1
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Hernández CL. Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era. Genes (Basel) 2023; 14:1534. [PMID: 37628587 PMCID: PMC10453943 DOI: 10.3390/genes14081534] [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] [Received: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is a small fraction of our hereditary material. However, this molecule has had an overwhelming presence in scientific research for decades until the arrival of high-throughput studies. Several appealing properties justify the application of mtDNA to understand how human populations are-from a genetic perspective-and how individuals exhibit phenotypes of biomedical importance. Here, I review the basics of mitochondrial studies with a focus on the dawn of the field, analysis methods and the connection between two sides of mitochondrial genetics: anthropological and biomedical. The particularities of mtDNA, with respect to inheritance pattern, evolutionary rate and dependence on the nuclear genome, explain the challenges of associating mtDNA composition and diseases. Finally, I consider the relevance of this single locus in the context of omics research. The present work may serve as a tribute to a tool that has provided important insights into the past and present of humankind.
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Affiliation(s)
- Candela L Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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2
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Ligotti ME, Aiello A, Accardi G, Calabrò A, Ciaccio M, Colomba C, Di Bona D, Lo Sasso B, Pojero F, Tuttolomondo A, Caruso C, Candore G, Duro G. Distribution of KIR Genes and Their HLA Ligands in Different Viral Infectious Diseases: Frequency Study in Sicilian Population. Int J Mol Sci 2022; 23:ijms232415466. [PMID: 36555106 PMCID: PMC9779783 DOI: 10.3390/ijms232415466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Natural killer (NK) cells play a role in defence against viral infections by killing infected cells or by producing cytokines and interacting with adaptive immune cells. Killer immunoglobulin-like receptors (KIRs) regulate the activation of NK cells through their interaction with human leucocyte antigens (HLA). Ninety-six Sicilian patients positive to Human Immunodeficiency Virus-1 (HIV) and ninety-two Sicilian patients positive to SARS-CoV-2 were genotyped for KIRs and their HLA ligands. We also included fifty-six Sicilian patients with chronic hepatitis B (CHB) already recruited in our previous study. The aim of this study was to compare the distribution of KIR-HLA genes/groups of these three different infected populations with healthy Sicilian donors from the literature. We showed that the inhibitory KIR3DL1 gene and the KIR3DL1/HLA-B Bw4 pairing were more prevalent in individual CHB. At the same time, the frequency of HLA-C2 was increased in CHB compared to other groups. In contrast, the HLA-C1 ligand seems to have no contribution to CHB progression whereas it was significantly higher in COVID-19 and HIV-positive than healthy controls. These results suggest that specific KIR-HLA combinations can predict the outcome/susceptibility of these viral infections and allows to plan successful customized therapeutic strategies.
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Affiliation(s)
- Mattia Emanuela Ligotti
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90134 Palermo, Italy
| | - Anna Aiello
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90134 Palermo, Italy
| | - Giulia Accardi
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90134 Palermo, Italy
- Correspondence:
| | - Anna Calabrò
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90134 Palermo, Italy
| | - Marcello Ciaccio
- Section of Clinical Biochemistry and Clinical Molecular Medicine, Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
| | - Claudia Colomba
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90127 Palermo, Italy
| | - Danilo Di Bona
- Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, 70124 Bari, Italy
| | - Bruna Lo Sasso
- Section of Clinical Biochemistry and Clinical Molecular Medicine, Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
| | - Fanny Pojero
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90134 Palermo, Italy
| | - Antonino Tuttolomondo
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90127 Palermo, Italy
| | - Calogero Caruso
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90134 Palermo, Italy
| | - Giuseppina Candore
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90134 Palermo, Italy
| | - Giovanni Duro
- Institute for Biomedical Research and Innovation, National Research Council of Italy, 90146 Palermo, Italy
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3
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Modi A, Vizzari MT, Catalano G, Boscolo Agostini R, Vai S, Lari M, Vergata C, Zaro V, Liccioli L, Fedi M, Barone S, Nigro L, Lancioni H, Achilli A, Sineo L, Caramelli D, Ghirotto S. Genetic structure and differentiation from early bronze age in the mediterranean island of sicily: Insights from ancient mitochondrial genomes. Front Genet 2022; 13:945227. [PMID: 36159977 PMCID: PMC9500526 DOI: 10.3389/fgene.2022.945227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Sicily is one of the main islands of the Mediterranean Sea, and it is characterized by a variety of archaeological records, material culture and traditions, reflecting the history of migrations and populations’ interaction since its first colonization, during the Paleolithic. These deep and complex demographic and cultural dynamics should have affected the genomic landscape of Sicily at different levels; however, the relative impact of these migrations on the genomic structure and differentiation within the island remains largely unknown. The available Sicilian modern genetic data gave a picture of the current genetic structure, but the paucity of ancient data did not allow so far to make predictions about the level of historical variation. In this work, we sequenced and analyzed the complete mitochondrial genomes of 36 individuals from five different locations in Sicily, spanning from Early Bronze Age to Iron Age, and with different cultural backgrounds. The comparison with coeval groups from the Mediterranean Basin highlighted structured genetic variation in Sicily since Early Bronze Age, thus supporting a demic impact of the cultural transitions within the Island. Explicit model testing through Approximate Bayesian Computation allowed us to make predictions about the origin of Sicanians, one of the three indigenous peoples of Sicily, whose foreign origin from Spain, historically attributed, was not confirmed by our analysis of genetic data. Sicilian modern mitochondrial data show a different, more homogeneous, genetic composition, calling for a recent genetic replacement in the Island of pre-Iron Age populations, that should be further investigated.
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Affiliation(s)
- Alessandra Modi
- Department of Biology, University of Florence, Firenze, Italy
- *Correspondence: Alessandra Modi, ; Silvia Ghirotto,
| | - Maria Teresa Vizzari
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Giulio Catalano
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | | | - Stefania Vai
- Department of Biology, University of Florence, Firenze, Italy
| | - Martina Lari
- Department of Biology, University of Florence, Firenze, Italy
| | - Chiara Vergata
- Department of Biology, University of Florence, Firenze, Italy
| | - Valentina Zaro
- Department of Biology, University of Florence, Firenze, Italy
| | - Lucia Liccioli
- INFN (Istituto Nazionale di Fisica Nucleare) Sezione di Firenze, Firenze, Italy
| | - Mariaelena Fedi
- INFN (Istituto Nazionale di Fisica Nucleare) Sezione di Firenze, Firenze, Italy
| | - Serena Barone
- INFN (Istituto Nazionale di Fisica Nucleare) Sezione di Firenze, Firenze, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Lorenzo Nigro
- Department “Italian Institute of Oriental Studies—ISO”, Sapienza University of Rome, Rome, Italy
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Luca Sineo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Firenze, Italy
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- *Correspondence: Alessandra Modi, ; Silvia Ghirotto,
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4
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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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Catanzaro R, Sciuto M, He F, Singh B, Marotta F. Non-alcoholic fatty liver disease: correlation with hyperuricemia in a European Mediterranean population. Acta Clin Belg 2022; 77:45-50. [PMID: 32559142 DOI: 10.1080/17843286.2020.1783907] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVES Non-alcoholic fatty liver disease (NAFLD) and metabolic syndrome (MetS) are two pathologies that intersect each other. It was found that there is an association between MetS/NAFLD and hyperuricemia. The aim of our study was to demonstrate this association in a European Mediterranean population. METHODS We compared 236 patients with NAFLD to 218 patients without NAFLD. We assessed laboratory metabolic parameters (serum uric acid - SUA, fasting glucose, triglycerides, total cholesterol, etc.) and the presence or absence of MetS in a retrospective, cross-sectional, case-control manner. RESULTS Analysis of the two main variables in study showed a moderate direct correlation (p< 0.01; Pearson coefficient 0.443) between SUA and NAFLD. Evaluation for SUA quartiles showed a decreased risk of NAFLD for the first and second quartiles (OR Q1 = 0.20; OR Q2 = 0.59), but increased for the third and fourth quartiles (OR Q3 = 2.22; OR Q4 = 6.97). In females, the risk of NAFLD was less compared to males for the first three quartiles of SUA, but it was more than double for the fourth quartile (OR Q1 0.21 vs 0.16; OR Q2 0.82 vs 0.45; OR Q3 2.50 vs 2.26; OR Q4 4.50 vs 9.83). In the NAFLD group, hyperuricemia was significantly correlated with sex, obesity, hypertension, and with the number of components of the MetS. In the Control group, SUA directly correlated with age, diabetes, and ALT, but not with obesity. CONCLUSION We have found a significant correlation between NAFLD and hyperuricemia. The higher SUA levels accompanied the risk of NAFLD.
