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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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Grugni V, Raveane A, Mattioli F, Battaglia V, Sala C, Toniolo D, Ferretti L, Gardella R, Achilli A, Olivieri A, Torroni A, Passarino G, Semino O. Reconstructing the genetic history of Italians: new insights from a male (Y-chromosome) perspective. Ann Hum Biol 2018; 45:44-56. [PMID: 29382284 DOI: 10.1080/03014460.2017.1409801] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Due to its central and strategic position in Europe and in the Mediterranean Basin, the Italian Peninsula played a pivotal role in the first peopling of the European continent and has been a crossroad of peoples and cultures since then. AIM This study aims to gain more information on the genetic structure of modern Italian populations and to shed light on the migration/expansion events that led to their formation. SUBJECTS AND METHODS High resolution Y-chromosome variation analysis in 817 unrelated males from 10 informative areas of Italy was performed. Haplogroup frequencies and microsatellite haplotypes were used, together with available data from the literature, to evaluate Mediterranean and European inputs and date their arrivals. RESULTS Fifty-three distinct Y-chromosome lineages were identified. Their distribution is in general agreement with geography, southern populations being more differentiated than northern ones. CONCLUSIONS A complex genetic structure reflecting the multifaceted peopling pattern of the Peninsula emerged: southern populations show high similarity with those from the Middle East and Southern Balkans, while those from Northern Italy are close to populations of North-Western Europe and the Northern Balkans. Interestingly, the population of Volterra, an ancient town of Etruscan origin in Tuscany, displays a unique Y-chromosomal genetic structure.
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Affiliation(s)
- Viola Grugni
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Alessandro Raveane
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Francesca Mattioli
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Vincenza Battaglia
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Cinzia Sala
- b Divisione di Genetica e Biologia Cellulare , Istituto Scientifico San Raffaele , Milano , Italy
| | - Daniela Toniolo
- b Divisione di Genetica e Biologia Cellulare , Istituto Scientifico San Raffaele , Milano , Italy
| | - Luca Ferretti
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Rita Gardella
- c Dipartimento di Medicina Molecolare e Traslazionale , Università di Brescia , Brescia , Italy
| | - Alessandro Achilli
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Anna Olivieri
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Antonio Torroni
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Giuseppe Passarino
- d Dipartimento di Biologia, Ecologia e Scienze della Terra , Università della Calabria , Arcavacata di Rende , Cosenza , Italy
| | - Ornella Semino
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
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Orrù A, De Iasio S, Frederic P, Girotti M, Boano R, Sanna E. Spatial diffusion of surnames by long transhumance routes between highland and lowland: A study in Sardinia. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2018; 69:127-138. [PMID: 30017379 DOI: 10.1016/j.jchb.2018.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/26/2018] [Indexed: 11/24/2022]
Abstract
RIASSUNTO.
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Affiliation(s)
- A Orrù
- Department of Life Sciences and Systems Biology, University of Turin, Italy.
| | - S De Iasio
- Department of Biosciences, University of Parma, Italy
| | - P Frederic
- Department of Economics "Marco Biagi", RECent (Center for Economic Research), University of Modena, Italy
| | - M Girotti
- Department of Life Sciences and Systems Biology, University of Turin, Italy
| | - R Boano
- Department of Life Sciences and Systems Biology, University of Turin, Italy
| | - E Sanna
- Department of Environmental and Life Sciences, University of Cagliari, Italy
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Modi A, Tassi F, Susca RR, Vai S, Rizzi E, Bellis GD, Lugliè C, Gonzalez Fortes G, Lari M, Barbujani G, Caramelli D, Ghirotto S. Complete mitochondrial sequences from Mesolithic Sardinia. Sci Rep 2017; 7:42869. [PMID: 28256601 PMCID: PMC5335606 DOI: 10.1038/srep42869] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 01/17/2017] [Indexed: 11/09/2022] Open
Abstract
Little is known about the genetic prehistory of Sardinia because of the scarcity of pre-Neolithic human remains. From a genetic perspective, modern Sardinians are known as genetic outliers in Europe, showing unusually high levels of internal diversity and a close relationship to early European Neolithic farmers. However, how far this peculiar genetic structure extends and how it originated was to date impossible to test. Here we present the first and oldest complete mitochondrial sequences from Sardinia, dated back to 10,000 yBP. These two individuals, while confirming a Mesolithic occupation of the island, belong to rare mtDNA lineages, which have never been found before in Mesolithic samples and that are currently present at low frequencies not only in Sardinia, but in the whole Europe. Preliminary Approximate Bayesian Computations, restricted by biased reference samples for Mesolithic Sardinia (the two typed samples) and Neolithic Europe (limited to central and north European sequences), suggest that the first inhabitants of the island have had a small or negligible contribution to the present-day Sardinian population, which mainly derives its genetic diversity from continental migration into the island by Neolithic times.
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Affiliation(s)
- Alessandra Modi
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Francesca Tassi
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
| | - Roberta Rosa Susca
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
| | - Stefania Vai
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Ermanno Rizzi
- Fondazione Telethon, 20121 Milano, Italy.,Istituto di Tecnologie Biomediche, CNR, 20090 Segrate, Milano, Italy
| | | | - Carlo Lugliè
- LASP, Dipartimento di Storia, Beni Culturali e Territorio, Università di Cagliari, 09124 Cagliari, Italy
| | - Gloria Gonzalez Fortes
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
| | - Martina Lari
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Guido Barbujani
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Silvia Ghirotto
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy
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Parolo S, Lisa A, Gentilini D, Di Blasio AM, Barlera S, Nicolis EB, Boncoraglio GB, Parati EA, Bione S. Characterization of the biological processes shaping the genetic structure of the Italian population. BMC Genet 2015; 16:132. [PMID: 26553317 PMCID: PMC4640365 DOI: 10.1186/s12863-015-0293-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/03/2015] [Indexed: 12/11/2022] Open
Abstract
Background The genetic structure of human populations is the outcome of the combined action of different processes such as demographic dynamics and natural selection. Several efforts toward the characterization of population genetic architectures and the identification of adaptation signatures were recently made. In this study, we provide a genome-wide depiction of the Italian population structure and the analysis of the major determinants of the current existing genetic variation. Results We defined and characterized 210 genomic loci associated with the first Principal Component calculated on the Italian genotypic data and correlated to the North–south genetic gradient. Using a gene-enrichment approach we identified the immune function as primarily involved in the Italian population differentiation and we described a locus on chromosome 13 showing combined evidence of North–south diversification in allele frequencies and signs of recent positive selection. In this region our bioinformatics analysis pinpointed an uncharacterized long intergenic non-coding (lincRNA), whose expression appeared specific for immune-related tissues suggesting its relevance for the immune function. Conclusions Our study, combining population genetic analyses with biological insights provides a description of the Italian genetic structure that in future could contribute to the evaluation of complex diseases risk in the population context. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0293-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Silvia Parolo
- Computational Biology Unit, Institute of Molecular Genetics-National Research Council, Pavia, Italy.
