c we have found a previously unexplored genetic connection between the studied Iranian populations and the Arabian Peninsula, India, Near East and Europe, likely the result of both ancient and recent gene flow. Our results for Persians and Qashqais point to a continuous increase of the population sizes from ∼24 kya to the present, although the phase between 14-24 kya is thought to be hyperarid according to the Gulf Oasis model. Since this would have affected hunter-gatherer ranges and mobility patterns and forced them to increasingly rely on coastal resources, this transition can explain the human expansion across the Persian Gulf region.
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Affiliation(s)
- Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
- * E-mail:
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Ardeshir Bahmanimehr
- Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, Armenia
| | - Galina Denisova
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Maria Perkova
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Shirin Farjadian
- Immunology Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Levon Yepiskoposyan
- Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, Armenia
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21
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Hagen CM, Aidt FH, Havndrup O, Hedley PL, Jespersgaard C, Jensen M, Kanters JK, Moolman-Smook JC, Møller DV, Bundgaard H, Christiansen M. MT-CYB mutations in hypertrophic cardiomyopathy. Mol Genet Genomic Med 2013; 1:54-65. [PMID: 24498601 PMCID: PMC3893158 DOI: 10.1002/mgg3.5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 02/18/2013] [Accepted: 02/21/2013] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial dysfunction is a characteristic of heart failure. Mutations in mitochondrial DNA, particularly in MT-CYB coding for cytochrome B in complex III (CIII), have been associated with isolated hypertrophic cardiomyopathy (HCM). We hypothesized that MT-CYB mutations might play an important causal or modifying role in HCM. The MT-CYB gene was sequenced from DNA isolated from blood from 91 Danish HCM probands. Nonsynonymous variants were analyzed by bioinformatics, molecular modeling and simulation. Two germline-inherited, putative disease-causing, nonsynonymous variants: m.15024G>A; p.C93Y and m.15482T>C; p.S246P were identified. Modeling showed that the p.C93Y mutation leads to disruption of the tertiary structure of Cytb by helix displacement, interfering with protein–heme interaction. The p.S246P mutation induces a diproline structure, which alters local secondary structure and induces a kink in the protein backbone, interfering with macromolecular interactions. These molecular effects are compatible with a leaky phenotype, that is, limited but progressive mitochondrial dysfunction. In conclusion, we find that rare, putative leaky mtDNA variants in MT-CYB can be identified in a cohort of HCM patients. We propose that further patients with HCM should be examined for mutations in MT-CYB in order to clarify the role of these variants.
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Affiliation(s)
- Christian M Hagen
- Department of Clinical Biochemistry, Immunology, and Genetics, Statens Serum Institut Copenhagen, Denmark ; Department of Biomedical Sciences, University of Copenhagen Copenhagen, Denmark
| | - Frederik H Aidt
- Department of Clinical Biochemistry, Immunology, and Genetics, Statens Serum Institut Copenhagen, Denmark ; Institute of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen Copenhagen, Denmark
| | - Ole Havndrup
- Department of Cardiology, Roskilde Sygehus Roskilde, Denmark
| | - Paula L Hedley
- Department of Clinical Biochemistry, Immunology, and Genetics, Statens Serum Institut Copenhagen, Denmark ; Department of Biomedical Sciences, Stellenbosch University Cape Town, South Africa
| | - Cathrine Jespersgaard
- Department of Clinical Biochemistry, Immunology, and Genetics, Statens Serum Institut Copenhagen, Denmark
| | - Morten Jensen
- Department of Medicine B, The Heart Center, Rigshospitalet Copenhagen, Denmark
| | - Jørgen K Kanters
- Department of Biomedical Sciences, University of Copenhagen Copenhagen, Denmark
| | | | - Daniel V Møller
- Department of Clinical Biochemistry, Immunology, and Genetics, Statens Serum Institut Copenhagen, Denmark
| | - Henning Bundgaard
- Department of Medicine B, The Heart Center, Rigshospitalet Copenhagen, Denmark
| | - Michael Christiansen
- Department of Clinical Biochemistry, Immunology, and Genetics, Statens Serum Institut Copenhagen, Denmark
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22
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Biino G, Parati G, Concas MP, Adamo M, Angius A, Vaccargiu S, Pirastu M. Environmental and genetic contribution to hypertension prevalence: data from an epidemiological survey on Sardinian genetic isolates. PLoS One 2013; 8:e59612. [PMID: 23527229 PMCID: PMC3603911 DOI: 10.1371/journal.pone.0059612] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 02/15/2013] [Indexed: 01/19/2023] Open
Abstract
Background and Objectives Hypertension represents a major cause of cardiovascular morbidity and mortality worldwide but its prevalence has been shown to vary in different countries. The reasons for such differences are still matter of debate, the relative contributions given by environmental and genetic factors being still poorly defined. We estimated the current prevalence, distribution and determinants of hypertension in isolated Sardinian populations and also investigated the environmental and genetic contribution to hypertension prevalence taking advantage of the characteristics of such populations. Methods and Results An epidemiological survey with cross-sectional design was carried out measuring blood pressure in 9845 inhabitants of 10 villages of Ogliastra region between 2002 and 2008. Regression analysis for assessing blood pressure determinants and variance component models for estimating heritability were performed. Overall 38.8% of this population had hypertension, its prevalence varying significantly by age, sex and among villages taking into account age and sex structure of their population. About 50% of hypertensives had prior cardiovascular disease. High blood pressure was independently associated with age, obesity related factors, heart rate, total cholesterol, alcohol consumption, low education and smoking status, all these factors contributing more in women than in men. Heritability was 27% for diastolic and 36% for systolic blood pressure, its contribution being significantly higher in men (57%) than in women (46%). Finally, the genetic correlation between systolic and diastolic blood pressure was 0.74, indicating incomplete pleiotropy. Conclusion Genetic factors involved in the expression of blood pressure traits account for about 30% of the phenotypic variance, but seem to play a larger role in men; comorbidities and environmental factors remain of predominant importance, but seem to contribute much more in women.
