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Yordanov G, Palova N, Mehandjyiski I, Hristov P. Mitochondrial DNA sequencing illuminates genetic diversity and origin of Hunagrian Nonius horse breed and his relatives - Danubian horse and Serbian Nonius. Anim Biotechnol 2023; 34:3897-3907. [PMID: 37489100 DOI: 10.1080/10495398.2023.2237533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
From a historical perspective, horse breeding in Bulgaria has been very well developed since the time of the Thracians (early Bronze Age c. 3000 BCE). Archaeological discoveries from this era present us with an extremely rich type diversity, including wild and local primitive horses, the prototype of heavy draft horses, and fine riding horses.The objective of this study was to investigate the genetic structure of unexamined populations of three closely related horse breeds - the Danubian Nonius Hungarian Nonius and Serbian Nonius horses. A 608 bp long fragment of the mtDNA D-loop region was amplified and sequenced. The obtained results showed completely different genetic profiles between the investigated breeds. We identified nine of the 17 haplogroups described in modern horses. Most of the obtained sequences fell into M, L, G, and O'P lineages, which reflects the genetic profiles of the ancestral mares that were probably used at the initial stages of formation of the breeds. The population of the Danubian horse was characterized by a high prevalence of Central Asian specific haplogroup G (45%), followed by Western Eurasian specific haplogroups L and M (both about 21%). In contrast to the Danubian horse, in the Nonius breed the highest frequency of Western Eurasian haplogroup M (43.5%) was found, followed by Middle Eastern haplogroups O'P (26.1%) Central Asian specific E (13.0%) and G (13.1%). The Serbian Nonius horse showed a completely different genetic profile with a prevalence of the rare for Europe haplogroup D (66.7%), followed by Central Asian specific G (16.7%). The high mitochondrial haplotype diversity (Hd = 0.886) found in the investigated samples is evidence for multiple maternal origins in all populations.In conclusion, the obtained results demonstrated a high percentage of haplogroup sharing especially in the Danubian and Hungarian Nonius horse breeds, which reflects the possible common origins of the two breeds. In contrast to these breeds, the Serbian Nonius, despite the small number of investigated animals, showed a specific genetic profile, which could be explained by different and independent origins.
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Affiliation(s)
- Georgi Yordanov
- Executive Agency for Selection and Reproduction in Animal Breeding, Sofia, Bulgaria
| | - Nadezhda Palova
- Scientific Center of Agriculture, Agricultural Academy, Sredets, Bulgaria
| | - Ivan Mehandjyiski
- Research Centre of Stockbreeding and Agriculture, Agricultural Academy, Smolyan, Bulgaria
| | - Peter Hristov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
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Kristjansson D, Schurr TG, Bohlin J, Jugessur A. Phylogeographic history of mitochondrial haplogroup J in Scandinavia. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:298-315. [PMID: 36790764 PMCID: PMC10100211 DOI: 10.1002/ajpa.24666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/10/2022] [Accepted: 11/13/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Mitochondrial DNA haplogroup J is the third most frequent haplogroup in modern-day Scandinavia, although it did not originate there. To infer the genetic history of haplogroup J in Scandinavia, we examined worldwide mitogenome sequences using a maximum-likelihood phylogenetic approach. METHODS Haplogroup J mitogenome sequences were gathered from GenBank (n = 2245) and aligned against the ancestral Reconstructed Sapiens Reference Sequence. We also analyzed haplogroup J Viking Age sequences from the European Nucleotide Archive (n = 54). Genetic distances were estimated from these data and projected onto a maximum likelihood rooted phylogenetic tree to analyze clustering and branching dates. RESULTS Haplogroup J originated approximately 42.6 kya (95% CI: 30.0-64.7), with several of its earliest branches being found within the Arabian Peninsula and Northern Africa. J1b was found most frequently in the Near East and Arabian Peninsula, while J1c occurred most frequently in Europe. Based on phylogenetic dating, subhaplogroup J1c has its early roots in the Mediterranean and Western Balkans. Otherwise, the majority of the branches found in Scandinavia are younger than those seen elsewhere, indicating that haplogroup J dispersed relatively recently into Northern Europe, most plausibly with Neolithic farmers. CONCLUSIONS Haplogroup J appeared when Scandinavia was transitioning to agriculture over 6 kya, with J1c being the most common lineage there today. Changes in the distribution of haplogroup J mtDNAs were likely driven by the expansion of farming from West Asia into Southern Europe, followed by a later expansion into Scandinavia, with other J subhaplogroups appearing among Scandinavian groups as early as the Viking Age.
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Affiliation(s)
- Dana Kristjansson
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jon Bohlin
- Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
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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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The role of mtDNA haplogroups on metabolic features in narcolepsy type 1. Mitochondrion 2022; 63:37-42. [PMID: 35051655 DOI: 10.1016/j.mito.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 11/24/2022]
Abstract
Narcolepsy type 1 (NT1) is due to selective loss of hypocretin (hcrt)-producing-neurons. Hcrt is a neuropeptide regulating the sleep/wake cycle, as well as feeding behavior. A subset of NT1 patients become overweight/obese, with a dysmetabolic phenotype. We hypothesized that mitochondrial DNA (mtDNA) sequence variation might contribute to the metabolic features in NT1 and we undertook an exploratory survey of mtDNA haplogroups in a cohort of well-characterized patients. We studied 246 NT1 Italian patients, fully defined for their metabolic features, including obesity, hypertension, low HDL, hypertriglyceridemia and hyperglycemia. For haplogroup assignment, the mtDNA control region was sequenced in combination with an assessment of diagnostic markers in the coding region. NT1 patients displayed the same mtDNA haplogroups (H, HV, J, K, T, U) frequency as those reported in the general Italian population. The majority of NT1 patients (64%) were overweight: amongst these, 35% were obese, 48% had low HDL cholesterol levels, and 31% had hypertriglyceridemia. We identified an association between haplogroups J, K and hypertriglyceridemia (P=0.03, 61.5% and 61.5%, respectively vs. 31.3% of the whole sample) and after correction for age and sex, we observed a reduction of these associations (OR=3.65, 95%CI=0.76-17.5, p=0.106 and 1.73, 0.52-5.69, p=0.368, respectively). The low HDL level showed a trend for association with haplogroup J (P=0.09, 83.3% vs. 47.4% of the whole sample) and after correction we observed an OR=6.73, 95%CI=0.65-69.9, p=0.110. Our study provides the first indication that mtDNA haplogroups J and K can modulate metabolic features of NT1 patients, linking mtDNA variation to the dysmetabolic phenotype in NT1.
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Posth C, Zaro V, Spyrou MA, Vai S, Gnecchi-Ruscone GA, Modi A, Peltzer A, Mötsch A, Nägele K, Vågene ÅJ, Nelson EA, Radzevičiūtė R, Freund C, Bondioli LM, Cappuccini L, Frenzel H, Pacciani E, Boschin F, Capecchi G, Martini I, Moroni A, Ricci S, Sperduti A, Turchetti MA, Riga A, Zavattaro M, Zifferero A, Heyne HO, Fernández-Domínguez E, Kroonen GJ, McCormick M, Haak W, Lari M, Barbujani G, Bondioli L, Bos KI, Caramelli D, Krause J. The origin and legacy of the Etruscans through a 2000-year archeogenomic time transect. SCIENCE ADVANCES 2021; 7:eabi7673. [PMID: 34559560 PMCID: PMC8462907 DOI: 10.1126/sciadv.abi7673] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The origin, development, and legacy of the enigmatic Etruscan civilization from the central region of the Italian peninsula known as Etruria have been debated for centuries. Here we report a genomic time transect of 82 individuals spanning almost two millennia (800 BCE to 1000 CE) across Etruria and southern Italy. During the Iron Age, we detect a component of Indo-European–associated steppe ancestry and the lack of recent Anatolian-related admixture among the putative non–Indo-European–speaking Etruscans. Despite comprising diverse individuals of central European, northern African, and Near Eastern ancestry, the local gene pool is largely maintained across the first millennium BCE. This drastically changes during the Roman Imperial period where we report an abrupt population-wide shift to ~50% admixture with eastern Mediterranean ancestry. Last, we identify northern European components appearing in central Italy during the Early Middle Ages, which thus formed the genetic landscape of present-day Italian populations.
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Affiliation(s)
- Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72074, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen 72074, Germany
| | - Valentina Zaro
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Maria A. Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72074, Germany
| | - Stefania Vai
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Guido A. Gnecchi-Ruscone
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Alexander Peltzer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Angela Mötsch
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Åshild J. Vågene
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen 1350, Denmark
| | - Elizabeth A. Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA
| | - Rita Radzevičiūtė
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Cäcilia Freund
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | | | - Luca Cappuccini
- Department of History, Archeology, Geography, Art and Entertainment, University of Florence, Firenze 50121, Italy
| | - Hannah Frenzel
- Anatomy Institute, University of Leipzig, Leipzig 04103, Germany
| | - Elsa Pacciani
- Superintendence of Archaeology, Fine Arts and Landscape for Firenze, Pistoia and Prato, Italy
| | - Francesco Boschin
- Department of Physical Sciences, Earth and Environment, Research Unit Prehistory and Anthropology, University of Siena, Siena 53100, Italy
| | - Giulia Capecchi
- Department of Physical Sciences, Earth and Environment, Research Unit Prehistory and Anthropology, University of Siena, Siena 53100, Italy
| | - Ivan Martini
- Department of Physical Sciences, Earth and Environment, University of Siena, Siena 53100, Italy
| | - Adriana Moroni
- Department of Physical Sciences, Earth and Environment, Research Unit Prehistory and Anthropology, University of Siena, Siena 53100, Italy
| | - Stefano Ricci
- Department of Physical Sciences, Earth and Environment, Research Unit Prehistory and Anthropology, University of Siena, Siena 53100, Italy
| | - Alessandra Sperduti
- Bioarchaeology Service, Museum of Civilizations, Rome 00144, Italy
- Asia, Africa and Mediterranean Department, University of Naples, Naples 80134, Italy
| | | | - Alessandro Riga
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Monica Zavattaro
- Museum of Anthropology and Ethnology, Museum System of the University of Florence, Florence 50122, Italy
| | - Andrea Zifferero
- Department of History and Cultural Heritage, University of Siena, Siena 53100, Italy
| | - Henrike O. Heyne
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
- Program for Medical and Population Genetics/Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Guus J. Kroonen
- Department of Nordic Studies and Linguistics, University of Copenhagen, Copenhagen 2300, Denmark
- Leiden University Center for Linguistics, Leiden 2311 BE, Netherlands
| | - Michael McCormick
- Initiative for the Science of the Human Past, Department of History-Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Harvard University, Cambridge, MA 02138, USA
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Martina Lari
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy
| | - Luca Bondioli
- Bioarchaeology Service, Museum of Civilizations, Rome 00144, Italy
- Department of Cultural Heritage, University of Padua, Padua 35139, Italy
| | - Kirsten I. Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - David Caramelli
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
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Aneli S, Caldon M, Saupe T, Montinaro F, Pagani L. Through 40,000 years of human presence in Southern Europe: the Italian case study. Hum Genet 2021; 140:1417-1431. [PMID: 34410492 PMCID: PMC8460580 DOI: 10.1007/s00439-021-02328-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/29/2021] [Indexed: 12/16/2022]
Abstract
The Italian Peninsula, a natural pier across the Mediterranean Sea, witnessed intricate population events since the very beginning of the human occupation in Europe. In the last few years, an increasing number of modern and ancient genomes from the area have been published by the international research community. This genomic perspective started unveiling the relevance of Italy to understand the post-Last Glacial Maximum (LGM) re-peopling of Europe, the earlier phase of the Neolithic westward migrations, and its linking role between Eastern and Western Mediterranean areas after the Iron Age. However, many open questions are still waiting for more data to be addressed in full. With this review, we summarize the current knowledge emerging from the available ancient Italian individuals and, by re-analysing them all at once, we try to shed light on the avenues future research in the area should cover. In particular, open questions concern (1) the fate of pre-Villabruna Europeans and to what extent their genomic components were absorbed by the post-LGM hunter-gatherers; (2) the role of Sicily and Sardinia before LGM; (3) to what degree the documented genetic structure within the Early Neolithic settlers can be described as two separate migrations; (4) what are the population events behind the marked presence of an Iranian Neolithic-like component in Bronze Age and Iron Age Italian and Southern European samples.