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Affiliation(s)
- Roberto Catanzaro
- Department of Clinical and Experimental Medicine - Gastroenterology Section "Gaspare Rodolico" Policlinico Hospital, University of Catania, Catania, Italy
| | - Morena Sciuto
- Department of Clinical and Experimental Medicine - Gastroenterology Section "Gaspare Rodolico" Policlinico Hospital, University of Catania, Catania, Italy
| | - Fang He
- Department of Nutrition, Food Safety and Toxicology, West China School of Public Health, Sichuan University, Chengdu, China
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station Palampur, Karnal, India
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6
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Archaeogenetics and Landscape Dynamics in Sicily during the Holocene: A Review. SUSTAINABILITY 2021. [DOI: 10.3390/su13179469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Mediterranean islands and their population history are of considerable importance to the interpretation of the population history of Europe as a whole. In this context, Sicily, because of its geographic position, represents a bridge between Africa, the Near East, and Europe that led to the stratification of settlements and admixture events. The genetic analysis of extant and ancient human samples has tried to reconstruct the population dynamics associated with the cultural and demographic changes that took place during the prehistory and history of Sicily. In turn, genetic, demographic and cultural changes need to be understood in the context of the environmental changes that took place over the Holocene. Based on this framework, this paper aims to discuss the cultural and demographic dimension of the island by reviewing archaeogenetic studies, and lastly, we discuss the ecological constraints related to human peopling in times of change in landscapes that occurred on the island in various periods. Finally, possible directions for future archaeogenetic studies of Sicily are discussed. Despite its long human history, Sicily is still one of the world’s biodiversity hotspots. The lessons we learn from the past use of landscape provide models for sustainable future management of the Mediterranean’s landscapes.
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7
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Sarno S, Boscolo Agostini R, De Fanti S, Ferri G, Ghirotto S, Modenini G, Pettener D, Boattini A. Y-chromosome variability and genetic history of Commons from Northern Italy. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 175:665-679. [PMID: 33969895 PMCID: PMC8360088 DOI: 10.1002/ajpa.24302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/19/2021] [Accepted: 04/17/2021] [Indexed: 12/31/2022]
Abstract
Objectives Genetic drift and admixture are driving forces in human evolution, but their concerted impact to population evolution in historical times and at a micro‐geographic scale is poorly assessed. In this study we test a demographic model encompassing both admixture and drift to the case of social‐cultural isolates such as the so‐called “Commons.” Materials and methods Commons are peculiar institutions of medieval origins whose key feature is the tight relationship between population and territory, mediated by the collective property of shared resources. Here, we analyze the Y‐chromosomal genetic structure of four Commons (for a total of 366 samples) from the Central and Eastern Padana plain in Northern Italy. Results Our results reveal that all these groups exhibit patterns of significant diversity reduction, peripheral/outlier position within the Italian/European genetic space and high frequency of Common‐specific haplogroups. By explicitly testing different drift‐admixture models, we show that a drift‐only model is more probable for Central Padana Commons, while additional admixture (~20%) from external population around the same time of their foundation cannot be excluded for the Eastern ones. Discussion Building on these results, we suggest central Middle Ages as the most probable age of foundation for three of the considered Commons, the remaining one pointing to late antiquity. We conclude that an admixture‐drift model is particularly useful for interpreting the genetic structure and recent demographic history of small‐scale populations in which social‐cultural features play a significant role.
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Affiliation(s)
- Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | | | - Sara De Fanti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
| | - Gianmarco Ferri
- Department of Diagnostic and Clinical Medicine and Public Health, University of Modena and Reggio Emilia, Modena, Italy
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Giorgia Modenini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Davide Pettener
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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8
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First Bronze Age Human Mitogenomes from Calabria (Grotta Della Monaca, Southern Italy). Genes (Basel) 2021; 12:genes12050636. [PMID: 33922908 PMCID: PMC8146030 DOI: 10.3390/genes12050636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/02/2021] [Accepted: 04/20/2021] [Indexed: 11/17/2022] Open
Abstract
The Italian peninsula was host to a strong history of migration processes that shaped its genomic variability since prehistoric times. During the Metal Age, Sicily and Southern Italy were the protagonists of intense trade networks and settlements along the Mediterranean. Nonetheless, ancient DNA studies in Southern Italy are, at present, still limited to prehistoric and Roman Apulia. Here, we present the first mitogenomes from a Middle Bronze Age cave burial in Calabria to address this knowledge gap. We adopted a hybridization capture approach, which enabled the recovery of one complete and one partial mitochondrial genome. Phylogenetic analysis assigned these two individuals to the H1e and H5 subhaplogroups, respectively. This preliminary phylogenetic analysis supports affinities with coeval Sicilian populations, along with Linearbandkeramik and Bell Beaker cultures maternal lineages from Central Europe and Iberia. Our work represents a starting point which contributes to the comprehension of migrations and population dynamics in Southern Italy, and highlights this knowledge gap yet to be filled by genomic studies.
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9
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Chironi S, Bacarella S, Altamore L, Columba P, Ingrassia M. Consumption of spices and ethnic contamination in the daily diet of Italians - consumers’ preferences and modification of eating habits. JOURNAL OF ETHNIC FOODS 2021; 8:6. [PMCID: PMC8179707 DOI: 10.1186/s42779-021-00082-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 05/19/2021] [Indexed: 06/18/2023]
Abstract
Currently, consumers appear to have diversified characteristics with regard to food tastes and consumption habits. The globalization of markets and the migration phenomenon contributed to the modification of food preferences of consumers who gradually introduce into their eating habits foods and recipes typical of the tradition of foreign countries. In this scenario, also in Italy, it is going to increase the use of “foreign products” with the consequent fusion of traditional cuisine techniques and recipes with ingredients that are typical of foreign countries and cultures. Foods and ingredients originally consumed in Asian or South American countries are increasingly consumed by Italian people, who have notoriously a strong “food identity,” who generally follow the Mediterranean Diet, and who consume typical products of the country. More particularly, the use of “new” or “novel” spices compared to those traditionally used in the preparation of Italian food has grown in the last 10 years. This study is an exploratory survey on the consumption of spices in Sicily (Southern Italy), which is an Italian Region with a high level of immigrated people and a good level of social integration and progressive inclusion. The objective of this study is to know whether and how Sicilian consumers’ consumption preferences, use, and purchasing behaviors with regard to spices changed in the last few years. The results highlight an increasing use of novel spices for the preparation of the traditional recipes and a good appreciation by consumers. These results are interesting because they provide information about spices’ market development and food product marketing and internationalization. The survey gives interesting inputs for reflections about the relationship between food contaminations and social integration and insight into consumers’ preferences in Italy.
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Affiliation(s)
- Stefania Chironi
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Viale delle Scienze, Building 4, Palermo, Italy
| | - Simona Bacarella
- Department of Economics, Business and Statistics, Università degli Studi di Palermo Viale delle Scienze, Building 13, Palermo, Italy
| | - Luca Altamore
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Viale delle Scienze, Building 4, Palermo, Italy
| | - Pietro Columba
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Viale delle Scienze, Building 4, Palermo, Italy
| | - Marzia Ingrassia
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Viale delle Scienze, Building 4, Palermo, Italy
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Ceolin A, Guardiano C, Irimia MA, Longobardi G. Formal Syntax and Deep History. Front Psychol 2020; 11:488871. [PMID: 33391062 PMCID: PMC7775603 DOI: 10.3389/fpsyg.2020.488871] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/24/2020] [Indexed: 11/13/2022] Open
Abstract
We show that, contrary to long-standing assumptions, syntactic traits, modeled here within the generative biolinguistic framework, provide insights into deep-time language history. To support this claim, we have encoded the diversity of nominal structures using 94 universally definable binary parameters, set in 69 languages spanning across up to 13 traditionally irreducible Eurasian families. We found a phylogenetic signal that distinguishes all such families and matches the family-internal tree topologies that are safely established through classical etymological methods and datasets. We have retrieved "near-perfect" phylogenies, which are essentially immune to homoplastic disruption and only moderately influenced by horizontal convergence, two factors that instead severely affect more externalized linguistic features, like sound inventories. This result allows us to draw some preliminary inferences about plausible/implausible cross-family classifications; it also provides a new source of evidence for testing the representation of diversity in syntactic theories.