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Affiliation(s)
- Ginevra Biino
- Institute of Population Genetics, National Research Council of Italy, Sassari, Italy.
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23
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Al-Ettribi GM, Effat LK, El-Bassyouni HT, Zaki MS, Shanab G, Karim AM. Clinical and molecular findings in eight Egyptian patients with suspected mitochondrial disorders and optic atrophy. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2013. [DOI: 10.1016/j.ejmhg.2012.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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24
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Pennarun E, Kivisild T, Metspalu E, Metspalu M, Reisberg T, Moisan JP, Behar DM, Jones SC, Villems R. Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa. BMC Evol Biol 2012. [PMID: 23206491 PMCID: PMC3582464 DOI: 10.1186/1471-2148-12-234] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background A Southwest Asian origin and dispersal to North Africa in the Early Upper Palaeolithic era has been inferred in previous studies for mtDNA haplogroups M1 and U6. Both haplogroups have been proposed to show similar geographic patterns and shared demographic histories. Results We report here 24 M1 and 33 U6 new complete mtDNA sequences that allow us to refine the existing phylogeny of these haplogroups. The resulting phylogenetic information was used to genotype a further 131 M1 and 91 U6 samples to determine the geographic spread of their sub-clades. No southwest Asian specific clades for M1 or U6 were discovered. U6 and M1 frequencies in North Africa, the Middle East and Europe do not follow similar patterns, and their sub-clade divisions do not appear to be compatible with their shared history reaching back to the Early Upper Palaeolithic. The Bayesian Skyline Plots testify to non-overlapping phases of expansion, and the haplogroups’ phylogenies suggest that there are U6 sub-clades that expanded earlier than those in M1. Some M1 and U6 sub-clades could be linked with certain events. For example, U6a1 and M1b, with their coalescent ages of ~20,000–22,000 years ago and earliest inferred expansion in northwest Africa, could coincide with the flourishing of the Iberomaurusian industry, whilst U6b and M1b1 appeared at the time of the Capsian culture. Conclusions Our high-resolution phylogenetic dissection of both haplogroups and coalescent time assessments suggest that the extant main branching pattern of both haplogroups arose and diversified in the mid-later Upper Palaeolithic, with some sub-clades concomitantly with the expansion of the Iberomaurusian industry. Carriers of these maternal lineages have been later absorbed into and diversified further during the spread of Afro-Asiatic languages in North and East Africa.
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Affiliation(s)
- Erwan Pennarun
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu, Estonia.
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Robledo R, Corrias L, Bachis V, Puddu N, Mameli A, Vona G, Calò CM. Analysis of a Genetic Isolate: The Case of Carloforte (Italy). Hum Biol 2012; 84:735-54. [DOI: 10.3378/027.084.0602] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2013] [Indexed: 01/19/2023]
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Gürkan H, Ozal SA, Esgin H. Results of Mitochondrial DNA Sequence Analysis in Patients with Clinically Diagnosed Leber's Hereditary Optic Neuropathy. Balkan Med J 2012; 29:306-9. [PMID: 25207020 DOI: 10.5152/balkanmedj.2012.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 02/24/2012] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE To investigate possible mitochondrial DNA (mtDNA) mutations in patients with Leber's hereditary optic neuropathy (LHON) in order to provide a precise diagnosis and genetic counseling. MATERIAL AND METHODS Between 1982 and 2007, ten patients were clinically diagnosed with LHON and six of these patients agreed to be involved in this study. Six healthy individuals were also included as a control group. mtDNA was isolated from peripheral blood samples and polymerase chain reaction and mtDNA sequence analysis were performed. RESULTS In one of the six patients, a homoplasmic mutant m.11778G>A mutation was detected. All of the clinically diagnosed LHON patients and the control groups had the m.14212C>T and m.14580G>A single nucleotide polymorphisms (SNPs). The m.11719A>G SNP was detected in three of six patients and four of the controls. Two of the six patients had the m.3197T>C SNP and, in addition, the m.14258G>A SNP was found in one of these two patients, while neither of these mutations were present in the control group. CONCLUSION The clinical diagnosis of LHON could be supported by molecular genetics only in one patient by the detection of one mutation. The m.3197T>C and m.14258G>A SNPs should be considered as potential mtDNA mutations due to the fact that they were detected in the patient group. These mutations should be investigated further in large case groups for suspected gene loci that could lead to optic neuropathy.
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Affiliation(s)
- Hakan Gürkan
- Department of Medical Biology, İstanbul Faculty of Medicine, İstanbul University, İstanbul, Turkey
| | - Sadık Altan Ozal
- Department of Ophtalmology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Haluk Esgin
- Department of Ophtalmology, Faculty of Medicine, Trakya University, Edirne, Turkey
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Evidence of high genetic variation among linguistically diverse populations on a micro-geographic scale: a case study of the Italian Alps. J Hum Genet 2012; 57:254-60. [PMID: 22418692 DOI: 10.1038/jhg.2012.14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Although essential for the fine-scale reconstruction of genetic structure, only a few micro-geographic studies have been carried out in European populations. This study analyzes mitochondrial variation (651 bp of the hypervariable region plus 17 single-nucleotide polymorphisms) in 393 samples from nine populations from Trentino (Eastern Italian Alps), a small area characterized by a complex geography and high linguistic diversity. A high level of genetic variation, comparable to geographically dispersed European groups, was observed. We found a difference in the intensity of peopling processes between two longitudinal areas, as populations from the west-central part of the region show stronger signatures of expansion, whereas those from the eastern area are closer to the expectations of a stationary demographic state. This may be explained by geomorphological factors and is also supported by archeological data. Finally, our results reveal a striking difference in the way in which the two linguistically isolated populations are genetically related to the neighboring groups. The Ladin speakers were found to be genetically close to the Italian-speaking populations and differentiated from the other Dolomitic Ladins, whereas the German-speaking Cimbri behave as an outlier, showing signatures of founder effects and low growth rate.
