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Kristjansson D, Schurr TG, Bohlin J, Jugessur A. Phylogeographic history of mitochondrial haplogroup J in Scandinavia. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:298-315. [PMID: 36790764 PMCID: PMC10100211 DOI: 10.1002/ajpa.24666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/10/2022] [Accepted: 11/13/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Mitochondrial DNA haplogroup J is the third most frequent haplogroup in modern-day Scandinavia, although it did not originate there. To infer the genetic history of haplogroup J in Scandinavia, we examined worldwide mitogenome sequences using a maximum-likelihood phylogenetic approach. METHODS Haplogroup J mitogenome sequences were gathered from GenBank (n = 2245) and aligned against the ancestral Reconstructed Sapiens Reference Sequence. We also analyzed haplogroup J Viking Age sequences from the European Nucleotide Archive (n = 54). Genetic distances were estimated from these data and projected onto a maximum likelihood rooted phylogenetic tree to analyze clustering and branching dates. RESULTS Haplogroup J originated approximately 42.6 kya (95% CI: 30.0-64.7), with several of its earliest branches being found within the Arabian Peninsula and Northern Africa. J1b was found most frequently in the Near East and Arabian Peninsula, while J1c occurred most frequently in Europe. Based on phylogenetic dating, subhaplogroup J1c has its early roots in the Mediterranean and Western Balkans. Otherwise, the majority of the branches found in Scandinavia are younger than those seen elsewhere, indicating that haplogroup J dispersed relatively recently into Northern Europe, most plausibly with Neolithic farmers. CONCLUSIONS Haplogroup J appeared when Scandinavia was transitioning to agriculture over 6 kya, with J1c being the most common lineage there today. Changes in the distribution of haplogroup J mtDNAs were likely driven by the expansion of farming from West Asia into Southern Europe, followed by a later expansion into Scandinavia, with other J subhaplogroups appearing among Scandinavian groups as early as the Viking Age.
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Affiliation(s)
- Dana Kristjansson
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jon Bohlin
- Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
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2
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Budowle B, Sajantila A. Revisiting informed consent in forensic genomics in light of current technologies and the times. Int J Legal Med 2023; 137:551-565. [PMID: 36642749 PMCID: PMC9902322 DOI: 10.1007/s00414-023-02947-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/14/2022] [Indexed: 01/17/2023]
Abstract
Informed consent is based on basic ethical principles that should be considered when conducting biomedical and behavioral research involving human subjects. These principles-respect, beneficence, and justice-form the foundations of informed consent which in itself is grounded on three fundamental elements: information, comprehension, and voluntary participation. While informed consent has focused on human subjects and research, the practice has been adopted willingly in the forensic science arena primarily to acquire reference samples from family members to assist in identifying missing persons. With advances in molecular biology technologies, data mining, and access to metadata, it is important to assess whether the past informed consent process and in particular associated risks are concomitant with these increased capabilities. Given the state-of-the-art, areas in which informed consent may need to be modified and augmented are as follows: reference samples from family members in missing persons or unidentified human remains cases; targeted analysis of an individual(s) during forensic genetic genealogy cases to reduce an investigative burden; donors who provide their samples for validation studies (to include population studies and entry into databases that would be applied to forensic statistical calculations) to support implementation of procedures and operations of the forensic laboratory; family members that may contribute samples or obtain genetic information from a molecular autopsy; and use of medical and other acquired samples that could be informative for identification purposes. The informed consent process should cover (1) purpose for collection of samples; (2) process to analyze the samples (to include type of data); (3) benefits (to donor, target, family, community, etc. as applicable); (4) risks (to donor, target, family, community, etc. as applicable); (5) access to data/reports by the donor; (6) sample disposition; (7) removal of data process (i.e., expungement); (8) process to ask questions/assessment of comprehension; (9) follow-up processes; and (10) voluntary, signed, and dated consent. Issues surrounding these topics are discussed with an emphasis on addressing risk factors. Addressing informed consent will allow human subjects to make decisions voluntarily and with autonomy as well as secure the use of samples for intended use.
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Affiliation(s)
- Bruce Budowle
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
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Kristjansson D, Bohlin J, Nguyen TT, Jugessur A, Schurr TG. Evolution and dispersal of mitochondrial DNA haplogroup U5 in Northern Europe: insights from an unsupervised learning approach to phylogeography. BMC Genomics 2022; 23:354. [PMID: 35525961 PMCID: PMC9080151 DOI: 10.1186/s12864-022-08572-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/20/2022] [Indexed: 12/28/2022] Open
Abstract
Background We combined an unsupervised learning methodology for analyzing mitogenome sequences with maximum likelihood (ML) phylogenetics to make detailed inferences about the evolution and diversification of mitochondrial DNA (mtDNA) haplogroup U5, which appears at high frequencies in northern Europe. Methods Haplogroup U5 mitogenome sequences were gathered from GenBank. The hierarchal Bayesian Analysis of Population Structure (hierBAPS) method was used to generate groups of sequences that were then projected onto a rooted maximum likelihood (ML) phylogenetic tree to visualize the pattern of clustering. The haplogroup statuses of the individual sequences were assessed using Haplogrep2. Results A total of 23 hierBAPS groups were identified, all of which corresponded to subclades defined in Phylotree, v.17. The hierBAPS groups projected onto the ML phylogeny accurately clustered all haplotypes belonging to a specific haplogroup in accordance with Haplogrep2. By incorporating the geographic source of each sequence and subclade age estimates into this framework, inferences about the diversification of U5 mtDNAs were made. Haplogroup U5 has been present in northern Europe since the Mesolithic, and spread in both eastern and western directions, undergoing significant diversification within Scandinavia. A review of historical and archeological evidence attests to some of the population interactions contributing to this pattern. Conclusions The hierBAPS algorithm accurately grouped mitogenome sequences into subclades in a phylogenetically robust manner. This analysis provided new insights into the phylogeographic structure of haplogroup U5 diversity in northern Europe, revealing a detailed perspective on the diversity of subclades in this region and their distribution in Scandinavian populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08572-y.
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Affiliation(s)
- Dana Kristjansson
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway. .,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.
| | - Jon Bohlin
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Truc Trung Nguyen
- IT Systems Bergen, Norwegian Institute of Public Health, Bergen, Norway
| | - Astanand Jugessur
- Center for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA, USA
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Kiiskilä J, Jokelainen J, Kytövuori L, Mikkola I, Härkönen P, Keinänen-Kiukaanniemi S, Majamaa K. Association of mitochondrial DNA haplogroups J and K with low response in exercise training among Finnish military conscripts. BMC Genomics 2021; 22:75. [PMID: 33482721 PMCID: PMC7821635 DOI: 10.1186/s12864-021-07383-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/12/2021] [Indexed: 11/10/2022] Open
Abstract
Background We have previously suggested that some of the mutations defining mitochondrial DNA (mtDNA) haplogroups J and K produce an uncoupling effect on oxidative phosphorylation and thus are detrimental for elite endurance performance. Here, the association between haplogroups J and K and physical performance was determined in a population-based cohort of 1036 Finnish military conscripts. Results Following a standard-dose training period, excellence in endurance performance was less frequent among subjects with haplogroups J or K than among subjects with non-JK haplogroups (p = 0.041), and this finding was more apparent among the best-performing subjects (p < 0.001). Conclusions These results suggest that mtDNA haplogroups are one of the genetic determinants explaining individual variability in the adaptive response to endurance training, and mtDNA haplogroups J and K are markers of low-responders in exercise training. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07383-x.
