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Pliss L, Timša L, Rootsi S, Tambets K, Pelnena I, Zole E, Puzuka A, Sabule A, Rozane S, Lace B, Kucinskas V, Krumina A, Ranka R, Baumanis V. Y-Chromosomal Lineages of Latvians in the Context of the Genetic Variation of the Eastern-Baltic Region. Ann Hum Genet 2015; 79:418-30. [PMID: 26411886 DOI: 10.1111/ahg.12130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 06/19/2015] [Accepted: 06/25/2015] [Indexed: 11/30/2022]
Abstract
Variations of the nonrecombining Y-chromosomal region were investigated in 159 unrelated Baltic-speaking ethnic Latvians from four different geographic regions, using 28 biallelic markers and 12 short tandem repeats. Eleven different haplogroups (hgs) were detected in a regionally homogeneous Latvian population, among which N1c, R1a, and I1 cover more than 85% of its paternal lineages. When compared its closest geographic neighbors, the composition of the Latvian Y-chromosomal gene pool was found to be very similar to those of Lithuanians and Estonians. Despite the comparable frequency distribution of hg N1c in Latvians and Lithuanians with the Finno-Ugric-speaking populations from the Eastern coast of the Baltic Sea, the observed differences in allelic variances of N1c haplotypes between these two groups are in concordance with the previously stated hypothesis of different dispersal ways of this lineage in the region. More than a third of Latvian paternal lineages belong specifically to a recently defined R1a-M558 hg, indicating an influence from a common source within Eastern Slavic populations on the formation of the present-day Latvian Y-chromosome gene pool.
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Affiliation(s)
- Liana Pliss
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Līga Timša
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | - Inese Pelnena
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Egija Zole
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Areta Sabule
- State Centre for Forensic Medical Examination of the Republic of Latvia, Riga, Latvia
| | - Sandra Rozane
- State Centre for Forensic Medical Examination of the Republic of Latvia, Riga, Latvia
| | - Baiba Lace
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Vaidutis Kucinskas
- Human Genome Research Centre, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | | | - Renate Ranka
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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Der Sarkissian C, Balanovsky O, Brandt G, Khartanovich V, Buzhilova A, Koshel S, Zaporozhchenko V, Gronenborn D, Moiseyev V, Kolpakov E, Shumkin V, Alt KW, Balanovska E, Cooper A, Haak W. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe. PLoS Genet 2013; 9:e1003296. [PMID: 23459685 PMCID: PMC3573127 DOI: 10.1371/journal.pgen.1003296] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 12/18/2012] [Indexed: 11/25/2022] Open
Abstract
North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across Eurasia. It contributes to the description of the spatio-temporal distribution of mitochondrial diversity and will be of significance for future reconstructions of the history of Europeans. The history of human populations can be retraced by studying the archaeological and anthropological record, but also by examining the current distribution of genetic markers, such as the maternally inherited mitochondrial DNA. Ancient DNA research allows the retrieval of DNA from ancient skeletal remains and contributes to the reconstruction of the human population history through the comparison of ancient and present-day genetic data. Here, we analysed the mitochondrial DNA of prehistoric remains from archaeological sites dated to 7,500 and 3,500 years Before Present. These sites are located in North East Europe, a region that displays a significant cultural and linguistic diversity today but for which no ancient human DNA was available before. We show that prehistoric hunter-gatherers of North East Europe were genetically similar to other European foragers. We also detected a prehistoric genetic input from Siberia, followed by migrations from Western Europe into North East Europe. Our research contributes to the understanding of the origins and past dynamics of human population in Europe.