| | - Antonella Lisa
- Computational Biology Unit, Institute of Molecular Genetics-National Research Council, Pavia, Italy.
| | - Davide Gentilini
- Molecular Biology Laboratory, Istituto Auxologico Italiano, Milan, Italy.
| | | | - Simona Barlera
- Department of Cardiovascular Research, IRCCS Mario Negri Institute for Pharmacological Research, Milan, Italy.
| | - Enrico B Nicolis
- Department of Cardiovascular Research, IRCCS Mario Negri Institute for Pharmacological Research, Milan, Italy.
| | - Giorgio B Boncoraglio
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
| | - Eugenio A Parati
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
| | - Silvia Bione
- Computational Biology Unit, Institute of Molecular Genetics-National Research Council, Pavia, Italy.
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Cappa C, Giulivi S, Schilirò A, Bastiani L, Muzio C, Meloni F. A screening on Specific Learning Disorders in an Italian speaking high genetic homogeneity area. RESEARCH IN DEVELOPMENTAL DISABILITIES 2015; 45-46:329-342. [PMID: 26296080 DOI: 10.1016/j.ridd.2015.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 07/09/2015] [Accepted: 07/13/2015] [Indexed: 06/04/2023]
Abstract
The aim of the present research is to investigate the prevalence of Specific Learning Disorders (SLD) in Ogliastra, an area of the island of Sardinia, Italy. Having experienced centuries of isolation, Ogliastra has become a high genetic homogeneity area, and is considered particularly interesting for studies on different kinds of pathologies. Here we are going to describe the results of a screening carried out throughout 2 consecutive years in 49 second grade classes (24 considered in the first year and 25 in the second year of the study) of the Ogliastra region. A total of 610 pupils (average age 7.54 years; 293 female, 317 male) corresponding to 68.69% of all pupils who were attending second grade in the area, took part in the study. The tool used for the screening was "RSR-DSA. Questionnaire for the detection of learning difficulties and disorders", which allowed the identification of 83 subjects at risk (13.61% of the whole sample involved in the study). These subjects took part in an enhancement training program of about 6 months. After the program, pupils underwent assessment for reading, writing and calculation abilities, as well as cognitive assessment. According to the results of the assessment, the prevalence of SLDs is 6.06%. For what concerns dyslexia, 4.75% of the total sample manifested this disorder either in isolation or in comorbidity with other disorders. According to the first national epidemiological investigation carried out in Italy, the prevalence of dyslexia is 3.1-3.2%, which is lower than the prevalence obtained in the present study. Given the genetic basis of SLDs, this result, together with the presence of several cases of SLD in isolation (17.14%) and with a 3:1 ratio of males to females diagnosed with a SLD, was to be expected in a sample coming from a high genetic homogeneity area.
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Affiliation(s)
- Claudia Cappa
- Institute of Clinical Physiology (IFC), CNR, Pisa, Italy.
| | - Sara Giulivi
- Department of Teaching and Learning (DFA) - University School of Applied Sciences and Arts of Southern Switzerland (SUPSI), Locarno, Switzerland.
| | - Antonino Schilirò
- Service of Child Neuropsychiatry, Azienda Sanitaria Locale 4, Lanusei, Italy.
| | - Luca Bastiani
- Institute of Clinical Physiology (IFC), CNR, Pisa, Italy.
| | - Carlo Muzio
- Istituto Santo Stefano, Porto Potenza Picena (MC), Italy.
| | - Fabrizio Meloni
- Service of Child Neuropsychiatry, Azienda Sanitaria Locale 4, Lanusei, Italy.
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Lisa A, Astolfi P, Zei G, Tentoni S. Consanguinity and late fertility: spatial analysis reveals positive association patterns. Ann Hum Genet 2014; 79:37-45. [PMID: 25441534 DOI: 10.1111/ahg.12092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 10/02/2014] [Indexed: 12/15/2022]
Abstract
The role of consanguinity on human complex traits is an important and controversial issue. In this work we focused on the Sardinian population and examined the effect of consanguineous unions on late female fertility. During the last century the island has been characterized by a high incidence of marriages between relatives, favoured by socio economic conditions and geographical isolation, and by high fertility despite a widespread tendency to delay reproduction. Through spatial analysis techniques, we explored the geographical heterogeneity of consanguinity and late fertility, and identified in Central-Eastern Sardinia a common area with an excess of both traits, where the traits are positively associated. We found that their association did not significantly affect women's fertility in the area, despite the expected negative role of both traits. Intriguingly, this critical zone corresponds well to areas reported by previous studies as being peculiar for a high frequency of centenarians and for lower risk in pregnancy outcome. The proposed approach can be generally exploited to identify target populations on which socioeconomic, biodemographic and genetic data can be collected at the individual level, and deeper analyses carried out to disentangle the determinants of complex biological traits and to investigate their association.
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Affiliation(s)
- Antonella Lisa
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100, Pavia, Italy
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Sardinians genetic background explained by runs of homozygosity and genomic regions under positive selection. PLoS One 2014; 9:e91237. [PMID: 24651212 PMCID: PMC3961211 DOI: 10.1371/journal.pone.0091237] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 02/10/2014] [Indexed: 11/19/2022] Open
Abstract
The peculiar position of Sardinia in the Mediterranean sea has rendered its population an interesting biogeographical isolate. The aim of this study was to investigate the genetic population structure, as well as to estimate Runs of Homozygosity and regions under positive selection, using about 1.2 million single nucleotide polymorphisms genotyped in 1077 Sardinian individuals. Using four different methods--fixation index, inflation factor, principal component analysis and ancestry estimation--we were able to highlight, as expected for a genetic isolate, the high internal homogeneity of the island. Sardinians showed a higher percentage of genome covered by RoHs>0.5 Mb (F(RoH%0.5)) when compared to peninsular Italians, with the only exception of the area surrounding Alghero. We furthermore identified 9 genomic regions showing signs of positive selection and, we re-captured many previously inferred signals. Other regions harbor novel candidate genes for positive selection, like TMEM252, or regions containing long non coding RNA. With the present study we confirmed the high genetic homogeneity of Sardinia that may be explained by the shared ancestry combined with the action of evolutionary forces.