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Affiliation(s)
- Jukka Kiiskilä
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland. .,Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland.
| | - Jari Jokelainen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland.,Unit of General Practice, Oulu University Hospital, Oulu, Finland
| | - Laura Kytövuori
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland
| | | | - Pirjo Härkönen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland.,Unit of General Practice, Oulu University Hospital, Oulu, Finland
| | - Sirkka Keinänen-Kiukaanniemi
- Center for Life Course Health Research, University of Oulu, Oulu, Finland.,Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland.,Healthcare and Social Services of Selänne, Pyhäjärvi, Finland
| | - Kari Majamaa
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland
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Lohi V, Ohtonen P, Aikio P, Sorri M, Mäki-Torkko E, Hannula S. Hearing impairment is common among Saami adults in Northern Finland. Int J Circumpolar Health 2017; 76:1398004. [PMID: 29132251 PMCID: PMC5700497 DOI: 10.1080/22423982.2017.1398004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Saami are the only indigenous population in Europe and their traditional living area is northern Scandinavia. Hearing impairment (HI) among Saami has not been studied before. The objective was to investigate the presence and type of HI among Saami adults, aged 49–77 years (median age 61 years), living in northern Finland. In addition, the presence of self-reported hearing difficulties, difficulties to hear in background noise and tinnitus were studied. An epidemiological, cross-sectional study encompassing a structured interview, otological examination and audiometry was performed. Bilateral HI was present in 42.9% of men and 29.4% of women, when HI was defined as a pure tone average (PTA) of at least 20 dB hearing level (HL) or more at the frequencies of 0.5, 1, 2 and 4 kHz. In one or both ears (worse ear hearing level, WEHL0.5,1,2,4≥20 dB HL) HI was present in 61.8% of men and 42.2% of women. Sensorineural high frequency hearing impairment was found to be most common. Nearly half (46.9%) of the study subjects reported hearing problems and more than half (55.6%) reported difficulties in following conversation in background noise. Measured HI and subjective hearing difficulties are common among the Saami adults. The healthcare personnel working in this area should be aware of the hearing problems of the Saami population. Abbreviations: ARHI, Age-related hearing impairment; PTA, Pure tone average; HI, Hearing impairment; HL, Hearing level; BEHL, Better ear hearing level; WEHL, Worse ear hearing level; CI, Confidence interval
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Affiliation(s)
- Venla Lohi
- a PEDEGO Research Unit , University of Oulu , Oulu , Finland.,b Medical Research Center Oulu , University of Oulu and Oulu University Hospital , Oulu , Finland.,c Department of Otorhinolaryngology and Head and Neck Surgery , Oulu University Hospital , Oulu , Finland
| | - Pasi Ohtonen
- d Division of Operative Care and Medical Research Center Oulu , Oulu University Hospital and University of Oulu , Oulu , Finland
| | - Pekka Aikio
- e Thule Institute , University of Oulu , Oulu , Finland
| | - Martti Sorri
- a PEDEGO Research Unit , University of Oulu , Oulu , Finland.,b Medical Research Center Oulu , University of Oulu and Oulu University Hospital , Oulu , Finland
| | - Elina Mäki-Torkko
- a PEDEGO Research Unit , University of Oulu , Oulu , Finland.,b Medical Research Center Oulu , University of Oulu and Oulu University Hospital , Oulu , Finland.,f School of Medical Sciences , Örebro University , Örebro , Sweden.,g Audiological Research Centre , Örebro University Hospital , Örebro , Sweden
| | - Samuli Hannula
- a PEDEGO Research Unit , University of Oulu , Oulu , Finland.,b Medical Research Center Oulu , University of Oulu and Oulu University Hospital , Oulu , Finland.,c Department of Otorhinolaryngology and Head and Neck Surgery , Oulu University Hospital , Oulu , Finland
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Ndou R, Schepartz LA. Morphometric Characteristics of the Humerus and Ulna in Limbs Bearing the Supratrochlear Aperture (STA). Anat Rec (Hoboken) 2015; 299:220-33. [PMID: 26579992 DOI: 10.1002/ar.23294] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/01/2015] [Accepted: 10/07/2015] [Indexed: 11/06/2022]
Abstract
The supratrochlear aperture (STA) is a perforation of the septum found between the olecranon and coronoid fossae of the humerus. Its prevalence is population specific and varies by sex. There is no consensus on the etiology of this feature despite decades of investigation. Two aspects of the mechanical theory, which states that the STA is formed when the ulnar olecranon and coronoid processes impinge upon the septum separating the olecranon and coronoid fossae, were investigated. First, osteometric measures of bone size were used to test the proposition that larger humeri are less prone to STA formation. We compared the dimensions of STA bearing humeri with those lacking STAs and investigated which skeletal features discriminate among South African populations. To specifically evaluate the mechanical theory that articulation with the olecranon and coronoid fossae may result in STA formation, dimensions of the olecranon and coronoid processes were compared. Our results verified that smaller individuals are prone to STA formation and that a significantly longer olecranon process is associated with the aperture. The olecranon process length and olecranon-coronoid distance were the main contributors to STA presence. Variables that contributed the most towards discrimination among the South African populations were the olecranon fossa depth and right humeral head circumference. An inverse relationship between the olecranon process length and olecranon fossa depth was also associated with presence of the STA.
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Affiliation(s)
- Robert Ndou
- School of Anatomical Sciences, Morphological Anatomy Division, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Parktown, 2193, South Africa
| | - Lynne Alison Schepartz
- School of Anatomical Sciences, Morphological Anatomy Division, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Parktown, 2193, South Africa
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7
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Longobardi G, Ghirotto S, Guardiano C, Tassi F, Benazzo A, Ceolin A, Barbujani G. Across language families: Genome diversity mirrors linguistic variation within Europe. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 157:630-40. [PMID: 26059462 PMCID: PMC5095809 DOI: 10.1002/ajpa.22758] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 04/02/2015] [Accepted: 04/14/2015] [Indexed: 01/23/2023]
Abstract
Objectives: The notion that patterns of linguistic and biological variation may cast light on each other and on population histories dates back to Darwin's times; yet, turning this intuition into a proper research program has met with serious methodological difficulties, especially affecting language comparisons. This article takes advantage of two new tools of comparative linguistics: a refined list of Indo‐European cognate words, and a novel method of language comparison estimating linguistic diversity from a universal inventory of grammatical polymorphisms, and hence enabling comparison even across different families. We corroborated the method and used it to compare patterns of linguistic and genomic variation in Europe. Materials and Methods: Two sets of linguistic distances, lexical and syntactic, were inferred from these data and compared with measures of geographic and genomic distance through a series of matrix correlation tests. Linguistic and genomic trees were also estimated and compared. A method (Treemix) was used to infer migration episodes after the main population splits. Results: We observed significant correlations between genomic and linguistic diversity, the latter inferred from data on both Indo‐European and non‐Indo‐European languages. Contrary to previous observations, on the European scale, language proved a better predictor of genomic differences than geography. Inferred episodes of genetic admixture following the main population splits found convincing correlates also in the linguistic realm. Discussion: These results pave the ground for previously unfeasible cross‐disciplinary analyses at the worldwide scale, encompassing populations of distant language families. Am J Phys Anthropol 157:630–640, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Giuseppe Longobardi
- Department of Language and Linguistic Science, University of York, York, UK.,Department of Humanities, University of Trieste, Trieste, Italy
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Cristina Guardiano
- Department of Communication and Economics, University of Modena-Reggio Emilia, Modena, Italy
| | - Francesca Tassi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Andrea Ceolin
- Department of Language and Linguistic Science, University of York, York, UK
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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Mitochondrial DNA genetic diversity and LCT-13910 and deltaF508 CFTR alleles typing in the medieval sample from Poland. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2015; 66:229-50. [PMID: 25896719 DOI: 10.1016/j.jchb.2014.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 11/10/2014] [Indexed: 11/22/2022]
Abstract
We attempted to confirm the resemblance of a local medieval population and to reconstruct their contribution to the formation of the modern Polish population at the DNA level. The HVR I mtDNA sequence and two nuclear alleles, LCT-13910C/T SNP and deltaF508 CFTR, were chosen as markers since the distribution of selected nuclear alleles varies among ethnic groups. A total of 47 specimens were selected from a medieval cemetery in Cedynia (located in the western Polish lowland). Regarding the HVR I profile, the analyzed population differed from the present-day population (P = 0.045, F(st) = 0.0103), in contrast to lactase persistence (LP) based on the LCT-13910T allele, thus indicating the lack of notable frequency changes of this allele during the last millennium (P = 0.141). The sequence of the HVR I mtDNA fragment allowed to identify six major haplogroups including H, U5, T, K, and HV0 within the medieval population of Cedynia which are common in today's central Europe. An analysis of haplogroup frequency and its comparison with modern European populations shows that the studied medieval population is more closely related to Finno-Ugric populations than to the present Polish population. Identification of less common haplogroups, i.e., Z and U2, both atypical of the modern Polish population and of Asian origin, provides evidence for some kind of connections between the studied and foreign populations. Furthermore, a comparison of the available aDNA sequences from medieval Europe suggests that populations differed from one another and a number of data from other locations are required to find out more about the features of the medieval gene pool profile.
