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Fan H, Xu Y, Zhao Y, Feng K, Hong L, Zhao Q, Lu X, Shi M, Li H, Wang L, Wen S. Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis. Forensic Sci Int Genet 2024; 71:103029. [PMID: 38518712 DOI: 10.1016/j.fsigen.2024.103029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 02/12/2024] [Accepted: 03/03/2024] [Indexed: 03/24/2024]
Abstract
Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.
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Affiliation(s)
- Haoliang Fan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China.
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China.
| | - Yutao Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Kai Feng
- Duanzhou Branch of Zhaoqing Public Security Bureau, Zhaoqing 526060, China.
| | - Liuxi Hong
- Sihui Public Security Bureau of Guangdong Province, Zhaoqing 526299, China.
| | - Qiancheng Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Xiaoyu Lu
- Deepreads Biotech Company Limited, Guangzhou 510663, China.
| | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing 100088, China.
| | - Haiyan Li
- Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou 510050, China.
| | - Lingxiang Wang
- MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
| | - Shaoqing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Institute of Archaeological Science, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
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Dmytrzak A, Lewandowska K, Boroń A, Łoniewska B, Grzesch N, Brodkiewicz A, Clark JSC, Ciechanowicz A, Kostrzewa-Nowak D. No Association of Polymorphisms in the Genes Encoding Interleukin-6 and Interleukin-6 Receptor Subunit Alpha with the Risk of Keloids in Polish Patients. Int J Mol Sci 2024; 25:5284. [PMID: 38791322 PMCID: PMC11121548 DOI: 10.3390/ijms25105284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
A keloid is a benign fibroproliferative hypertrophy of scar tissue that extends outside the original wound and invades adjacent healthy skin. Keloid formation is thought to be a complex process including overactivity of the interleukin-6 signaling pathway and genetic susceptibility. The aim of the study was to investigate possible associations between rs1800797, rs1800796, and rs1800795 polymorphisms in the promoter of the IL6 gene encoding interleukin-6 and the rs2228145 polymorphism in the IL6R gene encoding the interleukin-6 receptor subunit alpha with the predisposition to keloids in Polish patients. The genetic polymorphisms were identified either using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) or sequencing of samples of genomic DNA extracted from blood leukocytes of 86 adult patients with keloids and 100 newborns comprising a control group. No significant differences in the distributions of IL6 or IL6R alleles or genotypes were found between keloid patients and newborn controls. There were also no significant differences between both groups in the distribution of IL6 haplotypes. The IL6 rs1800797, rs1800796 and rs1800795 and IL6R rs2228145 polymorphisms were not found to predispose individuals in the study group to keloids. IL6 promoter haplotypes were not found to be associated with a higher risk of keloids in the studied group.
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Affiliation(s)
| | - Klaudyna Lewandowska
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.L.); (A.B.); (N.G.); (J.S.C.C.); (A.C.)
| | - Agnieszka Boroń
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.L.); (A.B.); (N.G.); (J.S.C.C.); (A.C.)
| | - Beata Łoniewska
- Department of Neonatal Diseases, Pomeranian Medical University, 70-111 Szczecin, Poland;
| | - Natalie Grzesch
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.L.); (A.B.); (N.G.); (J.S.C.C.); (A.C.)
| | - Andrzej Brodkiewicz
- Department of Pediatrics, Child Nephrology, Dialysotherapy and Management of Acute Poisoning, Pomeranian Medical University, 70-780 Szczecin, Poland;
| | - Jeremy S. C. Clark
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.L.); (A.B.); (N.G.); (J.S.C.C.); (A.C.)
| | - Andrzej Ciechanowicz
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.L.); (A.B.); (N.G.); (J.S.C.C.); (A.C.)
| | - Dorota Kostrzewa-Nowak
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-111 Szczecin, Poland; (K.L.); (A.B.); (N.G.); (J.S.C.C.); (A.C.)
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Milona M, Ciechanowicz A, Węsierska K, Gońda-Domin M, Zawiślak A, Jarząbek A, Sobalska-Kwapis M, Jarczak J, Gruszka R, Strapagiel D, Janiszewska-Olszowska J, Grocholewicz K. Association of Three Genetic Loci with Molar Incisor Hypomineralization in Polish Children. J Clin Med 2024; 13:857. [PMID: 38337551 PMCID: PMC10856562 DOI: 10.3390/jcm13030857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Molar incisor hypomineralization (MIH) is a qualitative, demarcated enamel defect of hypomineralization affecting one to four first permanent molars, often with incisor involvement. Its etiology is complex. However, evidence suggests the influence of genetic factors, potentially including the single nucleotide polymorphisms (SNPs) rs2889956, rs4811117 and rs13058467, which were previously linked to MIH in a genome-wide association study of German children. The aim was to replicate analyses of possible associations between the SNPs and molar incisor hypomineralization in Polish children. METHODS The final study group consisted of 778 children aged 126-168 months old. Saliva samples were taken, and genomic DNA was extracted and genotyped using beadchip microarrays. RESULTS Among the 778 subjects, there were 68 (8.7%) subjects with MIH and 710 (91.3%) subjects without MIH. There were no significant differences in distributions in age, sex, or the frequency of caries in permanent dentition between the MIH and non-MIH groups. The rs2889956, rs4811117, and rs13058467 genotype distributions in the studied group conformed to the expected Hardy-Weinberg equilibria, and there were no significant differences in the distributions of their alleles or genotypes between the MIH and non-MIH groups. CONCLUSION Our replication study did not confirm highly significant associations between the single nucleotide polymorphisms rs2889956, rs4811117, and rs13058467 with molar incisor hypomineralization in Polish children.
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Affiliation(s)
- Marta Milona
- Department of Hygiene and Epidemiology, Pomeranian Medical University, 70-111 Szczecin, Poland;
| | - Andrzej Ciechanowicz
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-111 Szczecin, Poland
| | | | | | - Alicja Zawiślak
- Department of Interdisciplinary Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland; (A.Z.); (J.J.-O.); (K.G.)
| | - Anna Jarząbek
- Laboratory of Paediatric Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland;
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland; (M.S.-K.); (D.S.)
| | - Justyna Jarczak
- Regenerative Medicine Laboratory, Medical University of Warsaw, 02-097 Warszawa, Poland;
| | - Renata Gruszka
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland;
| | - Dominik Strapagiel
- Biobank Lab, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland; (M.S.-K.); (D.S.)
| | - Joanna Janiszewska-Olszowska
- Department of Interdisciplinary Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland; (A.Z.); (J.J.-O.); (K.G.)
| | - Katarzyna Grocholewicz
- Department of Interdisciplinary Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland; (A.Z.); (J.J.-O.); (K.G.)
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Mut P, Bertoni B, Sapiro R, Hidalgo PC, Torres A, Azambuja C, Sans M. Insights into the Y chromosome human diversity in Uruguay. Am J Hum Biol 2023; 35:e23963. [PMID: 37493343 DOI: 10.1002/ajhb.23963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/26/2023] [Accepted: 07/04/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND With regard to the origin of its population and microevolutionary processes, Uruguay exhibits distinctive features that distinguish it from other countries in Latin America, while at the same time sharing several similarities. In this article, we will focus on the variability of paternal genetic lineages in two geographical regions with different histories that can be considered as examples of distinct populations for the continent. In general terms, the genetic diversity is a result of different demographic processes related to the American conquest and colonisation. These resulted in distinct ancestral components which vary geographical and depend on the distribution by sex within these components. In Uruguay, native maternal haplogroups are significantly more frequent in the North. Although there are several studies about the geneticvariability of Uruguay, little is known about male genetic lineages. AIMS The aim of this work is to present an updated study of the male genetic variability of the Uruguayan population. METHODS We analyzed 13 biallelic markers and 27 STRs located in the male-specific region of the Y chromosome for 157 males: 98 from the capital, Montevideo, and 59 from Tacuarembó. RESULTS Almost all haplogroups found in both locations are European (99% and 93.2% respectively). One Sub-Saharan African haplogroup was found in Montevideo (1%) and 2 in Tacuarembó (3%), while Native haplogroups were found only in Tacuarembó, evidencing a strong sex-biased admixture. By crossing genetic and genealogical information we could relate European haplogroups with different waves and times of migrations. DISCUSSION Network analysis indicated a very diverse male population, suggesting that European migrants came from heterogeneous geographic locations and in different waves. Tacuarembó has closer population affinities with Iberian populations while Montevideo is more diverse. Male population expansion expansion, can be explained by the large number of migrants that arrived during the XIX century and the first half of the XX century. CONCLUSIONS The Uruguayan male gene pool is the result of several migration waves with diverse origins, with strong sex-biased admixture that can be explained by the European migration, the violence against the indigenous males, and the segregation of the Africansadmixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation of hte Africans.