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Rossi P. Surname distribution in population genetics and in statistical physics. Phys Life Rev 2013; 10:395-415. [PMID: 23830614 DOI: 10.1016/j.plrev.2013.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 06/18/2013] [Indexed: 10/26/2022]
Abstract
Surnames tend to behave like neutral genes, and their distribution has attracted a growing attention from genetists and physicists. We review the century-long history of surname studies and discuss the most recent developments. Isonymy has been regarded as a tool for the measurement of consanguinity of individuals and populations and has been applied to the analysis of migrations. The analogy between patrilineal surname transmission and the propagation of Y chromosomes has been exploited for the genetic characterization of families, communities and control groups. Surname distribution is the result of a stochastic dynamics, which has been studied either as a Yule process or as a branching phenomenon: both approaches predict the asymptotic power-law behavior which has been observed in many empirical researches. Models of neutral evolution based on the theory of disordered systems have suggested the application of field-theoretical techniques, and in particular the Renormalization Group, to describe the dynamics leading to scale-invariant distributions and to compute the related (critical) exponents.
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Affiliation(s)
- Paolo Rossi
- Dipartimento di Fisica dell'Università di Pisa and I.N.F.N., Sezione di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy.
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Boattini A, Lisa A, Fiorani O, Zei G, Pettener D, Manni F. General method to unravel ancient population structures through surnames, final validation on Italian data. Hum Biol 2013; 84:235-70. [PMID: 23020096 DOI: 10.3378/027.084.0302] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We analyze the geographic location of 77,451 different Italian surnames (17,579,891 individuals) obtained from the lists of telephone subscribers of the year 1993. By using a specific neural network analysis (Self-Organizing Maps, SOMs), we automatically identify the geographic origin of 49,117 different surnames. To validate the methodology, we compare the results to a study, previously conducted, on the same database, with accurate supervised methods. By comparing the results, we find an overlap of 97%, meaning that the SOMs methodology is highly reliable and well traces back the geographic origin of surnames at the time of their introduction (Late Middle Ages/Renaissance in Italy). SOMs results enables one to distinguish monophyletic surnames from polyphyletic ones, that is surnames having had a single geographic and historic origin from those that started to be in use, with an identical spelling, in different locations (respectively, 76.06% and 21.05% of the total). As we are interested in geographic origins, polyphyletic surnames are excluded from further analyses. By comparing the present location of each monophyletic surname to its inferred geographic origin in late Middle Ages/Renaissance, we measure the extent of the migrations having occurred in Italy since that time. We find that the percentage of individuals presently living in the very area where their surname started to be in use centuries ago is extremely variable (ranging from 22.77% to 77.86% according to the province), thus meaning that self-assessed regional identities seldom correspond to the "autochthony" they imply. For example the upper part of the Thyrennian coast (Northern Latium, Tuscany) has a strong identity but few "autochthonous" inhabitants (∼28%) having been a passageway from the North to the South of Italy.
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Piras IS, De Montis A, Calò CM, Marini M, Atzori M, Corrias L, Sazzini M, Boattini A, Vona G, Contu L. Genome-wide scan with nearly 700,000 SNPs in two Sardinian sub-populations suggests some regions as candidate targets for positive selection. Eur J Hum Genet 2012; 20:1155-61. [PMID: 22535185 PMCID: PMC3476709 DOI: 10.1038/ejhg.2012.65] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 03/14/2012] [Accepted: 03/15/2012] [Indexed: 01/16/2023] Open
Abstract
This paper explores the genetic structure and signatures of natural selection in different sub-populations from the Island of Sardinia, exploiting information from nearly 700,000 autosomal SNPs genotyped with the Affymetrix Genome-Wide Human SNP 6.0 Array. The genetic structure of the Sardinian population and its position within the context of other Mediterranean and European human groups were investigated in depth by comparing our data with publicly available data sets. Principal components and admixture analyses suggest a clustering of the examined samples in two significantly differentiated sub-populations (Ogliastra and Southern Sardinia), as confirmed by AMOVA (F(ST)=0.011; P<0.001). Differentiation of these sub-populations was still evident when they were pooled together with supplementary Sardinian samples from HGDP and compared with several other European, North-African and Near Eastern populations, confirming the uniqueness of the Sardinian genetic background. Moreover, by applying several statistical approaches aimed at assessing differences at the SNP level, the highest differentiated genomic regions between Ogliastra and Southern Sardinia were thus investigated via an extended haplotype homozygosity (EHH)-based test to point out potential selective sweeps. Using this approach, 40 genomic regions were detected, with significant differences between Ogliastra and Southern Sardinia. These regions were subsequently investigated using a long-range haplotype test, which found significant REHH values for SNPs rs11070188 and rs11070192 in the Ogliastra sub-population. In the light of these results and the overlap of the different computed statistics, the region encompassing these loci can be considered a strong candidate to have undergone selective pressure in Ogliastra.
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Affiliation(s)
- Ignazio Stefano Piras
- Department of Experimental Biology, University of Cagliari, Cittadella Universitaria, Monserrato, Cagliari, Italy.
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Darlu P, Bloothooft G, Boattini A, Brouwer L, Brouwer M, Brunet G, Chareille P, Cheshire J, Coates R, Dräger K, Desjardins B, Hanks P, Longley P, Mandemakers K, Mateos P, Pettener D, Useli A, Manni F. The family name as socio-cultural feature and genetic metaphor: from concepts to methods. Hum Biol 2012; 84:169-214. [PMID: 22708820 DOI: 10.3378/027.084.0205] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A recent workshop entitled "The Family Name as Socio-Cultural Feature and Genetic Metaphor: From Concepts to Methods" was held in Paris in December 2010, sponsored by the French National Centre for Scientific Research (CNRS) and by the journal Human Biology. This workshop was intended to foster a debate on questions related to the family names and to compare different multidisciplinary approaches involving geneticists, historians, geographers, sociologists and social anthropologists. This collective paper presents a collection of selected communications.