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Affiliation(s)
- Andrea Ceolin
- Department of Linguistics, University of Pennsylvania, Philadelphia, PA, United States
| | - Cristina Guardiano
- Dipartimento di Comunicazione ed Economia, Università di Modena e Reggio Emilia, Reggio Emilia, Italy
| | - Monica Alexandrina Irimia
- Dipartimento di Comunicazione ed Economia, Università di Modena e Reggio Emilia, Reggio Emilia, Italy
| | - Giuseppe Longobardi
- Department of Language and Linguistic Science, University of York, York, United Kingdom
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11
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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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Sazzini M, Abondio P, Sarno S, Gnecchi-Ruscone GA, Ragno M, Giuliani C, De Fanti S, Ojeda-Granados C, Boattini A, Marquis J, Valsesia A, Carayol J, Raymond F, Pirazzini C, Marasco E, Ferrarini A, Xumerle L, Collino S, Mari D, Arosio B, Monti D, Passarino G, D'Aquila P, Pettener D, Luiselli D, Castellani G, Delledonne M, Descombes P, Franceschi C, Garagnani P. Genomic history of the Italian population recapitulates key evolutionary dynamics of both Continental and Southern Europeans. BMC Biol 2020; 18:51. [PMID: 32438927 PMCID: PMC7243322 DOI: 10.1186/s12915-020-00778-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/01/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The cline of human genetic diversity observable across Europe is recapitulated at a micro-geographic scale by variation within the Italian population. Besides resulting from extensive gene flow, this might be ascribable also to local adaptations to diverse ecological contexts evolved by people who anciently spread along the Italian Peninsula. Dissecting the evolutionary history of the ancestors of present-day Italians may thus improve the understanding of demographic and biological processes that contributed to shape the gene pool of European populations. However, previous SNP array-based studies failed to investigate the full spectrum of Italian variation, generally neglecting low-frequency genetic variants and examining a limited set of small effect size alleles, which may represent important determinants of population structure and complex adaptive traits. To overcome these issues, we analyzed 38 high-coverage whole-genome sequences representative of population clusters at the opposite ends of the cline of Italian variation, along with a large panel of modern and ancient Euro-Mediterranean genomes. RESULTS We provided evidence for the early divergence of Italian groups dating back to the Late Glacial and for Neolithic and distinct Bronze Age migrations having further differentiated their gene pools. We inferred adaptive evolution at insulin-related loci in people from Italian regions with a temperate climate, while possible adaptations to pathogens and ultraviolet radiation were observed in Mediterranean Italians. Some of these adaptive events may also have secondarily modulated population disease or longevity predisposition. CONCLUSIONS We disentangled the contribution of multiple migratory and adaptive events in shaping the heterogeneous Italian genomic background, which exemplify population dynamics and gene-environment interactions that played significant roles also in the formation of the Continental and Southern European genomic landscapes.
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Affiliation(s)
- Marco Sazzini
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy.
| | - Paolo Abondio
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Stefania Sarno
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | | | - Matteo Ragno
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Sara De Fanti
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Claudia Ojeda-Granados
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara "Fray Antonio Alcalde" and Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Alessio Boattini
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Julien Marquis
- Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
- Current Address: Lausanne Genomic Technologies Facility, University of Lausanne, Lausanne, Switzerland
| | - Armand Valsesia
- Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | - Jerome Carayol
- Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
| | | | - Chiara Pirazzini
- IRCCS Bologna Institute of Neurological Sciences, Bologna, Italy
| | - Elena Marasco
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna, Bologna, Italy
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, Bologna, Italy
| | - Alberto Ferrarini
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
- Current Address: Menarini Silicon Biosystems SpA, Castel Maggiore, Bologna, Italy
| | - Luciano Xumerle
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Daniela Mari
- Geriatric Unit, Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Beatrice Arosio
- Geriatric Unit, Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Patrizia D'Aquila
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Davide Pettener
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Gastone Castellani
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Massimo Delledonne
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Claudio Franceschi
- Department of Applied Mathematics, Institute of Information Technology, Lobachevsky University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Paolo Garagnani
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy.
- Department of Experimental, Diagnostic, and Specialty Medicine, University of Bologna, Bologna, Italy.
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden.
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Inlamea OF, Soares P, Ikuta CY, Heinemann MB, Achá SJ, Machado A, Ferreira Neto JS, Correia-Neves M, Rito T. Evolutionary analysis of Mycobacterium bovis genotypes across Africa suggests co-evolution with livestock and humans. PLoS Negl Trop Dis 2020; 14:e0008081. [PMID: 32119671 PMCID: PMC7077849 DOI: 10.1371/journal.pntd.0008081] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 03/17/2020] [Accepted: 01/22/2020] [Indexed: 01/05/2023] Open
Abstract
Mycobacterium bovis is the pathogenic agent responsible for bovine tuberculosis (bTB), a zoonotic disease affecting mostly cattle, but also transmittable to humans and wildlife. Genetic studies on M. bovis allow to detect possible routes of bTB transmission and the identification of genetic reservoirs that may provide an essential framework for public health action. We used a database with 1235 M. bovis genotypes collected from different regions in Africa with 45 new Mozambican samples. Our analyses, based on phylogeographic and population genetics’ approaches, allowed to identify two clear trends. First, the genetic diversity of M. bovis is geographically clustered across the continent, with the only incidences of long-distance sharing of genotypes, between South Africa and Algeria, likely due to recent European introductions. Second, there is a broad gradient of diversity from Northern to Southern Africa with a diversity focus on the proximity to the Near East, where M. bovis likely emerged with animal domestication in the last 10,000 years. Diversity indices are higher in Eastern Africa, followed successively by Northern, Central, Southern and Western Africa, roughly correlating with the regional archaeological records of introduction of animal domesticates. Given this scenario M. bovis in Africa was probably established millennia ago following a concomitant spread with cattle, sheep and goat. Such scenario could translate into long-term locally adapted lineages across Africa. This work describes a novel scenario for the spread of M. bovis in Africa using the available genetic data, opening the field to further studies using higher resolution genomic data. We describe the genetic diversity distribution in Africa of the pathogen Mycobacterium bovis, the responsible for bovine tuberculosis, mostly present in cattle but also transmittable to other animals including humans. This diversity is geographically clustered within the African continent meaning that the genetic diversity was established through independent evolution within different areas. Higher diversity values of M. bovis are found in Eastern and Northern Africa, followed by Central Africa, with Western and Southern Africa displaying the lowest diversity. These levels of diversity correlate well with the introduction of domesticated livestock in the different regions of Africa, following their domestication in the Near East 10,000 ago. We hypothesize that M. bovis emerged in the Near East and it was carried across Africa together with domesticated animals and people that developed herding practices and biological tolerance for digesting milk in adulthood. Such scenario implies a strong evolution and co-evolution of M. bovis across Africa leading to locally adapted strains that could prove a challenge for public health actions.
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Affiliation(s)
- Osvaldo Frederico Inlamea
- Programa de pós-graduação Ciência Para o desenvolvimento (PGCD)–Instituto Gulbenkian de Ciência–Portugal
- Faculdade de Medicina Veterinária e Zootecnia (VPS-FMVZ), Universidade de São Paulo, USP–Brasil
- Instituto Nacional de Saúde, Ministério de Saúde, Moçambique
- Faculdade de Veterinária (FAVET), Universidade Eduardo Mondlane, Maputo, Moçambique
- * E-mail: (OFI); (TR)
| | - Pedro Soares
- Centre of Molecular and Environmental Biology (CBMA), School of Sciences, University of Minho, Braga, Portugal
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Cassia Yumi Ikuta
- Faculdade de Medicina Veterinária e Zootecnia (VPS-FMVZ), Universidade de São Paulo, USP–Brasil
| | - Marcos Bryan Heinemann
- Faculdade de Medicina Veterinária e Zootecnia (VPS-FMVZ), Universidade de São Paulo, USP–Brasil
| | - Sara Juma Achá
- Direcção de Ciências Animais, Instituto de Investigação Agrária de Moçambique, Ministério de Agricultura e Segurança Alimentar, Maputo, Moçambique
| | - Adelina Machado
- Faculdade de Veterinária (FAVET), Universidade Eduardo Mondlane, Maputo, Moçambique
| | | | - Margarida Correia-Neves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Teresa Rito
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
- * E-mail: (OFI); (TR)
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14
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The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean. Nat Ecol Evol 2020; 4:334-345. [PMID: 32094539 PMCID: PMC7080320 DOI: 10.1038/s41559-020-1102-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 01/08/2020] [Indexed: 11/08/2022]
Abstract
Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 BC, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BC. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 BC) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 BC, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium BC, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island's early farmers until the first millennium BC, with the exception of an outlier from the third millennium BC, who had primarily North African ancestry and who-along with an approximately contemporary Iberian-documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium BC and, at present, no more than 56-62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people.