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Affiliation(s)
- Clio Der Sarkissian
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Guido Brandt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | | | | | - Sergey Koshel
- Faculty of Geography, Moscow State University, Moscow, Russia
| | - Valery Zaporozhchenko
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
| | | | | | - Eugen Kolpakov
- Institute for the History of Material Culture, Russian Academy of Science, St. Petersburg, Russia
| | - Vladimir Shumkin
- Institute for the History of Material Culture, Russian Academy of Science, St. Petersburg, Russia
| | - Kurt W. Alt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia, Australia
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Douroudis K, Nemvalts V, Rajasalu T, Kisand K, Uibo R. The CD226 gene in susceptibility of type 1 diabetes. ACTA ACUST UNITED AC 2009; 74:417-9. [PMID: 19624611 DOI: 10.1111/j.1399-0039.2009.01320.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The rs763361 single nucleotide polymorphism (SNP) within the CD226 gene has recently been reported as a novel susceptible locus for type 1 diabetes. The CD226 gene is implicated in the regulation of a number of cells involved in immune mechanisms leading to beta-cell destruction in type 1 diabetes. The aim of the present study was to confirm the association of the CD226 gene with type 1 diabetes in Estonian population. The TT genotype [odds ratio (OR) = 2.29, 95% confidence interval (CI) = 1.25-4.18, P = 0.0071) and the T allele (OR = 1.48, 95% CI = 1.11-1.98, P = 0.0084) of the rs763361 SNP were associated with the risk of type 1 diabetes. The current study replicates the novel association of the rs763361 SNP in susceptibility of type 1 diabetes and supports the CD226 gene as a susceptible candidate locus for type 1 diabetes outside the major histocompatibility complex region.
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Affiliation(s)
- K Douroudis
- Immunology Group, Institute of General and Molecular Pathology, University of Tartu, Tartu, Estonia
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Puschmann A. Unverricht-Lundborg disease-A misnomer? Mov Disord 2009; 24:629-30; author reply 630. [DOI: 10.1002/mds.22119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Stacey A, Sheffield NC, Crandall KA. Calculating expected DNA remnants from ancient founding events in human population genetics. BMC Genet 2008; 9:66. [PMID: 18928554 PMCID: PMC2588638 DOI: 10.1186/1471-2156-9-66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 10/17/2008] [Indexed: 11/10/2022] Open
Abstract
Background Recent advancements in sequencing and computational technologies have led to rapid generation and analysis of high quality genetic data. Such genetic data have achieved wide acceptance in studies of historic human population origins and admixture. However, in studies relating to small, recent admixture events, genetic factors such as historic population sizes, genetic drift, and mutation can have pronounced effects on data reliability and utility. To address these issues we conducted genetic simulations targeting influential genetic parameters in admixed populations. Results We performed a series of simulations, adjusting variable values to assess the affect of these genetic parameters on current human population studies and what these studies infer about past population structure. Final mean allele frequencies varied from 0.0005 to over 0.50, depending on the parameters. Conclusion The results of the simulations illustrate that, while genetic data may be sensitive and powerful in large genetic studies, caution must be used when applying genetic information to small, recent admixture events. For some parameter sets, genetic data will not be adequate to detect historic admixture. In such cases, studies should consider anthropologic, archeological, and linguistic data where possible.
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Affiliation(s)
- Andrew Stacey
- Department of Statistics, Brigham Young University, Provo, UT 84602, USA.
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Pliss L, Tambets K, Loogväli EL, Pronina N, Lazdins M, Krumina A, Baumanis V, Villems R. Mitochondrial DNA Portrait of Latvians: Towards the Understanding of the Genetic Structure of Baltic-Speaking Populations. Ann Hum Genet 2006; 70:439-58. [PMID: 16759178 DOI: 10.1111/j.1469-1809.2005.00238.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mitochondrial DNA (mtDNA) variation was investigated in a sample of 299 Latvians, a Baltic-speaking population from Eastern Europe. Sequencing of the first hypervariable segment (HVS-I) in combination with analysis of informative coding region markers revealed that the vast majority of observed mtDNAs belong to haplogroups (hgs) common to most European populations. Analysis of the spatial distribution of mtDNA haplotypes found in Latvians, as well as in Baltic-speaking populations in general, revealed that they share haplotypes with all neighbouring populations irrespective of their linguistic affiliation. Hence, the results of our mtDNA analysis show that the previously described sharp difference between the Y-chromosomal hg N3 distribution in the paternally inherited gene pool of Baltic-speaking populations and of other European Indo-European speakers does not have a corresponding maternal counterpart.
