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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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2
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Birolo G, Aneli S, Di Gaetano C, Cugliari G, Russo A, Allione A, Casalone E, Giorgio E, Paraboschi EM, Ardissino D, Duga S, Asselta R, Matullo G. Functional and clinical implications of genetic structure in 1686 Italian exomes. Hum Mutat 2021; 42:272-289. [PMID: 33326653 DOI: 10.1002/humu.24156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 11/13/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
To reconstruct the phenotypical and clinical implications of the Italian genetic structure, we thoroughly analyzed a whole-exome sequencing data set comprised of 1686 healthy Italian individuals. We found six previously unreported variants with remarkable frequency differences between Northern and Southern Italy in the HERC2, OR52R1, ADH1B, and THBS4 genes. We reported 36 clinically relevant variants (submitted as pathogenic, risk factors, or drug response in ClinVar) with significant frequency differences between Italy and Europe. We then explored putatively pathogenic variants in the Italian exome. On average, our Italian individuals carried 16.6 protein-truncating variants (PTVs), with 2.5% of the population having a PTV in one of the 59 American College of Medical Genetics (ACMG) actionable genes. Lastly, we looked for PTVs that are likely to cause Mendelian diseases. We found four heterozygous PTVs in haploinsufficient genes (KAT6A, PTCH1, and STXBP1) and three homozygous PTVs in genes causing recessive diseases (DPYD, FLG, and PYGM). Comparing frequencies from our data set to other public databases, like gnomAD, we showed the importance of population-specific databases for a more accurate assessment of variant pathogenicity. For this reason, we made aggregated frequencies from our data set publicly available as a tool for both clinicians and researchers (http://nigdb.cineca.it; NIG-ExIT).
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Affiliation(s)
- Giovanni Birolo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Serena Aneli
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | | | - Alessia Russo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | | | - Elisa Giorgio
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Elvezia M Paraboschi
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Diego Ardissino
- Division of Cardiology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy.,Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
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3
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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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4
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Grugni V, Raveane A, Colombo G, Nici C, Crobu F, Ongaro L, Battaglia V, Sanna D, Al-Zahery N, Fiorani O, Lisa A, Ferretti L, Achilli A, Olivieri A, Francalacci P, Piazza A, Torroni A, Semino O. Y-chromosome and Surname Analyses for Reconstructing Past Population Structures: The Sardinian Population as a Test Case. Int J Mol Sci 2019; 20:E5763. [PMID: 31744094 PMCID: PMC6888588 DOI: 10.3390/ijms20225763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 11/17/2022] Open
Abstract
Many anthropological, linguistic, genetic and genomic analyses have been carried out to evaluate the potential impact that evolutionary forces had in shaping the present-day Sardinian gene pool, the main outlier in the genetic landscape of Europe. However, due to the homogenizing effect of internal movements, which have intensified over the past fifty years, only partial information has been obtained about the main demographic events. To overcome this limitation, we analyzed the male-specific region of the Y chromosome in three population samples obtained by reallocating a large number of Sardinian subjects to the place of origin of their monophyletic surnames, which are paternally transmitted through generations in most of the populations, much like the Y chromosome. Three Y-chromosome founding lineages, G2-L91, I2-M26 and R1b-V88, were identified as strongly contributing to the definition of the outlying position of Sardinians in the European genetic context and marking a significant differentiation within the island. The present distribution of these lineages does not always mirror that detected in ancient DNAs. Our results show that the analysis of the Y-chromosome gene pool coupled with a sampling method based on the origin of the family name, is an efficient approach to unravelling past heterogeneity, often hidden by recent movements, in the gene pool of modern populations. Furthermore, the reconstruction and comparison of past genetic isolates represent a starting point to better assess the genetic information deriving from the increasing number of available ancient DNA samples.