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Affiliation(s)
- Pierre Darlu
- UMR7206, CNRS, Muséum National d'Histoire Naturelle, Université Paris 7 Paris, France.
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Grugni V, Battaglia V, Hooshiar Kashani B, Parolo S, Al-Zahery N, Achilli A, Olivieri A, Gandini F, Houshmand M, Sanati MH, Torroni A, Semino O. Ancient migratory events in the Middle East: new clues from the Y-chromosome variation of modern Iranians. PLoS One 2012; 7:e41252. [PMID: 22815981 PMCID: PMC3399854 DOI: 10.1371/journal.pone.0041252] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 06/19/2012] [Indexed: 11/18/2022] Open
Abstract
Knowledge of high resolution Y-chromosome haplogroup diversification within Iran provides important geographic context regarding the spread and compartmentalization of male lineages in the Middle East and southwestern Asia. At present, the Iranian population is characterized by an extraordinary mix of different ethnic groups speaking a variety of Indo-Iranian, Semitic and Turkic languages. Despite these features, only few studies have investigated the multiethnic components of the Iranian gene pool. In this survey 938 Iranian male DNAs belonging to 15 ethnic groups from 14 Iranian provinces were analyzed for 84 Y-chromosome biallelic markers and 10 STRs. The results show an autochthonous but non-homogeneous ancient background mainly composed by J2a sub-clades with different external contributions. The phylogeography of the main haplogroups allowed identifying post-glacial and Neolithic expansions toward western Eurasia but also recent movements towards the Iranian region from western Eurasia (R1b-L23), Central Asia (Q-M25), Asia Minor (J2a-M92) and southern Mesopotamia (J1-Page08). In spite of the presence of important geographic barriers (Zagros and Alborz mountain ranges, and the Dasht-e Kavir and Dash-e Lut deserts) which may have limited gene flow, AMOVA analysis revealed that language, in addition to geography, has played an important role in shaping the nowadays Iranian gene pool. Overall, this study provides a portrait of the Y-chromosomal variation in Iran, useful for depicting a more comprehensive history of the peoples of this area as well as for reconstructing ancient migration routes. In addition, our results evidence the important role of the Iranian plateau as source and recipient of gene flow between culturally and genetically distinct populations.
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Affiliation(s)
- Viola Grugni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | | | - Silvia Parolo
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Nadia Al-Zahery
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Massoud Houshmand
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohammad Hossein Sanati
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Pavia, Italy
- Centro Interdipartimentale “Studi di Genere”, Università di Pavia, Pavia, Italy
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Abstract
SummaryThis study examines local heterogeneity in the aptitude of Sardinian mothers towards late reproduction, and explores its temporal persistence and association with both post-reproductive longevity and propensity to consanguineous marriage. Data on women's fertility from 1961 and birth records for 1980–1996 from Vital Statistics were analysed by means of the following indicators: the incidence of old mothers at last childbirth, female mortality (1980–2001) at 80 years of age and over and the proportion of consanguineous marriages (1930–1969). A variable kernel-smoothing method was used to create interpretable representations of the true spatial structure of the indicators, and to highlight areas of higher than expected intensity. In particular, an area of reproductive and post-reproductive longevity was identified where the traits combine with a higher tendency to relatedness. Intriguingly, this area corresponds approximately to the geographically and historically well defined central-eastern zone, which was the refuge of Sardinians during past invasions, and overlaps the Ogliastra region, which has been widely studied for its genetic homogeneity.
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Balanovska EV, Romanov AG, Balanovsky OP. Namesakes or relatives? Approaches to investigating the relationship between Y chromosome haplogroups and surnames. Mol Biol 2011. [DOI: 10.1134/s0026893311030022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Craniofacial morphometric variation and the biological history of the peopling of Sardinia. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2010; 61:385-412. [PMID: 20979998 DOI: 10.1016/j.jchb.2010.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 07/17/2010] [Indexed: 11/22/2022]
Abstract
The aim of this work is to explore the pattern of craniofacial morphometric variation and the relationships among five prehistoric Sardinian groups dated from Late Neolithic to the Nuragic Period (Middle and Late Bronze Age), in order to formulate hypotheses on the peopling history of Sardinia. Biological relationships with coeval populations of central peninsular Italy were also analysed to detect influences from and towards extra-Sardinian sources. Furthermore, comparison with samples of contemporary populations from Sardinia and from continental Italy provided an indication of the trend leading to the final part of the peopling history. Finally, Upper Palaeolithic and Mesolithic samples were included in the analyses to compare the prehistoric Sardinians with some of their potential continental ancestors. The analysis is based on multivariate techniques including Mahalanobis D(2) distance, non-parametric multidimensional scaling (MDS) and principal component analysis (PCA). The results showed the tendency to progressive differentiation between Sardinian groups and peninsular Italian groups, with the possible exception of a discontinuity showed by the Bonnànaro (Early Bronze Age) Sardinian sample. Several aspects of the morphological results were found to agree with the current genetic evidence available for the present-day Sardinian population and a Nuragic sample: (1) biological divergence between the Sardinian and peninsular Italian populations; (2) similarity/continuity among Neolithic, Bronze Age and recent Sardinians; (3) biological separation between the Nuragic and Etruscan populations; (4) contribution of a Palaeo-Mesolithic gene pool to the genetic structure of current Sardinians.
