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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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Nuñez C, Baeta M, Sosa C, Casalod Y, Ge J, Budowle B, Martínez-Jarreta B. Reconstructing the population history of Nicaragua by means of mtDNA, Y-chromosome STRs, and autosomal STR markers. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 143:591-600. [PMID: 20721944 DOI: 10.1002/ajpa.21355] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 05/15/2010] [Indexed: 11/12/2022]
Abstract
Before the arrival of the Spaniards in Nicaragua, diverse Native American groups inhabited the territory. In colonial times, Native Nicaraguan populations interacted with Europeans and slaves from Africa. To ascertain the extent of this genetic admixture and provide genetic evidence about the origin of the Nicaraguan ancestors, we analyzed the mitochondrial control region (HVSI and HVSII), 17 Y chromosome STRs, and 15 autosomal STRs in 165 Mestizo individuals from Nicaragua. To carry out interpopulation comparisons, HVSI sequences from 29 American populations were compiled from the literature. The results reveal a close relationship between Oto-manguean, Uto-Aztecan, Mayan groups from Mexico, and a Chibchan group to Nicaraguan lineages. The Native American contribution to present-day Nicaraguan Mestizos accounts for most of the maternal lineages, whereas the majority of Nicaraguan Y chromosome haplogroups can be traced back to a West Eurasian origin. Pairwise Fst distances based on Y-STRs between Nicaragua and European, African and Native American populations show that Nicaragua is much closer to Europeans than the other populations. Additionally, admixture proportions based on autosomal STRs indicate a predominantly Spanish contribution. Our study reveals that the Nicaraguan Mestizo population harbors a high proportion of European male and Native American female substrate. Finally, the amount of African ancestry is also interesting, probably because of the contribution of Spanish conquerors with North African genetic traces or that of West African slaves.
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Affiliation(s)
- Carolina Nuñez
- Laboratory of Forensic Genetics, Faculty of Medicine, University of Zaragoza, 50009 Zaragoza, Spain.
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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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Schwengber SP, Kommers T, Matte CHF, Raimann PE, Carvalho BA, Leite FPN, Medeiros MA, Souza LF, Castro CS, Chassot FGC, Bonatto SL. Population data of 17 Y-STR loci from Rio Grande do Sul state (South Brazil). Forensic Sci Int Genet 2009; 4:e31-3. [PMID: 19948319 DOI: 10.1016/j.fsigen.2009.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 01/28/2009] [Accepted: 02/04/2009] [Indexed: 11/30/2022]
Abstract
A sample of 255 Brazilian males from Rio Grande do Sul (RS), the Brazilian southernmost state, was typed for 17 Y-STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA_H4.1 and DYS385ab). A total of 247 haplotypes were identified, of which 239 were unique and eight were found in two individuals each. The haplotype diversity (99.98%) and discrimination capacity (96.86%) were calculated. Pairwise haplotype distances showed that the RS population is not significantly different from Brazil, Rio de Janeiro, and Argentina, is different from São Paulo, Italy, and North Portugal, and is very distant from Spain, the Amazon region, Germany, and South Amerindians. When the RS data was separated in the seven geopolitical regions, some pairs of regions were significantly different; however no region was different from the whole Brazilian sample.
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Affiliation(s)
- Solange P Schwengber
- Setor de Genética Forense, Laboratório de Perícias, Instituto-Geral de Perícias, Secretaria da Segurança Pública do Estado do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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Rapone C, Geraci A, Capelli C, De Meo A, D'Errico G, Barni F, Berti A, Lago G. Y chromosome haplotypes in Central-South Italy: implication for reference database. Forensic Sci Int 2007; 172:67-71. [PMID: 16884881 DOI: 10.1016/j.forsciint.2006.06.072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2005] [Revised: 06/22/2006] [Accepted: 06/24/2006] [Indexed: 11/26/2022]
Abstract
One hundred and fifty individuals have been sampled across Central-South Italy and genotyped for Y chromosome STRs by PowerPlex Y system. Comparison with previous Italian databases revealed that majority of Y chromosome variation still need to be sampled. Identification of locus duplications, distribution of genetic variation and firstly identified alleles point to the necessity of more focused sampling strategies for reference databases.