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Gubina MA, Babenko VN, Damba LD, Ponomareva MN, Konovalova NA, Voevoda MI. Polymorphism of mitochondrial DNA in old believers from Siberia. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414060040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Hervella M, Izagirre N, Alonso S, Ioana M, Netea MG, de-la-Rua C. The Carpathian range represents a weak genetic barrier in South-East Europe. BMC Genet 2014; 15:56. [PMID: 24885208 PMCID: PMC4050216 DOI: 10.1186/1471-2156-15-56] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 05/07/2014] [Indexed: 11/15/2022] Open
Abstract
Background In the present study we have assessed whether the Carpathian Mountains represent a genetic barrier in East Europe. Therefore, we have analyzed the mtDNA of 128 native individuals of Romania: 62 of them from the North of Romania, and 66 from South Romania. Results We have analyzed their mtDNA variability in the context of other European and Near Eastern populations through multivariate analyses. The results show that regarding the mtDNA haplogroup and haplotype distributions the Romanian groups living outside the Carpathian range (South Romania) displayed some degree of genetic differentiation compared to those living within the Carpahian range (North Romania). Conclusion The main differentiation between the mtDNA variability of the groups from North and South Romania can be attributed to the demographic movements from East to West (prehistoric or historic) that differently affected in these regions, suggesting that the Carpathian mountain range represents a weak genetic barrier in South-East Europe.
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Affiliation(s)
| | | | | | | | | | - Concepción de-la-Rua
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Barrio Sarriena s/n 48940, Leioa, Bizkaia, Spain.
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Bernardo S, Hermida R, Desidério M, Silva DA, de Carvalho EF. MtDNA ancestry of Rio de Janeiro population, Brazil. Mol Biol Rep 2014; 41:1945-50. [PMID: 24420852 DOI: 10.1007/s11033-014-3041-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 01/04/2014] [Indexed: 11/30/2022]
Abstract
Polymorphism studies concerning HVI and HVII regions of mitochondrial DNA (mtDNA) have improved the understanding of the admixture genetic process related to the occupation of the continents by human population groups. We have analyzed the mtDNA lineages of 190 healthy and maternally unrelated individuals born in the metropolitan region of the Rio de Janeiro city, the capital of the State of Rio de Janeiro, southeastern Brazil. The data showing that 57.9, 25.3 and 16.8 % of the matrilineages found in Rio de Janeiro come from African, Amerindian and European population groups. They are, respectively, in close agreement with historical records which indicate that the admixture population of Brazil is the resulting of interethnic asymmetry crosses between individuals from those population groups. The high proportion of African mtDNA lineages in the population of Rio de Janeiro is in accordance with studies related to other Brazilian states.
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Affiliation(s)
- Suellen Bernardo
- Laboratório de Diagnósticos por DNA, Instituto de Biologia, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
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Soini HK, Moilanen JS, Vilmi-Kerälä T, Finnilä S, Majamaa K. Mitochondrial DNA variant m.15218A > G in Finnish epilepsy patients who have maternal relatives with epilepsy, sensorineural hearing impairment or diabetes mellitus. BMC MEDICAL GENETICS 2013; 14:73. [PMID: 23870133 PMCID: PMC3726289 DOI: 10.1186/1471-2350-14-73] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 07/17/2013] [Indexed: 01/04/2023]
Abstract
BACKGROUND Mitochondrial diseases caused by mutations in mitochondrial DNA (mtDNA) affect tissues with high energy demand. Epilepsy is one of the manifestations of mitochondrial dysfunction when the brain is affected. We have studied here 79 Finnish patients with epilepsy and who have maternal first- or second-degree relatives with epilepsy, sensorineural hearing impairment or diabetes mellitus. METHODS The entire mtDNA was studied by using conformation sensitive gel electrophoresis and PCR fragments that differed in mobility were directly sequenced. RESULTS We found a common nonsynonymous variant m.15218A > G (p.T158A, MTCYB) that occurs in haplogroup U5a1 to be more frequent in patients with epilepsy. The m.15218A > G variant was present in five patients with epilepsy and in four out of 403 population controls (p = 0.0077). This variant was present in two branches in the phylogenetic network constructed on the basis of mtDNA variation among the patients. Three algorithms predicted that m.15218A > G is damaging in effect. CONCLUSIONS We suggest that the m.15218A > G variant is mildly deleterious and that mtDNA involvement should be considered in patients with epilepsy and who have a maternal history of epilepsy, sensorineural hearing impairment or diabetes mellitus.
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Affiliation(s)
- Heidi K Soini
- Department of Neurology, Oulu University Hospital, P.O. Box 20, Oulu FI-90029, OYS, Finland
- Department of Clinical Medicine, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
- Clinical Research Center, Oulu University Hospital, P.O. Box 5000, FI-90014, Oulu, Finland
| | - Jukka S Moilanen
- Department of Clinical Genetics, Oulu University Hospital and University of Oulu P.O. Box 23, FI-90029, OYS, Oulu, Finland
| | - Tiina Vilmi-Kerälä
- Department of Neurology, Oulu University Hospital, P.O. Box 20, Oulu FI-90029, OYS, Finland
- Department of Clinical Medicine, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
- Clinical Research Center, Oulu University Hospital, P.O. Box 5000, FI-90014, Oulu, Finland
| | - Saara Finnilä
- Department of Neurology, Oulu University Hospital, P.O. Box 20, Oulu FI-90029, OYS, Finland
- Department of Clinical Medicine, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
- Clinical Research Center, Oulu University Hospital, P.O. Box 5000, FI-90014, Oulu, Finland
| | - Kari Majamaa
- Department of Neurology, Oulu University Hospital, P.O. Box 20, Oulu FI-90029, OYS, Finland
- Department of Clinical Medicine, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
- Clinical Research Center, Oulu University Hospital, P.O. Box 5000, FI-90014, Oulu, Finland
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Gubina MA, Girgol’kau LA, Babenko VN, Damba LD, Maksimov VN, Voevoda MI. Mitochondrial DNA polymorphism in populations of aboriginal residents of the Far East. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413070065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Gubina MA, Damba LD, Babenko VN, Romaschenko AG, Voevoda MI. Haplotype diversity in mtDNA and Y-chromosome in populations of Altai-Sayan region. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795412120034] [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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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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Forsius H, Eriksson AW, Fellman J. The international biological program/human adaptability studies among the Skolt Sami in Finland (1966-1970). Int J Circumpolar Health 2012; 71:1-5. [PMID: 22564462 PMCID: PMC3417680 DOI: 10.3402/ijch.v71i0.18186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 06/22/2011] [Accepted: 09/16/2011] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The population is increasingly lighter pigmented moving in a northward direction in Europe until reaching the Arctic Circle, where the Samis (Lapps) are clearly more pigmented. METHODS In 1966-1970, we investigated a total of 689 subjects in the villages of Sevettijärvi and Nellim, including persons with mixed Sami and Finnish heritage; of these, 487 (242 males, 245 females) had both parents classified as Skolt Sami. For estimation of the colour of the iris and hair, international scales were used. For translucency of the iris, pigmentation of the fundus was estimated in 3 different shades. The length and type of eyelashes were classified into 3 categories. To our knowledge, a simultaneous study of the pigmentation of eyebrows, eyelashes and eye fundus at different ages has not previously been published. RESULTS The age differences of iris colour were highly significant. Iris colour in children varied markedly, and they generally had lighter colours than later in life. Age and sex effects on the translucency of irises were found. Male irises were more translucent. Fundus pigmentation was scanty in the youngest age groups, with full pigmentation being reached at 20 years. Among young individuals hair colour darkens with increasing age. Eyebrow colour was slightly lighter for both sexes in the youngest age groups that in older cohorts. Women had longer eyelashes than males. CONCLUSIONS The main factor of the lighter skin is a higher ability to synthesize vitamin D, providing superior protection against rickets. The Skolt Samis are more pigmented than other Nordic people. In earlier times they had problems with rickets but our studies did not show any essential symptoms of rickets today. Visual acuity among Skolt Samis was good. They had lower prevalence of myopia compared to Finns. The stronger pigmentation of Skolt Samis is probably due to their origin from darker Eastern populations. Since our investigations were made, the Skolt Samis have been to a great part mixed with neighbouring populations and scattered throughout Finland. Even their old language is nowadays used mainly for traditional purposes. Therefore similar studies could not be performed anymore.