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Mirabal S, Varljen T, Gayden T, Regueiro M, Vujovic S, Popovic D, Djuric M, Stojkovic O, Herrera RJ. Human Y-chromosome short tandem repeats: A tale of acculturation and migrations as mechanisms for the diffusion of agriculture in the Balkan Peninsula. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 142:380-90. [DOI: 10.1002/ajpa.21235] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Ghirotto S, Mona S, Benazzo A, Paparazzo F, Caramelli D, Barbujani G. Inferring Genealogical Processes from Patterns of Bronze-Age and Modern DNA Variation in Sardinia. Mol Biol Evol 2009; 27:875-86. [DOI: 10.1093/molbev/msp292] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Novelletto A. Y chromosome variation in Europe: Continental and local processes in the formation of the extant gene pool. Ann Hum Biol 2009; 34:139-72. [PMID: 17558587 DOI: 10.1080/03014460701206843] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The polymorphism of the male-specific portion of the Y chromosome has been increasingly used to describe the composition of the European gene pool and to reconstruct its formation. Here the theoretical grounds and the limitations of this approach are presented, together with the different views on debated issues. The emerging picture for the composition of the male gene pool of the continent is illustrated, but local peculiarities that represent departures from the main trends are also highlighted, in order to illustrate the main unifying feature, i.e. the overlay of recent patterns onto more ancient ones. A synopsis of the main findings and conclusions obtained in regional studies has also been compiled.
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21
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Improved resolution haplogroup G phylogeny in the Y chromosome, revealed by a set of newly characterized SNPs. PLoS One 2009; 4:e5792. [PMID: 19495413 PMCID: PMC2686153 DOI: 10.1371/journal.pone.0005792] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 05/04/2009] [Indexed: 11/22/2022] Open
Abstract
Background Y-SNP haplogroup G (hgG), defined by Y-SNP marker M201, is relatively uncommon in the United States general population, with only 8 additional sub-markers characterized. Many of the previously described eight sub-markers are either very rare (2–4%) or do not distinguish between major populations within this hg. In fact, prior to the current study, only 2% of our reference Caucasian population belonged to hgG and all of these individuals were in sub-haplogroup G2a, defined by P15. Additional Y-SNPs are needed in order to differentiate between individuals within this haplogroup. Principal Findings In this work we have investigated whether we could differentiate between a population of 63 hgG individuals using previously uncharacterized Y-SNPs. We have designed assays to test these individuals using all known hgG SNPs (n = 9) and an additional 16 unreported/undefined Y-SNPS. Using a combination of DNA sequence and genetic genealogy databases, we have uncovered a total of 15 new hgG SNPs that had been previously reported but not phylogenetically characterized. Ten of the new Y-SNPs are phylogenetically equivalent to M201, one is equivalent to P15 and, interestingly, four create new, separate haplogroups. Three of the latter are more common than many of the previously defined Y-SNPs. Y-STR data from these individuals show that DYS385*12 is present in (70%) of G2a3b1-U13 individuals while only 4% of non-G2a3b1-U13 individuals posses the DYS385*12 allele. Conclusions This study uncovered several previously undefined Y-SNPs by using data from several database sources. The new Y-SNPs revealed in this paper will be of importance to those with research interests in population biology and human evolution.
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Pala M, Achilli A, Olivieri A, Kashani BH, Perego UA, Sanna D, Metspalu E, Tambets K, Tamm E, Accetturo M, Carossa V, Lancioni H, Panara F, Zimmermann B, Huber G, Al-Zahery N, Brisighelli F, Woodward SR, Francalacci P, Parson W, Salas A, Behar DM, Villems R, Semino O, Bandelt HJ, Torroni A. Mitochondrial haplogroup U5b3: a distant echo of the epipaleolithic in Italy and the legacy of the early Sardinians. Am J Hum Genet 2009; 84:814-21. [PMID: 19500771 PMCID: PMC2694970 DOI: 10.1016/j.ajhg.2009.05.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 05/15/2009] [Accepted: 05/15/2009] [Indexed: 11/16/2022] Open
Abstract
There are extensive data indicating that some glacial refuge zones of southern Europe (Franco-Cantabria, Balkans, and Ukraine) were major genetic sources for the human recolonization of the continent at the beginning of the Holocene. Intriguingly, there is no genetic evidence that the refuge area located in the Italian Peninsula contributed to this process. Here we show, through phylogeographic analyses of mitochondrial DNA (mtDNA) variation performed at the highest level of molecular resolution (52 entire mitochondrial genomes), that the most likely homeland for U5b3-a haplogroup present at a very low frequency across Europe-was the Italian Peninsula. In contrast to mtDNA haplogroups that expanded from other refugia, the Holocene expansion of haplogroup U5b3 toward the North was restricted by the Alps and occurred only along the Mediterranean coasts, mainly toward nearby Provence (southern France). From there, approximately 7,000-9,000 years ago, a subclade of this haplogroup moved to Sardinia, possibly as a result of the obsidian trade that linked the two regions, leaving a distinctive signature in the modern people of the island. This scenario strikingly matches the age, distribution, and postulated geographic source of a Sardinian Y chromosome haplogroup (I2a2-M26), a paradigmatic case in the European context of a founder event marking both female and male lineages.
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Affiliation(s)
- Maria Pala
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | - Alessandro Achilli
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia 06123, Italy
| | - Anna Olivieri
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | | | - Ugo A. Perego
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA
| | - Daria Sanna
- Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, Sassari 07100, Italy
| | - Ene Metspalu
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Kristiina Tambets
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Erika Tamm
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Matteo Accetturo
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | - Valeria Carossa
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | - Hovirag Lancioni
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia 06123, Italy
| | - Fausto Panara
- Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia 06123, Italy
| | - Bettina Zimmermann
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck A-6020, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck A-6020, Austria
| | - Nadia Al-Zahery
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
- Department of Biotechnology, College of Science, University of Baghdad, Iraq
| | - Francesca Brisighelli
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses; and Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia 15782, Spain
| | - Scott R. Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA
| | - Paolo Francalacci
- Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, Sassari 07100, Italy
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck A-6020, Austria
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses; and Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia 15782, Spain
| | - Doron M. Behar
- Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel
| | - Richard Villems
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu 51010, Estonia
| | - Ornella Semino
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
| | | | - Antonio Torroni
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia 27100, Italy
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Kim SH, Jung J, Cho NS, Hwang JH, Yoo SY, Seong KM, Han MS, Kim W. Y-STR genetic structure of the most common surnames in Korea. Genes Genomics 2009. [DOI: 10.1007/bf03191196] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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24
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Late reproduction behaviour in Sardinia: spatial analysis suggests local aptitude towards reproductive longevity. EVOL HUM BEHAV 2009. [DOI: 10.1016/j.evolhumbehav.2008.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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25
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Pistis G, Piras I, Pirastu N, Persico I, Sassu A, Picciau A, Prodi D, Fraumene C, Mocci E, Manias MT, Atzeni R, Cosso M, Pirastu M, Angius A. High differentiation among eight villages in a secluded area of Sardinia revealed by genome-wide high density SNPs analysis. PLoS One 2009; 4:e4654. [PMID: 19247500 PMCID: PMC2646134 DOI: 10.1371/journal.pone.0004654] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 01/29/2009] [Indexed: 01/21/2023] Open
Abstract
To better design association studies for complex traits in isolated populations it's important to understand how history and isolation moulded the genetic features of different communities. Population isolates should not “a priori” be considered homogeneous, even if the communities are not distant and part of a small region. We studied a particular area of Sardinia called Ogliastra, characterized by the presence of several distinct villages that display different history, immigration events and population size. Cultural and geographic isolation characterized the history of these communities. We determined LD parameters in 8 villages and defined population structure through high density SNPs (about 360 K) on 360 unrelated people (45 selected samples from each village). These isolates showed differences in LD values and LD map length. Five of these villages show high LD values probably due to their reduced population size and extreme isolation. High genetic differentiation among villages was detected. Moreover population structure analysis revealed a high correlation between genetic and geographic distances. Our study indicates that history, geography and biodemography have influenced the genetic features of Ogliastra communities producing differences in LD and population structure. All these data demonstrate that we can consider each village an isolate with specific characteristics. We suggest that, in order to optimize the study design of complex traits, a thorough characterization of genetic features is useful to identify the presence of sub-populations and stratification within genetic isolates.