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Fu Q, Rudan P, Pääbo S, Krause J. Complete mitochondrial genomes reveal neolithic expansion into Europe. PLoS One 2012; 7:e32473. [PMID: 22427842 PMCID: PMC3302788 DOI: 10.1371/journal.pone.0032473] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/31/2012] [Indexed: 11/18/2022] Open
Abstract
The Neolithic transition from hunting and gathering to farming and cattle breeding marks one of the most drastic cultural changes in European prehistory. Short stretches of ancient mitochondrial DNA (mtDNA) from skeletons of pre-Neolithic hunter-gatherers as well as early Neolithic farmers support the demic diffusion model where a migration of early farmers from the Near East and a replacement of pre-Neolithic hunter-gatherers are largely responsible for cultural innovation and changes in subsistence strategies during the Neolithic revolution in Europe. In order to test if a signal of population expansion is still present in modern European mitochondrial DNA, we analyzed a comprehensive dataset of 1,151 complete mtDNAs from present-day Europeans. Relying upon ancient DNA data from previous investigations, we identified mtDNA haplogroups that are typical for early farmers and hunter-gatherers, namely H and U respectively. Bayesian skyline coalescence estimates were then used on subsets of complete mtDNAs from modern populations to look for signals of past population expansions. Our analyses revealed a population expansion between 15,000 and 10,000 years before present (YBP) in mtDNAs typical for hunters and gatherers, with a decline between 10,000 and 5,000 YBP. These corresponded to an analogous population increase approximately 9,000 YBP for mtDNAs typical of early farmers. The observed changes over time suggest that the spread of agriculture in Europe involved the expansion of farming populations into Europe followed by the eventual assimilation of resident hunter-gatherers. Our data show that contemporary mtDNA datasets can be used to study ancient population history if only limited ancient genetic data is available.
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Affiliation(s)
- Qiaomei Fu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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Calò CM, Corrias L, Vona G, Bachis V, Robledo R. Sampling strategies in a linguistic isolate: results from mtDNA analysis. Am J Hum Biol 2012; 24:192-4. [PMID: 22287111 DOI: 10.1002/ajhb.22215] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 10/03/2011] [Accepted: 11/22/2011] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Sampling strategies are crucial issues in population genetics and anthropological studies. The sampling choice is related to the research question and the type of markers used. In this research, we compared two different sampling strategies in the Sardinian linguistic isolate of Carloforte (Italy). METHODS A first sampling (N = 49) was carried out through grandparents criterion: individuals selected for the study were born and resident in Carloforte, and unrelated for at least three generations. A second sampling (N = 50) was based on founders surnames (FS): selected participants were proved to be descendants of the village founders, and to have no ancestors in common, at least up to the grandparental generation. RESULTS The group selected through FS showed a greater gene diversity, which was confirmed by both network and haplogroup analysis. Among the shared haplogroups, we find clear differences in their frequencies. Sampling through grandparents criterion showed essentially the same haplogroups found in Sardinia, and with similar frequencies. Interesting results came from genetic tree. The FS sampling clustered with Northern African populations and it is located very far from Italian and Sardinian populations, whereas the grandparents criterion sampling clustered with Italian populations and it is located close to the other Sardinian populations. CONCLUSIONS Results showed that different sampling strategies can lead to contrasting results. As sampling through grandparents criterion is influenced by recent gene flow, we hypothesize that the difference observed with the two sampling strategies is due to the merging of Carloforte with Sardinian populations.
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Affiliation(s)
- Carla Maria Calò
- Department of Experimental Biology, University of Cagliari, 09042 Monserrato, Italy
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Scott TA, Arnold RS, Petros JA. Mitochondrial Cytochrome c Oxidase subunit 1 Sequence Variation in Prostate Cancer. SCIENTIFICA 2012; 2012:701810. [PMID: 24124627 PMCID: PMC3795349 DOI: 10.6064/2012/701810] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 05/03/2012] [Indexed: 06/02/2023]
Abstract
PURPOSE Mitochondrial DNA (mtDNA) gene mutations have been described in nearly every adult solid neoplasm including prostate cancer. There are marked racial differences in specific inherited mutations within the cytochrome c oxidase subunit 1 (COI) gene in individuals with prostate cancer (PCa). The purpose of this study was to identify the variation in COI gene sequence in prostate cancer patients and to compare the mutations in African and Caucasian Americans. MATERIALS AND METHODS We sequenced the COI gene in DNA derived from peripheral blood in 482 prostate cancer patients and 189 controls. All bases that differed from the revised Cambridge Reference Sequence (rCRS) were classified as either silent (non-amino acid altering) or missense (amino acid altering) and the compiled alterations were then compared between races and published reports of mutations in this gene in both Caucasian and African-Americans. RESULTS AND CONCLUSIONS We found inherited mtDNA COI missense variants in 8.8% of Caucasian prostate cancer patients (vs. 0.0% controls) and 72.8 % of African-American prostate cancer patients (vs. 64.3% controls) A total of 144 COI variants were identified, of which 30 were missense mutations. Of 482 PCa patients, 116 (24.1%) had one or more missense mutations. Further evaluation of this gene and these mutations may allow for the identification of genetically at-risk populations. The high rate of COI mutations in African-Americans may account for some of the racial disparity observed in prostate cancer.