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Affiliation(s)
- Henrik Forsius
- Department of Genetic Epidemiology, Folkhälsan Institute of Genetics, Helsinki, Finland.
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Evidence of high genetic variation among linguistically diverse populations on a micro-geographic scale: a case study of the Italian Alps. J Hum Genet 2012; 57:254-60. [PMID: 22418692 DOI: 10.1038/jhg.2012.14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Although essential for the fine-scale reconstruction of genetic structure, only a few micro-geographic studies have been carried out in European populations. This study analyzes mitochondrial variation (651 bp of the hypervariable region plus 17 single-nucleotide polymorphisms) in 393 samples from nine populations from Trentino (Eastern Italian Alps), a small area characterized by a complex geography and high linguistic diversity. A high level of genetic variation, comparable to geographically dispersed European groups, was observed. We found a difference in the intensity of peopling processes between two longitudinal areas, as populations from the west-central part of the region show stronger signatures of expansion, whereas those from the eastern area are closer to the expectations of a stationary demographic state. This may be explained by geomorphological factors and is also supported by archeological data. Finally, our results reveal a striking difference in the way in which the two linguistically isolated populations are genetically related to the neighboring groups. The Ladin speakers were found to be genetically close to the Italian-speaking populations and differentiated from the other Dolomitic Ladins, whereas the German-speaking Cimbri behave as an outlier, showing signatures of founder effects and low growth rate.
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Morozova I, Evsyukov A, Kon'kov A, Grosheva A, Zhukova O, Rychkov S. Russian ethnic history inferred from mitochondrial DNA diversity. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 147:341-51. [PMID: 22183855 DOI: 10.1002/ajpa.21649] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 11/01/2011] [Indexed: 11/07/2022]
Abstract
With the aim of gaining insight into the genetic history of the Russians, we have studied mitochondrial DNA diversity among a number of modern Russian populations. Polymorphisms in mtDNA markers (HVS-I and restriction sites of the coding region) of populations from 14 regions within present-day European Russia were investigated. Based on analysis of the mitochondrial gene pool geographic structure, we have identified three different elements in it and a vast "intermediate" zone between them. The analysis of the genetic distances from these elements to the European ethnic groups revealed the main causes of the Russian mitochondrial gene pool differentiation. The investigation of this pattern in historic perspective showed that the structure of the mitochondrial gene pool of the present-day Russians largely conforms to the tribal structure of the medieval Slavs who laid the foundation of modern Russians. Our results indicate that the formation of the genetic diversity currently observed among Russians can be traced to the second half of the first millennium A.D., the time of the colonization of the East European Plain by the Slavic tribes. Patterns of diversity are explained by both the impact of the native population of the East European Plain and by genetic differences among the early Slavs.
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Affiliation(s)
- Irina Morozova
- Human Genetics Laboratory, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.
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Balanovsky OP, Koshel SM, Zaporozhchenko VV, Pshenichnov AS, Frolova SA, Kuznetsova MA, Baranova EE, Teuchezh IE, Kuznetsova AA, Romashkina MV, Utevska OM, Churnosov ML, Villems R, Balanovska EV. Genetic ecological monitoring in human populations: Heterozygosity, mtDNA haplotype variation, and genetic load. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411110056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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KIR genotypic diversity can track ancestries in heterogeneous populations: a potential confounder for disease association studies. Immunogenetics 2011; 64:97-109. [PMID: 21898189 DOI: 10.1007/s00251-011-0569-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 08/25/2011] [Indexed: 10/17/2022]
Abstract
Killer cell immunoglobulin-like receptors (KIR) are encoded by highly polymorphic genes that regulate the activation of natural killer (NK) cells and other lymphocyte subsets and likely play key roles in innate and adaptive immunity. Association studies increasingly implicate KIR in disease predisposition and outcome but could be confounded by unknown KIR genetic structure in heterogeneous populations. To examine this, we characterized the diversity of 16 KIR genes in 712 Northern Californians (NC) stratified by self-assigned ethnicities and compared the profiles of KIR polymorphism with other US and global populations using a reference database. Sixty-eight distinct KIR genotypes were characterized: 58 in 457 Caucasians (NCC), 17 in 47 African Americans (NCAA), 21 in 80 Asians (NCA), 20 in 74 Hispanics (NCH), and 18 in 54 "other" ethnicities (NCO). KIR genotype patterns and frequencies in the 4 defined ethnicities were compared with each other and with 34 global populations by phylogenetic analysis. Although there were no population-specific genotypes, the KIR genotype frequency patterns faithfully traced the ancestry of NCC, NCAA, and NCA but not of NCH whose ancestries are known to be more heterogeneous. KIR genotype frequencies can therefore track ethnic ancestries in modern urban populations. Our data emphasize the importance of selecting ethnically matched controls in KIR-based studies to avert spurious associations.
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Denisova GA, Malyarchuk BA, Derenko MV, Kravtsova OA. Population structure of Volga Tatars inferred from the mitochondrial DNA diversity data. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411020086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Evolution of detoxifying systems: the role of environment and population history in shaping genetic diversity at human CYP2D6 locus. Pharmacogenet Genomics 2011; 20:485-99. [PMID: 20520586 DOI: 10.1097/fpc.0b013e32833bba25] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The transition from food collection to food production (FP) modified the nature of selective pressures, and several studies illustrate that genetic adaptation to new lifestyle has occurred in humans since the agricultural revolution. Here we test the hypothesis that high levels of genetic variation at CYP2D6, a locus coding for a detoxifying enzyme of the cytochrome P450 complex, reflect this change. METHODS We compared DNA sequences and predicted the levels of enzyme activity across 10 African, Asian and European populations, six of which currently rely on hunting and gathering (HG) while four on food production (FP). RESULTS AND CONCLUSION HG and FP showed similar levels of CYP2D6 diversity, but displayed different substitution patterns at coding DNA sites possibly related to selective differences. Comparison with variation at presumably neutral independent loci confirmed this finding, despite the confounding effects of population history, resulting in higher overall variation in Africans than in Eurasians. The differences between HG and FP populations suggest that new lifestyle and dietary habits acquired in the transition to agriculture affected the variation pattern at CYP2D6, leading to an increase in FP populations of the frequency of alleles that are associated with a slower rate of metabolism. These alleles reached a balanced co-existence with other important and previously selected variants. We suggest that the pronounced substrate-dependent activity of most of these enzymes expanded the spectrum of the metabolic response.
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Malyarchuk BA, Perkova MA, Derenko MV. On the origin of Mongoloid component in the mitochondrial gene pool of Slavs. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795408030162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Messina F, Scorrano G, Labarga CM, Rolfo MF, Rickards O. Mitochondrial DNA variation in an isolated area of Central Italy. Ann Hum Biol 2010; 37:385-402. [PMID: 20377493 DOI: 10.3109/03014461003720304] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND The genetic variation in Italy is the result of ancient population movement, demographic change, and geography. The increasing possibility of studying the maternal genetic structure of selected Italian population samples at a high level of phylogenetic resolution provides a particularly useful model to assess the presence of genetic traces of the ancient people who lived in Italy in pre-Roman times in present populations AIM In this study we reconstructed the genetic maternal history of Jenne and Vallepietra, two mountain communities in the Aniene Valley in the Simbruini Mountains near Rome. Both communities have been spared external invasion due to their geographic location, which very likely preserved the genetic pool of these autochthonous populations. SUBJECTS AND METHODS The study population (124 individuals from Jenne and Vallepietra) were investigated for D-loop mtDNA hypervariable segments I (HVS-I) and II (HVS-II) and for informative single nucleotide polymorphisms (SNPs) within the coding region. The detected haplotypes were then compared with those of other Italian, European and Mediterranean populations. RESULTS The distribution of mtDNA diversity in Jenne and Vallepietra, although similar to that found in other European populations, shows a basic variability and the typical signs of a certain degree of isolation between them and other populations analysed; in particular, the Vallepietra sample showed an unusually high frequency (71.3%) of mtDNA haplogroups which are typical of Near Eastern and South-Western Asian populations. CONCLUSION The high degree of differentiation between the two villages is intriguing, since it suggests a low level of gene flow between them, despite their close geographic proximity and shared linguistic features. The degree of their genetic isolation, also in comparison to other Italian, European and Mediterranean populations, is consistent with isolation among geographically separated populations.