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Affiliation(s)
- Giorgio Pistis
- Istituto di Genetica delle Popolazioni, CNR, Alghero, Sassari, Italy
| | | | | | - Ivana Persico
- Istituto di Genetica delle Popolazioni, CNR, Alghero, Sassari, Italy
| | | | | | | | | | | | | | | | | | - Mario Pirastu
- Istituto di Genetica delle Popolazioni, CNR, Alghero, Sassari, Italy
- Shardna Life Sciences, Pula, Cagliari, Italy
| | - Andrea Angius
- Istituto di Genetica delle Popolazioni, CNR, Alghero, Sassari, Italy
- Shardna Life Sciences, Pula, Cagliari, Italy
- * E-mail:
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Y-chromosomal evidence of the cultural diffusion of agriculture in Southeast Europe. Eur J Hum Genet 2008; 17:820-30. [PMID: 19107149 DOI: 10.1038/ejhg.2008.249] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The debate concerning the mechanisms underlying the prehistoric spread of farming to Southeast Europe is framed around the opposing roles of population movement and cultural diffusion. To investigate the possible involvement of local people during the transition of agriculture in the Balkans, we analysed patterns of Y-chromosome diversity in 1206 subjects from 17 population samples, mainly from Southeast Europe. Evidence from three Y-chromosome lineages, I-M423, E-V13 and J-M241, make it possible to distinguish between Holocene Mesolithic forager and subsequent Neolithic range expansions from the eastern Sahara and the Near East, respectively. In particular, whereas the Balkan microsatellite variation associated to J-M241 correlates with the Neolithic period, those related to E-V13 and I-M423 Balkan Y chromosomes are consistent with a late Mesolithic time frame. In addition, the low frequency and variance associated to I-M423 and E-V13 in Anatolia and the Middle East, support an European Mesolithic origin of these two clades. Thus, these Balkan Mesolithic foragers with their own autochthonous genetic signatures, were destined to become the earliest to adopt farming, when it was subsequently introduced by a cadre of migrating farmers from the Near East. These initial local converted farmers became the principal agents spreading this economy using maritime leapfrog colonization strategies in the Adriatic and transmitting the Neolithic cultural package to other adjacent Mesolithic populations. The ensuing range expansions of E-V13 and I-M423 parallel in space and time the diffusion of Neolithic Impressed Ware, thereby supporting a case of cultural diffusion using genetic evidence.
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Martinez L, Mirabal S, Luis JR, Herrera RJ. Middle Eastern and European mtDNA lineages characterize populations from eastern Crete. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2008; 137:213-23. [PMID: 18500747 DOI: 10.1002/ajpa.20857] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Throughout centuries, the geographic location of the island of Crete has been one of the leading factors shaping the composition of its population. Invasions and commercial and cultural ties at various time periods with European, Middle Eastern, and North African civilizations have created a collage of genetic and/or cultural influences from each of these regions within the island. Previous Y-chromosome diversity analyses uncovered pronounced differences in the frequency distribution of haplogroups from a mountain refugium and surrounding lowland populations of eastern Crete. In this study, the current geographic stratification of mtDNA haplotypes in eastern Crete was explored to elucidate potential sources of maternal gene flow. Our work includes a comparative characterization of two lowland collections from the Heraklion and Lasithi Prefectures in eastern Crete, as well as of an isolated mountain population from the Lasithi Plateau, all three previously examined using Y-chromosome markers. In addition to the presence of European mtDNA haplogroups in all three collections, our analyses reveal a significant contribution of Middle Eastern and Central Asian genetic signatures in the island of Crete, and particularly in the two populations from the Lasithi region at the eastern-most portion of the island. Close association between these Cretan groups and the Balkans can also be discerned, which in the case of the Lasithi Plateau corroborates previously uncovered Y-chromosome affiliations with the same geographic region.