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Boattini A, Sarno S, Mazzarisi AM, Viroli C, De Fanti S, Bini C, Larmuseau MHD, Pelotti S, Luiselli D. Estimating Y-Str Mutation Rates and Tmrca Through Deep-Rooting Italian Pedigrees. Sci Rep 2019; 9:9032. [PMID: 31227725 PMCID: PMC6588691 DOI: 10.1038/s41598-019-45398-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 06/06/2019] [Indexed: 02/06/2023] Open
Abstract
In the population genomics era, the study of Y-chromosome variability is still of the greatest interest for several fields ranging from molecular anthropology to forensics and genetic genealogy. In particular, mutation rates of Y-chromosomal Short Tandem Repeats markers (Y-STRs) are key parameters for different interdisciplinary applications. Among them, testing the patrilineal relatedness between individuals and calculating their Time of Most Recent Common Ancestors (TMRCAs) are of the utmost importance. To provide new valuable estimates and to address these issues, we typed 47 Y-STRs (comprising Yfiler, PowerPlex23 and YfilerPlus loci, the recently defined Rapidly Mutating [RM] panel and 11 additional markers often used in genetic genealogical applications) in 135 individuals belonging to 66 deep-rooting paternal genealogies from Northern Italy. Our results confirmed that the genealogy approach is an effective way to obtain reliable Y-STR mutation rate estimates even with a limited number of samples. Moreover, they showed that the impact of multi-step mutations and backmutations is negligible within the temporal scale usually adopted by forensic and genetic genealogy analyses. We then detected a significant association between the number of mutations within genealogies and observed TMRCAs. Therefore, we compared observed and expected TMRCAs by implementing a Bayesian procedure originally designed by Walsh (2001) and showed that the method yields a good performance (up to 96.72%), especially when using the Infinite Alleles Model (IAM).
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Affiliation(s)
- Alessio Boattini
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, 40126, Bologna, Italy.
| | - Stefania Sarno
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, 40126, Bologna, Italy
| | - Alessandra M Mazzarisi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, 40126, Bologna, Italy
| | - Cinzia Viroli
- Dipartimento di Scienze Statistiche "Paolo Fortunati", Università di Bologna, 40126, Bologna, Italy
| | - Sara De Fanti
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, 40126, Bologna, Italy
| | - Carla Bini
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, 40126, Bologna, Italy
| | - Maarten H D Larmuseau
- Laboratory of Forensic Genetics and Molecular Archaeology, Forensic Biomedical Sciences, KU Leuven, B-3000, Leuven, Belgium.,Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, B-3000, Leuven, Belgium
| | - Susi Pelotti
- Dipartimento di Scienze Mediche e Chirurgiche, Università di Bologna, 40126, Bologna, Italy
| | - Donata Luiselli
- Dipartimento di Beni Culturali, Università di Bologna, 48121, Ravenna, Italy
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16
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Hernández CL, Dugoujon JM, Sánchez-Martínez LJ, Cuesta P, Novelletto A, Calderón R. Paternal lineages in southern Iberia provide time frames for gene flow from mainland Europe and the Mediterranean world. Ann Hum Biol 2019; 46:63-76. [PMID: 30822152 DOI: 10.1080/03014460.2019.1587507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND The geography of southern Iberia and an abundant archaeological record of human occupation are ideal conditions for a full understanding of scenarios of genetic history in the area. Recent advances in the phylogeography of Y-chromosome lineages offer the opportunity to set upper bounds for the appearance of different genetic components. AIM To provide a global knowledge on the Y haplogroups observed in Andalusia with their Y microsatellite variation. Preferential attention is given to the vehement debate about the age, origin and expansion of R1b-M269 clade and sub-lineages. SUBJECT AND METHODS Four hundred and fourteen male DNA samples from western and eastern autochthonous Andalusians were genotyped for a set of Y-SNPs and Y-STRs. Gene diversity, potential population genetic structures and coalescent times were assessed. RESULTS Most of the analysed samples belong to the European haplogroup R1b1a1a2-M269, whereas haplogroups E, J, I, G and T show lower frequencies. A phylogenetic dissection of the R1b-M269 was performed and younger time frames than those previously reported in the literature were obtained for its sub-lineages. CONCLUSION The particular Andalusian R1b-M269 assemblage confirms the shallow topology of the clade. Moreover, the sharing of lineages with the rest of Europe indicates the impact in Iberia of an amount of pre-existing diversity, with the possible exception of R1b-DF27. Lineages such as J2-M172 and G-M201 highlight the importance of maritime travels of early farmers who reached the Iberian Peninsula.
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Affiliation(s)
- Candela L Hernández
- a Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología , Universidad Complutense , Madrid , Spain
| | - Jean-Michel Dugoujon
- b CNRS UMR 5288 Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse (AMIS) , Université Paul Sabatier Toulouse III , Toulouse , France
| | - Luis J Sánchez-Martínez
- a Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología , Universidad Complutense , Madrid , Spain
| | - Pedro Cuesta
- c Centro de Proceso de Datos , Universidad Complutense , Madrid , Spain
| | | | - Rosario Calderón
- a Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología , Universidad Complutense , Madrid , Spain
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Serventi P, Panicucci C, Bodega R, De Fanti S, Sarno S, Fondevila Alvarez M, Brisighelli F, Trombetta B, Anagnostou P, Ferri G, Vazzana A, Delpino C, Gruppioni G, Luiselli D, Cilli E. Iron Age Italic population genetics: the Piceni from Novilara (8th-7th century BC). Ann Hum Biol 2018; 45:34-43. [PMID: 29216758 DOI: 10.1080/03014460.2017.1414876] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Archaeological data provide evidence that Italy, during the Iron Age, witnessed the appearance of the first communities with well defined cultural identities. To date, only a few studies report genetic data about these populations and, in particular, the Piceni have never been analysed. AIMS To provide new data about mitochondrial DNA (mtDNA) variability of an Iron Age Italic population, to understand the contribution of the Piceni in shaping the modern Italian gene pool and to ascertain the kinship between some individuals buried in the same grave within the Novilara necropolis. SUBJECTS AND METHODS In a first set of 10 individuals from Novilara, we performed deep sequencing of the HVS-I region of the mtDNA, combined with the genotyping of 22 SNPs in the coding region and the analysis of several autosomal markers. RESULTS The results show a low nucleotide diversity for the inhabitants of Novilara and highlight a genetic affinity of this ancient population with the current inhabitants of central Italy. No family relationship was observed between the individuals analysed here. CONCLUSIONS This study provides a preliminary characterisation of the mtDNA variability of the Piceni of Novilara, as well as a kinship assessment of two peculiar burials.
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Affiliation(s)
- Patrizia Serventi
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy.,b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Chiara Panicucci
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Roberta Bodega
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Sara De Fanti
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Stefania Sarno
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Manuel Fondevila Alvarez
- c Instituto de Ciencias Forenses 'Luis Concheiro' , University of Santiago de Compostela, Santiago de Compostela , Galicia , Spain
| | - Francesca Brisighelli
- d Sezione di Medicina Legale-Istituto di Sanità Pubblica , Università Cattolica del Sacro Cuore , Roma , Italy
| | - Beniamino Trombetta
- e Department of Biology and Biotechnology 'Charles Darwin' , Sapienza University , Rome , Italy
| | - Paolo Anagnostou
- f Department of Environmental Biology , University of Rome 'La Sapienza' , Rome , Italy.,g ISItA, Istituto Italiano di Antropologia , Rome , Italy
| | - Gianmarco Ferri
- h Department of Diagnostic and Clinical Medicine and Public Health , University of Modena and Reggio Emilia , Modena , Italy
| | - Antonino Vazzana
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Chiara Delpino
- i Superintendence of Archaeological Heritage of Marche Region , Ancona , Italy
| | - Giorgio Gruppioni
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
| | - Donata Luiselli
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Elisabetta Cilli
- b Department of Cultural Heritage , University of Bologna , Ravenna , Italy
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Larmuseau MHD, Ottoni C. Mediterranean Y-chromosome 2.0-why the Y in the Mediterranean is still relevant in the postgenomic era. Ann Hum Biol 2018; 45:20-33. [PMID: 29382278 DOI: 10.1080/03014460.2017.1402956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CONTEXT Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour. OBJECTIVE For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available. METHODS A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. RESULTS Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. CONCLUSIONS There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.