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Affiliation(s)
- Francesco Messina
- Dipartimento di Biologia, Università di Roma Tor Vergata, Via della Ricerca Scientifica n. 1, 00173 Rome, Italy
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Xu S, Kangwanpong D, Seielstad M, Srikummool M, Kampuansai J, Jin L. Genetic evidence supports linguistic affinity of Mlabri--a hunter-gatherer group in Thailand. BMC Genet 2010; 11:18. [PMID: 20302622 PMCID: PMC2858090 DOI: 10.1186/1471-2156-11-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 03/19/2010] [Indexed: 01/03/2023] Open
Abstract
Background The Mlabri are a group of nomadic hunter-gatherers inhabiting the rural highlands of Thailand. Little is known about the origins of the Mlabri and linguistic evidence suggests that the present-day Mlabri language most likely arose from Tin, a Khmuic language in the Austro-Asiatic language family. This study aims to examine whether the genetic affinity of the Mlabri is consistent with this linguistic relationship, and to further explore the origins of this enigmatic population. Results We conducted a genome-wide analysis of genetic variation using more than fifty thousand single nucleotide polymorphisms (SNPs) typed in thirteen population samples from Thailand, including the Mlabri, Htin and neighboring populations of the Northern Highlands, speaking Austro-Asiatic, Tai-Kadai and Hmong-Mien languages. The Mlabri population showed higher LD and lower haplotype diversity when compared with its neighboring populations. Both model-free and Bayesian model-based clustering analyses indicated a close genetic relationship between the Mlabri and the Htin, a group speaking a Tin language. Conclusion Our results strongly suggested that the Mlabri share more recent common ancestry with the Htin. We thus provided, to our knowledge, the first genetic evidence that supports the linguistic affinity of Mlabri, and this association between linguistic and genetic classifications could reflect the same past population processes.
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Affiliation(s)
- Shuhua Xu
- Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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A genome-wide association study for age-related hearing impairment in the Saami. Eur J Hum Genet 2010; 18:685-93. [PMID: 20068591 DOI: 10.1038/ejhg.2009.234] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
This study aimed at contributing to the elucidation of the genetic basis of age-related hearing impairment (ARHI), a common multifactorial disease with an important genetic contribution as demonstrated by heritability studies. We conducted a genome-wide association study (GWAS) in the Finnish Saami, a small, ancient, genetically isolated population without evidence of demographic expansion. The choice of this study population was motivated by its anticipated higher extent of LD, potentially offering a substantial power advantage for association mapping. DNA samples and audiometric measurements were collected from 352 Finnish Saami individuals, aged between 50 and 75 years. To reduce the burden of multiple testing, we applied principal component (PC) analysis to the multivariate audiometric phenotype. The first three PCs captured 80% of the variation in hearing thresholds, while maintaining biologically important audiometric features. All subjects were genotyped with the Affymetrix 100 K chip. To account for multiple levels of relatedness among subjects, as well as for population stratification, association testing was performed using a mixed model. We summarised the top-ranking association signals for the three traits under study. The top-ranked SNP, rs457717 (P-value 3.55 x 10(-7)), was associated with PC3 and was localised in an intron of the IQ motif-containing GTPase-activating-like protein (IQGAP2). Intriguingly, the SNP rs161927 (P-value 0.000149), seventh-ranked for PC1, was positioned immediately downstream from the metabotropic glutamate receptor-7 gene (GRM7). As a previous GWAS of a European and Finnish sample set already suggested a role for GRM7 in ARHI, this study provides further evidence for the involvement of this gene.
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Genome-wide SNP analysis reveals no gain in power for association studies of common variants in the Finnish Saami. Eur J Hum Genet 2009; 18:569-74. [PMID: 19935831 DOI: 10.1038/ejhg.2009.210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The Saami from Fennoscandia are believed to represent an ancient, genetically isolated population with no evidence of population expansion. Theoretical work has indicated that under this demographic scenario, extensive linkage disequilibrium (LD) is generated by genetic drift. Therefore, it has been suggested that the Saami would be particularly suited for genetic association studies, offering a substantial power advantage and allowing more economic study designs. However, no study has yet assessed this claim. As part of a GWAS for a complex trait, we evaluated the relative power for association studies of common variants in the Finnish Saami. LD patterns in the Saami were very similar to those in the non-African HapMap reference panels. Haplotype diversity was reduced and, on average, levels of LD were higher in the Saami as compared with those in the HapMap panels. However, using a 'hidden' SNP approach we show that this does not translate into a power gain in association studies. Contrary to earlier claims, we show that for a given set of common SNPs, genomic coverage attained in the Saami is similar to that in the non-African HapMap panels. Nevertheless, the reduced haplotype diversity could potentially facilitate gene identification, especially if multiple rare variants play a role in disease etiology. Our results further indicate that the HapMap is a useful resource for genetic studies in the Saami.
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Mirabal S, Regueiro M, Cadenas AM, Cavalli-Sforza LL, Underhill PA, Verbenko DA, Limborska SA, Herrera RJ. Y-chromosome distribution within the geo-linguistic landscape of northwestern Russia. Eur J Hum Genet 2009; 17:1260-73. [PMID: 19259129 PMCID: PMC2986641 DOI: 10.1038/ejhg.2009.6] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 01/09/2009] [Accepted: 01/14/2009] [Indexed: 11/09/2022] Open
Abstract
Populations of northeastern Europe and the Uralic mountain range are found in close geographic proximity, but they have been subject to different demographic histories. The current study attempts to better understand the genetic paternal relationships of ethnic groups residing in these regions. We have performed high-resolution haplotyping of 236 Y-chromosomes from populations in northwestern Russia and the Uralic mountains, and compared them to relevant previously published data. Haplotype variation and age estimation analyses using 15 Y-STR loci were conducted for samples within the N1b, N1c1 and R1a1 single-nucleotide polymorphism backgrounds. Our results suggest that although most genetic relationships throughout Eurasia are dependent on geographic proximity, members of the Uralic and Slavic linguistic families and subfamilies, yield significant correlations at both levels of comparison making it difficult to denote either linguistics or geographic proximity as the basis for their genetic substrata. Expansion times for haplogroup R1a1 date approximately to 18,000 YBP, and age estimates along with Network topology of populations found at opposite poles of its range (Eastern Europe and South Asia) indicate that two separate haplotypic foci exist within this haplogroup. Data based on haplogroup N1b challenge earlier findings and suggest that the mutation may have occurred in the Uralic range rather than in Siberia and much earlier than has been proposed (12.9+/-4.1 instead of 5.2+/-2.7 kya). In addition, age and variance estimates for haplogroup N1c1 suggest that populations from the western Urals may have been genetically influenced by a dispersal from northeastern Europe (eg, eastern Slavs) rather than the converse.
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Affiliation(s)
- Sheyla Mirabal
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL, USA
| | - Maria Regueiro
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL, USA
| | - Alicia M Cadenas
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL, USA
| | | | | | - Dmitry A Verbenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | | | - Rene J Herrera
- Department of Molecular and Human Genetics, College of Medicine, Florida International University, Miami, FL, USA
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Abstract
The Finnish population in Northern Europe has been a target of extensive genetic studies during the last decades. The population is considered as a homogeneous isolate, well suited for gene mapping studies because of its reduced diversity and homogeneity. However, several studies have shown substantial differences between the eastern and western parts of the country, especially in the male-mediated Y chromosome. This divergence is evident in non-neutral genetic variation also and it is usually explained to stem from founder effects occurring in the settlement of eastern Finland as late as in the 16th century. Here, we have reassessed this population historical scenario using Y-chromosomal, mitochondrial and autosomal markers and geographical sampling covering entire Finland. The obtained results suggest substantial Scandinavian gene flow into south-western, but not into the eastern, Finland. Male-biased Scandinavian gene flow into the south-western parts of the country would plausibly explain the large inter-regional differences observed in the Y-chromosome, and the relative homogeneity in the mitochondrial and autosomal data. On the basis of these results, we suggest that the expression of 'Finnish Disease Heritage' illnesses, more common in the eastern/north-eastern Finland, stems from long-term drift, rather than from relatively recent founder effects.