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Affiliation(s)
- Patricia Mut
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, UdelaR, Montevideo, Uruguay
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - Rossana Sapiro
- Departamento de Histología y Embriología, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - Pedro C Hidalgo
- Polo de Desarrollo Universitario Diversidad Genética Humana, Centro Universitario Noreste, Tacuarembó, Uruguay
| | | | | | - Mónica Sans
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, UdelaR, Montevideo, Uruguay
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Gorący I, Łoniewska B, Lewandowska K, Boroń A, Grzegorczyk M, Nowak R, Clark JSC, Ciechanowicz A. Association of the rs3039851 Insertion/Deletion in the Gene PPP3R1, Which Encodes the Regulatory Calcineurin Subunit B Type 1, with Left Ventricular Mass in Polish Full-Term Newborns. Biomedicines 2023; 11:biomedicines11051415. [PMID: 37239086 DOI: 10.3390/biomedicines11051415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/02/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND The five base-pair (bp) insertion/deletion (rs3039851) polymorphism in the PPP3R1 gene, which encodes calcineurin subunit B type 1, has been found to be associated with left ventricular hypertrophy (LVH) in hypertensive patients and in athletes. The aim of this study is to analyze the possible association between PPP3R1:rs3039851 polymorphism and left ventricular mass (LVM) in full-term healthy newborns. METHODS The study group consisted of 162 consecutive, full-term, healthy newborns. Two-dimensional M-mode echocardiography was used to assess LVM. The PPP3R1:rs3039851 polymorphism was identified by PCR-RFLP in genomic DNA extracted from cord blood leukocytes. RESULTS No significant differences were found between newborns homozygous for the reference allele (5I/5I, n = 135) and newborns carrying at least one 5D allele (n = 27) for LVM standardized for body mass, body length or body surface area (LVM/BM, LVM/BL or LVM/BSA, respectively). However, the frequency of PPP3R1:rs3039851 genotypes with a 5D allele (5I/5D + 5D/5D) among newborns with the largest LVM/BM or LVM/BSA (upper tertile) was statistically significantly higher compared with the prevalence in individuals with the lowest values of both indices (lower tertile). CONCLUSIONS Our results suggest that the PPP3R1:rs3039851 polymorphism may contribute to subtle variation in left ventricular mass at birth.
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Affiliation(s)
- Iwona Gorący
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Beata Łoniewska
- Department of Neonatal Diseases, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Klaudyna Lewandowska
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Agnieszka Boroń
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Małgorzata Grzegorczyk
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Robert Nowak
- Institute of Physical Culture Sciences, University of Szczecin, 71-650 Szczecin, Poland
- Department of Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Jeremy Simon C Clark
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Andrzej Ciechanowicz
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, 70-111 Szczecin, Poland
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Population Genetic Data of 30 Insertion-Deletion Markers in the Polish Population. Genes (Basel) 2022; 13:genes13101683. [PMID: 36292568 PMCID: PMC9601377 DOI: 10.3390/genes13101683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
(1) Background: Insertion-deletion (InDel) markers show the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) and are considered alternative markers in forensic genetics. (2) Methods: Allelic frequencies and corresponding forensic efficiency parameters of 30 autosomal polymorphic InDel loci included in the Investigator DIPplex kit (Qiagen) were obtained in a sample of 631 unrelated Polish individuals. Allelic frequency data were compared with those reported for selected populations (3) Results: All the loci conformed with Hardy-Weinberg equilibrium after applying a Bonferroni correction and no pair-wise significant linkage disequilibrium was detected. (4) Conclusions: DIPplex Kit differences were high among populations worldwide. The InDel markers are highly discriminating for human identification purposes in the Polish population.
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Contrasting maternal and paternal genetic histories among five ethnic groups from Khyber Pakhtunkhwa, Pakistan. Sci Rep 2022; 12:1027. [PMID: 35046511 PMCID: PMC8770644 DOI: 10.1038/s41598-022-05076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022] Open
Abstract
Northwest Pakistan has served as a point of entry to South Asia for different populations since ancient times. However, relatively little is known about the population genetic history of the people residing within this region. To better understand human dispersal in the region within the broader history of the subcontinent, we analyzed mtDNA diversity in 659 and Y-chromosome diversity in 678 individuals, respectively, from five ethnic groups (Gujars, Jadoons, Syeds, Tanolis and Yousafzais), from Swabi and Buner Districts, Khyber Pakhtunkhwa Province, Pakistan. The mtDNAs of all individuals were subject to control region sequencing and SNP genotyping, while Y-chromosomes were analyzed using 54 SNPs and 19 STR loci. The majority of the mtDNAs belonged to West Eurasian haplogroups, with the rest belonging to either South or East Asian lineages. Four of the five Pakistani populations (Gujars, Jadoons, Syeds, Yousafzais) possessed strong maternal genetic affinities with other Pakistani and Central Asian populations, whereas one (Tanolis) did not. Four haplogroups (R1a, R1b, O3, L) among the 11 Y-chromosome lineages observed among these five ethnic groups contributed substantially to their paternal genetic makeup. Gujars, Syeds and Yousafzais showed strong paternal genetic affinities with other Pakistani and Central Asian populations, whereas Jadoons and Tanolis had close affinities with Turkmen populations from Central Asia and ethnic groups from northeast India. We evaluate these genetic data in the context of historical and archeological evidence to test different hypotheses concerning their origins and biological relationships.
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A reference database of forensic autosomal and gonosomal STR markers in the Tigray population of Ethiopia. Forensic Sci Int Genet 2021; 56:102618. [PMID: 34735940 DOI: 10.1016/j.fsigen.2021.102618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/31/2021] [Accepted: 10/20/2021] [Indexed: 11/20/2022]
Abstract
Allele frequencies of 21 autosomal STR markers (AmpF/STR GlobalFiler) and haplotype frequencies of 27 Y- and 12 X-STR markers (AmpF/STR YFiler Plus and Investigator Argus X-12, respectively) were investigated in the Tigray population of Ethiopia, representing the main population group in the Tigray regional state of Ethiopia and neighboring Eritrea. For autosomal STR allele frequencies, the average random match probability in the Tigray sample was 2.1 × 10-27. The average locus by locus FST distance calculated comparing autosomal STR allele frequencies from Tigray and from a broad regional reference dataset currently available for the Horn of Africa was 0.003. The Tigray male sample displayed high Y-STR diversity, with complete individualization of haplotypes using the AmpF/STR YFiler Plus panel. Analysis of molecular variance did not detect significant heterogeneity between Y-STR haplotypes observed in the present study and those previously reported in the literature for other Tigray population samples from Ethiopia and Eritrea. Study of the X-STR landscape in Tigray evidenced several distinctive features including: the molecular characterization of a novel null allele at locus DXS10146 with frequency > 1%; allele dependency between loci within linkage groups I and III; significant differences in haplotype distribution compared to other Horn of Africa populations, that should be taken into account in kinship analysis. The collected data can be used as a reference STR database by local forensic genetics services and in genetic identification procedures of victims of human trafficking in the Mediterranean Sea, which frequently involve individuals originating from the Horn of Africa.
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Phylogeographic review of Y chromosome haplogroups in Europe. Int J Legal Med 2021; 135:1675-1684. [PMID: 34216266 DOI: 10.1007/s00414-021-02644-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
The Y chromosome has been widely explored for the study of human migrations. Due to its paternal inheritance, the Y chromosome polymorphisms are helpful tools for understanding the geographical distribution of populations all over the world and for inferring their origin, which is really useful in forensics. The remarkable historical context of Europe, with numerous migrations and invasions, has turned this continent into a melting pot. For this reason, it is interesting to study the Y chromosome variability and how it has contributed to improving our knowledge of the distribution and development of European male genetic pool as it is today. The analysis of Y lineages in Europe shows the predominance of four haplogroups, R1b-M269, I1-M253, I2-M438 and R1a-M420. However, other haplogroups have been identified which, although less frequent, provide significant evidence about the paternal origin of the populations. In addition, the study of the Y chromosome in Europe is a valuable tool for revealing the genetic trace of the different European colonizations, mainly in several American countries, where the European ancestry is mostly detected by the presence of the R1b-M269 haplogroup. Therefore, the objective of this review is to compile the studies of the Y chromosome haplogroups in current European populations, in order to provide an outline of these haplogroups which facilitate their use in forensic studies.
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Middle eastern genetic legacy in the paternal and maternal gene pools of Chuetas. Sci Rep 2020; 10:21428. [PMID: 33293675 PMCID: PMC7722846 DOI: 10.1038/s41598-020-78487-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 11/19/2020] [Indexed: 11/08/2022] Open
Abstract
Chuetas are a group of descendants of Majorcan Crypto-Jews (Balearic Islands, Spain) who were socially stigmatized and segregated by their Majorcan neighbours until recently; generating a community that, although after the seventeenth century no longer contained Judaic religious elements, maintained strong group cohesion, Jewishness consciousness, and endogamy. Collective memory fixed 15 surnames as a most important defining element of Chueta families. Previous studies demonstrated Chuetas were a differentiated population, with a considerable proportion of their original genetic make-up. Genetic data of Y-chromosome polymorphism and mtDNA control region showed, in Chuetas’ paternal lineages, high prevalence of haplogroups J2-M172 (33%) and J1-M267 (18%). In maternal lineages, the Chuetas hallmark is the presence of a new sub-branching of the rare haplogroup R0a2m as their modal haplogroup (21%). Genetic diversity in both Y-chromosome and mtDNA indicates the Chueta community has managed to avoid the expected heterogeneity decrease in their gene pool after centuries of isolation and inbreeding. Moreover, the composition of their uniparentally transmitted lineages demonstrates a remarkable signature of Middle Eastern ancestry—despite some degree of host admixture—confirming Chuetas have retained over the centuries a considerable degree of ancestral genetic signature along with the cultural memory of their Jewish origin.