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Affiliation(s)
- Maarten H D Larmuseau
- a KU Leuven, Forensic Biomedical Sciences , Department of Imaging & Pathology , Leuven , Belgium.,b KU Leuven, Laboratory of Socioecology and Social Evolution , Department of Biology , Leuven , Belgium
| | - Claudio Ottoni
- c Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences , University of Oslo , Oslo , Norway
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19
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Boattini A, Sarno S, Fiorani O, Lisa A, Luiselli D, Pettener D. Ripples on the surface. Surnames and genes in Sicily and Southern Italy. Ann Hum Biol 2018; 45:57-65. [PMID: 29183201 DOI: 10.1080/03014460.2017.1411525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Southern Italy and Sicily played a key role in the peopling history of the Mediterranean. While genetic research showed the remarkable homogeneity of these regions, surname-based studies instead suggested low population mobility, hence potential structuring. AIM In order to better understand these different patterns, this study (1) thoroughly analysed the surname structure of Sicily and Southern Italy and (2) tested its relationships with a wide set of molecular markers. SUBJECTS AND METHODS Surname data were collected from 1213 municipalities and compared to uniparental and autosomal genetic markers typed in ∼300 individuals from 8-10 populations. Surname analyses were performed using different multivariate methods, while comparisons with genetic data relied on correlation tests. RESULTS Surnames were clearly structured according to regional geographic patterns, which likely emerged because of recent isolation-by-distance-like population dynamics. In general, genetic markers, hinting at a pervasive homogeneity, did not correlate with surname distribution. However, long autosomal haplotypes (>5 cM) that compared to genotypic (SNPs) data identify more "recent" relatedness, showing a clear association with surname patterns. CONCLUSION The apparent contradiction between surname structure and genetic homogeneity was resolved by figuring surnames as recent "ripples" deposited on a vast and ancient homogeneous genetic "surface".
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Affiliation(s)
- Alessio Boattini
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Stefania Sarno
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Ornella Fiorani
- b Institute of Molecular Genetics (IGM) , Consiglio Nazionale delle Ricerche (CNR) , Pavia , Italy
| | - Antonella Lisa
- b Institute of Molecular Genetics (IGM) , Consiglio Nazionale delle Ricerche (CNR) , Pavia , Italy
| | - Donata Luiselli
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Davide Pettener
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
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20
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A finely resolved phylogeny of Y chromosome Hg J illuminates the processes of Phoenician and Greek colonizations in the Mediterranean. Sci Rep 2018; 8:7465. [PMID: 29748665 PMCID: PMC5945646 DOI: 10.1038/s41598-018-25912-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/25/2018] [Indexed: 11/15/2022] Open
Abstract
In order to improve the phylogeography of the male-specific genetic traces of Greek and Phoenician colonizations on the Northern coasts of the Mediterranean, we performed a geographically structured sampling of seven subclades of haplogroup J in Turkey, Greece and Italy. We resequenced 4.4 Mb of Y-chromosome in 58 subjects, obtaining 1079 high quality variants. We did not find a preferential coalescence of Turkish samples to ancestral nodes, contradicting the simplistic idea of a dispersal and radiation of Hg J as a whole from the Middle East. Upon calibration with an ancient Hg J chromosome, we confirmed that signs of Holocenic Hg J radiations are subtle and date mainly to the Bronze Age. We pinpointed seven variants which could potentially unveil star clusters of sequences, indicative of local expansions. By directly genotyping these variants in Hg J carriers and complementing with published resequenced chromosomes (893 subjects), we provide strong temporal and distributional evidence for markers of the Greek settlement of Magna Graecia (J2a-L397) and Phoenician migrations (rs760148062). Our work generated a minimal but robust list of evolutionarily stable markers to elucidate the demographic dynamics and spatial domains of male-mediated movements across and around the Mediterranean, in the last 6,000 years.
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Capittini C, Messina F, Puglisi F, Azzaro M, Toscano S, De Silvestri A, Tinelli C, Sortino G. An historical approach to the genetic distribution of KIR and HLA ligands in Eastern Sicilians compared to modern descendants of their invaders. Hum Immunol 2018; 79:5-12. [DOI: 10.1016/j.humimm.2017.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 11/26/2022]
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Heraclides A, Bashiardes E, Fernández-Domínguez E, Bertoncini S, Chimonas M, Christofi V, King J, Budowle B, Manoli P, Cariolou MA. Y-chromosomal analysis of Greek Cypriots reveals a primarily common pre-Ottoman paternal ancestry with Turkish Cypriots. PLoS One 2017; 12:e0179474. [PMID: 28622394 PMCID: PMC5473566 DOI: 10.1371/journal.pone.0179474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/31/2017] [Indexed: 12/15/2022] Open
Abstract
Genetics can provide invaluable information on the ancestry of the current inhabitants of Cyprus. A Y-chromosome analysis was performed to (i) determine paternal ancestry among the Greek Cypriot (GCy) community in the context of the Central and Eastern Mediterranean and the Near East; and (ii) identify genetic similarities and differences between Greek Cypriots (GCy) and Turkish Cypriots (TCy). Our haplotype-based analysis has revealed that GCy and TCy patrilineages derive primarily from a single gene pool and show very close genetic affinity (low genetic differentiation) to Calabrian Italian and Lebanese patrilineages. In terms of more recent (past millennium) ancestry, as indicated by Y-haplotype sharing, GCy and TCy share much more haplotypes between them than with any surrounding population (7-8% of total haplotypes shared), while TCy also share around 3% of haplotypes with mainland Turks, and to a lesser extent with North Africans. In terms of Y-haplogroup frequencies, again GCy and TCy show very similar distributions, with the predominant haplogroups in both being J2a-M410, E-M78, and G2-P287. Overall, GCy also have a similar Y-haplogroup distribution to non-Turkic Anatolian and Southwest Caucasian populations, as well as Cretan Greeks. TCy show a slight shift towards Turkish populations, due to the presence of Eastern Eurasian (some of which of possible Ottoman origin) Y-haplogroups. Overall, the Y-chromosome analysis performed, using both Y-STR haplotype and binary Y-haplogroup data puts Cypriot in the middle of a genetic continuum stretching from the Levant to Southeast Europe and reveals that despite some differences in haplotype sharing and haplogroup structure, Greek Cypriots and Turkish Cypriots share primarily a common pre-Ottoman paternal ancestry.
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Affiliation(s)
- Alexandros Heraclides
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Department of Primary Care and Population Health, University of Nicosia Medical School, Nicosia, Cyprus
| | - Evy Bashiardes
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | | | - Marios Chimonas
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Vasilis Christofi
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Jonathan King
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Panayiotis Manoli
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marios A. Cariolou
- Department of Cardiovascular Genetics and The Laboratory of Forensic Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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Santovito A, Gendusa C, Matini A, Ferraro F, Musso I, Costanzo M, Delclos A, Cervella P. Frequency distribution of six cytokine gene polymorphisms in North- and South-Italy. Int J Immunogenet 2017; 44:158-163. [DOI: 10.1111/iji.12324] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/10/2017] [Accepted: 04/20/2017] [Indexed: 01/22/2023]
Affiliation(s)
- A. Santovito
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
| | - C. Gendusa
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
| | - A. Matini
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
| | - F. Ferraro
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
| | - I. Musso
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
| | - M. Costanzo
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
| | - A. Delclos
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
| | - P. Cervella
- Department of Life Sciences and Systems Biology; University of Turin; Torino Italy
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Ancient and recent admixture layers in Sicily and Southern Italy trace multiple migration routes along the Mediterranean. Sci Rep 2017; 7:1984. [PMID: 28512355 PMCID: PMC5434004 DOI: 10.1038/s41598-017-01802-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/04/2017] [Indexed: 12/12/2022] Open
Abstract
The Mediterranean shores stretching between Sicily, Southern Italy and the Southern Balkans witnessed a long series of migration processes and cultural exchanges. Accordingly, present-day population diversity is composed by multiple genetic layers, which make the deciphering of different ancestral and historical contributes particularly challenging. We address this issue by genotyping 511 samples from 23 populations of Sicily, Southern Italy, Greece and Albania with the Illumina GenoChip Array, also including new samples from Albanian- and Greek-speaking ethno-linguistic minorities of Southern Italy. Our results reveal a shared Mediterranean genetic continuity, extending from Sicily to Cyprus, where Southern Italian populations appear genetically closer to Greek-speaking islands than to continental Greece. Besides a predominant Neolithic background, we identify traces of Post-Neolithic Levantine- and Caucasus-related ancestries, compatible with maritime Bronze-Age migrations. We argue that these results may have important implications in the cultural history of Europe, such as in the diffusion of some Indo-European languages. Instead, recent historical expansions from North-Eastern Europe account for the observed differentiation of present-day continental Southern Balkan groups. Patterns of IBD-sharing directly reconnect Albanian-speaking Arbereshe with a recent Balkan-source origin, while Greek-speaking communities of Southern Italy cluster with their Italian-speaking neighbours suggesting a long-term history of presence in Southern Italy.