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Affiliation(s)
- Laisel Martinez
- Department of Biological Sciences, Florida International University, Miami, Florida 33199, USA
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De genotipos e isonimias: análisis de correlación entre el apellido y el patrimonio genético heredado en el cromosoma Y en la población de tres departamentos del suroccidente colombiano. BIOMEDICA 2008. [DOI: 10.7705/biomedica.v28i3.74] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Contu D, Morelli L, Santoni F, Foster JW, Francalacci P, Cucca F. Y-chromosome based evidence for pre-neolithic origin of the genetically homogeneous but diverse Sardinian population: inference for association scans. PLoS One 2008; 3:e1430. [PMID: 18183308 PMCID: PMC2174525 DOI: 10.1371/journal.pone.0001430] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 12/03/2007] [Indexed: 11/19/2022] Open
Abstract
The island of Sardinia shows a unique high incidence of several autoimmune diseases with multifactorial inheritance, particularly type 1 diabetes and multiple sclerosis. The prior knowledge of the genetic structure of this population is fundamental to establish the optimal design for association studies in these diseases. Previous work suggested that the Sardinians are a relatively homogenous population, but some reports were contradictory and data were largely based on variants subject to selection. For an unbiased assessment of genetic structure, we studied a combination of neutral Y-chromosome variants, 21 biallelic and 8 short tandem repeats (STRs) in 930 Sardinian males. We found a high degree of interindividual variation but a homogenous distribution of the detected variability in samples from three separate regions of the island. One haplogroup, I-M26, is rare or absent outside Sardinia and is very common (0.37 frequency) throughout the island, consistent with a founder effect. A Bayesian full likelihood analysis (BATWING) indicated that the time from the most recent common ancestor (TMRCA) of I-M26, was 21.0 (16.0–25.5) thousand years ago (KYA) and that the population began to expand 14.0 (7.8–22.0) KYA. These results suggest a largely pre-Neolithic settlement of the island with little subsequent gene flow from outside populations. Consequently, Sardinia is an especially attractive venue for case-control genome wide association scans in common multifactorial diseases. Concomitantly, the high degree of interindividual variation in the current population facilitates fine mapping efforts to pinpoint the aetiologic polymorphisms.
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Affiliation(s)
- Daniela Contu
- Laboratorio di Immunogenetica, Ospedale Microcitemico, Cagliari, Italy
| | - Laura Morelli
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Federico Santoni
- Center for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy
| | - Jamie W. Foster
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Paolo Francalacci
- Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, Sassari, Italy
| | - Francesco Cucca
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
- * To whom correspondence should be addressed. E-mail:
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Montesanto A, Passarino G, Senatore A, Carotenuto L, De Benedictis G. Spatial Analysis and Surname Analysis: Complementary Tools for Shedding Light on Human Longevity Patterns. Ann Hum Genet 2007; 72:253-60. [DOI: 10.1111/j.1469-1809.2007.00405.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. Montesanto
- Department of Cell Biology, University of Calabria. 87036 Rende, Italy
| | - G. Passarino
- Department of Cell Biology, University of Calabria. 87036 Rende, Italy
| | - A. Senatore
- Department of Soil Conservation, University of Calabria. 87036 Rende, Italy
| | - L. Carotenuto
- Department of Electronics, Informatics and System Science, University of Calabria. 87036 Rende, Italy
| | - G. De Benedictis
- Department of Cell Biology, University of Calabria. 87036 Rende, Italy
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Pollin TI, McBride DJ, Agarwala R, Schäffer AA, Shuldiner AR, Mitchell BD, O'Connell JR. Investigations of the Y chromosome, male founder structure and YSTR mutation rates in the Old Order Amish. Hum Hered 2007; 65:91-104. [PMID: 17898540 PMCID: PMC2857628 DOI: 10.1159/000108941] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2007] [Accepted: 06/06/2007] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Using Y chromosome short tandem repeat (YSTR) genotypes, (1) evaluate the accuracy and completeness of the Lancaster County Old Order Amish (OOA) genealogical records and (2) estimate YSTR mutation rates. METHODS Nine YSTR markers were genotyped in 739 Old Order Amish males who participated in several ongoing genetic studies of complex traits and could be connected into one of 28 all-male lineage pedigrees constructed using the Anabaptist Genealogy Database and the query software Ped-Hunter. A putative founder YSTR haplotype was constructed for each pedigree, and observed and inferred father-son transmissions were used to estimate YSTR mutation rates. RESULTS We inferred 27 distinct founder Y chromosome haplotypes in the 28 male lineages, which encompassed 27 surnames accounting for 98% of Lancaster OOA households. Nearly all deviations from founder haplotypes were consistent with mutation events rather than errors. The estimated marker-specific mutation rates ranged from 0 to 1.09% (average 0.33% using up to 283 observed meioses only and 0.28% using up to 1,232 observed and inferred meioses combined). CONCLUSIONS These data confirm the accuracy and completeness of the male lineage portion of the Anabaptist Genealogy Database and contribute mutation rate estimates for several commonly used Y chromosome STR markers.
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Affiliation(s)
- Toni I Pollin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
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Bürkle A, Caselli G, Franceschi C, Mariani E, Sansoni P, Santoni A, Vecchio G, Witkowski JM, Caruso C. Pathophysiology of ageing, longevity and age related diseases. IMMUNITY & AGEING 2007; 4:4. [PMID: 17683521 PMCID: PMC1973075 DOI: 10.1186/1742-4933-4-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Accepted: 08/02/2007] [Indexed: 01/10/2023]
Abstract
On April 18, 2007 an international meeting on Pathophysiology of Ageing, Longevity and Age-Related Diseases was held in Palermo, Italy. Several interesting topics on Cancer, Immunosenescence, Age-related inflammatory diseases and longevity were discussed. In this report we summarize the most important issues. However, ageing must be considered an unavoidable end point of the life history of each individual, nevertheless the increasing knowledge on ageing mechanisms, allows envisaging many different strategies to cope with, and delay it. So, a better understanding of pathophysiology of ageing and age-related disease is essential for giving everybody a reasonable chance for living a long and enjoyable final part of the life.