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The Y Chromosome: A Complex Locus for Genetic Analyses of Complex Human Traits. Genes (Basel) 2020; 11:genes11111273. [PMID: 33137877 PMCID: PMC7693691 DOI: 10.3390/genes11111273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/19/2020] [Accepted: 10/26/2020] [Indexed: 12/29/2022] Open
Abstract
The Human Y chromosome (ChrY) has been demonstrated to be a powerful tool for phylogenetics, population genetics, genetic genealogy and forensics. However, the importance of ChrY genetic variation in relation to human complex traits is less clear. In this review, we summarise existing evidence about the inherent complexities of ChrY variation and their use in association studies of human complex traits. We present and discuss the specific particularities of ChrY genetic variation, including Y chromosomal haplogroups, that need to be considered in the design and interpretation of genetic epidemiological studies involving ChrY.
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Grochowalski Ł, Jarczak J, Urbanowicz M, Słomka M, Szargut M, Borówka P, Sobalska-Kwapis M, Marciniak B, Ossowski A, Lorkiewicz W, Strapagiel D. Y-Chromosome Genetic Analysis of Modern Polish Population. Front Genet 2020; 11:567309. [PMID: 33193657 PMCID: PMC7644898 DOI: 10.3389/fgene.2020.567309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/27/2020] [Indexed: 01/11/2023] Open
Abstract
The study presents a full analysis of the Y-chromosome variability of the modern male Polish population. It is the first study of the Polish population to be conducted with such a large set of data (2,705 individuals), which includes genetic information from inhabitants of all voivodeships, i.e., the first administrative level, in the country and the vast majority of its counties, i.e., the second level. In addition, the available data were divided into clusters corresponding to more natural geographic regions. Genetic analysis included the estimation of FST distances, the visualization with the use of multidimensional scaling plots and analysis of molecular variance. Y-chromosome binary haplogroups were classified and visualized with the use of interpolation maps. Results showed that the level of differentiation within Polish population is quite low, but some differences were indicated. It was confirmed that the Polish population is characterized by a high degree of homogeneity, with only slight genetic differences being observed at the regional level. The use of regional clustering as an alternative to counties and voivodeships provided a more detailed view of the genetic structure of the population. Those regional differences identified in the present study highlighted the need for additional division of the population by cultural and ethnic criteria in such studies rather than just by geographical or administrative regionalization.
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Affiliation(s)
- Łukasz Grochowalski
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Justyna Jarczak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Maria Urbanowicz
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Marcin Słomka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Maria Szargut
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland.,The Polish Genetic Database of Totalitarianism Victims, Szczecin, Poland
| | - Paulina Borówka
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Błażej Marciniak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Andrzej Ossowski
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland.,The Polish Genetic Database of Totalitarianism Victims, Szczecin, Poland
| | - Wiesław Lorkiewicz
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
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13
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Ralf A, Lubach D, Kousouri N, Winkler C, Schulz I, Roewer L, Purps J, Lessig R, Krajewski P, Ploski R, Dobosz T, Henke L, Henke J, Larmuseau MHD, Kayser M. Identification and characterization of novel rapidly mutating Y‐chromosomal short tandem repeat markers. Hum Mutat 2020; 41:1680-1696. [DOI: 10.1002/humu.24068] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/05/2020] [Accepted: 06/22/2020] [Indexed: 01/06/2023]
Affiliation(s)
- Arwin Ralf
- Department of Genetic Identification Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | - Delano Lubach
- Department of Genetic Identification Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | - Nefeli Kousouri
- Department of Genetic Identification Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
| | | | - Iris Schulz
- Institut für Blutgruppenforschung LGC GmbH Cologne Germany
| | - Lutz Roewer
- Abteilung für Forensische Genetik, Institut für Rechtsmedizin und Forensische Wissenschaften Charite ́‐Universitätsmedizin Berlin Berlin Germany
| | - Josephine Purps
- Abteilung für Forensische Genetik, Institut für Rechtsmedizin und Forensische Wissenschaften Charite ́‐Universitätsmedizin Berlin Berlin Germany
| | - Rüdiger Lessig
- Institut für Rechtsmedizin Universitätsklinikum Halle Halle/Saale Germany
| | - Pawel Krajewski
- Department of Medical Genetics and Department of Forensic Medicine Medical University Warsaw Warsaw Poland
| | - Rafal Ploski
- Department of Medical Genetics and Department of Forensic Medicine Medical University Warsaw Warsaw Poland
| | - Tadeusz Dobosz
- Department of Forensic Medicine Wroclaw Medical University Wroclaw Poland
| | - Lotte Henke
- Institut für Blutgruppenforschung LGC GmbH Cologne Germany
| | - Jürgen Henke
- Institut für Blutgruppenforschung LGC GmbH Cologne Germany
| | | | - Manfred Kayser
- Department of Genetic Identification Erasmus MC University Medical Center Rotterdam Rotterdam The Netherlands
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14
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Roewer L, Andersen MM, Ballantyne J, Butler JM, Caliebe A, Corach D, D'Amato ME, Gusmão L, Hou Y, de Knijff P, Parson W, Prinz M, Schneider PM, Taylor D, Vennemann M, Willuweit S. DNA commission of the International Society of Forensic Genetics (ISFG): Recommendations on the interpretation of Y-STR results in forensic analysis. Forensic Sci Int Genet 2020; 48:102308. [PMID: 32622324 DOI: 10.1016/j.fsigen.2020.102308] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 05/06/2020] [Indexed: 10/24/2022]
Abstract
Forensic genetic laboratories perform a large amount of STR analyses of the Y chromosome, in particular to analyze the male part of complex DNA mixtures. However, the statistical interpretation of evidence retrieved from Y-STR haplotypes is challenging. Due to the uni-parental inheritance mode, Y-STR loci are connected to each other and thus haplotypes show patterns of relationship on the familial and population level. This precludes the treatment of Y-STR loci as independently inherited variables and the application of the product rule. Instead, the dependency structure of Y-STRs needs to be included in the haplotype frequency estimation process affecting also the current paradigm of a random match probability that is in the autosomal case approximated by the population frequency assuming unrelatedness of sampled individuals. Information on the degree of paternal relatedness in the suspect population as well as on the familial network is however needed to interpret Y-chromosomal results in the best possible way. The previous recommendations of the DNA commission of the ISFG on the use of Y-STRs in forensic analysis published more than a decade ago [1] cover the interpretation issue only marginally. The current recommendations address a number of topics (frequency estimators, databases, metapopulations, LR formulation, triage, rapidly mutating Y-STRs) with relevance for the Y-STR statistics and recommend a decision-based procedure, which takes into account legal requirements as well as availability of population data and statistical methods.
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Affiliation(s)
- Lutz Roewer
- Institute of Legal Medicine and Forensic Sciences, Dept. Forensic Genetics, Charité - Universitätsmedizin Berlin, Germany.
| | - Mikkel Meyer Andersen
- Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark; Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Jack Ballantyne
- National Center for Forensic Science, University of Central Florida, Orlando, USA
| | - John M Butler
- National Institute of Standards and Technology, Special Programs Office, Gaithersburg, USA
| | - Amke Caliebe
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Daniel Corach
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Immunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Buenos Aires, Argentina; National Research Council, CONICET, Buenos Aires, Argentina
| | - Maria Eugenia D'Amato
- University of the Western Cape, Department of Biotechnology, Forensic DNA Lab, Cape Town, South Africa
| | - Leonor Gusmão
- State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil; IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Portugal; Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, China
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - Mechthild Prinz
- John Jay College of Criminal Justice, Dept. of Sciences, New York, USA
| | - Peter M Schneider
- Institute of Legal Medicine, Medical Faculty, University of Cologne, Cologne, Germany
| | - Duncan Taylor
- Forensic Science South Australia, Adelaide, Australia; Flinders University, Adelaide, Australia
| | | | - Sascha Willuweit
- Institute of Legal Medicine and Forensic Sciences, Dept. Forensic Genetics, Charité - Universitätsmedizin Berlin, Germany
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15
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Distinct genetic variation and heterogeneity of the Iranian population. PLoS Genet 2019; 15:e1008385. [PMID: 31550250 PMCID: PMC6759149 DOI: 10.1371/journal.pgen.1008385] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 08/27/2019] [Indexed: 02/07/2023] Open
Abstract
Iran, despite its size, geographic location and past cultural influence, has largely been a blind spot for human population genetic studies. With only sparse genetic information on the Iranian population available, we pursued its genome-wide and geographic characterization based on 1021 samples from eleven ethnic groups. We show that Iranians, while close to neighboring populations, present distinct genetic variation consistent with long-standing genetic continuity, harbor high heterogeneity and different levels of consanguinity, fall apart into a cluster of similar groups and several admixed ones and have experienced numerous language adoption events in the past. Our findings render Iran an important source for human genetic variation in Western and Central Asia, will guide adequate study sampling and assist the interpretation of putative disease-implicated genetic variation. Given Iran's internal genetic heterogeneity, future studies will have to consider ethnic affiliations and possible admixture.