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Affiliation(s)
- Cesare Rapone
- Carabinieri Scientific Investigation, Department of Rome, DNA Unit, Viale di Tor di Quinto 151, 00191 Rome, Italy
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Capelli C, Brisighelli F, Scarnicci F, Blanco-Verea A, Brion M, Pascali VL. Phylogenetic evidence for multiple independent duplication events at the DYS19 locus. Forensic Sci Int Genet 2007; 1:287-90. [PMID: 19083776 DOI: 10.1016/j.fsigen.2007.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 05/10/2007] [Accepted: 06/01/2007] [Indexed: 11/19/2022]
Abstract
Duplication events at Y chromosome STR loci have been repeatedly described in human populations. DYS19 is probably the best known example and it exhibits duplicate state in individuals from all continents. Despite the large amount of available data, evolutionary relationship between DYS19 duplication-bearing chromosomes has not been so far investigated. We address the genealogical correlation among such chromosomes by analysing newly identified DYS19 duplicated Y chromosomes by SNP genotyping and microsatellite-based network analysis. SNP and network analysis show that DYS19 duplicated Y chromosomes associate with different Y chromosome lineages. These results indicate that DYS19 duplication occurred more than once during human evolution.
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Affiliation(s)
- Cristian Capelli
- Department of Zoology, University of Oxford, Tinbergen Building, South Parks Road, OX1 3PS Oxford, UK.
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Góis CC, Martins JA, Pereira GA, Freschi A, Paneto GG, Alvarenga VLS, Cicarelli RMB, Hirata MH, Oliveira RN. Genetic population data of 12 STR loci of the PowerPlex Y system in the state of São Paulo population (Southeast of Brazil). Forensic Sci Int 2007; 174:81-6. [PMID: 17433590 DOI: 10.1016/j.forsciint.2006.12.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Revised: 10/27/2006] [Accepted: 12/18/2006] [Indexed: 11/28/2022]
Abstract
Allele frequency distributions and population data for 12 Y-chromosomal short tandem repeats (STRs) included in the PowerPlex Y Systems (Promega) were obtained for a sample of 200 healthy unrelated males living in São Paulo State (Southeast of Brazil). A total of 192 haplotypes were identified, of which 184 were unique and 8 were found in 2 individuals. The average gene diversity of the 12 Y-STR was 0.6746 and the haplotype diversity was 0.9996. Pairwise analysis confirmed that our population is more similar with the Italy, North Portugal and Spain, being more distant of the Japan.
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Affiliation(s)
- C C Góis
- School of Dentistry, University of São Paulo, Brazil
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Y chromosome genetic variation in the Italian peninsula is clinal and supports an admixture model for the Mesolithic-Neolithic encounter. Mol Phylogenet Evol 2006; 44:228-39. [PMID: 17275346 DOI: 10.1016/j.ympev.2006.11.030] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 10/30/2006] [Accepted: 11/21/2006] [Indexed: 11/24/2022]
Abstract
The Italian peninsula, given its geographical location in the middle of the Mediterranean basin, was involved in the process of the peopling of Europe since the very beginning, with first settlements dating to the Upper Paleolithic. Later on, the Neolithic revolution left clear evidence in the archeological record, with findings going back to 7000 B.C. We have investigated the demographic consequences of the agriculture revolution in this area by genotyping Y chromosome markers for almost 700 individuals from 12 different regions. Data analysis showed a non-random distribution of the observed genetic variation, with more than 70% of the Y chromosome diversity distributed along a North-South axis. While the Greek colonisation during classical time appears to have left no significant contribution, the results support a male demic diffusion model, even if population replacement was not complete and the degree of Neolithic admixture with Mesolithic inhabitants was different in different areas of Italy.
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