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Balasus D, Way M, Fusilli C, Mazza T, Morgan MY, Cervello M, Giannitrapani L, Soresi M, Agliastro R, Vinciguerra M, Montalto G. The association of variants in PNPLA3 and GRP78 and the risk of developing hepatocellular carcinoma in an Italian population. Oncotarget 2016; 7:86791-86802. [PMID: 27888630 PMCID: PMC5349954 DOI: 10.18632/oncotarget.13558] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/07/2016] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) has one of the worst prognoses amongst all malignancies. It commonly arises in patients with established liver disease and the diagnosis often occurs at an advanced stage. Genetic variations, such as single nucleotide polymorphisms (SNPs), may alter disease risk and thus may have use as predictive markers of disease outcome. The aims of this study were (i) to assess the association of two SNPs, rs430397 in GRP78 and rs738409 in PNPLA3 with the risk of developing HCC in a Sicilian association cohort and, (ii) to use a machine learning technique to establish a predictive combinatorial phenotypic model for HCC including rs430397 and rs738409 genotypes and clinical and laboratory attributes. The controls comprised of 304 healthy subjects while the cases comprised of 170 HCC patients the majority of whom had hepatitis C (HCV)-related cirrhosis. Significant associations were identified between the risk of developing HCC and both rs430397 (p=0.0095) and rs738409 (p=0.0063). The association between rs738409 and HCC was significantly stronger in the HCV positive cases. In the best prediction model, represented graphically by a decision tree with an acceptable misclassification rate of 17.0%, the A/A and G/A genotypes of the rs430397 variant were fixed and combined with the three rs738409 genotypes; the attributes were age, sex and alcohol. These results demonstrate significant associations between both rs430397 and rs738409 and HCC development in a Sicilian cohort. The combinatorial predictive model developed to include these genetic variants may, if validated in independent cohorts, allow for earlier diagnosis of HCC.
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Affiliation(s)
- Daniele Balasus
- Biomedical Department of Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Michael Way
- Institute for Liver & Digestive Health, Division of Medicine, Royal Free Campus, University College London, London, UK
| | - Caterina Fusilli
- IRCCS Casa Sollievo della Sofferenza, Bioinformatics Unit, San Giovanni Rotondo (FG), Italy
| | - Tommaso Mazza
- IRCCS Casa Sollievo della Sofferenza, Bioinformatics Unit, San Giovanni Rotondo (FG), Italy
| | - Marsha Y. Morgan
- Institute for Liver & Digestive Health, Division of Medicine, Royal Free Campus, University College London, London, UK
| | - Melchiorre Cervello
- Institute of Biomedicine and Molecular Immunology, National Research Council (C.N.R.), Palermo, Italy
| | - Lydia Giannitrapani
- Biomedical Department of Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Maurizio Soresi
- Biomedical Department of Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Rosalia Agliastro
- Immunohematology and Transfusion Medicine Unit, “Civico” Reference Regional Hospital, Palermo, Italy
| | - Manlio Vinciguerra
- Institute for Liver & Digestive Health, Division of Medicine, Royal Free Campus, University College London, London, UK
- Center for Translational Medicine (CTM), International Clinical Research Center (ICRC), St. Anne's University Hospital, Brno, Czech Republic
| | - Giuseppe Montalto
- Biomedical Department of Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
- Institute of Biomedicine and Molecular Immunology, National Research Council (C.N.R.), Palermo, Italy
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Messina F, Finocchio A, Akar N, Loutradis A, Michalodimitrakis EI, Brdicka R, Jodice C, Novelletto A. Spatially Explicit Models to Investigate Geographic Patterns in the Distribution of Forensic STRs: Application to the North-Eastern Mediterranean. PLoS One 2016; 11:e0167065. [PMID: 27898725 PMCID: PMC5127579 DOI: 10.1371/journal.pone.0167065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/08/2016] [Indexed: 11/18/2022] Open
Abstract
Human forensic STRs used for individual identification have been reported to have little power for inter-population analyses. Several methods have been developed which incorporate information on the spatial distribution of individuals to arrive at a description of the arrangement of diversity. We genotyped at 16 forensic STRs a large population sample obtained from many locations in Italy, Greece and Turkey, i.e. three countries crucial to the understanding of discontinuities at the European/Asian junction and the genetic legacy of ancient migrations, but seldom represented together in previous studies. Using spatial PCA on the full dataset, we detected patterns of population affinities in the area. Additionally, we devised objective criteria to reduce the overall complexity into reduced datasets. Independent spatially explicit methods applied to these latter datasets converged in showing that the extraction of information on long- to medium-range geographical trends and structuring from the overall diversity is possible. All analyses returned the picture of a background clinal variation, with regional discontinuities captured by each of the reduced datasets. Several aspects of our results are confirmed on external STR datasets and replicate those of genome-wide SNP typings. High levels of gene flow were inferred within the main continental areas by coalescent simulations. These results are promising from a microevolutionary perspective, in view of the fast pace at which forensic data are being accumulated for many locales. It is foreseeable that this will allow the exploitation of an invaluable genotypic resource, assembled for other (forensic) purposes, to clarify important aspects in the formation of local gene pools.
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Affiliation(s)
| | | | - Nejat Akar
- Pediatrics Department, TOBB-Economy and Technology University Hospital, Ankara, Turkey
| | | | | | - Radim Brdicka
- Institute of Haematology and Blood Transfusion, Praha, Czech Republic
| | - Carla Jodice
- Department of Biology, University "Tor Vergata", Rome, Italy
| | - Andrea Novelletto
- Department of Biology, University "Tor Vergata", Rome, Italy
- * E-mail:
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27
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De Fanti S, Vianello D, Giuliani C, Quagliariello A, Cherubini A, Sevini F, Iaquilano N, Franceschi C, Sazzini M, Luiselli D. Massive parallel sequencing of human whole mitochondrial genomes with Ion Torrent technology: an optimized workflow for Anthropological and Population Genetics studies. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:843-850. [PMID: 27822964 DOI: 10.1080/24701394.2016.1197218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Investigation of human mitochondrial DNA variation patterns and phylogeny has been extensively used in Anthropological and Population Genetics studies and sequencing the whole mitochondrial genome is progressively becoming the gold standard. Among the currently available massive parallel sequencing technologies, Ion Torrent™ semiconductor sequencing represents a promising approach for such studies. Nevertheless, an experimental protocol conceived to enable the achievement of both as high as possible yield and of the most homogeneous sequence coverage through the whole mitochondrial genome is still not available. The present work was thus aimed at improving the overall performance of whole mitochondrial genomes Ion Torrent™ sequencing, with special focus on the capability to obtain robust coverage and highly reliable variants calling. For this purpose, a series of cost-effective modifications in standard laboratory workflows was fine-tuned to optimize them for medium- and large-scale population studies. A total of 54 human samples were thus subjected to sequencing of the whole mitochondrial genome with the Ion Personal Genome Machine™ System in four distinct experiments and using Ion 314 chips. Seven of the selected samples were also characterized by means of conventional Sanger sequencing for the sake of comparison. Obtained results demonstrated that the implemented optimizations had definitely improved sequencing outputs in terms of both variants calling efficiency and coverage uniformity, enabling to setup an effective and accurate protocol for whole mitochondrial genome sequencing and a considerable reduction in experimental time consumption and sequencing costs.