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Affiliation(s)
- Viola Grugni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Alessandro Raveane
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Giulia Colombo
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Carmen Nici
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Francesca Crobu
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), 09042 Monserrato, Italy
| | - Linda Ongaro
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Estonian Biocentre, Institute of Genomics, Riia 23, 51010 Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, Riia 23, 51010 Tartu, Estonia
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Daria Sanna
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy
| | - Nadia Al-Zahery
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Ornella Fiorani
- Istituto di Genetica Molecolare “L.L. Cavalli-Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy; (O.F.); (A.L.)
| | - Antonella Lisa
- Istituto di Genetica Molecolare “L.L. Cavalli-Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy; (O.F.); (A.L.)
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Paolo Francalacci
- Dipartimento di Scienza della Vita e dell’Ambiente, Università di Cagliari, 09123 Cagliari, Italy;
| | - Alberto Piazza
- Dipartimento di Scienze Mediche, Scuola di Medicina, Università di Torino, 10124 Torino, Italy;
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
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5
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Giuliani C, Sazzini M, Pirazzini C, Bacalini MG, Marasco E, Ruscone GAG, Fang F, Sarno S, Gentilini D, Di Blasio AM, Crocco P, Passarino G, Mari D, Monti D, Nacmias B, Sorbi S, Salvarani C, Catanoso M, Pettener D, Luiselli D, Ukraintseva S, Yashin A, Franceschi C, Garagnani P. Impact of demography and population dynamics on the genetic architecture of human longevity. Aging (Albany NY) 2019; 10:1947-1963. [PMID: 30089705 PMCID: PMC6128422 DOI: 10.18632/aging.101515] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 07/26/2018] [Indexed: 02/07/2023]
Abstract
The study of the genetics of longevity has been mainly addressed by GWASs that considered subjects from different populations to reach higher statistical power. The "price to pay" is that population-specific evolutionary histories and trade-offs were neglected in the investigation of gene-environment interactions. We propose a new “diachronic” approach that considers processes occurred at both evolutionary and lifespan timescales. We focused on a well-characterized population in terms of evolutionary history (i.e. Italians) and we generated genome-wide data for 333 centenarians from the peninsula and 773 geographically-matched healthy individuals. Obtained results showed that: (i) centenarian genomes are enriched for an ancestral component likely shaped by pre-Neolithic migrations; (ii) centenarians born in Northern Italy unexpectedly clustered with controls from Central/Southern Italy suggesting that Neolithic and Bronze Age gene flow did not favor longevity in this population; (iii) local past adaptive events in response to pathogens and targeting arachidonic acid metabolism became favorable for longevity; (iv) lifelong changes in the frequency of several alleles revealed pleiotropy and trade-off mechanisms crucial for longevity. Therefore, we propose that demographic history and ancient/recent population dynamics need to be properly considered to identify genes involved in longevity, which can differ in different temporal/spatial settings.
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Affiliation(s)
- Cristina Giuliani
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy.,School of Anthropology and Museum Ethnography, University of Oxford, Oxford, UK.,Interdepartmental Center "L. Galvani," (CIG), University of Bologna, Bologna, Italy
| | - Marco Sazzini
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Chiara Pirazzini
- IRCCS, Institute of Neurological Sciences of Bologna, Bologna, Italy
| | | | - Elena Marasco
- Interdepartmental Center "L. Galvani," (CIG), University of Bologna, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.,Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, Bologna, Italy
| | - Guido Alberto Gnecchi Ruscone
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Fang Fang
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Stefania Sarno
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Davide Gentilini
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | | | - Paolina Crocco
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Daniela Mari
- Geriatric Unit, Department of Medical Sciences and Community Health, Milan, Italy.,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
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
| | - Sandro Sorbi
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy.,IRCCS Don Gnocchi, Florence, Italy
| | - Carlo Salvarani
- Azienda Ospedaliera-IRCCS, Reggio Emilia, Italy.,Department of Surgical, Medical, Dental and Morphological Sciences with Interest Transplant, Oncological and Regenerative Medicine, , Italy
| | | | - Davide Pettener
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- Department for the Cultural Heritage (DBC), University of Bologna, Ravenna, Italy
| | - Svetlana Ukraintseva
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Anatoliy Yashin
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Claudio Franceschi
- IRCCS, Institute of Neurological Sciences of Bologna, Bologna, Italy.,Co-senior authors