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Affiliation(s)
- Alexander Bürkle
- Department of Biology, Box X911, University of Konstanz, Konstanz, Germany
| | - Graziella Caselli
- Department of Demographic Sciences, University "La Sapienza" of Rome, Rome, Italy
| | - Claudio Franceschi
- Department of Experimental Pathology and CIG – Interdepartmental Center "L. Galvani", University of Bologna, Italy
| | - Erminia Mariani
- Immunology and Genetics Laboratory, Institute Codivilla-Putti, Bologna, Italy
- Department of Internal Medicine and Gastroenterology of University of Bologna, Bologna, Italy
| | - Paolo Sansoni
- Department of Internal Medicine and Biomedical Sciences, University of Parma, Parma, Italy
| | - Angela Santoni
- Department of Experimental Medicine, University "La Sapienza" of Rome, Rome, Italy
| | - Giancarlo Vecchio
- Department of Cellular and Molecular Biology and Pathology, University of Naples Federico II, Naples, Italy
| | - Jacek M Witkowski
- Department of Pathophysiology, Medical University of Gdansk, Gdansk, Poland
| | - Calogero Caruso
- Immunosenescence Unit, Department of Pathobiology and Biomedical Methodologies, University of Palermo, Palermo, Italy
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Diéterlen F, Pinna A, Berriche S, Mercier G, Lucotte G. Characterization of the Y-Chromosome Sardinian–Corsican Haplotype. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/s11599-006-9012-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Immel UD, Krawczak M, Udolph J, Richter A, Rodig H, Kleiber M, Klintschar M. Y-chromosomal STR haplotype analysis reveals surname-associated strata in the East-German population. Eur J Hum Genet 2006; 14:577-82. [PMID: 16435000 DOI: 10.1038/sj.ejhg.5201572] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
In human populations, the correct historical interpretation of a genetic structure is often hampered by an almost inherent inability to differentiate between ancient and more recent influences upon extant gene pools. One method to trace recent population movements is the analysis of surnames, which, at least in Central Europe, can be thought of as traits 'linked' to the Y chromosome. Illegitimacy, extramarital birth and changes of surnames may have substantially obscured this linkage. In order to assess the actual extent of correlation between surnames and Y-chromosomal haplotypes in Central Europe, we typed Y-chromosomal short tandem repeat markers in 419 German males from Halle. These individuals were subdivided into three groups according to the origin of their respective surname, namely German (G), Slavic (S) or 'Mixed' (M). The distribution of the haplotypes was compared by Analysis of Molecular Variance. While the M group was indistinguishable from group G (PhiST=-0.0008, P>0.5), a highly significant difference (PhiST=0.0277, P<0.001) was observed between the S group and the combined G+M group. This surprisingly strong differentiation is comparable to that of European populations of much larger geographic and linguistic difference. In view of the major migration from Slavic countries into Germany in the 19th century, it appears likely that the observed concurrence of Slavic surnames and Y chromosomes is of a recent rather than an early origin. Our results suggest that surnames may provide a simple means to stratify, and thereby to render more efficient, Y-chromosomal analyses of Central Europeans that target more ancient events.
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Affiliation(s)
- Uta-Dorothee Immel
- Department of Legal Medicine, Martin-Luther-University, Halle (Saale), Germany.
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Montiel R, Bettencourt C, Silva C, Santos C, Prata MJ, Lima M. Analysis of Y-chromosome Variability and its Comparison with mtDNA Variability Reveals Different Demographic Histories Between Islands in the Azores Archipelago (Portugal). Ann Hum Genet 2005. [DOI: 10.1046/j.1469-1809.2004.00146.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Flores C, Maca-Meyer N, González AM, Oefner PJ, Shen P, Pérez JA, Rojas A, Larruga JM, Underhill PA. Reduced genetic structure of the Iberian peninsula revealed by Y-chromosome analysis: implications for population demography. Eur J Hum Genet 2004; 12:855-63. [PMID: 15280900 DOI: 10.1038/sj.ejhg.5201225] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Europe has been influenced by both intra- and intercontinental migrations. Since the Iberian peninsula was a refuge during the Last Glacial Maximum, demographic factors associated with contraction, isolation, subsequent expansion and gene flow episodes have contributed complexity to its population history. In this work, we analysed 26 Y-chromosome biallelic markers in 568 chromosomes from 11 different Iberian population groups and compared them to published data on the Basques and Catalans to gain insight into the paternal gene pool of these populations and find out to what extent major demographic processes account for their genetic structure. Our results reveal a reduced, although geographically correlated, Y-chromosomal interpopulation variance (1.2%), which points to a limited heterogeneity in the region. Coincidentally, spatial analysis of genetic distances points to a focal distribution of Y-chromosome haplogroups in this area. These results indicate that neither old or recent Levantine expansions nor North African contacts have influenced the current Iberian Y-chromosome diversity so that geographical patterns can be identified.
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Affiliation(s)
- Carlos Flores
- Departamento de Genética, Universidad de La Laguna, Tenerife E-38271, Spain.
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Rootsi S, Magri C, Kivisild T, Benuzzi G, Help H, Bermisheva M, Kutuev I, Barać L, Pericić M, Balanovsky O, Pshenichnov A, Dion D, Grobei M, Zhivotovsky LA, Battaglia V, Achilli A, Al-Zahery N, Parik J, King R, Cinnioğlu C, Khusnutdinova E, Rudan P, Balanovska E, Scheffrahn W, Simonescu M, Brehm A, Goncalves R, Rosa A, Moisan JP, Chaventre A, Ferak V, Füredi S, Oefner PJ, Shen P, Beckman L, Mikerezi I, Terzić R, Primorac D, Cambon-Thomsen A, Krumina A, Torroni A, Underhill PA, Santachiara-Benerecetti AS, Villems R, Semino O. Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in europe. Am J Hum Genet 2004; 75:128-37. [PMID: 15162323 PMCID: PMC1181996 DOI: 10.1086/422196] [Citation(s) in RCA: 184] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2004] [Accepted: 04/26/2004] [Indexed: 11/03/2022] Open
Abstract
To investigate which aspects of contemporary human Y-chromosome variation in Europe are characteristic of primary colonization, late-glacial expansions from refuge areas, Neolithic dispersals, or more recent events of gene flow, we have analyzed, in detail, haplogroup I (Hg I), the only major clade of the Y phylogeny that is widespread over Europe but virtually absent elsewhere. The analysis of 1,104 Hg I Y chromosomes, which were identified in the survey of 7,574 males from 60 population samples, revealed several subclades with distinct geographic distributions. Subclade I1a accounts for most of Hg I in Scandinavia, with a rapidly decreasing frequency toward both the East European Plain and the Atlantic fringe, but microsatellite diversity reveals that France could be the source region of the early spread of both I1a and the less common I1c. Also, I1b*, which extends from the eastern Adriatic to eastern Europe and declines noticeably toward the southern Balkans and abruptly toward the periphery of northern Italy, probably diffused after the Last Glacial Maximum from a homeland in eastern Europe or the Balkans. In contrast, I1b2 most likely arose in southern France/Iberia. Similarly to the other subclades, it underwent a postglacial expansion and marked the human colonization of Sardinia approximately 9,000 years ago.
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Affiliation(s)
- Siiri Rootsi
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Riia, Tartu, Estonia.
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