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Affiliation(s)
- Serena Aneli
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.
| | - Matteo Caldon
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia.,Department of Biology-Genetics, University of Bari, Via Edoardo Orabona 4, 70125, Bari, Italy
| | - Luca Pagani
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.,Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
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7
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Yordanov G, Zlatanovic N, Palova N, Mehandjyiski I, Neov B, Radoslavov G, Hristov P. Sequence analysis of the mitochondrial D-loop region throws a new light on the origin of Hungarian Nonius, Danubian Horse and Serbian Nonius. Acta Vet Hung 2021; 69:239-248. [PMID: 34343110 DOI: 10.1556/004.2021.00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/07/2021] [Indexed: 11/19/2022]
Abstract
The objective of our study was to investigate the genetic structure of yet uninvestigated populations of three closely related horse breeds - the Danubian Horse, the Hungarian Nonius and the Serbian Nonius - in order to clarify their origin and genetic diversity. A 640-bp-long fragment of the mtDNA D-loop region was amplified and sequenced. The results showed that the investigated breeds have different genetic profiles although they share some common characteristics. We identified nine of the 17 haplogroups described in modern horses. Most of the obtained sequences fall into the M, L, G, and O'P lineages, which is indicative of the genetic profile of the ancestral mares that had probably been used at the initial stages of the formation of the breeds. The population of the Danubian Horse is characterised by a high prevalence of the Anatolian specific haplogroup G (45%), followed by the Western Eurasian specific haplogroups L and M (both about 21%). In the Hungarian Nonius breed we found the highest frequency of the Western Eurasian haplogroup M (44%), followed by the Middle Eastern O'P (26%) and the Central Asian specific E (13%) and G (13%). The Serbian Nonius showed a distinct genetic profile, characterised by a high prevalence of the rare European haplogroup D (67%), followed by the Central Asian specific haplogroup G (17%). The high percentage of haplogroups shared especially between the Danubian and the Hungarian Nonius indicates the possibility of a common origin of the two breeds. In contrast, the Serbian Nonius showed a specific genetic profile, which can be explained by a different and independent origin.
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Affiliation(s)
- Georgi Yordanov
- 1 Executive Agency for Selection and Reproduction in Animal Breeding, Sofia, Bulgaria
| | | | - Nadezhda Palova
- 3 Scientific Center of Agriculture, Agricultural Academy, Sredets, Bulgaria
| | - Ivan Mehandjyiski
- 4 Research Centеr of Stockbreeding and Agriculture, Agricultural Academy, Smolyan, Bulgaria
| | - Boyko Neov
- 5 Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, ‘Acad. G. Bonchev’ Str., Bl. 25, 1113, Sofia, Bulgaria
| | - Georgi Radoslavov
- 5 Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, ‘Acad. G. Bonchev’ Str., Bl. 25, 1113, Sofia, Bulgaria
| | - Peter Hristov
- 5 Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, ‘Acad. G. Bonchev’ Str., Bl. 25, 1113, Sofia, Bulgaria
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8
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Modi A, Lancioni H, Cardinali I, Capodiferro MR, Rambaldi Migliore N, Hussein A, Strobl C, Bodner M, Schnaller L, Xavier C, Rizzi E, Bonomi Ponzi L, Vai S, Raveane A, Cavadas B, Semino O, Torroni A, Olivieri A, Lari M, Pereira L, Parson W, Caramelli D, Achilli A. The mitogenome portrait of Umbria in Central Italy as depicted by contemporary inhabitants and pre-Roman remains. Sci Rep 2020; 10:10700. [PMID: 32612271 PMCID: PMC7329865 DOI: 10.1038/s41598-020-67445-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/22/2020] [Indexed: 12/19/2022] Open
Abstract
Umbria is located in Central Italy and took the name from its ancient inhabitants, the Umbri, whose origins are still debated. Here, we investigated the mitochondrial DNA (mtDNA) variation of 545 present-day Umbrians (with 198 entire mitogenomes) and 28 pre-Roman individuals (obtaining 19 ancient mtDNAs) excavated from the necropolis of Plestia. We found a rather homogeneous distribution of western Eurasian lineages across the region, with few notable exceptions. Contemporary inhabitants of the eastern part, delimited by the Tiber River and the Apennine Mountains, manifest a peculiar mitochondrial proximity to central-eastern Europeans, mainly due to haplogroups U4 and U5a, and an overrepresentation of J (30%) similar to the pre-Roman remains, also excavated in East Umbria. Local genetic continuities are further attested to by six terminal branches (H1e1, J1c3, J2b1, U2e2a, U8b1b1 and K1a4a) shared between ancient and modern mitogenomes. Eventually, we identified multiple inputs from various population sources that likely shaped the mitochondrial gene pool of ancient Umbri over time, since early Neolithic, including gene flows with central-eastern Europe. This diachronic mtDNA portrait of Umbria fits well with the genome-wide population structure identified on the entire peninsula and with historical sources that list the Umbri among the most ancient Italic populations.
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Affiliation(s)
- Alessandra Modi
- Department of Biology, University of Florence, 50122, Florence, Italy
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123, Perugia, Italy.
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123, Perugia, Italy
| | - Marco R Capodiferro
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Abir Hussein
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Lisa Schnaller
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Ermanno Rizzi
- Istituto di Tecnologie Biomediche, CNR, Segrate, 20090, Milan, Italy
| | | | - Stefania Vai
- Department of Biology, University of Florence, 50122, Florence, Italy
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Bruno Cavadas
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Porto, Portugal.,i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200-135, Porto, Portugal
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Martina Lari
- Department of Biology, University of Florence, 50122, Florence, Italy
| | - Luisa Pereira
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Porto, Portugal.,i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200-135, Porto, Portugal
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, University Park, PA, 16801, USA
| | - David Caramelli
- Department of Biology, University of Florence, 50122, Florence, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy.
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9
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Arauna LR, Hellenthal G, Comas D. Dissecting human North African gene-flow into its western coastal surroundings. Proc Biol Sci 2020; 286:20190471. [PMID: 31039721 DOI: 10.1098/rspb.2019.0471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
North African history and populations have exerted a pivotal influence on surrounding geographical regions, although scant genetic studies have addressed this issue. Our aim is to understand human historical migrations in the coastal surroundings of North Africa. We built a refined genome-wide dataset of North African populations to unearth the fine-scale genetic structure of the region, using haplotype information. The results suggest that the gene-flow from North Africa into the European Mediterranean coast (Tuscany and the Iberian Peninsula) arrived mainly from the Mediterranean coast of North Africa. In Tuscany, this North African admixture date estimate suggests the movement of peoples during the fall of the Roman Empire around the fourth century. In the Iberian Peninsula, the North African component probably reflects the impact of the Arab expansion since the seventh century and the subsequent expansion of the Christian Kingdoms. By contrast, the North African component in the Canary Islands has a source genetically related to present-day people from the Atlantic North African coast. We also find sub-Saharan gene-flow from the Senegambia region in the Canary Islands. Specifically, we detect a complex signal of admixture involving Atlantic, Senegambian and European sources intermixing around the fifteenth century, soon after the Castilian conquest. Our results highlight the differential genetic influence of North Africa into the surrounding coast and show that specific historical events have not only had a socio-cultural impact but additionally modified the gene pool of the populations.
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Affiliation(s)
- Lara R Arauna
- 1 Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra , Barcelona , Spain
| | - Garrett Hellenthal
- 2 UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London , London , UK
| | - David Comas
- 1 Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra , Barcelona , Spain
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10
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Poma A, Cesare P, Bonfigli A, Vecchiotti G, Colafarina S, Savini F, Redi F, Zarivi O. Analysis of ancient mtDNA from the medieval archeological site of Amiternum (L'Aquila), central Italy. Heliyon 2019; 5:e02586. [PMID: 31646208 PMCID: PMC6804371 DOI: 10.1016/j.heliyon.2019.e02586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/11/2019] [Accepted: 10/01/2019] [Indexed: 11/17/2022] Open
Abstract
Study of ancient DNA makes it possible to analyze genetic relationships between individuals and populations of past and present. In this paper we have analyzed remains of human bones, dating back to the 8th-10th century AD, from the burials found in the Cathedral of Santa Maria in Civitate, archaeological site of Amiternum, L'Aquila, Italy. As a genetic marker, the hypervariable region 1 of mitochondrial DNA (HVR1) was selected. To obtain reliable sequences from the hypervariable region 1 of mtDNA (HVR1) were performed: multiple extractions, template quantification and cloning of PCR products. The sequences obtained were compared with Anderson's sequence for the identification of polymorphisms (SNP) and haplogroups. The data obtained were analyzed with various software and phylogenetic methods. For the comparison between populations, ancient and modern sequences found in databases and literature have been used. This work provides preliminary information on the correlation between the population of Amiternum, the migrant populations transited and/or established in the territory of Amiternum such as Byzantines, Longobards (Lombards), which dominated the Italian peninsula between 568 and 774 AD, and the current populations of Italy. The study of haplogroups, the analysis of genetic variability and phylogenesis studies on the sequences considered show a genetic closeness between the individuals of Amiternum, the current population of central-northern Italy and the Germanic tribe of Longobards, however, also highlights genetic traits of Byzantines in some samples of Amiternum. Using the analysis of amelogenin gene fragments, we successfully determined the sex of the bone remains on all samples.
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Affiliation(s)
- Anna Poma
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
- Corresponding author.
| | - Patrizia Cesare
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Antonella Bonfigli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giulia Vecchiotti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Sabrina Colafarina
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Francesca Savini
- Department of Human Sciences, University of L'Aquila, L'Aquila, Italy
| | - Fabio Redi
- Department of Human Sciences, University of L'Aquila, L'Aquila, Italy
| | - Osvaldo Zarivi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
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11
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Yankova I, Marinov M, Neov B, Petrova M, Spassov N, Hristov P, Radoslavov G. Evidence for Early European Neolithic Dog Dispersal: New Data on Southeastern European Subfossil Dogs from the Prehistoric and Antiquity Ages. Genes (Basel) 2019; 10:genes10100757. [PMID: 31561553 PMCID: PMC6826387 DOI: 10.3390/genes10100757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 01/03/2023] Open
Abstract
The history of dog domestication is still under debate, but it is doubtless the process of an ancient partnership between dogs (Canis familiaris) and humans. Although data on ancient DNA for dog diversity are still incomplete, it is clear that several regional dog populations had formed in Eurasia up to the Holocene. During the Neolithic Revolution and the transition from hunter-gatherer to farmer societies, followed by civilization changes in the Antiquity period, the dog population structure also changed. This process was due to replacement with newly formed dog populations. In this study, we present for the first time mitochondrial data of ancient dog remains from the Early Neolithic (8000 years before present (BP)) to Late Antiquity (up to 3th century AD) from southeastern Europe (the Balkans). A total of 16 samples were analyzed, using the mitochondrial D-loop region (HVR1). The results show the presence of A (70%) and B (25%) clades throughout the Early and Late Neolithic Period. In order to clarify the position of our results within the ancient dog population in Eneolithic Eurasia, we performed phylogenetic analysis with the available genetic data sets. This data showed a similarity of the ancient Bulgarian dogs to Italian (A, B, and C clades) and Iberian (clades A and C) dogs’ populations. A clear border can be seen between southern European genetic dog structure, on the one hand, and on the other hand, central-western (clade C), eastern (clade D) and northern Europe (clades A and C). This corresponds to genetic data for European humans during the same period, without admixture between dog populations. Also, our data have shown the presence of clade B in ancient Eurasia. This is not unexpected, as the B haplogroup is widely distributed in extant Balkan dogs and wolves. The presence of this clade both in dogs and in wolves on the Balkans may be explained with hybridization events before the Neolithic period. The spreading of this clade across Europe, together with the A clade, is related to the possible dissemination of newly formed dog breeds from Ancient Greece, Thrace, and the Roman Empire.