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16
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The Dutch Y-chromosomal landscape. Eur J Hum Genet 2019; 28:287-299. [PMID: 31488894 PMCID: PMC7029002 DOI: 10.1038/s41431-019-0496-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/09/2019] [Accepted: 08/02/2019] [Indexed: 12/05/2022] Open
Abstract
Previous studies indicated existing, albeit limited, genetic-geographic population substructure in the Dutch population based on genome-wide data and a lack of this for mitochondrial SNP based data. Despite the aforementioned studies, Y-chromosomal SNP data from the Netherlands remain scarce and do not cover the territory of the Netherlands well enough to allow a reliable investigation of genetic-geographic population substructure. Here we provide the first substantial dataset of detailed spatial Y-chromosomal haplogroup information in 2085 males collected across the Netherlands and supplemented with previously published data from northern Belgium. We found Y-chromosomal evidence for genetic–geographic population substructure, and several Y-haplogroups demonstrating significant clinal frequency distributions in different directions. By means of prediction surface maps we could visualize (complex) distribution patterns of individual Y-haplogroups in detail. These results highlight the value of a micro-geographic approach and are of great use for forensic and epidemiological investigations and our understanding of the Dutch population history. Moreover, the previously noted absence of genetic-geographic population substructure in the Netherlands based on mitochondrial DNA in contrast to our Y-chromosome results, hints at different population histories for women and men in the Netherlands.
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17
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Jankova R, Seidel M, Videtič Paska A, Willuweit S, Roewer L. Y-chromosome diversity of the three major ethno-linguistic groups in the Republic of North Macedonia. Forensic Sci Int Genet 2019; 42:165-170. [PMID: 31351212 DOI: 10.1016/j.fsigen.2019.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/31/2019] [Accepted: 07/10/2019] [Indexed: 10/26/2022]
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18
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Bánfai Z, Melegh BI, Sümegi K, Hadzsiev K, Miseta A, Kásler M, Melegh B. Revealing the Genetic Impact of the Ottoman Occupation on Ethnic Groups of East-Central Europe and on the Roma Population of the Area. Front Genet 2019; 10:558. [PMID: 31263480 PMCID: PMC6585392 DOI: 10.3389/fgene.2019.00558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/28/2019] [Indexed: 12/03/2022] Open
Abstract
History of East-Central Europe has been intertwined with the history of Turks in the past. A significant part of this region of Europe has been fallen under Ottoman control during the 150 years of Ottoman occupation in the 16–17th centuries. The presence of the Ottoman Empire affected this area not only culturally but also demographically. The Romani people, the largest ethnic minority of the East-Central European area, share an even more eventful past with Turkish people from the time of their migration throughout Eurasia and they were a notable ethnic group in East-Central Europe in the Ottoman era already. The relationship of Turks with East-Central European ethnic groups and with regional Roma ethnicity was investigated based on genome-wide autosomal single nucleotide polymorphism data. Population structure analysis, ancestry estimation, various formal tests of admixture and DNA segment analyses were carried out in order to shed light to the conclusion of these events on a genome-wide basis. Analyses show that the Ottoman occupation of Europe left detectable impact in the affected East-Central European area and shaped the ancestry of the Romani people as well. We estimate that the investigated European populations have an average identity-by-descent share of 0.61 with Turks, which is notable, compared to other European populations living in West and North Europe far from the affected area, and compared to the share of Sardinians, living isolated from these events. Admixture of Roma and Turks during the Ottoman rule show also high extent.
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Affiliation(s)
- Zsolt Bánfai
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Béla I Melegh
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Katalin Sümegi
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Kinga Hadzsiev
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Attila Miseta
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
| | | | - Béla Melegh
- Department of Medical Genetics, Clinical Centre, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
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19
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Mitochondrial DNA variability of the Polish population. Eur J Hum Genet 2019; 27:1304-1314. [PMID: 30903113 PMCID: PMC6777467 DOI: 10.1038/s41431-019-0381-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 03/04/2019] [Accepted: 03/07/2019] [Indexed: 01/24/2023] Open
Abstract
The aim of the present study was to define the mtDNA variability of Polish population and to visualize the genetic relations between Poles. For the first time, the study of Polish population was conducted on such a large number of individuals (5852) representing administrative units of both levels of local administration in Poland (voivodeships and counties). Additionally, clustering was used as a method of population subdivision. Performed genetic analysis, included FST, MDS plot, AMOVA and SAMOVA. Haplogroups were classified and their geographical distribution was visualized using surface interpolation maps. Results of the present study showed that Poles are characterized by the main West Eurasian mtDNA haplogroups. Furthermore, the level of differentiation within the Polish population was quite low but the existing genetic differences could be explained well with geographic distances. This may lead to a conclusion that Poles can be considered as genetically homogenous but with slight differences, highlighted at the regional level. Some patterns of variability were observed and could be explained by the history of demographic processes in Poland such as resettlements and migrations of women or relatively weaker urbanisation and higher rural population retention of some regions.
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20
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Diepenbroek M, Cytacka S, Szargut M, Arciszewska J, Zielińska G, Ossowski A. Analysis of male specific region of the human Y chromosome sheds light on historical events in Nazi occupied eastern Poland. Int J Legal Med 2018; 133:395-409. [PMID: 30327924 PMCID: PMC6373375 DOI: 10.1007/s00414-018-1943-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 10/10/2018] [Indexed: 11/25/2022]
Abstract
In Poland, during the World War II, almost 3 million people were killed during the Nazi occupation, and about 570,000 during the Soviet occupation. Furthermore, historians have estimated that after the World War II at least 30,000 people were killed during the Stalinist regime in Poland (1944–1956). The exact number is unknown, because both executions and burials were kept secret. Thousands of people just vanished. As a response to those events, forensic scientists from the Pomeranian Medical University in Szczecin in cooperation with historians from the Institute of National Remembrance started the project of the Polish Genetic Database of Victims of Totalitarianism, which aim is to identify victims killed in the years 1939–1956. Several exhumations were done under the project, with the biggest one done in Białystok. According to the information gathered by local historians, a detention centre in Białystok was the place of the secret burials in late 1940s and 1950s. Surprisingly, except few graves from the post-war period, most of the burials found in Białystok indicated that majority the victims were probably local civilians who died during the Nazi occupation. Unfortunately, data concerning what happened in the detention ward during that period of time is not very detailed. What was known is that people who got incarcerated were “political prisoners” what, according to Nazi politics, was based on their nationality, religion and activity against the Third Reich. The aim of this research was to test genetically the remains found in Białystok to determine their possible ethnic background, in order to shed new light on the victims and what happened in the Białystok detention centre during the Nazi occupation. The analysis of male specific region of the human Y chromosome shows that including phylogenetic analysis into the complex process led by the Polish Genetic Database of Victims of Totalitarianism may help with the final identification of hundreds of anonymous victims.
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Affiliation(s)
- Marta Diepenbroek
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich Street 72, Szczecin, Poland.
| | - Sandra Cytacka
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich Street 72, Szczecin, Poland
| | - Maria Szargut
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich Street 72, Szczecin, Poland
| | - Joanna Arciszewska
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich Street 72, Szczecin, Poland
| | - Grażyna Zielińska
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich Street 72, Szczecin, Poland
| | - Andrzej Ossowski
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Powstańców Wielkopolskich Street 72, Szczecin, Poland
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21
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A glance of genetic relations in the Balkan populations utilizing network analysis based on in silico assigned Y-DNA haplogroups. ANTHROPOLOGICAL REVIEW 2018. [DOI: 10.2478/anre-2018-0021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study is to provide an insight into Balkan populations’ genetic relations utilizing in silico analysis of Y-STR haplotypes and performing haplogroup predictions together with network analysis of the same haplotypes for visualization of the relations between chosen haplotypes and Balkan populations in general. The population dataset used in this study was obtained using 23, 17, 12, 9 and 7 Y-STR loci for 13 populations. The 13 populations include: Bosnia and Herzegovina (B&H), Croatia, Macedonia, Slovenia, Greece, Romany (Hungary), Hungary, Serbia, Montenegro, Albania, Kosovo, Romania and Bulgaria. The overall dataset contains a total of 2179 samples with 1878 different haplotypes.
I2a was detected as the major haplogroup in four out of thirteen analysed Balkan populations. The four populations (B&H, Croatia, Montenegro and Serbia) which had I2a as the most prevalent haplogroup were all from the former Yugoslavian republic. The remaining two major populations from former Yugoslavia, Macedonia and Slovenia, had E1b1b and R1a haplogroups as the most prevalent, respectively.
The populations with E1b1b haplogroup as the most prevalent one are Macedonian, Romanian, as well as Albanian populations from Kosovo and Albania. The I2a haplogroup cluster is more compact when compared to E1b1b and R1b haplogroup clusters, indicating a larger degree of homogeneity within the haplotypes that belong to the I2a haplogroup. Our study demonstrates that a combination of haplogroup prediction and network analysis represents an effective approach to utilize publicly available Y-STR datasets for population genetics.