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Affiliation(s)
- Takara A. Scott
- Department of Urology, Emory University, Atlanta, GA 30322, USA
| | - Rebecca S. Arnold
- Department of Urology, Emory University, Atlanta, GA 30322, USA
- Atlanta VA Medical Center, Decatur, GA 30033, USA
| | - John A. Petros
- Department of Urology, Emory University, Atlanta, GA 30322, USA
- Atlanta VA Medical Center, Decatur, GA 30033, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
- Department of Hematology & Medical Oncology, Emory University, Atlanta, GA 30322, USA
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Sanna D, Pala M, Cossu P, Dedola GL, Melis S, Fresu G, Morelli L, Obinu D, Tonolo G, Secchi G, Triunfo R, Lorenz JG, Scheinfeldt L, Torroni A, Robledo R, Francalacci P. Mendelian breeding units versus standard sampling strategies: Mitochondrial DNA variation in southwest Sardinia. Genet Mol Biol 2011; 34:187-94. [PMID: 21734814 PMCID: PMC3115307 DOI: 10.1590/s1415-47572011000200003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Accepted: 02/08/2011] [Indexed: 11/22/2022] Open
Abstract
We report a sampling strategy based on Mendelian Breeding Units (MBUs), representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and coding region) in unrelated healthy subjects from two different areas of Sardinia: the area around the town of Cabras and the western Campidano area. No statistically significant differences were observed when the two sampling methods were compared, indicating that the stringent sample selection needed to establish a MBU does not alter original genetic variability and haplogroup distribution. Therefore, the MBU sampling strategy can be considered a useful tool in association studies of complex traits.
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Affiliation(s)
- Daria Sanna
- Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, Sassari, Italy
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Application of a new method for GWAS in a related case/control sample with known pedigree structure: identification of new loci for nephrolithiasis. PLoS Genet 2011; 7:e1001281. [PMID: 21283782 PMCID: PMC3024262 DOI: 10.1371/journal.pgen.1001281] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 12/17/2010] [Indexed: 12/24/2022] Open
Abstract
In contrast to large GWA studies based on thousands of individuals and large meta-analyses combining GWAS results, we analyzed a small case/control sample for uric acid nephrolithiasis. Our cohort of closely related individuals is derived from a small, genetically isolated village in Sardinia, with well-characterized genealogical data linking the extant population up to the 16(th) century. It is expected that the number of risk alleles involved in complex disorders is smaller in isolated founder populations than in more diverse populations, and the power to detect association with complex traits may be increased when related, homogeneous affected individuals are selected, as they are more likely to be enriched with and share specific risk variants than are unrelated, affected individuals from the general population. When related individuals are included in an association study, correlations among relatives must be accurately taken into account to ensure validity of the results. A recently proposed association method uses an empirical genotypic covariance matrix estimated from genome-screen data to allow for additional population structure and cryptic relatedness that may not be captured by the genealogical data. We apply the method to our data, and we also investigate the properties of the method, as well as other association methods, in our highly inbred population, as previous applications were to outbred samples. The more promising regions identified in our initial study in the genetic isolate were then further investigated in an independent sample collected from the Italian population. Among the loci that showed association in this study, we observed evidence of a possible involvement of the region encompassing the gene LRRC16A, already associated to serum uric acid levels in a large meta-analysis of 14 GWAS, suggesting that this locus might lead a pathway for uric acid metabolism that may be involved in gout as well as in nephrolithiasis.
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Pereira L, Silva NM, Franco-Duarte R, Fernandes V, Pereira JB, Costa MD, Martins H, Soares P, Behar DM, Richards MB, Macaulay V. Population expansion in the North African late Pleistocene signalled by mitochondrial DNA haplogroup U6. BMC Evol Biol 2010; 10:390. [PMID: 21176127 PMCID: PMC3016289 DOI: 10.1186/1471-2148-10-390] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 12/21/2010] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The archaeology of North Africa remains enigmatic, with questions of population continuity versus discontinuity taking centre-stage. Debates have focused on population transitions between the bearers of the Middle Palaeolithic Aterian industry and the later Upper Palaeolithic populations of the Maghreb, as well as between the late Pleistocene and Holocene. RESULTS Improved resolution of the mitochondrial DNA (mtDNA) haplogroup U6 phylogeny, by the screening of 39 new complete sequences, has enabled us to infer a signal of moderate population expansion using Bayesian coalescent methods. To ascertain the time for this expansion, we applied both a mutation rate accounting for purifying selection and one with an internal calibration based on four approximate archaeological dates: the settlement of the Canary Islands, the settlement of Sardinia and its internal population re-expansion, and the split between haplogroups U5 and U6 around the time of the first modern human settlement of the Near East. CONCLUSIONS A Bayesian skyline plot placed the main expansion in the time frame of the Late Pleistocene, around 20 ka, and spatial smoothing techniques suggested that the most probable geographic region for this demographic event was to the west of North Africa. A comparison with U6's European sister clade, U5, revealed a stronger population expansion at around this time in Europe. Also in contrast with U5, a weak signal of a recent population expansion in the last 5,000 years was observed in North Africa, pointing to a moderate impact of the late Neolithic on the local population size of the southern Mediterranean coast.
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Affiliation(s)
- Luísa Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal.