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Affiliation(s)
- Sara De Fanti
- a Laboratory of Molecular Anthropology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy.,b Centre for Genome Biology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy
| | - Dario Vianello
- c Department of Experimental, Diagnostic & Specialty Medicine (DIMES) , University of Bologna , Bologna , Italy
| | - Cristina Giuliani
- a Laboratory of Molecular Anthropology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy.,b Centre for Genome Biology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy
| | - Andrea Quagliariello
- a Laboratory of Molecular Anthropology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy.,b Centre for Genome Biology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy
| | - Anna Cherubini
- a Laboratory of Molecular Anthropology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy.,b Centre for Genome Biology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy
| | - Federica Sevini
- c Department of Experimental, Diagnostic & Specialty Medicine (DIMES) , University of Bologna , Bologna , Italy
| | - Nicoletta Iaquilano
- c Department of Experimental, Diagnostic & Specialty Medicine (DIMES) , University of Bologna , Bologna , Italy
| | - Claudio Franceschi
- c Department of Experimental, Diagnostic & Specialty Medicine (DIMES) , University of Bologna , Bologna , Italy
| | - Marco Sazzini
- a Laboratory of Molecular Anthropology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy.,b Centre for Genome Biology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy
| | - Donata Luiselli
- a Laboratory of Molecular Anthropology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy.,b Centre for Genome Biology, Department of Biological, Geological & Environmental Sciences (BiGeA) , University of Bologna , Bologna , Italy
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28
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Complex interplay between neutral and adaptive evolution shaped differential genomic background and disease susceptibility along the Italian peninsula. Sci Rep 2016; 6:32513. [PMID: 27582244 PMCID: PMC5007512 DOI: 10.1038/srep32513] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 08/08/2016] [Indexed: 01/23/2023] Open
Abstract
The Italian peninsula has long represented a natural hub for human migrations across
the Mediterranean area, being involved in several prehistoric and historical
population movements. Coupled with a patchy environmental landscape entailing
different ecological/cultural selective pressures, this might have produced peculiar
patterns of population structure and local adaptations responsible for heterogeneous
genomic background of present-day Italians. To disentangle this complex scenario,
genome-wide data from 780 Italian individuals were generated and set into the
context of European/Mediterranean genomic diversity by comparison with genotypes
from 50 populations. To maximize possibility of pinpointing functional genomic
regions that have played adaptive roles during Italian natural history, our survey
included also ~250,000 exomic markers and ~20,000
coding/regulatory variants with well-established clinical relevance. This enabled
fine-grained dissection of Italian population structure through the identification
of clusters of genetically homogeneous provinces and of genomic regions underlying
their local adaptations. Description of such patterns disclosed crucial implications
for understanding differential susceptibility to some inflammatory/autoimmune
disorders, coronary artery disease and type 2 diabetes of diverse Italian
subpopulations, suggesting the evolutionary causes that made some of them
particularly exposed to the metabolic and immune challenges imposed by dietary and
lifestyle shifts that involved western societies in the last centuries.
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29
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Matisoo-Smith EA, Gosling AL, Boocock J, Kardailsky O, Kurumilian Y, Roudesli-Chebbi S, Badre L, Morel JP, Sebaï LL, Zalloua PA. A European Mitochondrial Haplotype Identified in Ancient Phoenician Remains from Carthage, North Africa. PLoS One 2016; 11:e0155046. [PMID: 27224451 PMCID: PMC4880306 DOI: 10.1371/journal.pone.0155046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/22/2016] [Indexed: 11/18/2022] Open
Abstract
While Phoenician culture and trade networks had a significant impact on Western civilizations, we know little about the Phoenicians themselves. In 1994, a Punic burial crypt was discovered on Byrsa Hill, near the entry to the National Museum of Carthage in Tunisia. Inside this crypt were the remains of a young man along with a range of burial goods, all dating to the late 6th century BCE. Here we describe the complete mitochondrial genome recovered from the Young Man of Byrsa and identify that he carried a rare European haplogroup, likely linking his maternal ancestry to Phoenician influenced locations somewhere on the North Mediterranean coast, the islands of the Mediterranean or the Iberian Peninsula. This result not only provides the first direct ancient DNA evidence of a Phoenician individual but the earliest evidence of a European mitochondrial haplogroup, U5b2c1, in North Africa.
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Affiliation(s)
| | - Anna L. Gosling
- Department of Anatomy and Allan Wilson Centre, University of Otago, Dunedin, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - James Boocock
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Olga Kardailsky
- Department of Anatomy and Allan Wilson Centre, University of Otago, Dunedin, New Zealand
| | - Yara Kurumilian
- School of Medicine, Lebanese American University, Byblos, Lebanon
| | | | - Leila Badre
- Archaeological Museum, American University of Beirut, Beirut, Lebanon
| | - Jean-Paul Morel
- Université d’Aix-Marseille, Centre Camille Jullian, Aix-en-Provence, France
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30
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Fiorito G, Di Gaetano C, Guarrera S, Rosa F, Feldman MW, Piazza A, Matullo G. The Italian genome reflects the history of Europe and the Mediterranean basin. Eur J Hum Genet 2015; 24:1056-62. [PMID: 26554880 DOI: 10.1038/ejhg.2015.233] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 11/09/2022] Open
Abstract
Recent scientific literature has highlighted the relevance of population genetic studies both for disease association mapping in admixed populations and for understanding the history of human migrations. Deeper insight into the history of the Italian population is critical for understanding the peopling of Europe. Because of its crucial position at the centre of the Mediterranean basin, the Italian peninsula has experienced a complex history of colonization and migration whose genetic signatures are still present in contemporary Italians. In this study, we investigated genomic variation in the Italian population using 2.5 million single-nucleotide polymorphisms in a sample of more than 300 unrelated Italian subjects with well-defined geographical origins. We combined several analytical approaches to interpret genome-wide data on 1272 individuals from European, Middle Eastern, and North African populations. We detected three major ancestral components contributing different proportions across the Italian peninsula, and signatures of continuous gene flow within Italy, which have produced remarkable genetic variability among contemporary Italians. In addition, we have extracted novel details about the Italian population's ancestry, identifying the genetic signatures of major historical events in Europe and the Mediterranean basin from the Neolithic (e.g., peopling of Sardinia) to recent times (e.g., 'barbarian invasion' of Northern and Central Italy). These results are valuable for further genetic, epidemiological and forensic studies in Italy and in Europe.
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Affiliation(s)
- Giovanni Fiorito
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
| | - Cornelia Di Gaetano
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
| | - Simonetta Guarrera
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
| | - Fabio Rosa
- HuGeF Human Genetics Foundation, Turin, Italy
| | | | - Alberto Piazza
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy.,HuGeF Human Genetics Foundation, Turin, Italy
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31
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Charoute H, Bakhchane A, Benrahma H, Romdhane L, Gabi K, Rouba H, Fakiri M, Abdelhak S, Lenaers G, Barakat A. Mediterranean Founder Mutation Database (MFMD): Taking Advantage from Founder Mutations in Genetics Diagnosis, Genetic Diversity and Migration History of the Mediterranean Population. Hum Mutat 2015; 36:E2441-53. [PMID: 26173767 DOI: 10.1002/humu.22835] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 06/26/2015] [Indexed: 01/09/2023]
Abstract
The Mediterranean basin has been the theater of migration crossroads followed by settlement of several societies and cultures in prehistoric and historical times, with important consequences on genetic and genomic determinisms. Here, we present the Mediterranean Founder Mutation Database (MFMD), established to offer web-based access to founder mutation information in the Mediterranean population. Mutation data were collected from the literature and other online resources and systematically reviewed and assembled into this database. The information provided for each founder mutation includes DNA change, amino-acid change, mutation type and mutation effect, as well as mutation frequency and coalescence time when available. Currently, the database contains 383 founder mutations found in 210 genes related to 219 diseases. We believe that MFMD will help scientists and physicians to design more rapid and less expensive genetic diagnostic tests. Moreover, the coalescence time of founder mutations gives an overview about the migration history of the Mediterranean population. MFMD can be publicly accessed from http://mfmd.pasteur.ma.