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Affiliation(s)
- Iskra Yankova
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Miroslav Marinov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Boyko Neov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Maria Petrova
- Department of Structure and Function of Chromatin, Institute of Molecular Biology, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Nikolai Spassov
- Palaeontology and Mineralogy Department, National Museum of Natural History, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Peter Hristov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
| | - Georgi Radoslavov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1040 Sofia, Bulgaria.
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12
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Tamm E, Di Cristofaro J, Mazières S, Pennarun E, Kushniarevich A, Raveane A, Semino O, Chiaroni J, Pereira L, Metspalu M, Montinaro F. Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy. Sci Rep 2019; 9:13581. [PMID: 31537848 PMCID: PMC6753063 DOI: 10.1038/s41598-019-49901-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/31/2019] [Indexed: 01/13/2023] Open
Abstract
Despite being the fourth largest island in the Mediterranean basin, the genetic variation of Corsica has not been explored as exhaustively as Sardinia, which is situated only 11 km South. However, it is likely that the populations of the two islands shared, at least in part, similar demographic histories. Moreover, the relative small size of the Corsica may have caused genetic isolation, which, in turn, might be relevant under medical and translational perspectives. Here we analysed genome wide data of 16 Corsicans, and integrated with newly (33 individuals) and previously generated samples from West Eurasia and North Africa. Allele frequency, haplotype-based, and ancient genome analyses suggest that although Sardinia and Corsica may have witnessed similar isolation and migration events, the latter is genetically closer to populations from continental Europe, such as Northern and Central Italians.
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Affiliation(s)
- Erika Tamm
- Institute of Genomics, University of Tartu, Tartu, Estonia.
| | - Julie Di Cristofaro
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France.,Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | | | - Erwan Pennarun
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Alena Kushniarevich
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, 220072, Belarus
| | - Alessandro Raveane
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani" Università di Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani" Università di Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Jacques Chiaroni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France.,Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - Luisa Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), 4200-135, Porto, Portugal
| | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Francesco Montinaro
- Institute of Genomics, University of Tartu, Tartu, Estonia. .,Department of Zoology, University of Oxford, Oxford, UK.
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13
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Grugni V, Raveane A, Mattioli F, Battaglia V, Sala C, Toniolo D, Ferretti L, Gardella R, Achilli A, Olivieri A, Torroni A, Passarino G, Semino O. Reconstructing the genetic history of Italians: new insights from a male (Y-chromosome) perspective. Ann Hum Biol 2018; 45:44-56. [PMID: 29382284 DOI: 10.1080/03014460.2017.1409801] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Due to its central and strategic position in Europe and in the Mediterranean Basin, the Italian Peninsula played a pivotal role in the first peopling of the European continent and has been a crossroad of peoples and cultures since then. AIM This study aims to gain more information on the genetic structure of modern Italian populations and to shed light on the migration/expansion events that led to their formation. SUBJECTS AND METHODS High resolution Y-chromosome variation analysis in 817 unrelated males from 10 informative areas of Italy was performed. Haplogroup frequencies and microsatellite haplotypes were used, together with available data from the literature, to evaluate Mediterranean and European inputs and date their arrivals. RESULTS Fifty-three distinct Y-chromosome lineages were identified. Their distribution is in general agreement with geography, southern populations being more differentiated than northern ones. CONCLUSIONS A complex genetic structure reflecting the multifaceted peopling pattern of the Peninsula emerged: southern populations show high similarity with those from the Middle East and Southern Balkans, while those from Northern Italy are close to populations of North-Western Europe and the Northern Balkans. Interestingly, the population of Volterra, an ancient town of Etruscan origin in Tuscany, displays a unique Y-chromosomal genetic structure.
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Affiliation(s)
- Viola Grugni
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Alessandro Raveane
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Francesca Mattioli
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Vincenza Battaglia
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Cinzia Sala
- b Divisione di Genetica e Biologia Cellulare , Istituto Scientifico San Raffaele , Milano , Italy
| | - Daniela Toniolo
- b Divisione di Genetica e Biologia Cellulare , Istituto Scientifico San Raffaele , Milano , Italy
| | - Luca Ferretti
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Rita Gardella
- c Dipartimento di Medicina Molecolare e Traslazionale , Università di Brescia , Brescia , Italy
| | - Alessandro Achilli
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Anna Olivieri
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Antonio Torroni
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Giuseppe Passarino
- d Dipartimento di Biologia, Ecologia e Scienze della Terra , Università della Calabria , Arcavacata di Rende , Cosenza , Italy
| | - Ornella Semino
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
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14
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Messina F, Finocchio A, Akar N, Loutradis A, Michalodimitrakis EI, Brdicka R, Jodice C, Novelletto A. Enlarging the gene-geography of Europe and the Mediterranean area to STR loci of common forensic use: longitudinal and latitudinal frequency gradients. Ann Hum Biol 2018; 45:77-85. [PMID: 29382282 DOI: 10.1080/03014460.2017.1409365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Tetranucleotide Short Tandem Repeats (STRs) for human identification and common use in forensic cases have recently been used to address the population genetics of the North-Eastern Mediterranean area. However, to gain confidence in the inferences made using STRs, this kind of analysis should be challenged with changes in three main aspects of the data, i.e. the sizes of the samples, their distance across space and the genetic background from which they are drawn. AIM To test the resilience of the gradients previously detected in the North-Eastern Mediterranean to the enlargement of the surveyed area and population set, using revised data. SUBJECTS AND METHODS STR genotype profiles were obtained from a publicly available database (PopAffilietor databank) and a dataset was assembled including >7000 subjects from the Arabian Peninsula to Scandinavia, genotyped at eight loci. Spatial principal component analysis (sPCA) was applied and the frequency maps of the nine alleles which contributed most strongly to sPC1 were examined in detail. RESULTS By far the greatest part of diversity was summarised by a single spatial principal component (sPC1), oriented along a SouthEast-to-NorthWest axis. The alleles with the top 5% squared loadings were TH01(9.3), D19S433(14), TH01(6), D19S433(15.2), FGA(20), FGA(24), D3S1358(14), FGA(21) and D2S1338(19). These results confirm a clinal pattern over the whole range for at least four loci (TH01, D19S433, FGA, D3S1358). CONCLUSIONS Four of the eight STR loci (or even alleles) considered here can reproducibly capture continental arrangements of diversity. This would, in principle, allow for the exploitation of forensic data to clarify important aspects in the formation of local gene pools.
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Affiliation(s)
- Francesco Messina
- a Department of Biology , University of Rome Tor Vergata , Rome , Italy
| | - Andrea Finocchio
- a Department of Biology , University of Rome Tor Vergata , Rome , Italy
| | - Nejat Akar
- b Pediatrics Department , TOBB-Economy and Technology University Hospital , Ankara , Turkey
| | | | | | - Radim Brdicka
- e Institute of Hematology and Blood Transfusion , Praha , Czech Republic
| | - Carla Jodice
- a Department of Biology , University of Rome Tor Vergata , Rome , Italy
| | - Andrea Novelletto
- a Department of Biology , University of Rome Tor Vergata , Rome , Italy
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15
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Marinov M, Teofanova D, Gadjev D, Radoslavov G, Hristov P. Mitochondrial diversity of Bulgarian native dogs suggests dual phylogenetic origin. PeerJ 2018; 6:e5060. [PMID: 29967734 PMCID: PMC6026455 DOI: 10.7717/peerj.5060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/04/2018] [Indexed: 11/20/2022] Open
Abstract
The dog has been the first domesticated animal to have a central role in human society from ancient times to present day. Although there have been numerous investigations of dog phylogeny and origin, genetic data of dogs in the region of the Balkan Peninsula (South-Eastern Europe) are still scarce. Therefore, the aim of the present study was to perform phylogenetic analysis of three native Bulgarian dog breeds. A total of 130 samples were analyzed at HVR1 (hypervariable region, D-loop region). The samples were taken from two hunting dog breeds (Bulgarian Hound Dog: Barak, n = 34; Bulgarian Scenthound Dog: Gonche, n = 45) as well as from a Bulgarian Shepherd Dog (n = 51). The first two breeds are reared in a flat region of the country (the Northern part of Bulgaria, the Danubian Plain), while the last breed is a typical representative of the mountainous part of the country. The results have shown the presence of almost all main clades—A, B, C and D—in the three dog breeds taken together, except clades E and F, as expected. With regard to haplogroups distribution, there are clear differences among investigated breeds. While hunting breeds exhibit a prevalence of clade C, the mountainous Shepherd dog shows presence of the D2 haplogroup but absence of the C clade. In conclusion, the present study has been the first to investigate the mitochondrial DNA diversity of native dog breeds in Bulgaria. The results have revealed a clear difference of haplogroups dissemination in native hunting and shepherd dogs, which suggests a dual independent phylogenetic origin, without hybridization events between these dogs.
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Affiliation(s)
- Miroslav Marinov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Denitsa Teofanova
- Department of Biochemistry, Faculty of Biology, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | - Dimitar Gadjev
- Agricultural and Stockbreeding Experimental Station, Agricultural Academy, Smolyan, Bulgaria
| | - Georgi Radoslavov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Peter Hristov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
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16
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Di Lorenzo P, Lancioni H, Ceccobelli S, Colli L, Cardinali I, Karsli T, Capodiferro MR, Sahin E, Ferretti L, Ajmone Marsan P, Sarti FM, Lasagna E, Panella F, Achilli A. Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin. PLoS One 2018; 13:e0192567. [PMID: 29462170 PMCID: PMC5819780 DOI: 10.1371/journal.pone.0192567] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/25/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Over the past 15 years, 300 out of 6000 breeds of all farm animal species identified by the Food and Agriculture Organization of the United Nations (FAO) have gone extinct. Among cattle, many Podolian breeds are seriously endangered in various European areas. Podolian cattle include a group of very ancient European breeds, phenotypically close to the aurochs ancestors (Bos primigenius). The aim of the present study was to assess the genetic diversity of Podolian breeds and to reconstruct their origin. METHODOLOGY The mitochondrial DNA (mtDNA) control-regions of 18 Podolian breeds have been phylogenetically assessed. Nine non-Podolian breeds have been also included for comparison. CONCLUSION The overall analysis clearly highlights some peculiarities in the mtDNA gene pool of some Podolian breeds. In particular, a principal component analysis point to a genetic proximity between five breeds (Chianina, Marchigiana, Maremmana, Podolica Italiana and Romagnola) reared in Central Italy and the Turkish Grey. We here propose the suggestive hypothesis of a dual ancestral contribution to the present gene pool of Podolian breeds, one deriving from Eastern European cattle; the other arising from the arrival of Middle Eastern cattle into Central Italy through a different route, perhaps by sea, ferried by Etruscan boats. The historical migration of Podolian cattle from North Eastern Europe towards Italy has not cancelled the mtDNA footprints of this previous ancient migration.