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22
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Nothnagel M, Fan G, Guo F, He Y, Hou Y, Hu S, Huang J, Jiang X, Kim W, Kim K, Li C, Li H, Li L, Li S, Li Z, Liang W, Liu C, Lu D, Luo H, Nie S, Shi M, Sun H, Tang J, Wang L, Wang CC, Wang D, Wen SQ, Wu H, Wu W, Xing J, Yan J, Yan S, Yao H, Ye Y, Yun L, Zeng Z, Zha L, Zhang S, Zheng X, Willuweit S, Roewer L. Revisiting the male genetic landscape of China: a multi-center study of almost 38,000 Y-STR haplotypes. Hum Genet 2017; 136:485-497. [PMID: 28138773 DOI: 10.1007/s00439-017-1759-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/13/2017] [Indexed: 02/05/2023]
Abstract
China has repeatedly been the subject of genetic studies to elucidate its prehistoric and historic demography. While some studies reported a genetic distinction between Northern and Southern Han Chinese, others showed a more clinal picture of small differences within China. Here, we investigated the distribution of Y chromosome variation along administrative as well as ethnic divisions in the mainland territory of the People's Republic of China, including 28 administrative regions and 19 recognized Chinese nationalities, to assess the impact of recent demographic processes. To this end, we analyzed 37,994 Y chromosomal 17-marker haplotype profiles from the YHRD database with respect to forensic diversity measures and genetic distance between groups defined by administrative boundaries and ethnic origin. We observed high diversity throughout all Chinese provinces and ethnicities. Some ethnicities, including most prominently Kazakhs and Tibetans, showed significant genetic differentiation from the Han and other groups. However, differences between provinces were, except for those located on the Tibetan plateau, less pronounced. This discrepancy is explicable by the sizeable presence of Han speakers, who showed high genetic homogeneity all across China, in nearly all studied provinces. Furthermore, we observed a continuous genetic North-South gradient in the Han, confirming previous reports of a clinal distribution of Y chromosome variation and being in notable concordance with the previously observed spatial distribution of autosomal variation. Our findings shed light on the demographic changes in China accrued by a fast-growing and increasingly mobile population.
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Affiliation(s)
- Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931, Cologne, Germany.
| | - Guangyao Fan
- Department of Public Security Technology, The Center for Forensic Science Research, Railway Police College, Zhengzhou, 450053, People's Republic of China
| | - Fei Guo
- Department of Forensic Medicine, National Police University of China, Shenyang, 110854, People's Republic of China
| | - Yongfeng He
- Department of Criminal Investigation, Shaanxi Provincial Public Security Bureau, Xi'an, 710016, People's Republic of China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Shengping Hu
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, People's Republic of China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Beijing Road, 9th, Guiyang, 550004, People's Republic of China
| | - Xianhua Jiang
- Liaoning Criminal and Science Technology Research Institute, Shenyang, 110032, People's Republic of China
| | - Wook Kim
- Department of Biological Sciences, Dankook University, Cheonan, 330-714, Republic of Korea
| | - Kicheol Kim
- Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, People's Republic of China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Liming Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Shilin Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Zhao Li
- Department of Criminal Investigation, Hebei Provincial Public Security Bureau, Shijiazhuang City, 050000, People's Republic of China
| | - Weibo Liang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Chao Liu
- Guangzhou Forensic Science Institute, Guangzhou, 510030, People's Republic of China
| | - Di Lu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, People's Republic of China
| | - Haibo Luo
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, People's Republic of China
| | - Meisen Shi
- Center of Cooperative Innovation for Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Ministry of Education, Beijing, 100088, People's Republic of China
| | - Hongyu Sun
- Department of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510089, People's Republic of China
| | - Jianpin Tang
- Department of Forensic Medicine, Guangdong Medical University, Dongguan, 523808, People's Republic of China
| | - Lei Wang
- Department of Forensic Sciences, Police Station of Zhengzhou, Zhengzhou, Henan, 450008, People's Republic of China
| | - Chuan-Chao Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Dan Wang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, People's Republic of China
| | - Shao-Qing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Hongyan Wu
- Xinxiang Medical University School of Basic Medical, Xinxiang, Henan, 453003, People's Republic of China
| | - Weiwei Wu
- Institute of Forensic Science, Zhejiang Provincial Public Security Bureau, Hangzhou, 310009, People's Republic of China
| | - Jiaxin Xing
- School of Forensic Medicine, China Medical University, Shenyang, People's Republic of China
| | - Jiangwei Yan
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Shi Yan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China
| | - Hongbing Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu Institute of Political Science and Law, Lanzhou, 730070, People's Republic of China
| | - Yi Ye
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Libing Yun
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Zhaoshu Zeng
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, People's Republic of China
| | - Lagabaiyila Zha
- Forensic Science Department, School of Basic Medical Sciences, Central South University, Changsha, 410013, People's Republic of China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, People's Republic of China
| | - Xiufen Zheng
- Department of Pathology, Department of Surgery, Department of Oncology, University of Western Ontario, Lawson Health Research Institute, London, Canada
| | - Sascha Willuweit
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Balanovsky O, Gurianov V, Zaporozhchenko V, Balaganskaya O, Urasin V, Zhabagin M, Grugni V, Canada R, Al-Zahery N, Raveane A, Wen SQ, Yan S, Wang X, Zalloua P, Marafi A, Koshel S, Semino O, Tyler-Smith C, Balanovska E. Phylogeography of human Y-chromosome haplogroup Q3-L275 from an academic/citizen science collaboration. BMC Evol Biol 2017; 17:18. [PMID: 28251872 PMCID: PMC5333174 DOI: 10.1186/s12862-016-0870-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background The Y-chromosome haplogroup Q has three major branches: Q1, Q2, and Q3. Q1 is found in both Asia and the Americas where it accounts for about 90% of indigenous Native American Y-chromosomes; Q2 is found in North and Central Asia; but little is known about the third branch, Q3, also named Q1b-L275. Here, we combined the efforts of population geneticists and genetic genealogists to use the potential of full Y-chromosome sequencing for reconstructing haplogroup Q3 phylogeography and suggest possible linkages to events in population history. Results We analyzed 47 fully sequenced Y-chromosomes and reconstructed the haplogroup Q3 phylogenetic tree in detail. Haplogroup Q3-L275, derived from the oldest known split within Eurasian/American haplogroup Q, most likely occurred in West or Central Asia in the Upper Paleolithic period. During the Mesolithic and Neolithic epochs, Q3 remained a minor component of the West Asian Y-chromosome pool and gave rise to five branches (Q3a to Q3e), which spread across West, Central and parts of South Asia. Around 3–4 millennia ago (Bronze Age), the Q3a branch underwent a rapid expansion, splitting into seven branches, some of which entered Europe. One of these branches, Q3a1, was acquired by a population ancestral to Ashkenazi Jews and grew within this population during the 1st millennium AD, reaching up to 5% in present day Ashkenazi. Conclusions This study dataset was generated by a massive Y-chromosome genotyping effort in the genetic genealogy community, and phylogeographic patterns were revealed by a collaboration of population geneticists and genetic genealogists. This positive experience of collaboration between academic and citizen science provides a model for further joint projects. Merging data and skills of academic and citizen science promises to combine, respectively, quality and quantity, generalization and specialization, and achieve a well-balanced and careful interpretation of the paternal-side history of human populations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0870-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oleg Balanovsky
- Vavilov Institute of General Genetics, Moscow, Russia. .,Research Centre for Medical Genetics, Moscow, Russia.
| | | | - Valery Zaporozhchenko
- Vavilov Institute of General Genetics, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia
| | | | | | - Maxat Zhabagin
- National Laboratory Astana, Nazarbayev University, Astana, Republic of Kazakhstan
| | - Viola Grugni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | | | - Nadia Al-Zahery
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Shao-Qing Wen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shi Yan
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xianpin Wang
- Department of Criminal Investigation, Xuanwei Public Security Bureau, Xuanwei, China
| | | | | | - Sergey Koshel
- Faculty of Geography, Lomonosov Moscow State University, Moscow, Russia
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elena Balanovska
- Vavilov Institute of General Genetics, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia
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Molecular Genealogy of a Mongol Queen's Family and Her Possible Kinship with Genghis Khan. PLoS One 2016; 11:e0161622. [PMID: 27627454 PMCID: PMC5023095 DOI: 10.1371/journal.pone.0161622] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 07/12/2016] [Indexed: 11/28/2022] Open
Abstract
Members of the Mongol imperial family (designated the Golden family) are buried in a secret necropolis; therefore, none of their burial grounds have been found. In 2004, we first discovered 5 graves belonging to the Golden family in Tavan Tolgoi, Eastern Mongolia. To define the genealogy of the 5 bodies and the kinship among them, SNP and/or STR profiles of mitochondria, autosomes, and Y chromosomes were analyzed. Four of the 5 bodies were determined to carry the mitochondrial DNA haplogroup D4, while the fifth carried haplogroup CZ, indicating that this individual had no kinship with the others. Meanwhile, Y-SNP and Y-STR profiles indicate that the males examined belonged to the R1b-M343 haplogroup. Thus, their East Asian D4 or CZ matrilineal and West Eurasian R1b-M343 patrilineal origins reveal genealogical admixture between Caucasoid and Mongoloid ethnic groups, despite a Mongoloid physical appearance. In addition, Y chromosomal and autosomal STR profiles revealed that the four D4-carrying bodies bore the relationship of either mother and three sons or four full siblings with almost the same probability. Moreover, the geographical distribution of R1b-M343-carrying modern-day individuals demonstrates that descendants of Tavan Tolgoi bodies today live mainly in Western Eurasia, with a high frequency in the territories of the past Mongol khanates. Here, we propose that Genghis Khan and his family carried Y-haplogroup R1b-M343, which is prevalent in West Eurasia, rather than the Y-haplogroup C3c-M48, which is prevalent in Asia and which is widely accepted to be present in the family members of Genghis Khan. Additionally, Tavan Tolgoi bodies may have been the product of marriages between the lineage of Genghis Khan’s Borjigin clan and the lineage of either the Ongud or Hongirad clans, indicating that these individuals were members of Genghis Khan’s immediate family or his close relatives.