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Affiliation(s)
- L Pliss
- Biomedical Research and Study Centre, University of Latvia, Riga, Latvia.
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Pliss L, Tambets K, Loogvali EL, Pronina N, Lazdins M, Krumina A, Baumanis V, Villems R. Mitochondrial DNA Portrait of Latvians: Towards the Understanding of the Genetic Structure of Baltic-Speaking Populations. Ann Hum Genet 2005. [DOI: 10.1111/j.1529-8817.2005.00238.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kasperaviciūte D, Kucinskas V, Stoneking M. Y chromosome and mitochondrial DNA variation in Lithuanians. Ann Hum Genet 2004; 68:438-52. [PMID: 15469421 DOI: 10.1046/j.1529-8817.2003.00119.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genetic composition of the Lithuanian population was investigated by analysing mitochondrial DNA hypervariable region 1, RFLP polymorphisms and Y chromosomal biallelic and STR markers in six ethnolinguistic groups of Lithuanians, to address questions about the origin and genetic structure of the present day population. There were no significant genetic differences among ethnolinguistic groups, and an analysis of molecular variance confirmed the homogeneity of the Lithuanian population. MtDNA diversity revealed that Lithuanians are close to both Slavic (Indo-European) and Finno-Ugric speaking populations of Northern and Eastern Europe. Y-chromosome SNP haplogroup analysis showed Lithuanians to be closest to Latvians and Estonians. Significant differences between Lithuanian and Estonian Y chromosome STR haplotypes suggested that these populations have had different demographic histories. We suggest that the observed pattern of Y chromosome diversity in Lithuanians may be explained by a population bottleneck associated with Indo-European contact. Different Y chromosome STR distributions in Lithuanians and Estonians might be explained by different origins or, alternatively, be the result of some period of isolation and genetic drift after the population split.
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Affiliation(s)
- D Kasperaviciūte
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Santariskiu str. 2, LT-08661 Vilnius, Lithuania.
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Haller K, Kisand K, Nemvalts V, Laine AP, Ilonen J, Uibo R. Type 1 diabetes is insulin -2221 MspI and CTLA-4 +49 A/G polymorphism dependent. Eur J Clin Invest 2004; 34:543-8. [PMID: 15305888 DOI: 10.1111/j.1365-2362.2004.01385.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Several studies have demonstrated an association of type 1 diabetes with specific alleles of HLA class II molecules, as with polymorphisms of insulin gene region. The aim of our study was to evaluate the interaction of insulin -2221 MspI polymorphism to type 1 diabetes susceptibility in connection with autoimmunity associated gene--CTLA-4 polymorphism. MATERIALS AND METHODS Insulin -2221 MspI C/T and CTLA-4 +49 A/G polymorphisms were detected by restriction fragment-length polymorphism analysis or oligonucleotide hybridization in type 1 (n = 69), type 2 diabetes (n = 301) patients and 158 healthy controls. Regression model adjusted for age, gender and gene polymorphisms was studied. RESULTS C-allele of insulin -2221 MspI and G-allele of +49 CTLA-4 were significant risk factors for type 1 diabetes (crude OR 3.53 and 1.59, respectively) and this impact increased in the homozygous form of both alleles. The regression model supported the idea of insulin CC and CTLA-4 GG genotypes for an independent and clearly significant risk for developing type 1 diabetes. We could not detect any significant correlation between investigated polymorphisms and type 2 diabetes. CONCLUSIONS There exists a significant association between the C-allele of -2221 MspI in the insulin gene and type 1 diabetes. The CTLA-4 G-allele is also positively correlated with type 1 diabetes. According to the regression model the investigated gene polymorphisms are independent risk factors for development of type 1 diabetes in the Estonian population. We propose that -2221 MspI is a good marker for evaluation of risk of insulin gene haplotype in type 1 diabetes patients.