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Affiliation(s)
- Piera Di Lorenzo
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
- * E-mail: (HL); (AA)
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Licia Colli
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, Italy
- Biodiversity and Ancient DNA Research Center–BioDNA, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, University of Akdeniz, Antalya, Turkey
| | | | - Emine Sahin
- Korkuteli Vocational School, University of Akdeniz, Antalya, Turkey
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
| | - Paolo Ajmone Marsan
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, Italy
- Biodiversity and Ancient DNA Research Center–BioDNA, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Francesca Maria Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Francesco Panella
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
- * E-mail: (HL); (AA)
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17
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Molto JE, Loreille O, Mallott EK, Malhi RS, Fast S, Daniels-Higginbotham J, Marshall C, Parr R. Complete Mitochondrial Genome Sequencing of a Burial from a Romano-Christian Cemetery in the Dakhleh Oasis, Egypt: Preliminary Indications. Genes (Basel) 2017; 8:genes8100262. [PMID: 28984839 PMCID: PMC5664112 DOI: 10.3390/genes8100262] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/15/2017] [Accepted: 09/26/2017] [Indexed: 11/17/2022] Open
Abstract
The curse of ancient Egyptian DNA was lifted by a recent study which sequenced the mitochondrial genomes (mtGenome) of 90 ancient Egyptians from the archaeological site of Abusir el-Meleq. Surprisingly, these ancient inhabitants were more closely related to those from the Near East than to contemporary Egyptians. It has been accepted that the timeless highway of the Nile River seeded Egypt with African genetic influence, well before pre-Dynastic times. Here we report on the successful recovery and analysis of the complete mtGenome from a burial recovered from a remote Romano–Christian cemetery, Kellis 2 (K2). K2 serviced the ancient municipality of Kellis, a village located in the Dakhleh Oasis in the southwest desert in Egypt. The data were obtained by high throughput sequencing (HTS) performed independently at two ancient DNA facilities (Armed Forces DNA Identification Laboratory, Dover, DE, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA). These efforts produced concordant haplotypes representing a U1a1a haplogroup lineage. This result indicates that Near Eastern maternal influence previously identified at Abusir el-Meleq was also present further south, in ancient Kellis during the Romano–Christian period.
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Affiliation(s)
- J Eldon Molto
- Department of Anthropology, Western University, London, ON N6A 3K7, Canada.
| | - Odile Loreille
- Armed Forces Medical Examiner System-Armed Forces DNA Identification Laboratory (AFMES/AFDIL), Dover, DE 19902, USA.
| | - Elizabeth K Mallott
- Department of Anthropology, Northwestern University, Evanston, IL 60208, USA.
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, 109 Davenport Hall, 607 S. Mathews Ave, Urbana, IL 61801, USA & Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Spence Fast
- Armed Forces Medical Examiner System-Armed Forces DNA Identification Laboratory (AFMES/AFDIL), Dover, DE 19902, USA.
| | - Jennifer Daniels-Higginbotham
- Armed Forces Medical Examiner System-Armed Forces DNA Identification Laboratory (AFMES/AFDIL), Dover, DE 19902, USA.
| | - Charla Marshall
- Armed Forces Medical Examiner System-Armed Forces DNA Identification Laboratory (AFMES/AFDIL), Dover, DE 19902, USA.
| | - Ryan Parr
- Department of Anthropology, Lakehead University, Thunder Bay, ON P7B 5E1, Canada.
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18
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Georgiou A, Demetriou CA, Heraclides A, Christou YP, Leonidou E, Loukaides P, Yiasoumi E, Panagiotou D, Manoli P, Thomson P, Loizidou MA, Hadjisavvas A, Zamba-Papanicolaou E. Mitochondrial superclusters influence age of onset of Parkinson's disease in a gender specific manner in the Cypriot population: A case-control study. PLoS One 2017; 12:e0183444. [PMID: 28877188 PMCID: PMC5587277 DOI: 10.1371/journal.pone.0183444] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 08/06/2017] [Indexed: 01/25/2023] Open
Abstract
Background Despite evidence supporting an involvement of mitochondrial dysfunction in the pathogenesis of some neurodegenerative disorders, there are inconsistent findings concerning mitochondrial haplogroups and their association to neurodegenerative disorders, including idiopathic Parkinson’s disease (PD). Methods To test this hypothesis for the Greek-Cypriot population, a cohort of 230 PD patients and 457 healthy matched controls were recruited. Mitochondrial haplogroup distributions for cases and controls were determined. Association tests were carried out between mitochondrial haplogroups and PD. Results Mitochondrial haplogroup U was associated with a reduced PD risk in the Cypriot population. After pooling mitochondrial haplogroups together into haplogroup clusters and superclusters, association tests demonstrated a significantly protective effect of mitochondrial haplogroup cluster N (xR) and supercluster LMN for PD risk only in females. In addition, for female PD cases belonging to UKJT and R (xH, xUKJT) haplogroup, the odds of having a later age of onset of PD were 13 and 15 times respectively higher than the odds for female cases with an H haplogroup. Conclusion Statistically significant associations regarding PD risk and PD age of onset were mostly detected for females thus suggesting that gender is a risk modifier between mitochondrial haplogroups and PD status / PD age of onset. The biological mechanisms behind this gender specificity remain to be determined.
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Affiliation(s)
- Andrea Georgiou
- Neurology Clinic D, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Christiana A. Demetriou
- Neurology Clinic D, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Alexandros Heraclides
- Department of Primary Care and Population Health, University of Nicosia Medical School, Nicosia, Cyprus
| | - Yiolanda P. Christou
- Neurology Clinic D, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Neurology Clinic B, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Eleni Leonidou
- Neurology Clinic C, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | | | | | - Panayiotis Manoli
- Department of Cardiovascular Genetics and the Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Pippa Thomson
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Maria A. Loizidou
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Electron Microscopy and Molecular Pathology Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Andreas Hadjisavvas
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Electron Microscopy and Molecular Pathology Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Eleni Zamba-Papanicolaou
- Neurology Clinic D, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- * E-mail:
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Margaryan A, Derenko M, Hovhannisyan H, Malyarchuk B, Heller R, Khachatryan Z, Avetisyan P, Badalyan R, Bobokhyan A, Melikyan V, Sargsyan G, Piliposyan A, Simonyan H, Mkrtchyan R, Denisova G, Yepiskoposyan L, Willerslev E, Allentoft ME. Eight Millennia of Matrilineal Genetic Continuity in the South Caucasus. Curr Biol 2017; 27:2023-2028.e7. [DOI: 10.1016/j.cub.2017.05.087] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 04/25/2017] [Accepted: 05/26/2017] [Indexed: 01/27/2023]
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Turchi C, Stanciu F, Paselli G, Buscemi L, Parson W, Tagliabracci A. The mitochondrial DNA makeup of Romanians: A forensic mtDNA control region database and phylogenetic characterization. Forensic Sci Int Genet 2016; 24:136-142. [DOI: 10.1016/j.fsigen.2016.06.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/26/2016] [Accepted: 06/18/2016] [Indexed: 01/13/2023]
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Nesheva DV, Karachanak-Yankova S, Lari M, Yordanov Y, Galabov A, Caramelli D, Toncheva D. Mitochondrial DNA Suggests a Western Eurasian Origin for Ancient (Proto-) Bulgarians. Hum Biol 2016; 87:19-28. [PMID: 26416319 DOI: 10.13110/humanbiology.87.1.0019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ancient (proto-) Bulgarians have long been thought of as a Turkic population. However, evidence found in the past three decades shows that this is not the case. Until now, this evidence has not included ancient mitochondrial DNA (mtDNA) analysis. To fill this void, we collected human remains from the 8th to the 10th century AD located in three necropolises in Bulgaria: Nojarevo (Silistra region) and Monastery of Mostich (Shumen region), both in northeastern Bulgaria, and Tuhovishte (Satovcha region) in southwestern Bulgaria. The phylogenetic analysis of 13 ancient DNA samples (extracted from teeth) identified 12 independent haplotypes, which we further classified into mtDNA haplogroups found in present-day European and western Eurasian populations. Our results suggest a western Eurasian matrilineal origin for proto-Bulgarians, as well as a genetic similarity between proto- and modern Bulgarians. Our future work will provide additional data that will further clarify proto-Bulgarian origins, thereby adding new clues to the current understanding of European genetic evolution.
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Affiliation(s)
- D V Nesheva
- 1 Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria
| | | | - M Lari
- 2 Department of Biology, Laboratory of Anthropology, Molecular Anthropology/Paleogenetics Unit, University of Florence, Florence, Italy
| | - Y Yordanov
- 3 Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - A Galabov
- 4 Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - D Caramelli
- 2 Department of Biology, Laboratory of Anthropology, Molecular Anthropology/Paleogenetics Unit, University of Florence, Florence, Italy
| | - D Toncheva
- 1 Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria
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Cardinali I, Lancioni H, Giontella A, Capodiferro MR, Capomaccio S, Buttazzoni L, Biggio GP, Cherchi R, Albertini E, Olivieri A, Cappelli K, Achilli A, Silvestrelli M. An Overview of Ten Italian Horse Breeds through Mitochondrial DNA. PLoS One 2016; 11:e0153004. [PMID: 27054850 PMCID: PMC4824442 DOI: 10.1371/journal.pone.0153004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/21/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The climatic and cultural diversity of the Italian Peninsula triggered, over time, the development of a great variety of horse breeds, whose origin and history are still unclear. To clarify this issue, analyses on phenotypic traits and genealogical data were recently coupled with molecular screening. METHODOLOGY To provide a comprehensive overview of the horse genetic variability in Italy, we produced and phylogenetically analyzed 407 mitochondrial DNA (mtDNA) control-region sequences from ten of the most important Italian riding horse and pony breeds: Bardigiano, Esperia, Giara, Lipizzan, Maremmano, Monterufolino, Murgese, Sarcidano, Sardinian Anglo-Arab, and Tolfetano. A collection of 36 Arabian horses was also evaluated to assess the genetic consequences of their common use for the improvement of some local breeds. CONCLUSIONS In Italian horses, all previously described domestic mtDNA haplogroups were detected as well as a high haplotype diversity. These findings indicate that the ancestral local mares harbored an extensive genetic diversity. Moreover, the limited haplotype sharing (11%) with the Arabian horse reveals that its impact on the autochthonous mitochondrial gene pools during the final establishment of pure breeds was marginal, if any. The only significant signs of genetic structure and differentiation were detected in the geographically most isolated contexts (i.e. Monterufolino and Sardinian breeds). Such a geographic effect was also confirmed in a wider breed setting, where the Italian pool stands in an intermediate position together with most of the other Mediterranean stocks. However, some notable exceptions and peculiar genetic proximities lend genetic support to historical theories about the origin of specific Italian breeds.
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Affiliation(s)
- Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Andrea Giontella
- Centro di Studio del Cavallo Sportivo, Dipartimento di Medicina Veterinaria, Università di Perugia, Perugia, Italy
| | | | - Stefano Capomaccio
- Centro di Studio del Cavallo Sportivo, Dipartimento di Medicina Veterinaria, Università di Perugia, Perugia, Italy
| | - Luca Buttazzoni
- Centro di ricerca per la produzione delle carni e il miglioramento genetico, Sede centrale–Monterotondo, Roma, Italy
| | | | - Raffaele Cherchi
- Agenzia per la ricerca in agricoltura–AGRIS Sardegna, Sassari, Italy
| | - Emidio Albertini
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università di Perugia, Perugia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
| | - Katia Cappelli
- Centro di Studio del Cavallo Sportivo, Dipartimento di Medicina Veterinaria, Università di Perugia, Perugia, Italy
| | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
- * E-mail:
| | - Maurizio Silvestrelli
- Centro di Studio del Cavallo Sportivo, Dipartimento di Medicina Veterinaria, Università di Perugia, Perugia, Italy
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Messina F, Scano G, Contini I, Martínez-Labarga C, De Stefano GF, Rickards O. Linking between genetic structure and geographical distance: Study of the maternal gene pool in the Ethiopian population. Ann Hum Biol 2016; 44:53-69. [PMID: 26883569 DOI: 10.3109/03014460.2016.1155646] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background The correlation between genetics and geographical distance has already been examined through the study of the dispersion of human populations, especially in terms of uniparental genetic markers. Aim The present work characterises, at the level of the mitochondrial DNA (mtDNA), two new samples of Amhara and Oromo populations from Ethiopia to evaluate the possible pattern of distribution for mtDNA variation and to test the hypothesis of the Isolation-by-Distance (IBD) model among African, European and Middle-Eastern populations. Subjects and methods This study analysed 173 individuals belonging to two ethnic groups of Ethiopia, Amhara and Oromo, by assaying HVS-I and HVS-II of mtDNA D-loop and informative coding region SNPs of mtDNA. Results The analysis suggests a relationship between genetic and geographic distances, affirming that the mtDNA pool of Africa, Europe and the Middle East might be coherent with the IBD model. Moreover, the mtDNA gene pools of the Sub-Saharan African and Mediterranean populations were very different. Conclusion In this study the pattern of mtDNA distribution, beginning with the Ethiopian plateau, was tested in the IBD model. It could be affirmed that, on a continent scale, the mtDNA pool of Africa, Europe and the Middle East might fall under the IBD model.