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Wiig O. Perthes' disease in Norway. A prospective study on 425 patients. ACTA ORTHOPAEDICA. SUPPLEMENTUM 2009; 80:1-44. [PMID: 19757732 DOI: 10.1080/17453690610046594] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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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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INFANT BURIALS IN DWELLINGS AT CHICHA-1, IN THE BARABA FOREST-STEPPE: RESULTS OF DNA ANALYSIS. ARCHAEOLOGY ETHNOLOGY AND ANTHROPOLOGY OF EURASIA 2008. [DOI: 10.1016/j.aeae.2008.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Pimenoff VN, Comas D, Palo JU, Vershubsky G, Kozlov A, Sajantila A. Northwest Siberian Khanty and Mansi in the junction of West and East Eurasian gene pools as revealed by uniparental markers. Eur J Hum Genet 2008; 16:1254-64. [DOI: 10.1038/ejhg.2008.101] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Johansson Å, Ingman M, Mack SJ, Erlich H, Gyllensten U. Genetic origin of the Swedish Sami inferred from HLA class I and class II allele frequencies. Eur J Hum Genet 2008; 16:1341-9. [DOI: 10.1038/ejhg.2008.88] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Reconstructing the phylogeny of African mitochondrial DNA lineages in Slavs. Eur J Hum Genet 2008; 16:1091-6. [PMID: 18398433 DOI: 10.1038/ejhg.2008.70] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
To elucidate the origin of African-specific mtDNA lineages, revealed previously in Slavonic populations (at frequency of about 0.4%), we completely sequenced eight African genomes belonging to haplogroups L1b, L2a, L3b, L3d and M1 gathered from Russians, Czechs, Slovaks and Poles. Results of phylogeographic analysis suggest that at least part of the African mtDNA lineages found in Slavs (such as L1b, L3b1, L3d) appears to be of West African origin, testifying to an opportunity of their occurrence as a result of migrations to Eastern Europe through Iberia. However, a prehistoric introgression of African mtDNA lineages into Eastern Europe (approximately 10 000 years ago) seems to be probable only for European-specific subclade L2a1a, defined by coding region mutations at positions 6722 and 12903 and detected in Czechs and Slovaks. Further studies of the nature of African admixture in gene pools of Europeans require the essential enlargement of databases of African complete mitochondrial genomes.
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Hassler S, Sjölander P, Grönberg H, Johansson R, Damber L. Cancer in the Sami population of Sweden in relation to lifestyle and genetic factors. Eur J Epidemiol 2008; 23:273-80. [PMID: 18322808 DOI: 10.1007/s10654-008-9232-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Accepted: 02/12/2008] [Indexed: 11/30/2022]
Abstract
The reindeer herding Sami of Sweden have low incidences of cancer. The aim of the present study was to investigate the cancer risk in a large cohort of Swedish Sami, containing Sami with different lifestyle and genetic Sami heritage. A cohort of 41,721 Sami identified in official national registers between 1960 and 1997, was divided into two sub-populations -- reindeer herding Sami (RS) and non-reindeer herding Sami (NRS). A demographically matched non-Sami reference population (NS) was used as standard when incidence and mortality ratios were calculated. Incidence and mortality data were obtained from the Swedish Cancer and Cause of Death Registers for the period 1961-2003. For Sami men, lower risks were found for cancers of the colon and prostate, and for malignant melanoma and non-Hodkins lymphoma, but higher for stomach cancer. The Sami women showed higher risks for cancers of the stomach and the ovaries, but lower risk for cancer of the bladder. The RS demonstrated lower relative cancer risks compared with the NRS. The lowest relative risk was found among the RS men, while the highest were observed among the NRS women. The RS men who had adopted a more westernized lifestyle showed a similar relative risk for prostate cancer as that of the NS living in the same region. Most of these differences in cancer risks could probably be ascribed to differences in lifestyle. It is concluded that the traditional Sami lifestyle contains elements, e.g. dietary contents and physical activity that may protect them from developing cancer.
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Affiliation(s)
- Sven Hassler
- Southern Lapland Research Department, Vilhelmina, Sweden
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Malyarchuk BA, Perkova MA, Derenko MV, Vanecek T, Lazur J, Gomolcak P. Mitochondrial DNA variability in Slovaks, with application to the Roma origin. Ann Hum Genet 2008; 72:228-40. [PMID: 18205894 DOI: 10.1111/j.1469-1809.2007.00410.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To gain insight into the mitochondrial gene pool diversity of European populations, we studied mitochondrial DNA (mtDNA) variability in 207 subjects from western and eastern areas of Slovakia. Sequencing of two hypervariable segments, HVS I and HVS II, in combination with screening of coding region haplogroup-specific RFLP-markers, revealed that the majority of Slovak mtDNAs belong to the common West Eurasian mitochondrial haplogroups (HV, J, T, U, N1, W, and X). However, a few sub-Saharan African (L2a) mtDNAs were detected in a population from eastern part of Slovakia. In addition, about 3% of mtDNAs from eastern Slovakia encompass Roma-specific lineages. By means of complete mtDNA sequencing we demonstrate here that the Roma-specific M-lineages observed in gene pools of different Slavonic populations (Slovaks, Poles and Russians), belong to Indian-specific haplogroups M5a1 and M35. Moreover, we show that haplogroup J lineages found in gene pools of the Roma and some Slavonic populations (Czechs and Slovaks) belong to new subhaplogroup J1a, which is defined by coding region mutation at position 8460.
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Affiliation(s)
- B A Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya str. 18, Magadan, Russia.
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Tömöry G, Csányi B, Bogácsi-Szabó E, Kalmár T, Czibula A, Csosz A, Priskin K, Mende B, Langó P, Downes CS, Raskó I. Comparison of maternal lineage and biogeographic analyses of ancient and modern Hungarian populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 134:354-68. [PMID: 17632797 DOI: 10.1002/ajpa.20677] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Hungarian language belongs to the Finno-Ugric branch of the Uralic family, but Hungarian speakers have been living in Central Europe for more than 1000 years, surrounded by speakers of unrelated Indo-European languages. In order to study the continuity in maternal lineage between ancient and modern Hungarian populations, polymorphisms in the HVSI and protein coding regions of mitochondrial DNA sequences of 27 ancient samples (10th-11th centuries), 101 modern Hungarian, and 76 modern Hungarian-speaking Sekler samples from Transylvania were analyzed. The data were compared with sequences derived from 57 European and Asian populations, including Finno-Ugric populations, and statistical analyses were performed to investigate their genetic relationships. Only 2 of 27 ancient Hungarian samples are unambiguously Asian: the rest belong to one of the western Eurasian haplogroups, but some Asian affinities, and the genetic effect of populations who came into contact with ancient Hungarians during their migrations are seen. Strong differences appear when the ancient Hungarian samples are analyzed according to apparent social status, as judged by grave goods. Commoners show a predominance of mtDNA haplotypes and haplogroups (H, R, T), common in west Eurasia, while high-status individuals, presumably conquering Hungarians, show a more heterogeneous haplogroup distribution, with haplogroups (N1a, X) which are present at very low frequencies in modern worldwide populations and are absent in recent Hungarian and Sekler populations. Modern Hungarian-speaking populations seem to be specifically European. Our findings demonstrate that significant genetic differences exist between the ancient and recent Hungarian-speaking populations, and no genetic continuity is seen.