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History, geography and population structure influence the distribution and heritability of blood and anthropometric quantitative traits in nine Sardinian genetic isolates. Genet Res (Camb) 2010; 92:199-208. [PMID: 20667164 DOI: 10.1017/s001667231000025x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Isolated founder populations which exhibit great genetic and environmental homogeneity provide an attractive setting for the study of quantitative traits (QTs). Geneticists have repeatedly turned to population isolates and the past successes have prompted increased interest among medical researchers. We studied nine small isolated villages of a secluded area of Sardinia (Ogliastra), all of them characterized by a few founders, high endogamy rates, slow population expansion and a distinct genetic makeup. Anthropometric and blood parameters, 43 QTs in all, were analysed in about 9000 voluntary subjects for whom extended genealogical information was available. We explored the distribution and examined mean differences of each trait among villages by analysis of variance (ANOVA). A heritability analysis with the variance component (VC) method was performed. Results show significant differences in the distribution of most traits between groups of villages located in two distinct geographical areas already identified by a previous population structure analysis, thus supporting the existence of differentiation among sub-populations in the same region. Heritability estimates range between 30 and 89%, demonstrating that genetic effects substantially contribute to phenotypic variation of all investigated traits and that this population provides excellent research conditions for gene-mapping projects. Results suggest that history, geographic location and population structure may have influenced the genetic and phenotypic features of these isolates. Our findings may be useful for the ongoing linkage and association studies in these isolates and suggest that a thorough characterization of population is valuable to better identify genes or variants that may be rare in the population at large and peculiar to single villages.
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Craniofacial morphometric variation and the biological history of the peopling of Sardinia. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2010; 61:385-412. [PMID: 20979998 DOI: 10.1016/j.jchb.2010.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 07/17/2010] [Indexed: 11/22/2022]
Abstract
The aim of this work is to explore the pattern of craniofacial morphometric variation and the relationships among five prehistoric Sardinian groups dated from Late Neolithic to the Nuragic Period (Middle and Late Bronze Age), in order to formulate hypotheses on the peopling history of Sardinia. Biological relationships with coeval populations of central peninsular Italy were also analysed to detect influences from and towards extra-Sardinian sources. Furthermore, comparison with samples of contemporary populations from Sardinia and from continental Italy provided an indication of the trend leading to the final part of the peopling history. Finally, Upper Palaeolithic and Mesolithic samples were included in the analyses to compare the prehistoric Sardinians with some of their potential continental ancestors. The analysis is based on multivariate techniques including Mahalanobis D(2) distance, non-parametric multidimensional scaling (MDS) and principal component analysis (PCA). The results showed the tendency to progressive differentiation between Sardinian groups and peninsular Italian groups, with the possible exception of a discontinuity showed by the Bonnànaro (Early Bronze Age) Sardinian sample. Several aspects of the morphological results were found to agree with the current genetic evidence available for the present-day Sardinian population and a Nuragic sample: (1) biological divergence between the Sardinian and peninsular Italian populations; (2) similarity/continuity among Neolithic, Bronze Age and recent Sardinians; (3) biological separation between the Nuragic and Etruscan populations; (4) contribution of a Palaeo-Mesolithic gene pool to the genetic structure of current Sardinians.
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Biino G, Balduini CL, Casula L, Cavallo P, Vaccargiu S, Parracciani D, Serra D, Portas L, Murgia F, Pirastu M. Analysis of 12,517 inhabitants of a Sardinian geographic isolate reveals that predispositions to thrombocytopenia and thrombocytosis are inherited traits. Haematologica 2010; 96:96-101. [PMID: 20823129 DOI: 10.3324/haematol.2010.029934] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Thrombocytopenia is a common finding in several diseases but almost nothing is known about the prevalence of thrombocytopenia in the general population. We examined the prevalence of thrombocytopenia and determinants of platelet count in a healthy population with a wide age range. DESIGN AND METHODS We performed a cross-sectional study on 12,517 inhabitants of ten villages (80% of residents) in a secluded area of Sardinia (Ogliastra). Participants underwent a complete blood count evaluation and a structured questionnaire, used to collect epidemiological data. RESULTS We observed a platelet count lower than 150 × 10⁹/L in 3.2% (2.8%-3.6%) of females and 4.8% (4.3%-5.4%) of males, with a value of 3.9% (3.6%-4.3%) in the entire population. Thrombocytopenia was mild (platelet count: 100 × 10⁹/L-150 × 10⁹/L), asymptomatic and not associated with other cytopenias or overt disorders in most cases. Its standardized prevalence was quite different in different villages, with values ranging from 1.5% to 6.8%, and was negatively correlated with the prevalence of a mild form of thrombocytosis, which ranged from 0.9% to 4.5%. Analysis of platelet counts across classes of age revealed that platelet number decreased progressively with aging. As a consequence, thrombocytopenia was nearly absent in young people and its prevalence increased regularly during lifetime. The opposite occurred for thrombocytosis. CONCLUSIONS Given the high genetic differentiation among Ogliastra villages with "high" and "low" platelet counts and the substantial heritability of this quantitative trait (54%), we concluded that the propensity to present mild and transient thrombocytosis in youth and to acquire mild thrombocytopenia during aging are new genetic traits.