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, S-141 86 Stockholm, Sweden.,CNR Institute of Molecular Genetics, Unit of Bologna, Bologna, Italy.,Rizzoli Orthopaedic Institute, Laboratory of Cell Biology, Bologna, Italy.,Co-senior authors
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6
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Raveane A, Aneli S, Montinaro F, Athanasiadis G, Barlera S, Birolo G, Boncoraglio G, Di Blasio AM, Di Gaetano C, Pagani L, Parolo S, Paschou P, Piazza A, Stamatoyannopoulos G, Angius A, Brucato N, Cucca F, Hellenthal G, Mulas A, Peyret-Guzzon M, Zoledziewska M, Baali A, Bycroft C, Cherkaoui M, Chiaroni J, Di Cristofaro J, Dina C, Dugoujon JM, Galan P, Giemza J, Kivisild T, Mazieres S, Melhaoui M, Metspalu M, Myers S, Pereira L, Ricaut FX, Brisighelli F, Cardinali I, Grugni V, Lancioni H, Pascali VL, Torroni A, Semino O, Matullo G, Achilli A, Olivieri A, Capelli C. Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe. SCIENCE ADVANCES 2019; 5:eaaw3492. [PMID: 31517044 PMCID: PMC6726452 DOI: 10.1126/sciadv.aaw3492] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/10/2019] [Accepted: 08/06/2019] [Indexed: 05/10/2023]
Abstract
European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.
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Affiliation(s)
- A. Raveane
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- Department of Zoology, University of Oxford, Oxford, UK
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - S. Aneli
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - F. Montinaro
- Department of Zoology, University of Oxford, Oxford, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - G. Athanasiadis
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - S. Barlera
- Department of Cardiovascular Research, Istituto di Ricovero e Cura a Carattere Scientifico–Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - G. Birolo
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - G. Boncoraglio
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
- PhD Program in Neuroscience, University Milano-Bicocca, Monza, Italy
| | - A. M. Di Blasio
- Istituto Auxologico Italiano, IRCCS, Centro di Ricerche e Tecnologie Biomediche, Milano, Italy
| | - C. Di Gaetano
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - L. Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- APE lab, Department of Biology, University of Padua, Padua, Italy
| | - S. Parolo
- Computational Biology Unit, Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - P. Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - A. Piazza
- Department of Medical Sciences, University of Turin, Turin, Italy
- Academy of Sciences, Turin, Italy
| | - G. Stamatoyannopoulos
- Department of Medicine and Genome Sciences, University of Washington, Seattle, WA, USA
| | - A. Angius
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - N. Brucato
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - F. Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - G. Hellenthal
- University College London Genetics Institute (UGI), University College London, London, UK
| | - A. Mulas
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Lanusei, Italy
| | - M. Peyret-Guzzon
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M. Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - A. Baali
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - C. Bycroft
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M. Cherkaoui
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - J. Chiaroni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - J. Di Cristofaro
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - C. Dina
- l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - J. M. Dugoujon
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - P. Galan
- Equipe de Recherche en Epidémiologie Nutritionnelle (EREN), Centre de Recherche en Epidémiologie et Statistiques, Université Paris 13/Inserm U1153/Inra U1125/ Cnam, COMUE Sorbonne Paris Cité, F-93017 Bobigny, France
| | - J. Giemza
- l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - T. Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Herestraat 49, box 604, Leuven 3000, Belgium
| | - S. Mazieres
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - M. Melhaoui
- Faculté des Sciences, Université Mohammed Premier, Oujda, Morocco
| | - M. Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - S. Myers
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - L. Pereira
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - F. X. Ricaut
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - F. Brisighelli
- Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - I. Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - V. Grugni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - H. Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - V. L. Pascali
- Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - A. Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - O. Semino
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - G. Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - A. Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - A. Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - C. Capelli
- Department of Zoology, University of Oxford, Oxford, UK
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
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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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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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