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Affiliation(s)
- Francesco Messina
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Giuseppina Scano
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Irene Contini
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Cristina Martínez-Labarga
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Gian Franco De Stefano
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
| | - Olga Rickards
- a Center of Molecular Anthropology for Ancient DNA Study, Department of Biology , University of Rome 'Tor Vergata' , Via della Ricerca Scientifica n. 1 , 00133 Rome , Italy
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Zupan A, Hauptman N, Glavač D. The maternal perspective for five Slovenian regions: The importance of regional sampling. Ann Hum Biol 2015; 43:57-66. [PMID: 26065896 DOI: 10.3109/03014460.2015.1006678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND The Slovenian territory is geographically positioned between the Alps, Adriatic Sea, Pannonian basin and the Dinaric Mountains and, as such, has served as a passageway for various populations in different periods of time. Turbulent historic events and diverse geography of the region have produced a diverse contemporary population whose genetic analysis could provide insight into past demographic events. AIM The aims of this study were to characterize the Slovenian mitochondrial gene pool at the micro-geographic level and to compare it with surrounding populations. SUBJECTS AND METHODS A total of 402 individuals from five Slovenian regions were analysed in this study by typing HVR I, HVR II and coding region polymorphisms of mtDNA. RESULTS Analysis revealed 47 haplogroups and sub-haplogroups, the most common of which were H*, H1, J1c, T2 and U5a. Intra-population comparisons revealed a sharp gradient of the J1c haplogroup between Slovenian regions, with a peak frequency of 24.5% being observed in the population of the Littoral Region. CONCLUSION The sharp gradient of the J1c haplogroup between Slovenian regions is in line with the archaeological horizon known as Impressed Ware culture and could, therefore, represent a genetic trace of the early Neolithic expansion route along the East Adriatic coastal region.
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Affiliation(s)
- Andrej Zupan
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
| | - Nina Hauptman
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
| | - Damjan Glavač
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
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Mitogenomes from The 1000 Genome Project reveal new Near Eastern features in present-day Tuscans. PLoS One 2015; 10:e0119242. [PMID: 25786119 PMCID: PMC4365045 DOI: 10.1371/journal.pone.0119242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/13/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Genetic analyses have recently been carried out on present-day Tuscans (Central Italy) in order to investigate their presumable recent Near East ancestry in connection with the long-standing debate on the origins of the Etruscan civilization. We retrieved mitogenomes and genome-wide SNP data from 110 Tuscans analyzed within the context of The 1000 Genome Project. For phylogeographic and evolutionary analysis we made use of a large worldwide database of entire mitogenomes (>26,000) and partial control region sequences (>180,000). RESULTS Different analyses reveal the presence of typical Near East haplotypes in Tuscans representing isolated members of various mtDNA phylogenetic branches. As a whole, the Near East component in Tuscan mitogenomes can be estimated at about 8%; a proportion that is comparable to previous estimates but significantly lower than admixture estimates obtained from autosomal SNP data (21%). Phylogeographic and evolutionary inter-population comparisons indicate that the main signal of Near Eastern Tuscan mitogenomes comes from Iran. CONCLUSIONS Mitogenomes of recent Near East origin in present-day Tuscans do not show local or regional variation. This points to a demographic scenario that is compatible with a recent arrival of Near Easterners to this region in Italy with no founder events or bottlenecks.
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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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Regueiro M, Garcia-Bertrand R, Fadhlaoui-Zid K, Álvarez J, Herrera RJ. From Arabia to Iberia: A Y chromosome perspective. Gene 2015; 564:141-52. [PMID: 25701402 DOI: 10.1016/j.gene.2015.02.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/08/2015] [Accepted: 02/15/2015] [Indexed: 12/31/2022]
Abstract
At different times during recent human evolution, northern Africa has served as a conduit for migrations from the Arabian Peninsula. Although previous researchers have investigated the possibility of the Strait of Gibraltar as a pathway of migration from North Africa to Iberia, we now revisit this issue and theorize that although the Strait of Gibraltar, at the west end of this corridor, has acted as a barrier for human dispersal into Southwest Europe, it has not provided an absolute seal to gene flow. To test this hypothesis, here we use the spatial frequency distributions, STR diversity and expansion time estimates of Y chromosome haplogroups J1-P58 and E-M81 to investigate the genetic imprints left by the Arabian and Berber expansions into the Iberian Peninsula, respectively. The data generated indicate that Arabian and Berber genetic markers are detected in Iberia. We present evidence that suggest that Iberia has received gene flow from Northwest Africa during and prior to the Islamic colonization of 711A.D. It is interesting that the highest frequencies of Arabia and Berber markers are not found in southern Spain, where Islam remained the longest and was culturally most influential, but in Northwest Iberia, specifically Galicia. We propose that Moriscos' relocations to the north during the Reconquista, the migration of cryptic Muslims seeking refuge in a more lenient society and/or more geographic extensive pre-Islamic incursions may explain the higher frequencies and older time estimates of mutations in the north of the Peninsula. These scenarios are congruent with the higher diversities of some diagnostic makers observed in Northwest Iberia.
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Affiliation(s)
- María Regueiro
- Biology Department, Colorado College, Colorado Springs, CO 80903, USA
| | | | - Karima Fadhlaoui-Zid
- Laboratoire de Genetique, Immunologie et Pathologies Humaines, Faculte des Sciences de Tunis, Campus Universitaire El Manar II, Universite el Manar, Tunis, Tunisia
| | - Joseph Álvarez
- Biology Department, Colorado College, Colorado Springs, CO 80903, USA
| | - Rene J Herrera
- Biology Department, Colorado College, Colorado Springs, CO 80903, USA
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Vai S, Ghirotto S, Pilli E, Tassi F, Lari M, Rizzi E, Matas-Lalueza L, Ramirez O, Lalueza-Fox C, Achilli A, Olivieri A, Torroni A, Lancioni H, Giostra C, Bedini E, Baricco LP, Matullo G, Di Gaetano C, Piazza A, Veeramah K, Geary P, Caramelli D, Barbujani G. Genealogical relationships between early medieval and modern inhabitants of Piedmont. PLoS One 2015; 10:e0116801. [PMID: 25635682 PMCID: PMC4312042 DOI: 10.1371/journal.pone.0116801] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 12/16/2014] [Indexed: 11/18/2022] Open
Abstract
In the period between 400 to 800 AD, also known as the period of the Barbarian invasions, intense migration is documented in the historical record of Europe. However, little is known about the demographic impact of these historical movements, potentially ranging from negligible to substantial. As a pilot study in a broader project on Medieval Europe, we sampled 102 specimens from 5 burial sites in Northwestern Italy, archaeologically classified as belonging to Lombards or Longobards, a Germanic people ruling over a vast section of the Italian peninsula from 568 to 774. We successfully amplified and typed the mitochondrial hypervariable region I (HVR-I) of 28 individuals. Comparisons of genetic diversity with other ancient populations and haplotype networks did not suggest that these samples are heterogeneous, and hence allowed us to jointly compare them with three isolated contemporary populations, and with a modern sample of a large city, representing a control for the effects of recent immigration. We then generated by serial coalescent simulations 16 millions of genealogies, contrasting a model of genealogical continuity with one in which the contemporary samples are genealogically independent from the medieval sample. Analyses by Approximate Bayesian Computation showed that the latter model fits the data in most cases, with one exception, Trino Vercellese, in which the evidence was compatible with persistence up to the present time of genetic features observed among this early medieval population. We conclude that it is possible, in general, to detect evidence of genealogical ties between medieval and specific modern populations. However, only seldom did mitochondrial DNA data allow us to reject with confidence either model tested, which indicates that broader analyses, based on larger assemblages of samples and genetic markers, are needed to understand in detail the effects of medieval migration.
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Affiliation(s)
- Stefania Vai
- Dipartimento di Biologia Evoluzionistica, Università di Firenze, 50122 Florence, Italy
| | - Silvia Ghirotto
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
| | - Elena Pilli
- Dipartimento di Biologia Evoluzionistica, Università di Firenze, 50122 Florence, Italy
| | - Francesca Tassi
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
| | - Martina Lari
- Dipartimento di Biologia Evoluzionistica, Università di Firenze, 50122 Florence, Italy
| | - Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, 20090 Segrate, Milan, Italy
| | | | - Oscar Ramirez
- Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Spain
| | | | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100,Pavia,Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100,Pavia,Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, 06123 Perugia, Italy
| | - Caterina Giostra
- Dipartimento di Storia, Archeologia e Storia dell’arte, Università Cattolica del Sacro Cuore, 20123 Milano, Italy
| | - Elena Bedini
- Anthropozoologica L.B.A. s.n.c., 57123 Livorno, Italy
| | | | | | | | | | - Krishna Veeramah
- Department of Ecology and Evolution, State University of New York, Stony Brook, New York 11794–5245, United States of America
| | - Patrick Geary
- School of Historical Studies, Institute for Advanced Study, Princeton, New Jersey 08540, United States of America
| | - David Caramelli
- Dipartimento di Biologia Evoluzionistica, Università di Firenze, 50122 Florence, Italy
| | - Guido Barbujani
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
- * E-mail:
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Davidovic S, Malyarchuk B, Aleksic JM, Derenko M, Topalovic V, Litvinov A, Stevanovic M, Kovacevic-Grujicic N. Mitochondrial DNA perspective of Serbian genetic diversity. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 156:449-65. [PMID: 25418795 DOI: 10.1002/ajpa.22670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/04/2014] [Indexed: 11/08/2022]
Abstract
Although south-Slavic populations have been studied to date from various aspects, the population of Serbia, occupying the central part of the Balkan Peninsula, is still genetically understudied at least at the level of mitochondrial DNA (mtDNA) variation. We analyzed polymorphisms of the first and the second mtDNA hypervariable segments (HVS-I and HVS-II) and informative coding-region markers in 139 Serbians to shed more light on their mtDNA variability, and used available data on other Slavic and neighboring non-Slavic populations to assess their interrelations in a broader European context. The contemporary Serbian mtDNA profile is consistent with the general European maternal landscape having a substantial proportion of shared haplotypes with eastern, central, and southern European populations. Serbian population was characterized as an important link between easternmost and westernmost south-Slavic populations due to the observed lack of genetic differentiation with all other south-Slavic populations and its geographical positioning within the Balkan Peninsula. An increased heterogeneity of south Slavs, most likely mirroring turbulent demographic events within the Balkan Peninsula over time (i.e., frequent admixture and differential introgression of various gene pools), and a marked geographical stratification of Slavs to south-, east-, and west-Slavic groups, were also found. A phylogeographic analyses of 20 completely sequenced Serbian mitochondrial genomes revealed not only the presence of mtDNA lineages predominantly found within the Slavic gene pool (U4a2a*, U4a2a1, U4a2c, U4a2g, HV10), supporting a common Slavic origin, but also lineages that may have originated within the southern Europe (H5*, H5e1, H5a1v) and the Balkan Peninsula in particular (H6a2b and L2a1k).