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Kujanová M, Pereira L, Fernandes V, Pereira JB, Cerný V. Near eastern neolithic genetic input in a small oasis of the Egyptian Western Desert. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2009; 140:336-46. [PMID: 19425100 DOI: 10.1002/ajpa.21078] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Egyptian Western Desert lies on an important geographic intersection between Africa and Asia. Genetic diversity of this region has been shaped, in part, by climatic changes in the Late Pleistocene and Holocene epochs marked by oscillating humid and arid periods. We present here a whole genome analysis of mitochondrial DNA (mtDNA) and high-resolution molecular analysis of nonrecombining Y-chromosomal (NRY) gene pools of a demographically small but autochthonous population from the Egyptian Western Desert oasis el-Hayez. Notwithstanding signs of expected genetic drift, we still found clear genetic evidence of a strong Near Eastern input that can be dated into the Neolithic. This is revealed by high frequencies and high internal variability of several mtDNA lineages from haplogroup T. The whole genome sequencing strategy and molecular dating allowed us to detect the accumulation of local mtDNA diversity to 5,138 +/- 3,633 YBP. Similarly, theY-chromosome gene pool reveals high frequencies of the Near Eastern J1 and the North African E1b1b1b lineages, both generally known to have expanded within North Africa during the Neolithic. These results provide another piece of evidence of the relatively young population history of North Africa.
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Affiliation(s)
- Martina Kujanová
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
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Pala M, Achilli A, Olivieri A, Kashani BH, Perego UA, Sanna D, Metspalu E, Tambets K, Tamm E, Accetturo M, Carossa V, Lancioni H, Panara F, Zimmermann B, Huber G, Al-Zahery N, Brisighelli F, Woodward SR, Francalacci P, Parson W, Salas A, Behar DM, Villems R, Semino O, Bandelt HJ, Torroni A. Mitochondrial haplogroup U5b3: a distant echo of the epipaleolithic in Italy and the legacy of the early Sardinians. Am J Hum Genet 2009; 84:814-21. [PMID: 19500771 PMCID: PMC2694970 DOI: 10.1016/j.ajhg.2009.05.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 05/15/2009] [Accepted: 05/15/2009] [Indexed: 11/16/2022] Open
Abstract
There are extensive data indicating that some glacial refuge zones of southern Europe (Franco-Cantabria, Balkans, and Ukraine) were major genetic sources for the human recolonization of the continent at the beginning of the Holocene. Intriguingly, there is no genetic evidence that the refuge area located in the Italian Peninsula contributed to this process. Here we show, through phylogeographic analyses of mitochondrial DNA (mtDNA) variation performed at the highest level of molecular resolution (52 entire mitochondrial genomes), that the most likely homeland for U5b3-a haplogroup present at a very low frequency across Europe-was the Italian Peninsula. In contrast to mtDNA haplogroups that expanded from other refugia, the Holocene expansion of haplogroup U5b3 toward the North was restricted by the Alps and occurred only along the Mediterranean coasts, mainly toward nearby Provence (southern France). From there, approximately 7,000-9,000 years ago, a subclade of this haplogroup moved to Sardinia, possibly as a result of the obsidian trade that linked the two regions, leaving a distinctive signature in the modern people of the island. This scenario strikingly matches the age, distribution, and postulated geographic source of a Sardinian Y chromosome haplogroup (I2a2-M26), a paradigmatic case in the European context of a founder event marking both female and male lineages.
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Affiliation(s)
- Maria Pala
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | - Alessandro Achilli
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia 06123, Italy
| | - Anna Olivieri
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | | | - Ugo A. Perego
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA
| | - Daria Sanna
- Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, Sassari 07100, Italy
| | - Ene Metspalu
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Kristiina Tambets
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Erika Tamm
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Matteo Accetturo
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | - Valeria Carossa
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | - Hovirag Lancioni
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia 06123, Italy
| | - Fausto Panara
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia 06123, Italy
| | - Bettina Zimmermann
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck A-6020, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck A-6020, Austria
| | - Nadia Al-Zahery
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
- Department of Biotechnology, College of Science, University of Baghdad, Iraq
| | - Francesca Brisighelli
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses; and Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia 15782, Spain
| | - Scott R. Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA
| | - Paolo Francalacci
- Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, Sassari 07100, Italy
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck A-6020, Austria
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses; and Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia 15782, Spain
| | - Doron M. Behar
- Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel
| | - Richard Villems
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Ornella Semino
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | | | - Antonio Torroni
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
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Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards MB. Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 2009; 84:740-59. [PMID: 19500773 DOI: 10.1016/j.ajhg.2009.05.001] [Citation(s) in RCA: 487] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Revised: 04/20/2009] [Accepted: 05/01/2009] [Indexed: 11/15/2022] Open
Abstract
There is currently no calibration available for the whole human mtDNA genome, incorporating both coding and control regions. Furthermore, as several authors have pointed out recently, linear molecular clocks that incorporate selectable characters are in any case problematic. We here confirm a modest effect of purifying selection on the mtDNA coding region and propose an improved molecular clock for dating human mtDNA, based on a worldwide phylogeny of > 2000 complete mtDNA genomes and calibrating against recent evidence for the divergence time of humans and chimpanzees. We focus on a time-dependent mutation rate based on the entire mtDNA genome and supported by a neutral clock based on synonymous mutations alone. We show that the corrected rate is further corroborated by archaeological dating for the settlement of the Canary Islands and Remote Oceania and also, given certain phylogeographic assumptions, by the timing of the first modern human settlement of Europe and resettlement after the Last Glacial Maximum. The corrected rate yields an age of modern human expansion in the Americas at approximately 15 kya that-unlike the uncorrected clock-matches the archaeological evidence, but continues to indicate an out-of-Africa dispersal at around 55-70 kya, 5-20 ky before any clear archaeological record, suggesting the need for archaeological research efforts focusing on this time window. We also present improved rates for the mtDNA control region, and the first comprehensive estimates of positional mutation rates for human mtDNA, which are essential for defining mutation models in phylogenetic analyses.