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Affiliation(s)
- Hicham Charoute
- Laboratoire de Génétique Moléculaire Humaine, Institut Pasteur du Maroc, 1 Place Louis Pasteur, 20360, Casablanca, Morocco.,Laboratory of Agri-food and Health, Faculty of Sciences and Techniques, Hassan 1st University, BP 577, 26000, Settat, Morocco
| | - Amina Bakhchane
- Laboratoire de Génétique Moléculaire Humaine, Institut Pasteur du Maroc, 1 Place Louis Pasteur, 20360, Casablanca, Morocco
| | - Houda Benrahma
- Laboratoire de Génétique Moléculaire Humaine, Institut Pasteur du Maroc, 1 Place Louis Pasteur, 20360, Casablanca, Morocco
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics LR11IPT05, Institut Pasteur de Tunis, 1002, Tunis, Tunisia
| | - Khalid Gabi
- Laboratoire de Génétique Moléculaire Humaine, Institut Pasteur du Maroc, 1 Place Louis Pasteur, 20360, Casablanca, Morocco
| | - Hassan Rouba
- Laboratoire de Génétique Moléculaire Humaine, Institut Pasteur du Maroc, 1 Place Louis Pasteur, 20360, Casablanca, Morocco
| | - Malika Fakiri
- Laboratory of Agri-food and Health, Faculty of Sciences and Techniques, Hassan 1st University, BP 577, 26000, Settat, Morocco
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics LR11IPT05, Institut Pasteur de Tunis, 1002, Tunis, Tunisia
| | - Guy Lenaers
- Pôle de Recherche et d'Enseignement en Médecine Mitochondriale (PREMMi), Université d'Angers, CHU Bât IRIS/IBS, Rue des Capucins, 49933, Angers cedex 9, France
| | - Abdelhamid Barakat
- Laboratoire de Génétique Moléculaire Humaine, Institut Pasteur du Maroc, 1 Place Louis Pasteur, 20360, Casablanca, Morocco
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Sarno S, Tofanelli S, De Fanti S, Quagliariello A, Bortolini E, Ferri G, Anagnostou P, Brisighelli F, Capelli C, Tagarelli G, Sineo L, Luiselli D, Boattini A, Pettener D. Shared language, diverging genetic histories: high-resolution analysis of Y-chromosome variability in Calabrian and Sicilian Arbereshe. Eur J Hum Genet 2015; 24:600-6. [PMID: 26130483 PMCID: PMC4929864 DOI: 10.1038/ejhg.2015.138] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/02/2015] [Accepted: 04/14/2015] [Indexed: 11/25/2022] Open
Abstract
The relationship between genetic and linguistic diversification in human populations has been often explored to interpret some specific issues in human history. The Albanian-speaking minorities of Sicily and Southern Italy (Arbereshe) constitute an important portion of the ethnolinguistic variability of Italy. Their linguistic isolation from neighboring Italian populations and their documented migration history, make such minorities particularly effective for investigating the interplay between cultural, geographic and historical factors. Nevertheless, the extent of Arbereshe genetic relationships with the Balkan homeland and the Italian recipient populations has been only partially investigated. In the present study we address the genetic history of Arbereshe people by combining highly resolved analyses of Y-chromosome lineages and extensive computer simulations. A large set of slow- and fast-evolving molecular markers was typed in different Arbereshe communities from Sicily and Southern Italy (Calabria), as well as in both the putative Balkan source and Italian sink populations. Our results revealed that the considered Arbereshe groups, despite speaking closely related languages and sharing common cultural features, actually experienced diverging genetic histories. The estimated proportions of genetic admixture confirm the tight relationship of Calabrian Arbereshe with modern Albanian populations, in accordance with linguistic hypotheses. On the other hand, population stratification and/or an increased permeability of linguistic and geographic barriers may be hypothesized for Sicilian groups, to account for their partial similarity with Greek populations and their higher levels of local admixture. These processes ultimately resulted in the differential acquisition or preservation of specific paternal lineages by the present-day Arbereshe communities.
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Affiliation(s)
- Stefania Sarno
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | | | - Sara De Fanti
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Andrea Quagliariello
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Eugenio Bortolini
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Gianmarco Ferri
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Università degli Studi di Modena e Reggio Emilia, Modena, Italia
| | - Paolo Anagnostou
- Dipartimento Biologia Ambientale, Sapienza Università di Roma, Roma, Italia.,Istituto Italiano di Antropologia, Roma, Italia
| | - Francesca Brisighelli
- Department of Zoology, University of Oxford, Oxford, UK.,Sezione di medicina Legale-Istituto di Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italia
| | | | | | - Luca Sineo
- Dipartimento Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italia
| | - Donata Luiselli
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Alessio Boattini
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
| | - Davide Pettener
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italia
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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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Bonura C, Gomgnimbou MK, Refrégier G, Aleo A, Fasciana T, Giammanco A, Sola C, Mammina C. Molecular epidemiology of tuberculosis in Sicily, Italy: what has changed after a decade? BMC Infect Dis 2014; 14:602. [PMID: 25407589 PMCID: PMC4241219 DOI: 10.1186/s12879-014-0602-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/31/2014] [Indexed: 11/10/2022] Open
Abstract
Background We aimed to investigate the molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) isolates in the province of Palermo, Sicily, Italy, by characterizing 183 isolates identified in the years 2004-2012. A comparison with 104 MTBC strains identified in the same geographic area in the years 1994-2000 was also carried out. Methods One hundred eighty-three MTBC isolates identified in Palermo, Italy, in the years 2004-2012 were analyzed by spoligotyping and the 24 mycobacterial interspersed repetitive unit (MIRU)-variable-number tandem-repeat (VNTR) method typing. Susceptibility testing to streptomycin, isoniazid, rifampin and ethambutol was also performed. Furthermore, the spoligotyping dataset obtained from 104 MTBC isolates identified from 1994 to 2000 was reanalyzed. Distribution into lineages and clustering of isolates in the two periods was compared. Results One hundred seventy-seven out of the 183 isolates of MTBC submitted to molecular typing were fully characterized. Of these, 108 were from Italian-born and 69 from foreign-born individuals. Eleven different lineages and 35 families-subfamilies were identified with the most represented lineages being Haarlem (26.5%), T (19.2%), LAM (13.6%) and S (8.5%). Except for the Haarlem lineage, where isolates from foreign-born patients were overrepresented, the distribution of isolates in the families belonging to the Euro-American clone reflected the proportions of the two subpopulations. A total of 27 (15.2%) strains were clustered and three clusters were mixed. Approximately 25% of the 183 MTBC isolates under study proved to be resistant to at least one antiTB drug, with only three isolates categorized as multidrug resistant (MDR). When MTBC isolates identified in the years 1994-2000 were reanalyzed, lineages T (30.8%), LAM (29.8%), Haarlem (16.3%) and S (13.5%) proved to be predominant. No MTBC isolates belonging to CAM, U, CAS, Turkish and Ural lineages were identified. Conclusions A wide heterogeneity was detected among the MTBC strains isolated in the years 2004-2012. Six lineages were not present among the isolates of the period 1994-2000. Comparison between distribution of lineages in the two consecutive periods depicts rapid and deep changes in the TB epidemiology in Palermo, Italy. An universal and continued laboratory-based surveillance of TB in Sicily is required. Electronic supplementary material The online version of this article (doi:10.1186/s12879-014-0602-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Celestino Bonura
- Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy.
| | - Michel K Gomgnimbou
- CNRS-Université Paris-Sud, Institut de Génétique et Microbiologie, UMR8621, Infection Genetics Emerging Pathogen Evolution Team, Orsay, France.
| | - Guislaine Refrégier
- CNRS-Université Paris-Sud, Institut de Génétique et Microbiologie, UMR8621, Infection Genetics Emerging Pathogen Evolution Team, Orsay, France.
| | - Aurora Aleo
- Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy.
| | - Teresa Fasciana
- Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy.
| | - Anna Giammanco
- Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy.
| | - Christophe Sola
- CNRS-Université Paris-Sud, Institut de Génétique et Microbiologie, UMR8621, Infection Genetics Emerging Pathogen Evolution Team, Orsay, France.
| | - Caterina Mammina
- Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy.
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Traces of medieval migrations in a socially stratified population from Northern Italy. Evidence from uniparental markers and deep-rooted pedigrees. Heredity (Edinb) 2014; 114:155-62. [PMID: 25204305 DOI: 10.1038/hdy.2014.77] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/25/2014] [Accepted: 07/23/2014] [Indexed: 02/03/2023] Open
Abstract
Social and cultural factors had a critical role in determining the genetic structure of Europe. Therefore, socially stratified populations may help to focus on specific episodes of European demographic history. In this study, we use uniparental markers to analyse the genetic structure of Partecipanza in San Giovanni in Persiceto (Northern Italy), a peculiar institution whose origins date back to the Middle Ages and whose members form the patrilineal descent of a group of founder families. From a maternal point of view (mtDNA), Partecipanza is genetically homogeneous with the rest of the population. However, we observed a significant differentiation for Y-chromosomes. In addition, by comparing 17 Y-STR profiles with deep-rooted paternal pedigrees, we estimated a Y-STR mutation rate equal to 3.90 * 10(-3) mutations per STR per generation and an average generation duration time of 33.38 years. When we used these values for tentative dating, we estimated 1300-600 years ago for the origins of the Partecipanza. These results, together with a peculiar Y-chromosomal composition and historical evidence, suggest that Germanic populations (Lombards in particular) settled in the area during the Migration Period (400-800 AD, approximately) and may have had an important role in the foundation of this community.
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