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Schregel J, Eiken HG, Grøndahl FA, Hailer F, Aspi J, Kojola I, Tirronen K, Danilov P, Rykov A, Poroshin E, Janke A, Swenson JE, Hagen SB. Y chromosome haplotype distribution of brown bears (Ursus arctos
) in Northern Europe provides insight into population history and recovery. Mol Ecol 2015; 24:6041-60. [DOI: 10.1111/mec.13448] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 10/17/2015] [Accepted: 10/26/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Julia Schregel
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; 1432 Ås Norway
| | - Hans Geir Eiken
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
| | | | - Frank Hailer
- School of Biosciences; Cardiff University; Cardiff CF10 3AX Wales UK
- Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt am Main Germany
| | - Jouni Aspi
- Department of Genetics and Physiology; University of Oulu; P.O. Box 3000 90014 Oulu Finland
| | - Ilpo Kojola
- Natural Resources Institute; P.O. Box 16 96301 Rovaniemi Finland
| | - Konstantin Tirronen
- Institute of Biology; Karelian Research Centre of the Russian Academy of Science; 185910 Petrozavodsk Russian Federation
| | - Piotr Danilov
- Institute of Biology; Karelian Research Centre of the Russian Academy of Science; 185910 Petrozavodsk Russian Federation
| | - Alexander Rykov
- Pinezhsky Strict Nature Reserve; Pervomayskaja 123a 164610 Pinega Russian Federation
| | - Eugene Poroshin
- Institute of Biology; Komi Research Centre of the Russian Academy of Science; 016761 Syktvkar Russian Federation
| | - Axel Janke
- Biodiversity and Climate Research Centre (BiK-F); Senckenberg Gesellschaft für Naturforschung; Senckenberganlage 25 60325 Frankfurt am Main Germany
- Goethe University Frankfurt; Institute for Ecology; Evolution & Diversity; 60438 Frankfurt am Main Germany
| | - Jon E. Swenson
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; 1432 Ås Norway
- Norwegian Institute for Nature Research; 7485 Trondheim Norway
| | - Snorre B. Hagen
- Norwegian Institute of Bioeconomy Research; NIBIO - Svanhovd; 9925 Svanvik Norway
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Genetic Heritage of the Balto-Slavic Speaking Populations: A Synthesis of Autosomal, Mitochondrial and Y-Chromosomal Data. PLoS One 2015; 10:e0135820. [PMID: 26332464 PMCID: PMC4558026 DOI: 10.1371/journal.pone.0135820] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/27/2015] [Indexed: 11/20/2022] Open
Abstract
The Slavic branch of the Balto-Slavic sub-family of Indo-European languages underwent rapid divergence as a result of the spatial expansion of its speakers from Central-East Europe, in early medieval times. This expansion–mainly to East Europe and the northern Balkans–resulted in the incorporation of genetic components from numerous autochthonous populations into the Slavic gene pools. Here, we characterize genetic variation in all extant ethnic groups speaking Balto-Slavic languages by analyzing mitochondrial DNA (n = 6,876), Y-chromosomes (n = 6,079) and genome-wide SNP profiles (n = 296), within the context of other European populations. We also reassess the phylogeny of Slavic languages within the Balto-Slavic branch of Indo-European. We find that genetic distances among Balto-Slavic populations, based on autosomal and Y-chromosomal loci, show a high correlation (0.9) both with each other and with geography, but a slightly lower correlation (0.7) with mitochondrial DNA and linguistic affiliation. The data suggest that genetic diversity of the present-day Slavs was predominantly shaped in situ, and we detect two different substrata: ‘central-east European’ for West and East Slavs, and ‘south-east European’ for South Slavs. A pattern of distribution of segments identical by descent between groups of East-West and South Slavs suggests shared ancestry or a modest gene flow between those two groups, which might derive from the historic spread of Slavic people.
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Willuweit S, Roewer L. The new Y Chromosome Haplotype Reference Database. Forensic Sci Int Genet 2015; 15:43-8. [DOI: 10.1016/j.fsigen.2014.11.024] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 11/21/2014] [Accepted: 11/26/2014] [Indexed: 11/25/2022]
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Rothe J, Melisch C, Powers N, Geppert M, Zander J, Purps J, Spors B, Nagy M. Genetic research at a fivefold children's burial from medieval Berlin. Forensic Sci Int Genet 2015; 15:90-7. [DOI: 10.1016/j.fsigen.2014.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/20/2014] [Accepted: 10/24/2014] [Indexed: 10/24/2022]
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Messina F, Finocchio A, Rolfo MF, De Angelis F, Rapone C, Coletta M, Martínez-Labarga C, Biondi G, Berti A, Rickards O. Traces of forgotten historical events in mountain communities in Central Italy: A genetic insight. Am J Hum Biol 2015; 27:508-19. [PMID: 25728801 DOI: 10.1002/ajhb.22677] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 11/20/2014] [Accepted: 12/20/2014] [Indexed: 01/16/2023] Open
Abstract
OBJECTIVES Analysis of human genetic variation in mountain communities can shed light on the peopling of mountainous regions, perhaps revealing whether the remote geographic location spared them from outside invasion and preserved their gene pool from admixture. In this study, we created a model to assess genetic traces of historical events by reconstructing the paternal and maternal genetic history of seven small mountain villages in inland valleys of Central Italy. METHODS The communities were selected for their geographic isolation, attested biodemographic stability, and documented history prior to the Roman conquest. We studied the genetic structure by analyzing two hypervariable segments (HVS-I and HVS-II) of the mtDNA D-loop and several informative single nucleotide polymorphisms (SNPs) of the mtDNA coding region in 346 individuals, in addition to 17 short tandem repeats (STRs) and Y-chromosome SNPs in 237 male individuals. RESULTS For both uniparental markers, most of the haplogroups originated in Western Europe while some Near Eastern haplogroups were identified at low frequencies. However, there was an evident genetic similarity between the Central Italian samples and Near Eastern populations mainly in the male genetic pool. CONCLUSIONS The samples highlight an overall European genetic pattern both for mtDNA and Y chromosome. Notwithstanding this scenario, Y chromosome haplogroup Q, a common paternal lineage in Central/Western Asia but almost Europe-wide absent, was found, suggesting that Central Italy could have hosted a settlement from Anatolia that might be supported by cultural, topographic and genetic evidence.
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Affiliation(s)
- Francesco Messina
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Andrea Finocchio
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Mario Federico Rolfo
- Department of Historical, Philosophical and Social Sciences, Cultural and Territory Heritage, University of Rome 'Tor Vergata', Via Columbia n. 1, 00173, Rome, Italy
| | - Flavio De Angelis
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Cesare Rapone
- Carabinieri, Scientific Investigation Department, Viale di Tor di Quinto 151, 00191, Rome, Italy
| | - Martina Coletta
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Cristina Martínez-Labarga
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
| | - Gianfranco Biondi
- Department of Environmental Sciences, University of L'Aquila, Via Vetoio, 67010, L'Aquila, Italy
| | - Andrea Berti
- Carabinieri, Scientific Investigation Department, Viale di Tor di Quinto 151, 00191, Rome, Italy
| | - Olga Rickards
- Department of Biology, Center of Molecular Anthropology for ancient DNA study, University of Rome 'Tor Vergata', Via della Ricerca Scientifica n. 1, 00133, Rome, Italy
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Cárdenas JM, Heinz T, Pardo-Seco J, Álvarez-Iglesias V, Taboada-Echalar P, Sánchez-Diz P, Carracedo Á, Salas A. The multiethnic ancestry of Bolivians as revealed by the analysis of Y-chromosome markers. Forensic Sci Int Genet 2015; 14:210-8. [DOI: 10.1016/j.fsigen.2014.10.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/20/2014] [Accepted: 10/27/2014] [Indexed: 10/24/2022]
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Davidovic S, Malyarchuk B, Aleksic JM, Derenko M, Topalovic V, Litvinov A, Stevanovic M, Kovacevic-Grujicic N. Mitochondrial DNA perspective of Serbian genetic diversity. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 156:449-65. [PMID: 25418795 DOI: 10.1002/ajpa.22670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/04/2014] [Indexed: 11/08/2022]
Abstract
Although south-Slavic populations have been studied to date from various aspects, the population of Serbia, occupying the central part of the Balkan Peninsula, is still genetically understudied at least at the level of mitochondrial DNA (mtDNA) variation. We analyzed polymorphisms of the first and the second mtDNA hypervariable segments (HVS-I and HVS-II) and informative coding-region markers in 139 Serbians to shed more light on their mtDNA variability, and used available data on other Slavic and neighboring non-Slavic populations to assess their interrelations in a broader European context. The contemporary Serbian mtDNA profile is consistent with the general European maternal landscape having a substantial proportion of shared haplotypes with eastern, central, and southern European populations. Serbian population was characterized as an important link between easternmost and westernmost south-Slavic populations due to the observed lack of genetic differentiation with all other south-Slavic populations and its geographical positioning within the Balkan Peninsula. An increased heterogeneity of south Slavs, most likely mirroring turbulent demographic events within the Balkan Peninsula over time (i.e., frequent admixture and differential introgression of various gene pools), and a marked geographical stratification of Slavs to south-, east-, and west-Slavic groups, were also found. A phylogeographic analyses of 20 completely sequenced Serbian mitochondrial genomes revealed not only the presence of mtDNA lineages predominantly found within the Slavic gene pool (U4a2a*, U4a2a1, U4a2c, U4a2g, HV10), supporting a common Slavic origin, but also lineages that may have originated within the southern Europe (H5*, H5e1, H5a1v) and the Balkan Peninsula in particular (H6a2b and L2a1k).