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Affiliation(s)
- Pedro Soares
- Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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Bandelt HJ, Salas A, Taylor RW, Yao YG. Exaggerated status of "novel" and "pathogenic" mtDNA sequence variants due to inadequate database searches. Hum Mutat 2009; 30:191-6. [PMID: 18800376 DOI: 10.1002/humu.20846] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Given its relative ease, screening the entire mitochondrial DNA (mtDNA) for heteroplasmic or novel homoplasmic mutations has become part of the routine diagnostic workup for the molecular geneticist confronted with a disease case exhibiting clinical and biochemical features of mitochondrial dysfunction. "Novelty" of a given mtDNA variant is most often equated with nonregistration in the extensive MITOMAP database (www.mitomap.org). This practice has led to a number of spurious findings and wrong conclusions concerning the pathogenic status of specific mtDNA mutations, especially in the absence of proper evaluation and pathogenicity scoring. We demonstrate by way of real cases targeting the mt-tRNA(Cys) (MT-TC) gene and a stretch within the MT-ND3 gene, that a straightforward Google search can identify twice as many previously observed mutations than any MITOMAP query could achieve. Further, we reassess the recent rediscovery of m.15287T>C by listing all known occurrences and, where possible, providing the haplogroup context, shedding new light on the potential pathogenicity status of m.15287T>C.
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Pistis G, Piras I, Pirastu N, Persico I, Sassu A, Picciau A, Prodi D, Fraumene C, Mocci E, Manias MT, Atzeni R, Cosso M, Pirastu M, Angius A. High differentiation among eight villages in a secluded area of Sardinia revealed by genome-wide high density SNPs analysis. PLoS One 2009; 4:e4654. [PMID: 19247500 PMCID: PMC2646134 DOI: 10.1371/journal.pone.0004654] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 01/29/2009] [Indexed: 01/21/2023] Open
Abstract
To better design association studies for complex traits in isolated populations it's important to understand how history and isolation moulded the genetic features of different communities. Population isolates should not “a priori” be considered homogeneous, even if the communities are not distant and part of a small region. We studied a particular area of Sardinia called Ogliastra, characterized by the presence of several distinct villages that display different history, immigration events and population size. Cultural and geographic isolation characterized the history of these communities. We determined LD parameters in 8 villages and defined population structure through high density SNPs (about 360 K) on 360 unrelated people (45 selected samples from each village). These isolates showed differences in LD values and LD map length. Five of these villages show high LD values probably due to their reduced population size and extreme isolation. High genetic differentiation among villages was detected. Moreover population structure analysis revealed a high correlation between genetic and geographic distances. Our study indicates that history, geography and biodemography have influenced the genetic features of Ogliastra communities producing differences in LD and population structure. All these data demonstrate that we can consider each village an isolate with specific characteristics. We suggest that, in order to optimize the study design of complex traits, a thorough characterization of genetic features is useful to identify the presence of sub-populations and stratification within genetic isolates.
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Affiliation(s)
- Giorgio Pistis
- Istituto di Genetica delle Popolazioni, CNR, Alghero, Sassari, Italy
| | | | | | - Ivana Persico
- Istituto di Genetica delle Popolazioni, CNR, Alghero, Sassari, Italy
| | | | | | | | | | | | | | | | | | - Mario Pirastu
- Istituto di Genetica delle Popolazioni, CNR, Alghero, Sassari, Italy
- Shardna Life Sciences, Pula, Cagliari, Italy
| | - Andrea Angius
- Istituto di Genetica delle Popolazioni, CNR, Alghero, Sassari, Italy
- Shardna Life Sciences, Pula, Cagliari, Italy
- * E-mail:
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Ennafaa H, Cabrera VM, Abu-Amero KK, González AM, Amor MB, Bouhaha R, Dzimiri N, Elgaaïed AB, Larruga JM. Mitochondrial DNA haplogroup H structure in North Africa. BMC Genet 2009; 10:8. [PMID: 19243582 PMCID: PMC2657161 DOI: 10.1186/1471-2156-10-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 02/25/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Strait of Gibraltar separating the Iberian Peninsula from North Africa is thought to be a stronger barrier to gene flow for male than for female lineages. However, the recent subdivision of the haplogroup H at mitochondrial DNA (mtDNA) level has revealed greater genetic differentiation among geographic regions than previously detected. The dissection of the mtDNA haplogroup H in North Africa, and its comparison with the Iberian Peninsula and Near-East profiles would help clarify the relative affinities among these regions. RESULTS Like the Iberian Peninsula, the dominant mtDNA haplogroup H subgroups in North Africa are H1 (42%) and H3 (13%). The similarity between these regions is stronger in the North-West edge affecting mainly Moroccan Arabs, West Saharans and Mauritanians, and decreases eastwards probably due to gene flow from Near East as attested for the higher frequencies of H4, H5, H7, H8 and H11 subgroups. Moroccan Berbers show stronger affinities with Tunisian and Tunisian Berbers than with Moroccan Arabs. Coalescence ages for H1 (11 +/- 2 ky) and H3 (11 +/- 4 ky) in North Africa point to the possibility of a late Palaeolithic settlement for these lineages similar to those found for other mtDNA haplogroups. Total and partial mtDNA genomic sequencing unveiled stronger mtDNA differentiation among regions than previously found using HVSI mtDNA based analysis. CONCLUSION The subdivision of the mtDNA haplogroup H in North Africa has confirmed that the genetic differentiation found among Western and Eastern populations is mainly due to geographical rather than cultural barriers. It also shows that the historical Arabian role on the region had more a cultural than a demic effect. Whole mtDNA sequencing of identical H haplotypes based on HVSI and RFLP information has unveiled additional mtDNA differences between North African and Iberian Peninsula lineages, pointing to an older mtDNA genetic flow between regions than previously thought. Based on this new information, it seems that the Strait of Gibraltar barrier affected both male and female gene flow in a similar fashion.