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Affiliation(s)
- Slobodan Davidovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11010, Belgrade, Serbia
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Derenko M, Malyarchuk B, Denisova G, Perkova M, Litvinov A, Grzybowski T, Dambueva I, Skonieczna K, Rogalla U, Tsybovsky I, Zakharov I. Western Eurasian ancestry in modern Siberians based on mitogenomic data. BMC Evol Biol 2014; 14:217. [PMID: 25301575 PMCID: PMC4195960 DOI: 10.1186/s12862-014-0217-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/29/2014] [Indexed: 11/30/2022] Open
Abstract
Background Although the genetic heritage of aboriginal Siberians is mostly of eastern Asian ancestry, a substantial western Eurasian component is observed in the majority of northern Asian populations. Traces of at least two migrations into southern Siberia, one from eastern Europe and the other from western Asia/the Caucasus have been detected previously in mitochondrial gene pools of modern Siberians. Results We report here 166 new complete mitochondrial DNA (mtDNA) sequences that allow us to expand and re-analyze the available data sets of western Eurasian lineages found in northern Asian populations, define the phylogenetic status of Siberian-specific subclades and search for links between mtDNA haplotypes/subclades and events of human migrations. From a survey of 158 western Eurasian mtDNA genomes found in Siberia we estimate that nearly 40% of them most likely have western Asian and another 29% European ancestry. It is striking that 65 of northern Asian mitogenomes, i.e. ~41%, fall into 19 branches and subclades which can be considered as Siberian-specific being found so far only in Siberian populations. From the coalescence analysis it is evident that the sequence divergence of Siberian-specific subclades was relatively small, corresponding to only 0.6-9.5 kya (using the complete mtDNA rate) and 1–6 kya (coding region rate). Conclusions The phylogeographic analysis implies that the western Eurasian founders, giving rise to Siberian specific subclades, may trace their ancestry only to the early and mid-Holocene, though some of genetic lineages may trace their ancestry back to the end of Last Glacial Maximum (LGM). We have not found the modern northern Asians to have western Eurasian genetic components of sufficient antiquity to indicate traces of pre-LGM expansions. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0217-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia.
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A genome-wide study of modern-day Tuscans: revisiting Herodotus's theory on the origin of the Etruscans. PLoS One 2014; 9:e105920. [PMID: 25230205 PMCID: PMC4167696 DOI: 10.1371/journal.pone.0105920] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/25/2014] [Indexed: 11/21/2022] Open
Abstract
Background The origin of the Etruscan civilization (Etruria, Central Italy) is a long-standing subject of debate among scholars from different disciplines. The bulk of the information has been reconstructed from ancient texts and archaeological findings and, in the last few years, through the analysis of uniparental genetic markers. Methods By meta-analyzing genome-wide data from The 1000 Genomes Project and the literature, we were able to compare the genomic patterns (>540,000 SNPs) of present day Tuscans (N = 98) with other population groups from the main hypothetical source populations, namely, Europe and the Middle East. Results Admixture analysis indicates the presence of 25–34% of Middle Eastern component in modern Tuscans. Different analyses have been carried out using identity-by-state (IBS) values and genetic distances point to Eastern Anatolia/Southern Caucasus as the most likely geographic origin of the main Middle Eastern genetic component observed in the genome of modern Tuscans. Conclusions The data indicate that the admixture event between local Tuscans and Middle Easterners could have occurred in Central Italy about 2,600–3,100 years ago (y.a.). On the whole, the results validate the theory of the ancient historian Herodotus on the origin of Etruscans.
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Capocasa M, Taglioli L, Anagnostou P, Paoli G, Danubio ME. Determinants of marital behaviour in five Apennine communities of Central Italy inferred by surname analysis, repeated pairs and kinship estimates. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2013; 65:64-74. [PMID: 24012323 DOI: 10.1016/j.jchb.2013.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 07/23/2013] [Indexed: 10/26/2022]
Abstract
The work makes use of surname analysis, repeated pairs and kinship estimates in 11,009 marriage records celebrated in five communities of the Italian Central Apennine (Celano, Lecce dei Marsi, Ortucchio, Roio, Villavallelonga) from 1802 to 1965 with the objective to deepen knowledge of the relative influence of several determinants on their marital behaviour. These towns are part of the same geographic and economic environment: the slopes of the ancient Fucino Lake. This work further elaborates the results from previous studies on the bio-demographic model of the region. The data were analyzed according to three periods of approximately 50 years. Results show the highest inbreeding coefficients in the pastoral towns of Roio and Villavallelonga. Repeated pair analysis highlights a certain degree of population subdivision which declined in time in Celano, Lecce dei Marsi and Ortucchio. The highest and increasing values of RP-RPr in time in Roio suggest a general reduction in genetic heterogeneity. This is possibly due to the celebration of marriages among families selected on the economic basis of pastoralism, as this town historically has had a leading tradition of sheep-farming. Villavallelonga, excluding isonymous marriages, shows an increase in repeated pair unions in time, thus revealing a substructure with marriages among preferred lineages. This is in line with previous results on consanguineous marriages which indicated the tendency of avoiding unions between close relatives in this small geographic isolate. This study demonstrates the influence of geographical (altitude) and social factors (pastoralism) on the marital structures of the investigated populations.
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Affiliation(s)
- M Capocasa
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; Istituto Italiano di Antropologia, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - L Taglioli
- Dipartimento di Biologia, Università di Pisa, Via Luca Ghini 13, 56126 Pisa, Italy
| | - P Anagnostou
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy; Istituto Italiano di Antropologia, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - G Paoli
- Dipartimento di Biologia, Università di Pisa, Via Luca Ghini 13, 56126 Pisa, Italy
| | - M E Danubio
- Dipartimento di Medicina clinica, sanità pubblica, scienze della vita e dell'ambiente, Università di L'Aquila, Piazzale Salvatore Tommasi 1, L'Aquila, Italy; Istituto Italiano di Antropologia, Piazzale Aldo Moro 5, 00185 Rome, Italy
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Tassi F, Ghirotto S, Caramelli D, Barbujani G. Genetic evidence does not support an Etruscan origin in Anatolia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 152:11-8. [PMID: 23900768 DOI: 10.1002/ajpa.22319] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 05/20/2013] [Indexed: 01/22/2023]
Abstract
The debate on the origins of Etruscans, documented in central Italy between the eighth century BC and the first century AD, dates back to antiquity. Herodotus described them as a group of immigrants from Lydia, in Western Anatolia, whereas for Dionysius of Halicarnassus they were an indigenous population. Dionysius' view is shared by most modern archeologists, but the observation of similarities between the (modern) mitochondrial DNAs (mtDNAs) of Turks and Tuscans was interpreted as supporting an Anatolian origin of the Etruscans. However, ancient DNA evidence shows that only some isolates, and not the bulk of the modern Tuscan population, are genetically related to the Etruscans. In this study, we tested alternative models of Etruscan origins by Approximate Bayesian Computation methods, comparing levels of genetic diversity in the mtDNAs of modern and ancient populations with those obtained by millions of computer simulations. The results show that the observed genetic similarities between modern Tuscans and Anatolians cannot be attributed to an immigration wave from the East leading to the onset of the Etruscan culture in Italy. Genetic links between Tuscany and Anatolia do exist, but date back to a remote stage of prehistory, possibly but not necessarily to the spread of farmers during the Neolithic period.
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Affiliation(s)
- Francesca Tassi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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Matullo G, Guarrera S, Betti M, Fiorito G, Ferrante D, Voglino F, Cadby G, Di Gaetano C, Rosa F, Russo A, Hirvonen A, Casalone E, Tunesi S, Padoan M, Giordano M, Aspesi A, Casadio C, Ardissone F, Ruffini E, Betta PG, Libener R, Guaschino R, Piccolini E, Neri M, Musk AWB, de Klerk NH, Hui J, Beilby J, James AL, Creaney J, Robinson BW, Mukherjee S, Palmer LJ, Mirabelli D, Ugolini D, Bonassi S, Magnani C, Dianzani I. Genetic variants associated with increased risk of malignant pleural mesothelioma: a genome-wide association study. PLoS One 2013; 8:e61253. [PMID: 23626673 PMCID: PMC3634031 DOI: 10.1371/journal.pone.0061253] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/06/2013] [Indexed: 12/19/2022] Open
Abstract
Asbestos exposure is the main risk factor for malignant pleural mesothelioma (MPM), a rare aggressive tumor. Nevertheless, only 5-17% of those exposed to asbestos develop MPM, suggesting the involvement of other environmental and genetic risk factors. To identify the genetic risk factors that may contribute to the development of MPM, we conducted a genome-wide association study (GWAS; 370,000 genotyped SNPs, 5 million imputed SNPs) in Italy, among 407 MPM cases and 389 controls with a complete history of asbestos exposure. A replication study was also undertaken and included 428 MPM cases and 1269 controls from Australia. Although no single marker reached the genome-wide significance threshold, several associations were supported by haplotype-, chromosomal region-, gene- and gene-ontology process-based analyses. Most of these SNPs were located in regions reported to harbor aberrant alterations in mesothelioma (SLC7A14, THRB, CEBP350, ADAMTS2, ETV1, PVT1 and MMP14 genes), causing at most a 2-3-fold increase in MPM risk. The Australian replication study showed significant associations in five of these chromosomal regions (3q26.2, 4q32.1, 7p22.2, 14q11.2, 15q14). Multivariate analysis suggested an independent contribution of 10 genetic variants, with an Area Under the ROC Curve (AUC) of 0.76 when only exposure and covariates were included in the model, and of 0.86 when the genetic component was also included, with a substantial increase of asbestos exposure risk estimation (odds ratio, OR: 45.28, 95% confidence interval, CI: 21.52-95.28). These results showed that genetic risk factors may play an additional role in the development of MPM, and that these should be taken into account to better estimate individual MPM risk in individuals who have been exposed to asbestos.