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Affiliation(s)
- Gyöngyvér Tömöry
- Institute of Genetics, Biological Research Center of the Hungarian Academy of Sciences, 6726 Szeged, Hungary
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Verbenko DA, Slominsky PA, Spitsyn VA, Bebyakova NA, Khusnutdinova EK, Mikulich AI, Tarskaia LA, Sorensen MV, Ivanov VP, Bets LV, Limborska SA. Polymorphisms at locus D1S80 and other hypervariable regions in the analysis of Eastern European ethnic group relationships. Ann Hum Biol 2007; 33:570-84. [PMID: 17381055 DOI: 10.1080/03014460601012077] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND It has been hypothesized that, whereas many loci are used to generate phylogenetic relationships, the utilization of those that yield the most information could increase the accuracy of any multilocus phylogenetic reconstruction. Among these is the D1S80 hypervariable minisatellite region, which has been shown to be highly polymorphic globally, and it was of interest to compare the nearest neighbours and distant populations of Eastern Europe using the D1S80 polymorphism. AIM The study evaluated the capacity of the D1S80 locus to discriminate between populations from different ethnic groups in Russia and the Republic of Belarus, revealing the polymorphism parameters of the populations studied. SUBJECTS AND METHODS Hypervariable D1S80 minisatellite polymorphism was studied in 15 populations, belonging to six distinct ethnic groups from the Russian Federation (Russians, Komis, Maris, Udmurts, Kalmyks, and Yakuts) and the Republic of Belarus (Byelorussians). The data were analysed with other results reported for D1S80 polymorphism among Eastern Europeans, and were analysed together with those previously reported for Eastern European populations for the 3'ApoB, DMPK, DRPLA, and SCA1 hypervariable loci. Genetic diversity analysis was carried out using multidimensional scaling (MDS) of Nei's genetic distances. RESULTS The Eastern Slavonic populations (Russians, Ukrainians, and Byelorussians) are closely associated, and outermost from populations of Asian origin (Kalmyks and Yakuts). The populations that inhabit the Volga-Ural region (Udmurt, Komi, Mari, and Bashkir ethnic groups) revealed intermediate characteristics. CONCLUSION The clustering of populations demonstrated here using D1S80 alone coincides with the analysis of five hypervariable region (HVR) loci, and is consistent with linguistic, geographic, and ethnohistorical data. These results are in agreement with most studies of mtDNA, Y-chromosomal, and autosomal DNA diversity in Eastern Europe. The D1S80 locus is convenient for population analyses, and may be used as part of a set of similar markers, which should allow the easy resolution of small differences in population structures.
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Affiliation(s)
- D A Verbenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.
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Grzybowski T, Malyarchuk BA, Derenko MV, Perkova MA, Bednarek J, Woźniak M. Complex interactions of the Eastern and Western Slavic populations with other European groups as revealed by mitochondrial DNA analysis. Forensic Sci Int Genet 2007; 1:141-7. [PMID: 19083745 DOI: 10.1016/j.fsigen.2007.01.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Accepted: 01/27/2007] [Indexed: 10/23/2022]
Abstract
Mitochondrial DNA sequence variation was examined by the control region sequencing (HVS I and HVS II) and RFLP analysis of haplogroup-diagnostic coding region sites in 570 individuals from four regional populations of Poles and two Russian groups from northwestern part of the country. Additionally, sequences of complete mitochondrial genomes representing K1a1b1a subclade in Polish and Polish Roma populations have been determined. Haplogroup frequency patterns revealed in Poles and Russians are similar to those characteristic of other Europeans. However, there are several features of Slavic mtDNA pools seen on the level of regional populations which are helpful in the understanding of complex interactions of the Eastern and Western Slavic populations with other European groups. One of the most important is the presence of subhaplogroups U5b1b1, D5, Z1 and U8a with simultaneous scarcity of haplogroup K in populations of northwestern Russia suggesting the participation of Finno-Ugrian tribes in the formation of mtDNA pools of Russians from this region. The results of genetic structure analyses suggest that Russians from Velikii Novgorod area (northwestern Russia) and Poles from Suwalszczyzna (northeastern Poland) differ from all remaining Polish and Russian samples. Simultaneously, northwestern Russians and northeastern Poles bear some similarities to Baltic (Latvians) and Finno-Ugrian groups (Estonians) of northeastern Europe, especially on the level of U5 haplogroup frequencies. The occurrence of K1a1b1a subcluster in Poles and Polish Roma is one of the first direct proofs of the presence of Ashkenazi-specific mtDNA lineages in non-Jewish European populations.
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Affiliation(s)
- Tomasz Grzybowski
- The Nicolaus Copernicus University, Ludwik Rydygier Collegium Medicum, Department of Molecular and Forensic Genetics, M. Curie-Skłodowskiej Str. 9, 85-094 Bydgoszcz, Poland.
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Finnish mitochondrial DNA HVS-I and HVS-II population data. Forensic Sci Int 2007; 172:171-8. [PMID: 17336475 DOI: 10.1016/j.forsciint.2006.09.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 09/26/2006] [Accepted: 09/26/2006] [Indexed: 11/16/2022]
Abstract
We have analyzed the two hypervariable regions HVS-I and HVS-II of 200 Finnish male individuals for forensic purposes. The distribution of the haplotypes within Finland was determined by the geographical knowledge of the donors' maternal ancestors. In our population sample, we identified 135 different mtDNA haplotypes. Different mtDNA sequences were further divided to haplogroups using the EMPOP software. The most common haplogroups were H (40.0%) and U (27.5%). Subgroup U5b, which contains earlier described "Saami motif", consisted majority (65.5%) of the sample in the U haplogroup. Analysis of the mtDNA sequence hypervariable regions I and II showed that the mtDNA diversity within the Finnish population sample was comparable to other European populations and uniformly distributed. This is contrary to the Y-STR "minimal haplotype" diversity, which in Finland is lower than in any of the other European populations studied so far.
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Cerný V, Salas A, Hájek M, Zaloudková M, Brdicka R. A bidirectional corridor in the Sahel-Sudan belt and the distinctive features of the Chad Basin populations: a history revealed by the mitochondrial DNA genome. Ann Hum Genet 2007; 71:433-52. [PMID: 17233755 DOI: 10.1111/j.1469-1809.2006.00339.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Chad Basin was sparsely inhabited during the Stone Age, and its continual settlement began with the Holocene. The role played by Lake Chad in the history and migration patterns of Africa is still unclear. We studied the mitochondrial DNA (mtDNA) variability in 448 individuals from 12 ethnically and/or economically (agricultural/pastoral) different populations from Cameroon, Chad, Niger and Nigeria. The data indicate the importance of this region as a corridor connecting East and West Africa; however, this bidirectional flow of people in the Sahel-Sudan Belt did not erase features peculiar to the original Chad Basin populations. A new sub-clade, L3f2, is described, which together with L3e5 is most probably autochthonous in the Chad Basin. The phylogeography of these two sub-haplogroups seems to indicate prehistoric expansion events in the Chad Basin around 28,950 and 11,400 Y.B.P., respectively. The distribution of L3f2 is virtually restricted to the Chad Basin alone, and in particular to Chadic speaking populations, while L3e5 shows evidence for diffusion into North Africa at about 7,100 Y.B.P. The absence of L3f2 and L3e5 in African-Americans, and the limited number of L-haplotypes shared between the Chad Basin populations and African-Americans, indicate the low contribution of the Chad region to the Atlantic slave trade.
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Affiliation(s)
- V Cerný
- Department of Anthropology and Environment, Institute of Archaeology, Czech Academy of Sciences, 118 01 Prague 1, Czech Republic.
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Belle EMS, Barbujani G. Worldwide analysis of multiple microsatellites: Language diversity has a detectable influence on DNA diversity. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 133:1137-46. [PMID: 17506490 DOI: 10.1002/ajpa.20622] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Previous studies of the correlations between the languages spoken by human populations and the genes carried by the members of those populations have been limited by the small amount of genetic markers available and by approximations in the treatment of linguistic data. In this study we analyzed a large collection of polymorphic microsatellite loci (377), distributed on all autosomes, and used Ruhlen's linguistic classification, to investigate the relative roles of geography and language in shaping the distribution of human DNA diversity at a worldwide scale. For this purpose, we performed three different kinds of analysis: (i) we partitioned genetic variances at three hierarchical levels of population subdivision according to language group by means of a molecular analysis of variance (AMOVA); (ii) we quantified by a series of Mantel's tests the correlation between measures of genetic and linguistic differentiation; and (iii) we tested whether linguistic differences are increased across known zones of increased genetic change between populations. Genetic differences appear to more closely reflect geographic than linguistic differentiation. However, our analyses show that language differences also have a detectable effect on DNA diversity at the genomic level, above and beyond the effects of geographic distance.