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Affiliation(s)
- Hajer Ennafaa
- Laboratory of Genetics, Immunology and Human Pathology at the Faculty of Sciences of Tunis, Faculty of Sciences of Tunis, University El Manar I, Tunis, Tunisia.
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Costa MD, Cherni L, Fernandes V, Freitas F, Ammar El Gaaied AB, Pereira L. Data from complete mtDNA sequencing of Tunisian centenarians: testing haplogroup association and the "golden mean" to longevity. Mech Ageing Dev 2008; 130:222-6. [PMID: 19133286 DOI: 10.1016/j.mad.2008.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2008] [Revised: 11/18/2008] [Accepted: 12/06/2008] [Indexed: 10/21/2022]
Abstract
Since the mitochondrial theory of ageing was proposed, mitochondrial DNA (mtDNA) diversity has been largely studied in old people, however complete genomes are still rare, being limited to Japanese and UK/US samples. In this work, we evaluated possible longevity associated polymorphisms/haplogroups in an African population, from Tunisia, by performing complete mtDNA sequencing. This population has a mixed Eurasian/sub-Saharan mtDNA gene pool, which could potentially facilitate the evaluation of association for sub-Saharan lineages. Sub-Saharan haplogroups were shown to be significantly less represented in centenarians (9.5%) than in controls (54.5%), but it is not possible to rule out an influence of population structure, which is high in these populations. No recurrent polymorphism were more frequent in centenarians than in controls, and although the Tunisian centenarians presented less synonymous and replacement polymorphisms than controls, this difference was not statistically significant. So far, it does not seem that centenarians have significantly less mildly deleterious substitutions, not only in Tunisia but also in Japanese and UK/US samples, as tested here, not favouring a "golden mean" to longevity.
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Affiliation(s)
- Marta D Costa
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Porto, Portugal
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Ermini L, Olivieri C, Rizzi E, Corti G, Bonnal R, Soares P, Luciani S, Marota I, De Bellis G, Richards MB, Rollo F. Complete mitochondrial genome sequence of the Tyrolean Iceman. Curr Biol 2008; 18:1687-93. [PMID: 18976917 DOI: 10.1016/j.cub.2008.09.028] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 08/22/2008] [Accepted: 09/03/2008] [Indexed: 11/29/2022]
Abstract
The Tyrolean Iceman was a witness to the Neolithic-Copper Age transition in Central Europe 5350-5100 years ago, and his mummified corpse was recovered from an Alpine glacier on the Austro-Italian border in 1991 [1]. Using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products, we have retrieved the first complete mitochondrial-genome sequence of a prehistoric European. We have then compared it with 115 related extant lineages from mitochondrial haplogroup K. We found that the Iceman belonged to a branch of mitochondrial haplogroup K1 that has not yet been identified in modern European populations. This is the oldest complete Homo sapiens mtDNA genome generated to date. The results point to the potential significance of complete-ancient-mtDNA studies in addressing questions concerning the genetic history of human populations that the phylogeography of modern lineages is unable to tackle.
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Affiliation(s)
- Luca Ermini
- Laboratorio di Archeo-Antropologia Molecolare/DNA Antico, Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, 62032 Camerino, Italy
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45
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Sridhar S, Lam F, Blelloch GE, Ravi R, Schwartz R. Direct maximum parsimony phylogeny reconstruction from genotype data. BMC Bioinformatics 2007; 8:472. [PMID: 18053244 PMCID: PMC2222657 DOI: 10.1186/1471-2105-8-472] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Accepted: 12/05/2007] [Indexed: 11/18/2022] Open
Abstract
Background Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. Results In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Conclusion Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.
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Affiliation(s)
- Srinath Sridhar
- Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA.
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Bandelt HJ, Salas A, Bravi CM. What is a 'novel' mtDNA mutation--and does 'novelty' really matter? J Hum Genet 2006; 51:1073-1082. [PMID: 17021933 DOI: 10.1007/s10038-006-0066-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2006] [Accepted: 08/29/2006] [Indexed: 01/08/2023]
Abstract
The hunt for pathogenic mitochondrial DNA (mtDNA) mutations is often fueled by the seeming novelty of mutations that are either nonsynonymous or affect the protein synthesis machinery in patients. In order to determine the novelty of a detected mutation, the working geneticist nearly always consults MITOMAP--often exclusively. By reanalyzing some case studies of refractory anemia with ring sideroblasts, prostate cancer, and hearing impairment, we demonstrate that the practice of solely relying on MITOMAP can be most misleading. A notorious example is the T1243C mutation, which was assessed to be novel and deemed to be associated with some (rare) disease simply because researchers did not realize that T1243C defines a deep branch in the Eurasian mtDNA phylogeny. The majority of 'novel' mutations suspected of being pathogenic are in actual fact known (and presumably neutral) polymorphisms (although unknown to MITOMAP), and this becomes glaringly evident when proper database searches and straightforward Internet queries are carried out.
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Affiliation(s)
- Hans-Jürgen Bandelt
- Department of Mathematics, University of Hamburg, Bundesstr. 55, 20146, Hamburg, Germany.
| | - Antonio Salas
- Unidad de Genética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, 15782, Galicia, Spain
- Centro Nacional de Genotipado (CeGen), Hospital Clínico Universitario, 15706, Galicia, Spain
| | - Claudio M Bravi
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), P.O. Box 403, 1900, La Plata, Argentina
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