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Affiliation(s)
- Giuseppe Matullo
- Human Genetics Foundation, HuGeF, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Marta Betti
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | | | - Daniela Ferrante
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | | | - Gemma Cadby
- Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
- Centre for Genetic Epidemiology and Biostatistics, University of Western Australia, Nedlands, Western Australia, Australia
| | - Cornelia Di Gaetano
- Human Genetics Foundation, HuGeF, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Fabio Rosa
- Human Genetics Foundation, HuGeF, Turin, Italy
| | - Alessia Russo
- Human Genetics Foundation, HuGeF, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Ari Hirvonen
- Centre of Expertise for Health and Work Ability, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Elisabetta Casalone
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Sara Tunesi
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Marina Padoan
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Mara Giordano
- Laboratory of Genetics, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Anna Aspesi
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
| | - Caterina Casadio
- Thoracic Surgery Unit, University of Piemonte Orientale, Novara, Italy
| | - Francesco Ardissone
- Chest Surgery, Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
| | - Enrico Ruffini
- Thoracic Surgery Unit, University of Turin, Turin, Italy
| | - Pier Giacomo Betta
- Pathology Unit, Azienda Ospedaliera Nazionale SS, Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Roberta Libener
- Pathology Unit, Azienda Ospedaliera Nazionale SS, Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Roberto Guaschino
- Transfusion Centre, Azienda Ospedaliera Nazionale SS, Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Ezio Piccolini
- Pneumology Unit, Santo Spirito Hospital, Casale Monferrato, Italy
| | - Monica Neri
- Unit of Clinical and Molecular Epidemiology IRCCS San Raffaele Pisana, Rome, Italy
| | - Arthur W. B. Musk
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Nicholas H. de Klerk
- Centre for Child Health Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Jennie Hui
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - John Beilby
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
- PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - Alan L. James
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Jenette Creaney
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Bruce W. Robinson
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Western Australia, Australia
| | - Sutapa Mukherjee
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Women's College Research Institute and Women's College Hospital, Toronto, Ontario, Canada
| | - Lyle J. Palmer
- Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
| | - Dario Mirabelli
- Unit of Cancer Epidemiology, CPO-Piemonte and University of Turin, Turin, Italy
- Interdepartmental Center for Studies on Asbestos and other Toxic Particulates “G. Scansetti”, University of Turin, Turin, Italy
| | - Donatella Ugolini
- Department of Internal Medicine, University of Genoa and IRCSS AOU San Martino-IST-Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Stefano Bonassi
- Unit of Clinical and Molecular Epidemiology IRCCS San Raffaele Pisana, Rome, Italy
| | - Corrado Magnani
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
- Interdepartmental Center for Studies on Asbestos and other Toxic Particulates “G. Scansetti”, University of Turin, Turin, Italy
| | - Irma Dianzani
- Laboratory of Genetic Pathology, Department Health Sciences, University of Piemonte Orientale, Novara, Italy
- Interdepartmental Center for Studies on Asbestos and other Toxic Particulates “G. Scansetti”, University of Turin, Turin, Italy
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Ghirotto S, Tassi F, Fumagalli E, Colonna V, Sandionigi A, Lari M, Vai S, Petiti E, Corti G, Rizzi E, De Bellis G, Caramelli D, Barbujani G. Origins and evolution of the Etruscans' mtDNA. PLoS One 2013; 8:e55519. [PMID: 23405165 PMCID: PMC3566088 DOI: 10.1371/journal.pone.0055519] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 12/24/2012] [Indexed: 11/25/2022] Open
Abstract
The Etruscan culture is documented in Etruria, Central Italy, from the 8th to the 1st century BC. For more than 2,000 years there has been disagreement on the Etruscans’ biological origins, whether local or in Anatolia. Genetic affinities with both Tuscan and Anatolian populations have been reported, but so far all attempts have failed to fit the Etruscans’ and modern populations in the same genealogy. We extracted and typed the hypervariable region of mitochondrial DNA of 14 individuals buried in two Etruscan necropoleis, analyzing them along with other Etruscan and Medieval samples, and 4,910 contemporary individuals from the Mediterranean basin. Comparing ancient (30 Etruscans, 27 Medieval individuals) and modern DNA sequences (370 Tuscans), with the results of millions of computer simulations, we show that the Etruscans can be considered ancestral, with a high degree of confidence, to the current inhabitants of Casentino and Volterra, but not to the general contemporary population of the former Etruscan homeland. By further considering two Anatolian samples (35 and 123 individuals) we could estimate that the genetic links between Tuscany and Anatolia date back to at least 5,000 years ago, strongly suggesting that the Etruscan culture developed locally, and not as an immediate consequence of immigration from the Eastern Mediterranean shores.
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Affiliation(s)
- Silvia Ghirotto
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | - Francesca Tassi
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
| | - Erica Fumagalli
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Vincenza Colonna
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
- Institute of Genetics e Biophysics “Adriano Buzzati-Traverso”, National Research Council, Naples, Italy
| | - Anna Sandionigi
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Martina Lari
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Stefania Vai
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Emmanuele Petiti
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Giorgio Corti
- Institute for Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - Gianluca De Bellis
- Institute for Biomedical Technologies, National Research Council, Segrate, Milan, Italy
| | - David Caramelli
- Department of Evolutionary Biology, University of Florence, Florence, Italy
| | - Guido Barbujani
- Department of Biology and Evolution, University of Ferrara, Ferrara, Italy
- * E-mail:
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Brisighelli F, Álvarez-Iglesias V, Fondevila M, Blanco-Verea A, Carracedo Á, Pascali VL, Capelli C, Salas A. Uniparental markers of contemporary Italian population reveals details on its pre-Roman heritage. PLoS One 2012; 7:e50794. [PMID: 23251386 PMCID: PMC3519480 DOI: 10.1371/journal.pone.0050794] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 10/24/2012] [Indexed: 11/18/2022] Open
Abstract
Background According to archaeological records and historical documentation, Italy has been a melting point for populations of different geographical and ethnic matrices. Although Italy has been a favorite subject for numerous population genetic studies, genetic patterns have never been analyzed comprehensively, including uniparental and autosomal markers throughout the country. Methods/Principal Findings A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities — and from two linguistic isolates (Ladins, Grecani Salentini). All samples were first typed for the mitochondrial DNA (mtDNA) control region and selected coding region SNPs (mtSNPs). This data was pooled for analysis with 3,778 mtDNA control-region profiles collected from the literature. Secondly, a set of Y-chromosome SNPs and STRs were also analyzed in 479 individuals together with a panel of autosomal ancestry informative markers (AIMs) from 441 samples. The resulting genetic record reveals clines of genetic frequencies laid according to the latitude slant along continental Italy – probably generated by demographical events dating back to the Neolithic. The Ladins showed distinctive, if more recent structure. The Neolithic contribution was estimated for the Y-chromosome as 14.5% and for mtDNA as 10.5%. Y-chromosome data showed larger differentiation between North, Center and South than mtDNA. AIMs detected a minor sub-Saharan component; this is however higher than for other European non-Mediterranean populations. The same signal of sub-Saharan heritage was also evident in uniparental markers. Conclusions/Significance Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times.
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Affiliation(s)
- Francesca Brisighelli
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
| | - Manuel Fondevila
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
| | - Alejandro Blanco-Verea
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
- Fundación Pública Galega de Medicina Xenómica (FPGMX-SERGAS), CIBER enfermedades raras, Santiago de Compostela, Galicia, Spain
| | - Vincenzo L. Pascali
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Antonio Salas
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
- * E-mail:
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An overview of the genetic structure within the Italian population from genome-wide data. PLoS One 2012; 7:e43759. [PMID: 22984441 PMCID: PMC3440425 DOI: 10.1371/journal.pone.0043759] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 07/24/2012] [Indexed: 12/21/2022] Open
Abstract
In spite of the common belief of Europe as reasonably homogeneous at genetic level, advances in high-throughput genotyping technology have resolved several gradients which define different geographical areas with good precision. When Northern and Southern European groups were considered separately, there were clear genetic distinctions. Intra-country genetic differences were also evident, especially in Finland and, to a lesser extent, within other European populations. Here, we present the first analysis using the 125,799 genome-wide Single Nucleotide Polymorphisms (SNPs) data of 1,014 Italians with wide geographical coverage. We showed by using Principal Component analysis and model-based individual ancestry analysis, that the current population of Sardinia can be clearly differentiated genetically from mainland Italy and Sicily, and that a certain degree of genetic differentiation is detectable within the current Italian peninsula population. Pair-wise F(ST) statistics Northern and Southern Italy amounts approximately to 0.001 between, and around 0.002 between Northern Italy and Utah residents with Northern and Western European ancestry (CEU). The Italian population also revealed a fine genetic substructure underscoring by the genomic inflation (Sardinia vs. Northern Italy = 3.040 and Northern Italy vs. CEU = 1.427), warning against confounding effects of hidden relatedness and population substructure in association studies.
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Distinguishing the co-ancestries of haplogroup G Y-chromosomes in the populations of Europe and the Caucasus. Eur J Hum Genet 2012; 20:1275-82. [PMID: 22588667 DOI: 10.1038/ejhg.2012.86] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Haplogroup G, together with J2 clades, has been associated with the spread of agriculture, especially in the European context. However, interpretations based on simple haplogroup frequency clines do not recognize underlying patterns of genetic diversification. Although progress has been recently made in resolving the haplogroup G phylogeny, a comprehensive survey of the geographic distribution patterns of the significant sub-clades of this haplogroup has not been conducted yet. Here we present the haplogroup frequency distribution and STR variation of 16 informative G sub-clades by evaluating 1472 haplogroup G chromosomes belonging to 98 populations ranging from Europe to Pakistan. Although no basal G-M201* chromosomes were detected in our data set, the homeland of this haplogroup has been estimated to be somewhere nearby eastern Anatolia, Armenia or western Iran, the only areas characterized by the co-presence of deep basal branches as well as the occurrence of high sub-haplogroup diversity. The P303 SNP defines the most frequent and widespread G sub-haplogroup. However, its sub-clades have more localized distribution with the U1-defined branch largely restricted to Near/Middle Eastern and the Caucasus, whereas L497 lineages essentially occur in Europe where they likely originated. In contrast, the only U1 representative in Europe is the G-M527 lineage whose distribution pattern is consistent with regions of Greek colonization. No clinal patterns were detected suggesting that the distributions are rather indicative of isolation by distance and demographic complexities.
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Hervella M, Izagirre N, Alonso S, Fregel R, Alonso A, Cabrera VM, de la Rúa C. Ancient DNA from hunter-gatherer and farmer groups from Northern Spain supports a random dispersion model for the Neolithic expansion into Europe. PLoS One 2012; 7:e34417. [PMID: 22563371 PMCID: PMC3340892 DOI: 10.1371/journal.pone.0034417] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 02/28/2012] [Indexed: 11/25/2022] Open
Abstract
Background/Principal Findings The phenomenon of Neolithisation refers to the transition of prehistoric
populations from a hunter-gatherer to an agro-pastoralist lifestyle.
Traditionally, the spread of an agro-pastoralist economy into Europe has
been framed within a dichotomy based either on an acculturation phenomenon
or on a demic diffusion. However, the nature and speed of this transition is
a matter of continuing scientific debate in archaeology, anthropology, and
human population genetics. In the present study, we have analyzed the
mitochondrial DNA diversity in hunter-gatherers and first farmers from
Northern Spain, in relation to the debate surrounding the phenomenon of
Neolithisation in Europe. Methodology/Significance Analysis of mitochondrial DNA was carried out on 54 individuals from Upper
Paleolithic and Early Neolithic, which were recovered from nine
archaeological sites from Northern Spain (Basque Country, Navarre and
Cantabria). In addition, to take all necessary precautions to avoid
contamination, different authentication criteria were applied in this study,
including: DNA quantification, cloning, duplication (51% of the
samples) and replication of the results (43% of the samples) by two
independent laboratories. Statistical and multivariate analyses of the
mitochondrial variability suggest that the genetic influence of
Neolithisation did not spread uniformly throughout Europe, producing
heterogeneous genetic consequences in different geographical regions,
rejecting the traditional models that explain the Neolithisation in
Europe. Conclusion The differences detected in the mitochondrial DNA lineages of Neolithic
groups studied so far (including these ones of this study) suggest different
genetic impact of Neolithic in Central Europe, Mediterranean Europe and the
Cantabrian fringe. The genetic data obtained in this study provide support
for a random dispersion model for Neolithic farmers. This random dispersion
had a different impact on the various geographic regions, and thus
contradicts the more simplistic total acculturation and replacement models
proposed so far to explain Neolithisation.
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Affiliation(s)
- Montserrat Hervella
- Department of Genetics, Physical Anthropology
and Animal Physiology, University of the Basque Country, Bizkaia,
Spain
| | - Neskuts Izagirre
- Department of Genetics, Physical Anthropology
and Animal Physiology, University of the Basque Country, Bizkaia,
Spain
| | - Santos Alonso
- Department of Genetics, Physical Anthropology
and Animal Physiology, University of the Basque Country, Bizkaia,
Spain
| | - Rosa Fregel
- Department of Genetics, University of La
Laguna, La Laguna, Santa Cruz de Tenerife, Spain
| | - Antonio Alonso
- Department of Biology, National Institute of
Toxicology and Forensic Sciences, Madrid, Spain
| | - Vicente M. Cabrera
- Department of Genetics, University of La
Laguna, La Laguna, Santa Cruz de Tenerife, Spain
| | - Concepción de la Rúa
- Department of Genetics, Physical Anthropology
and Animal Physiology, University of the Basque Country, Bizkaia,
Spain
- * E-mail:
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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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Salihović MP, Barešić A, Klarić IM, Cukrov S, Lauc LB, Janićijević B. The role of the Vlax Roma in shaping the European Romani maternal genetic history. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:262-70. [DOI: 10.1002/ajpa.21566] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 05/09/2011] [Indexed: 11/07/2022]
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Sans M, Figueiro G, Ackermann E, Barreto I, Egaña A, Bertoni B, Poittevin-Gilmet E, Maytia D, Hidalgo PC. Mitochondrial DNA in Basque descendants from the city of Trinidad, Uruguay: Uruguayan- or Basque-like population? Hum Biol 2011; 83:55-70. [PMID: 21453004 DOI: 10.3378/027.083.0104] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Like other countries in the Americas, during its colonization Uruguay was the recipient of immigrants from several ethnic groups from Europe, as well as of enslaved Africans. After its independence in 1830, Basques were the first group of Europeans to arrive in the country. In this paper, we aim to contribute to the understanding of the process of integration of these migratory waves into the Uruguayan society. For that purpose, individuals of Basque origin from the city of Trinidad, Uruguay, were chosen to participate in this study. Particularly, we wanted to determine if Basque descendants in Uruguay remained relatively isolated or if they mixed with other ethnic groups. Mitochondrial DNA (mtDNA) of 60 self-identified Basque descendants, taken from a larger sample of subjects with Basque ancestors, was analyzed. The origin of mtDNA haplogroups was 77.8% European, 20.4% Amerindian, and 1.8% African, showing similar frequencies to other Uruguayan regions. Very few sequences showed a clear Basque origin, although other sources such as the Canary Islands are likely. Moreover, genetic distances clearly show that Basque descendants are genetically closer to other Uruguayan groups than to European populations, including Basques. It is possible to conclude that Basques and their descendants in the region of Trinidad did not remain isolated and that their marriage behavior was similar to that of other Uruguayan populations. However, to have a more accurate picture of the way Basques intermarried with other populations in Uruguay, new analyses are needed that take into account paternal lineages as well as biparental genetic markers.