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Affiliation(s)
- Slobodan Davidovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11010, Belgrade, Serbia
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Nováčková J, Dreslerová D, Černý V, Poloni ES. The place of Slovakian paternal diversity in the clinal European landscape. Ann Hum Biol 2014; 42:511-22. [PMID: 25374405 DOI: 10.3109/03014460.2014.974668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Several demographic events have been postulated to explain the contemporaneous structure of European genetic diversity. First, an initial settlement of the continent by anatomically modern humans; second, the re-settlement of northern latitudes after the Last Glacial Maximum; third, the demic diffusion of Neolithic farmers from the Near East; and, fourth, several historical events such as the Slavic migration. AIM The aim of this study was to provide a more integrated picture of male-specific genetic relationships of Slovakia within the broader pan-European genetic landscape. SUBJECTS AND METHODS This study analysed a new Y-chromosome data-set (156 individuals) for both SNP and STR polymorphisms in population samples from five different Slovakian localities. RESULTS It was found that the male diversity of Slovakia is embedded in the clinal pattern of the major R1a and R1b clades extending over the continent and a similar pattern of population structure is found with Y-specific SNP or STR variation. CONCLUSION The highly significant correlation between the results based on fast evolving STRs on one hand and slow evolving SNPs on the other hand suggests a recent timeframe for the settlement of the area.
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Affiliation(s)
- Jana Nováčková
- a Department of Anthropology and Human Genetics, Faculty of Science , Charles University , Prague , Czech Republic
| | - Dagmar Dreslerová
- b Department of the Archaeology of Landscape and Archaeobiology , Institute of Archaeology of the Academy of Sciences of the Czech Republic , Czech Republic
| | - Viktor Černý
- c Archaeogenetics Laboratory, Department of the Archaeology of Landscape and Archaeobiology, Institute of Archaeology of the Academy of Sciences of the Czech Republic , Czech Republic , and
| | - Estella S Poloni
- d Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution , University of Geneva , Geneva , Switzerland
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Ballantyne KN, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ, Ayub Q, Balažic J, Ballantyne J, Ballard DJ, Berger B, Bobillo C, Bouabdellah M, Burri H, Capal T, Caratti S, Cárdenas J, Cartault F, Carvalho EF, Carvalho M, Cheng B, Coble MD, Comas D, Corach D, D'Amato ME, Davison S, de Knijff P, De Ungria MCA, Decorte R, Dobosz T, Dupuy BM, Elmrghni S, Gliwiński M, Gomes SC, Grol L, Haas C, Hanson E, Henke J, Henke L, Herrera-Rodríguez F, Hill CR, Holmlund G, Honda K, Immel UD, Inokuchi S, Jobling MA, Kaddura M, Kim JS, Kim SH, Kim W, King TE, Klausriegler E, Kling D, Kovačević L, Kovatsi L, Krajewski P, Kravchenko S, Larmuseau MHD, Lee EY, Lessig R, Livshits LA, Marjanović D, Minarik M, Mizuno N, Moreira H, Morling N, Mukherjee M, Munier P, Nagaraju J, Neuhuber F, Nie S, Nilasitsataporn P, Nishi T, Oh HH, Olofsson J, Onofri V, Palo JU, Pamjav H, Parson W, Petlach M, Phillips C, Ploski R, Prasad SPR, Primorac D, Purnomo GA, Purps J, Rangel-Villalobos H, Rębała K, Rerkamnuaychoke B, Gonzalez DR, Robino C, Roewer L, Rosa A, Sajantila A, Sala A, Salvador JM, Sanz P, Schmitt C, Sharma AK, Silva DA, Shin KJ, Sijen T, Sirker M, Siváková D, Skaro V, Solano-Matamoros C, Souto L, Stenzl V, Sudoyo H, Syndercombe-Court D, Tagliabracci A, Taylor D, Tillmar A, Tsybovsky IS, Tyler-Smith C, van der Gaag KJ, Vanek D, Völgyi A, Ward D, Willemse P, Yap EPH, Yong RYY, Pajnič IZ, Kayser M. Toward male individualization with rapidly mutating y-chromosomal short tandem repeats. Hum Mutat 2014; 35:1021-32. [PMID: 24917567 PMCID: PMC4145662 DOI: 10.1002/humu.22599] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/26/2014] [Indexed: 11/30/2022]
Abstract
Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836–0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father–son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database.
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Affiliation(s)
- Kaye N Ballantyne
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, Victoria, Australia
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The phylogenetic and geographic structure of Y-chromosome haplogroup R1a. Eur J Hum Genet 2014; 23:124-31. [PMID: 24667786 DOI: 10.1038/ejhg.2014.50] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 02/07/2014] [Accepted: 02/13/2014] [Indexed: 12/31/2022] Open
Abstract
R1a-M420 is one of the most widely spread Y-chromosome haplogroups; however, its substructure within Europe and Asia has remained poorly characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-chromosomes and analyzed them to a highly granular phylogeographic resolution. Whole Y-chromosome sequence analysis of eight R1a and five R1b individuals suggests a divergence time of ∼25,000 (95% CI: 21,300-29,000) years ago and a coalescence time within R1a-M417 of ∼5800 (95% CI: 4800-6800) years. The spatial frequency distributions of R1a sub-haplogroups conclusively indicate two major groups, one found primarily in Europe and the other confined to Central and South Asia. Beyond the major European versus Asian dichotomy, we describe several younger sub-haplogroups. Based on spatial distributions and diversity patterns within the R1a-M420 clade, particularly rare basal branches detected primarily within Iran and eastern Turkey, we conclude that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran.
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Coronary artery disease predisposing haplogroup I of the Y chromosome, aggression and sex steroids – Genetic association analysis. Atherosclerosis 2014; 233:160-4. [DOI: 10.1016/j.atherosclerosis.2013.12.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 11/26/2013] [Accepted: 12/03/2013] [Indexed: 11/21/2022]
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Kostrzewa G, Broda G, Konarzewska M, Krajewki P, Płoski R. Genetic polymorphism of human Y chromosome and risk factors for cardiovascular diseases: a study in WOBASZ cohort. PLoS One 2013; 8:e68155. [PMID: 23935855 PMCID: PMC3723826 DOI: 10.1371/journal.pone.0068155] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 05/30/2013] [Indexed: 11/18/2022] Open
Abstract
Genetic variants of Y chromosome predispose to hypertension in rodents, whereas in humans the evidence is conflicting. Our purpose was to study the distribution of a panel of Y chromosome markers in a cohort from a cross-sectional population-based study on the prevalence of cardiovascular risk factors in Poland (WOBASZ study). The HindIII, YAP Y chromosome variants, previously shown to influence blood pressure, lipid traits or height, as well as SNPs defining main Y chromosome haplogroups, were typed in 3026, 2783 and 2652 samples, respectively. In addition, 4 subgroups (N∼100 each) representing extremes of LDL concentration or blood pressure (BP) were typed for a panel of 17 STRs. The HindIII and YAP polymorphism were not associated with any of the studied traits. Analysis of the haplogroup distribution showed an association between higher HDL level and hg I-M170 (P = 0.02), higher LDL level and hg F*(xI-M170, J2-M172, K-M9) (P = 0.03) and lower BMI and hg N3-Tat (P = 0.04). Analysis of STRs did not show statistically significant differences. Since all these associations lost statistical significance after Bonferroni correction, we conclude that a major role of Y chromosome genetic variation (defined by HindIII, YAP or main Y chromosome haplogroups) in determining cardiovascular risk in Poles is unlikely.