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Affiliation(s)
- K Haller
- University of Tartu, Tartu, Estonia
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Laitinen V, Lahermo P, Sistonen P, Savontaus ML. Y-chromosomal diversity suggests that Baltic males share common Finno-Ugric-speaking forefathers. Hum Hered 2002; 53:68-78. [PMID: 12037406 DOI: 10.1159/000057985] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To elucidate the genetic relationships between Estonian, Latvian and Lithuanian men by studying Y-chromosomal variation in these people. METHODS The allelic status of five deep-rooted marker loci (YAP, Tat, M9, 92R7 and SRY-1532) was determined for 346 Baltic males. On the basis of single nucleotide polymorphism (SNP) haplotypes, Y chromosomes were divided into six haplogroups, and the Baltic haplogroup distribution compared with that in 7 European reference populations. Haplogroup frequencies, diversities and genetic distances (F(ST) values) were calculated. The relationships between populations were further illustrated using Mantel test, neighbor-joining tree and principal-component map. RESULTS We found the Indo-European-speaking Latvians and Lithuanians to be genetically very similar to the Finno-Ugric-speaking Estonians. When compared to the reference populations, Baltic males were most closely related to the Finno-Ugric-speaking Mari, followed by their Finnish and Slavonic neighbors. CONCLUSIONS The genetic similarity existing between Estonian, Latvian and Lithuanian men suggests that they originate from the same male founder population. Since the Baltic Y-chromosomal haplogroup distribution more closely resembles that of Finno-Ugric than Indo-European-speaking populations, we propose a hypothesis that Baltic males share a common Finno-Ugric ancestry.
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Affiliation(s)
- Virpi Laitinen
- Department of Medical Genetics, Biomedical Institute, University of Turku, Finland.
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Zerjal T, Beckman L, Beckman G, Mikelsaar AV, Krumina A, Kucinskas V, Hurles ME, Tyler-Smith C. Geographical, linguistic, and cultural influences on genetic diversity: Y-chromosomal distribution in Northern European populations. Mol Biol Evol 2001; 18:1077-87. [PMID: 11371596 DOI: 10.1093/oxfordjournals.molbev.a003879] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We analyzed 10 Y-chromosomal binary markers in 363 males from 8 populations in Northern Europe and 5 Y microsatellites in 346 of these individuals. These populations can be grouped according to cultural, linguistic, or geographical criteria, and the groupings are different in each case. We can therefore ask which criterion best corresponds to the distribution of genetic variation. In an AMOVA analysis using the binary markers, 13% of the Y variation was found between populations, indicating a high level of differentiation within this small area. No significant difference was seen between the traditionally nomadic Saami and the neighboring, historically farming, populations. When the populations were divided into Uralic speakers and Indo-European speakers, 8% of the variation was found between groups, but when they were divided according to geographical location, 14% of the variation was between groups. Geographical factors have thus been the most important in limiting gene flow between these populations, but linguistic differences have also been important in the east.
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Affiliation(s)
- T Zerjal
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
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Beckman L, Sikström C, Mikelsaar A, Krumina A, Kucinskas V, Beckman G. alpha1-antitrypsin (PI) alleles as markers of Westeuropean influence in the Baltic Sea region. Hum Hered 1999; 49:52-5. [PMID: 9858859 DOI: 10.1159/000022841] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The distribution of alpha1-antitrypsin (PI) alleles was studied in an attempt to elucidate migrations and admixture between populations in the Baltic Sea region. The frequency of the PI Z allele, a typically Northwesteuropean marker gene, showed a highly significant regional variation in the Baltic Sea region. The highest frequency (4.5%) was found in the western part of Latvia (Courland). The PI S allele, another marker of Westeuropean influence, also showed an increased frequency in the Courland population. These results indicate that among the populations east of the Baltic Sea the Curonian population has the most pronounced Westeuropean influence. Archaeological data have shown that from the 7th century and for several hundreds of years Courland received immigrations from mainland Sweden and the island of Gotland. We speculate that the increased frequencies of the PI Z alleles and S alleles in Courland may have been caused by these migrations.
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Affiliation(s)
- L Beckman
- Department of Medical Genetics, Umeâ University, Umeâ, Sweden.
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