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Affiliation(s)
- Elise M S Belle
- Dipartimento di Biologia ed Evoluzione, Università di Ferrara, Via Borsari, 46, 44100 Ferrara, Italy
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Nasidze I, Quinque D, Udina I, Kunizheva S, Stoneking M. The Gagauz, a Linguistic Enclave, are not a Genetic Isolate. Ann Hum Genet 2006; 71:379-89. [PMID: 17147693 DOI: 10.1111/j.1469-1809.2006.00330.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Gagauz are a Turkic-speaking group that migrated from Turkey to their present location in the southern part of the Republic of Moldova about 150 years ago. Surrounded by Indo-European-speaking populations, they thus form a linguistic enclave, which raises the following question: to what extent have they remained in genetic isolation from their geographic neighbours? Analyses of mtDNA and Y chromosome variation indicate that despite their linguistic differences, the Gagauz have admixed extensively with neighbouring groups. Our data suggest that there has been more mtDNA than Y chromosome admixture, in keeping with the patrilocal nature of these groups. Moreover, when compared with another linguistic enclave, the Kalmyks there appears to be a correlation between the amount of genetic admixture and the amount of linguistic influence that these two linguistic enclaves have experienced from neighbouring groups.
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Affiliation(s)
- Ivan Nasidze
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Deutscher Platz 6, D-04103, Leipzig, Germany.
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Roostalu U, Kutuev I, Loogväli EL, Metspalu E, Tambets K, Reidla M, Khusnutdinova EK, Usanga E, Kivisild T, Villems R. Origin and expansion of haplogroup H, the dominant human mitochondrial DNA lineage in West Eurasia: the Near Eastern and Caucasian perspective. Mol Biol Evol 2006; 24:436-48. [PMID: 17099056 DOI: 10.1093/molbev/msl173] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
More than a third of the European pool of human mitochondrial DNA (mtDNA) is fragmented into a number of subclades of haplogroup (hg) H, the most frequent hg throughout western Eurasia. Although there has been considerable recent progress in studying mitochondrial genome variation in Europe at the complete sequence resolution, little data of comparable resolution is so far available for regions like the Caucasus and the Near and Middle East-areas where most of European genetic lineages, including hg H, have likely emerged. This gap in our knowledge causes a serious hindrance for progress in understanding the demographic prehistory of Europe and western Eurasia in general. Here we describe the phylogeography of hg H in the populations of the Near East and the Caucasus. We have analyzed 545 samples of hg H at high resolution, including 15 novel complete mtDNA sequences. As in Europe, most of the present-day Near Eastern-Caucasus area variants of hg H started to expand after the last glacial maximum (LGM) and presumably before the Holocene. Yet importantly, several hg H subclades in Near East and Southern Caucasus region coalesce to the pre-LGM period. Furthermore, irrespective of their common origin, significant differences between the distribution of hg H sub-hgs in Europe and in the Near East and South Caucasus imply limited post-LGM maternal gene flow between these regions. In a contrast, the North Caucasus mitochondrial gene pool has received an influx of hg H variants, arriving from the Ponto-Caspian/East European area.
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Affiliation(s)
- U Roostalu
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia
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Ingman M, Gyllensten U. A recent genetic link between Sami and the Volga-Ural region of Russia. Eur J Hum Genet 2006; 15:115-20. [PMID: 16985502 DOI: 10.1038/sj.ejhg.5201712] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The genetic origin of the Sami is enigmatic and contributions from Continental Europe, Eastern Europe and Asia have been proposed. To address the evolutionary history of northern and southern Swedish Sami, we have studied their mtDNA haplogroup frequencies and complete mtDNA genome sequences. While the majority of mtDNA diversity in the northern Swedish, Norwegian and Finnish Sami is accounted for by haplogroups V and U5b1b1, the southern Swedish Sami have other haplogroups and a frequency distribution similar to that of the Continental European population. Stratification of the southern Sami on the basis of occupation indicates that this is the result of recent admixture with the Swedish population. The divergence time for the Sami haplogroup V sequences is 7600 YBP (years before present), and for U5b1b1, 5500 YBP amongst Sami and 6600 YBP amongst Sami and Finns. This suggests an arrival in the region soon after the retreat of the glacial ice, either by way of Continental Europe and/or the Volga-Ural region. Haplogroup Z is found at low frequency in the Sami and Northern Asian populations but is virtually absent in Europe. Several conserved substitutions group the Sami Z lineages strongly with those from Finland and the Volga-Ural region of Russia, but distinguish them from Northeast Asian representatives. This suggests that some Sami lineages shared a common ancestor with lineages from the Volga-Ural region as recently as 2700 years ago, indicative of a more recent contribution of people from the Volga-Ural region to the Sami population.
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Affiliation(s)
- Max Ingman
- Department of Genetics and Pathology, Rudbeck Laboratory, University of Uppsala, Uppsala, Sweden
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Lappalainen T, Koivumäki S, Salmela E, Huoponen K, Sistonen P, Savontaus ML, Lahermo P. Regional differences among the Finns: A Y-chromosomal perspective. Gene 2006; 376:207-15. [PMID: 16644145 DOI: 10.1016/j.gene.2006.03.004] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2005] [Revised: 03/10/2006] [Accepted: 03/12/2006] [Indexed: 11/20/2022]
Abstract
Twenty-two Y-chromosomal markers, consisting of fourteen biallelic markers (YAP/DYS287, M170, M253, P37, M223, 12f2, M9, P43, Tat, 92R7, P36, SRY-1532, M17, P25) and eight STRs (DYS19, DYS385a/b, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393), were analyzed in 536 unrelated Finnish males from eastern and western subpopulations of Finland. The aim of the study was to analyze regional differences in genetic variation within the country, and to analyze the population history of the Finns. Our results gave further support to the existence of a sharp genetic border between eastern and western Finns so far observed exclusively in Y-chromosomal variation. Both biallelic haplogroup and STR haplotype networks showed bifurcated structures, and similar clustering was evident in haplogroup and haplotype frequencies and genetic distances. These results suggest that the western and eastern parts of the country have been subject to partly different population histories, which is also supported by earlier archaeological, historical and genetic data. It seems probable that early migrations from Finno-Ugric sources affected the whole country, whereas subsequent migrations from Scandinavia had an impact mainly on the western parts of the country. The contacts between Finland and neighboring Finno-Ugric, Scandinavian and Baltic regions are evident. However, there is no support for recent migrations from Siberia and Central Europe. Our results emphasize the importance of incorporating Y-chromosomal data to reveal the population substructure which is often left undetected in mitochondrial DNA variation. Early assumptions of the homogeneity of the isolated Finnish population have now proven to be false, which may also have implications for future association studies.
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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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50
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Warner JB, Bruin EJ, Hannig H, Hellenkamp F, Hörning A, Mittmann K, van der Steege G, de Leij LFMH, Garritsen HSP. Use of sequence variation in three highly variable regions of the mitochondrial DNA for the discrimination of allogeneic platelets. Transfusion 2006; 46:554-61. [PMID: 16584431 DOI: 10.1111/j.1537-2995.2006.00775.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Human mitochondrial DNA (mtDNA) polymorphisms can be used to detect allogeneic transfused platelets. To increase the number of informative polymorphisms we investigated three hypervariable regions (HVR1, HVR2, and HVR3) within the displacement loop (D-loop) region of the mtDNA. STUDY DESIGN AND METHODS mtDNA was obtained from 119 unrelated blood donors. Forward and reverse primers were designed and conditions optimized to amplify and sequence the template mtDNA by dye terminator cycle sequencing. RESULTS We established a sequencing protocol for all three HVRs of the mtDNA. Polymorphic sites were found in all three regions: 66 in HVR1, 44 in HVR2, and 18 in HVR3. Combining the sequence information of HVR1, -2, and -3 resulted in 105 different genotypes of which 95 were unique. We were able to discriminate between two randomly chosen individuals with a random match probability of 1.2 percent. CONCLUSION The D-loop region of mtDNA contains a wealth of informative molecular markers for chimerism and survival studies after transfusions of cellular blood components.
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Affiliation(s)
- Jessica B Warner
- Medical Biology Division, University of Groningen, the Netherlands
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