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Affiliation(s)
- M Sans
- Department of Biological Anthropology, Facultad de Humanidades y Ciencias de la Educación, Universidad de la República, 11200 Montevideo, Uruguay
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Bulgarians vs the other European populations: a mitochondrial DNA perspective. Int J Legal Med 2011; 126:497-503. [DOI: 10.1007/s00414-011-0589-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 06/01/2011] [Indexed: 10/18/2022]
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Achilli A, Olivieri A, Pala M, Hooshiar Kashani B, Carossa V, Perego UA, Gandini F, Santoro A, Battaglia V, Grugni V, Lancioni H, Sirolla C, Bonfigli AR, Cormio A, Boemi M, Testa I, Semino O, Ceriello A, Spazzafumo L, Gadaleta MN, Marra M, Testa R, Franceschi C, Torroni A. Mitochondrial DNA backgrounds might modulate diabetes complications rather than T2DM as a whole. PLoS One 2011; 6:e21029. [PMID: 21695278 PMCID: PMC3111471 DOI: 10.1371/journal.pone.0021029] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 05/17/2011] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial dysfunction has been implicated in rare and common forms of type 2 diabetes (T2DM). Additionally, rare mitochondrial DNA (mtDNA) mutations have been shown to be causal for T2DM pathogenesis. So far, many studies have investigated the possibility that mtDNA variation might affect the risk of T2DM, however, when found, haplogroup association has been rarely replicated, even in related populations, possibly due to an inadequate level of haplogroup resolution. Effects of mtDNA variation on diabetes complications have also been proposed. However, additional studies evaluating the mitochondrial role on both T2DM and related complications are badly needed. To test the hypothesis of a mitochondrial genome effect on diabetes and its complications, we genotyped the mtDNAs of 466 T2DM patients and 438 controls from a regional population of central Italy (Marche). Based on the most updated mtDNA phylogeny, all 904 samples were classified into 57 different mitochondrial sub-haplogroups, thus reaching an unprecedented level of resolution. We then evaluated whether the susceptibility of developing T2DM or its complications differed among the identified haplogroups, considering also the potential effects of phenotypical and clinical variables. MtDNA backgrounds, even when based on a refined haplogroup classification, do not appear to play a role in developing T2DM despite a possible protective effect for the common European haplogroup H1, which harbors the G3010A transition in the MTRNR2 gene. In contrast, our data indicate that different mitochondrial haplogroups are significantly associated with an increased risk of specific diabetes complications: H (the most frequent European haplogroup) with retinopathy, H3 with neuropathy, U3 with nephropathy, and V with renal failure.
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Affiliation(s)
- Alessandro Achilli
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy
| | - Anna Olivieri
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
| | - Maria Pala
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
| | | | - Valeria Carossa
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
| | - Ugo A. Perego
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | - Francesca Gandini
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
| | - Aurelia Santoro
- Dipartimento di Patologia Sperimentale, Università di Bologna, Bologna, Italy
- CIG-Interdepartmental Center for Biophysics and Biocomplexity Studies, Università di Bologna, Bologna, Italy
| | - Vincenza Battaglia
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
| | - Viola Grugni
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
| | - Hovirag Lancioni
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy
| | - Cristina Sirolla
- Department of Gerontology Research, Statistic and Biometry Center, Italian National Research Center on Aging (INRCA), Ancona, Italy
| | - Anna Rita Bonfigli
- Metabolic and Nutrition Research Center on Diabetes, Italian National Research Center on Aging, INRCA-IRCCS, Ancona, Italy
| | - Antonella Cormio
- Dipartimento di Biochimica e Biologia Molecolare “E. Quagliariello”, Università di Bari, Bari, Italy
| | - Massimo Boemi
- Metabolic and Nutrition Research Center on Diabetes, Italian National Research Center on Aging, INRCA-IRCCS, Ancona, Italy
| | - Ivano Testa
- Metabolic and Nutrition Research Center on Diabetes, Italian National Research Center on Aging, INRCA-IRCCS, Ancona, Italy
| | - Ornella Semino
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
- Centro Interdipartimentale “Studi di Genere”, Università di Pavia, Pavia, Italy
| | - Antonio Ceriello
- Institut d'Investigacions Biomèdiques August Pi Sunyer (IDIBAPS) and Centro de Investigacion Biomedica en Red de Diabetes y Enfermedades Metabolicas Asociadis (CIBERDEM), Barcelona, Spain
| | - Liana Spazzafumo
- Department of Gerontology Research, Statistic and Biometry Center, Italian National Research Center on Aging (INRCA), Ancona, Italy
| | - Maria Nicola Gadaleta
- Dipartimento di Biochimica e Biologia Molecolare “E. Quagliariello”, Università di Bari, Bari, Italy
| | - Maurizio Marra
- Metabolic and Nutrition Research Center on Diabetes, Italian National Research Center on Aging, INRCA-IRCCS, Ancona, Italy
| | - Roberto Testa
- Metabolic and Nutrition Research Center on Diabetes, Italian National Research Center on Aging, INRCA-IRCCS, Ancona, Italy
| | - Claudio Franceschi
- Dipartimento di Patologia Sperimentale, Università di Bologna, Bologna, Italy
- CIG-Interdepartmental Center for Biophysics and Biocomplexity Studies, Università di Bologna, Bologna, Italy
| | - Antonio Torroni
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
- * E-mail:
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Peng MS, He JD, Liu HX, Zhang YP. Tracing the legacy of the early Hainan Islanders--a perspective from mitochondrial DNA. BMC Evol Biol 2011; 11:46. [PMID: 21324107 PMCID: PMC3048540 DOI: 10.1186/1471-2148-11-46] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 02/15/2011] [Indexed: 02/20/2023] Open
Abstract
BACKGROUND Hainan Island is located around the conjunction of East Asia and Southeast Asia, and during the Last Glacial Maximum (LGM) was connected with the mainland. This provided an opportunity for the colonization of Hainan Island by modern human in the Upper Pleistocene. Whether the ancient dispersal left any footprints in the contemporary gene pool of Hainan islanders is debatable. RESULTS We collected samples from 285 Li individuals and analyzed mitochondrial DNA (mtDNA) variations of hypervariable sequence I and II (HVS-I and II), as well as partial coding regions. By incorporating previously reported data, the phylogeny of Hainan islanders was reconstructed. We found that Hainan islanders showed a close relationship with the populations in mainland southern China, especially from Guangxi. Haplotype sharing analyses suggested that the recent gene flow from the mainland might play important roles in shaping the maternal pool of Hainan islanders. More importantly, haplogroups M12, M7e, and M7c1* might represent the genetic relics of the ancient population that populated this region; thus, 14 representative complete mtDNA genomes were further sequenced. CONCLUSIONS The detailed phylogeographic analyses of haplogroups M12, M7e, and M7c1* indicated that the early peopling of Hainan Island by modern human could be traced back to the early Holocene and/or even the late Upper Pleistocene, around 7-27 kya. These results correspond to both Y-chromosome and archaeological studies.
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Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, PR China
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47
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Fadhlaoui-Zid K, Rodríguez-Botigué L, Naoui N, Benammar-Elgaaied A, Calafell F, Comas D. Mitochondrial DNA structure in North Africa reveals a genetic discontinuity in the Nile Valley. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 145:107-17. [PMID: 21312180 DOI: 10.1002/ajpa.21472] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 11/16/2010] [Indexed: 11/08/2022]
Abstract
Human population movements in North Africa have been mostly restricted to an east-west direction due to the geographical barriers imposed by the Sahara Desert and the Mediterranean Sea. Although these barriers have not completely impeded human migrations, genetic studies have shown that an east-west genetic gradient exists. However, the lack of genetic information of certain geographical areas and the focus of some studies in parts of the North African landscape have limited the global view of the genetic pool of North African populations. To provide a global view of the North African genetic landscape and population structure, we have analyzed ∼2,300 North African mitochondrial DNA lineages (including 269 new sequences from Libya, in the first mtDNA study of the general Libyan population). Our results show a clinal distribution of certain haplogroups, some of them more frequent in Western (H, HV0, L1b, L3b, U6) or Eastern populations (L0a, R0a, N1b, I, J) that might be the result of human migrations from the Middle East, sub-Saharan Africa, and Europe. Despite this clinal pattern, a genetic discontinuity is found in the Libyan/Egyptian border, suggesting a differential gene flow in the Nile River Valley. Finally, frequency of the post-LGM subclades H1 and H3 is predominant in Libya within the H sequences, highlighting the magnitude of the LGM expansion in North Africa.
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Affiliation(s)
- Karima Fadhlaoui-Zid
- Laboratory of Genetics, Immunology, and Human Pathology, Faculty of Science of Tunis, University Tunis El Manar, Tunisia
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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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Somatic point mutations in mtDNA control region are influenced by genetic background and associated with healthy aging: a GEHA study. PLoS One 2010; 5:e13395. [PMID: 20976236 PMCID: PMC2954809 DOI: 10.1371/journal.pone.0013395] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 09/18/2010] [Indexed: 02/02/2023] Open
Abstract
Tissue specific somatic mutations occurring in the mtDNA control region have been proposed to provide a survival advantage. Data on twins and on relatives of long-lived subjects suggested that the occurrence/accumulation of these mutations may be genetically influenced. To further investigate control region somatic heteroplasmy in the elderly, we analyzed the segment surrounding the nt 150 position (previously reported as specific of Leukocytes) in various types of leukocytes obtained from 195 ultra-nonagenarians sib-pairs of Italian or Finnish origin collected in the frame of the GEHA Project. We found a significant correlation of the mtDNA control region heteroplasmy between sibs, confirming a genetic influence on this phenomenon. Furthermore, many subjects showed heteroplasmy due to mutations different from the C150T transition. In these cases heteroplasmy was correlated within sibpairs in Finnish and northern Italian samples, but not in southern Italians. This suggested that the genetic contribution to control region mutations may be population specific. Finally, we observed a possible correlation between heteroplasmy and Hand Grip strength, one of the best markers of physical performance and of mortality risk in the elderly. Our study provides new evidence on the relevance of mtDNA somatic mutations in aging and longevity and confirms that the occurrence of specific point mutations in the mtDNA control region may represent a strategy for the age-related remodelling of organismal functions.
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50
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Ajmone-Marsan P, Garcia JF, Lenstra JA. On the origin of cattle: How aurochs became cattle and colonized the world. Evol Anthropol 2010. [DOI: 10.1002/evan.20267] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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