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Affiliation(s)
- Grażyna Kostrzewa
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Grażyna Broda
- Department of Cardiovascular Epidemiology and Prevention, and Health Promotion, Institute of Cardiology, Warsaw, Poland
| | | | - Paweł Krajewki
- Department of Forensic Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
- * E-mail:
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Ben-Efraim YJ, Wasserman D, Wasserman J, Sokolowski M. Family-based study of AVPR1B association and interaction with stressful life events on depression and anxiety in suicide attempts. Neuropsychopharmacology 2013; 38:1504-11. [PMID: 23422793 PMCID: PMC3682145 DOI: 10.1038/npp.2013.49] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The cortisol response to psychosocial stress may become dysregulated in stress-related disorders. It is potentiated by pituitary secretion of adrenocorticotropic hormone (ACTH), which is, in part, regulated by arginine vasopressin receptor-1B (AVPR1B). AVPR1B variants were previously reported to associate with mood and anxiety disorders. This study aims, for the first time, to investigate association of AVPR1B genetic variants with mood and anxiety outcomes in suicidal behavior.Using a family-based study design of 660 complete nuclear family trios with offspring who have made a suicide attempt (SA), we tested the direct association and linkage of AVPR1B single nucleotide polymorphisms (SNPs) with SA, as well as with depression and anxiety in SA. Main findings were the association and linkage of AVPR1B exon 1 SNP rs33990840 and a major 6-SNP haplotype representative of all common AVPR1B-SNPs, on the outcome of high Beck Depression Inventory scores in SA. By contrast, genetic associations with lifetime diagnoses of depression and anxiety in SA or gene-environment interactions between AVPR1B variants and stressful life events (SLEs) were not significant. An exploratory screen of interactions between AVPR1B and CRHR1 (corticotropin-releasing hormone receptor-1), the principal pituitary regulator of ACTH secretion, showed no support for gene-gene interactions on the studied outcomes. The results suggest that AVPR1B genetic variation, eg, non-synonymous SNP rs33990840 mediating putative consequences on ligand binding, has a role in SA etiology characterized by elevated depression symptoms, without involving AVPR1B-moderation of SLEs.
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Affiliation(s)
- Yair J Ben-Efraim
- The National Centre for Suicide Research and Prevention of Mental Ill-Health (NASP), Karolinska Institute (KI), Stockholm, Sweden
| | - Danuta Wasserman
- The National Centre for Suicide Research and Prevention of Mental Ill-Health (NASP), Karolinska Institute (KI), Stockholm, Sweden
| | - Jerzy Wasserman
- The National Centre for Suicide Research and Prevention of Mental Ill-Health (NASP), Karolinska Institute (KI), Stockholm, Sweden
| | - Marcus Sokolowski
- The National Centre for Suicide Research and Prevention of Mental Ill-Health (NASP), Karolinska Institute (KI), Stockholm, Sweden,National Centre for Suicide Research and Prevention of Mental Ill-Health (NASP), Karolinska Institute (KI), Stockholm S-171 77, Sweden. Tel: +468 5248 6938, Fax: +4683 06439, E-mail:
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Isaacs S, Geduld-Ullah T, Benjeddou M. Reconstruction of major maternal and paternal lineages of the Cape Muslim population. Genet Mol Biol 2013; 36:167-76. [PMID: 23885197 PMCID: PMC3715281 DOI: 10.1590/s1415-47572013005000019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 03/12/2013] [Indexed: 11/28/2022] Open
Abstract
The earliest Cape Muslims were brought to the Cape (Cape Town - South Africa) from Africa and Asia from 1652 to 1834. They were part of an involuntary migration of slaves, political prisoners and convicts, and they contributed to the ethnic diversity of the present Cape Muslim population of South Africa. The history of the Cape Muslims has been well documented and researched however no in-depth genetic studies have been undertaken. The aim of the present study was to determine the respective African, Asian and European contributions to the mtDNA (maternal) and Y-chromosomal (paternal) gene pool of the Cape Muslim population, by analyzing DNA samples of 100 unrelated Muslim males born in the Cape Metropolitan area. A panel of six mtDNA and eight Y-chromosome SNP markers were screened using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP). Overall admixture estimates for the maternal line indicated Asian (0.4168) and African mtDNA (0.4005) as the main contributors. The admixture estimates for the paternal line, however, showed a predominance of the Asian contribution (0.7852). The findings are in accordance with historical data on the origins of the early Cape Muslims.
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Affiliation(s)
- Shafieka Isaacs
- Department of Biotechnology, University of the Western Cape, Bellville, Cape Town, South Africa
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Kushniarevich A, Sivitskaya L, Danilenko N, Novogrodskii T, Tsybovsky I, Kiseleva A, Kotova S, Chaubey G, Metspalu E, Sahakyan H, Bahmanimehr A, Reidla M, Rootsi S, Parik J, Reisberg T, Achilli A, Hooshiar Kashani B, Gandini F, Olivieri A, Behar DM, Torroni A, Davydenko O, Villems R. Uniparental genetic heritage of belarusians: encounter of rare middle eastern matrilineages with a central European mitochondrial DNA pool. PLoS One 2013; 8:e66499. [PMID: 23785503 PMCID: PMC3681942 DOI: 10.1371/journal.pone.0066499] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 05/06/2013] [Indexed: 11/19/2022] Open
Abstract
Ethnic Belarusians make up more than 80% of the nine and half million people inhabiting the Republic of Belarus. Belarusians together with Ukrainians and Russians represent the East Slavic linguistic group, largest both in numbers and territory, inhabiting East Europe alongside Baltic-, Finno-Permic- and Turkic-speaking people. Till date, only a limited number of low resolution genetic studies have been performed on this population. Therefore, with the phylogeographic analysis of 565 Y-chromosomes and 267 mitochondrial DNAs from six well covered geographic sub-regions of Belarus we strove to complement the existing genetic profile of eastern Europeans. Our results reveal that around 80% of the paternal Belarusian gene pool is composed of R1a, I2a and N1c Y-chromosome haplogroups – a profile which is very similar to the two other eastern European populations – Ukrainians and Russians. The maternal Belarusian gene pool encompasses a full range of West Eurasian haplogroups and agrees well with the genetic structure of central-east European populations. Our data attest that latitudinal gradients characterize the variation of the uniparentally transmitted gene pools of modern Belarusians. In particular, the Y-chromosome reflects movements of people in central-east Europe, starting probably as early as the beginning of the Holocene. Furthermore, the matrilineal legacy of Belarusians retains two rare mitochondrial DNA haplogroups, N1a3 and N3, whose phylogeographies were explored in detail after de novo sequencing of 20 and 13 complete mitogenomes, respectively, from all over Eurasia. Our phylogeographic analyses reveal that two mitochondrial DNA lineages, N3 and N1a3, both of Middle Eastern origin, might mark distinct events of matrilineal gene flow to Europe: during the mid-Holocene period and around the Pleistocene-Holocene transition, respectively.
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Roewer L, Nothnagel M, Gusmão L, Gomes V, González M, Corach D, Sala A, Alechine E, Palha T, Santos N, Ribeiro-Dos-Santos A, Geppert M, Willuweit S, Nagy M, Zweynert S, Baeta M, Núñez C, Martínez-Jarreta B, González-Andrade F, Fagundes de Carvalho E, da Silva DA, Builes JJ, Turbón D, Lopez Parra AM, Arroyo-Pardo E, Toscanini U, Borjas L, Barletta C, Ewart E, Santos S, Krawczak M. Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in native South Americans. PLoS Genet 2013; 9:e1003460. [PMID: 23593040 PMCID: PMC3623769 DOI: 10.1371/journal.pgen.1003460] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 03/04/2013] [Indexed: 01/07/2023] Open
Abstract
Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans. In the largest population genetic study of South Americans to date, we analyzed the Y-chromosomal makeup of more than 1,000 male natives. We found that the male-specific genetic variation of Native Americans lacks any clear structure that could sensibly be related to their geographic and/or linguistic relationships. This finding is consistent with a rapid initial peopling of South America, followed by long periods of isolation in small tribal groups. The observed continent-wide decoupling of geography, spoken language, and genetics contrasts strikingly with previous reports of such correlation from many parts of Europe and Asia. Moreover, we identified a cluster of Native American founding lineages of Y chromosomes, called C-M217 (C3*), within a restricted area of Ecuador in North-Western South America. The same haplogroup occurs at high frequency in Central, East, and North East Asia, but is virtually absent from North (except Alaska) and Central America. Possible scenarios for the introduction of C-M217 (C3*) into Ecuador may thus include a coastal or trans-Pacific route, an idea also supported by occasional archeological evidence and the recent coalescence of the C3* haplotypes, estimated from our data to have occurred some 6,000 years ago.
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Affiliation(s)
- Lutz Roewer
- Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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Malukiewicz G, Lesiewska-Junk H, Linkowska K, Grzybowski T, Kaźmierczak K. Analysis of CNTNAP2 polymorphisms in Polish population with pseudoexfoliation syndrome. Acta Ophthalmol 2012; 90:e660-1. [PMID: 22429864 DOI: 10.1111/j.1755-3768.2012.02395.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rębała K, Martínez-Cruz B, Tönjes A, Kovacs P, Stumvoll M, Lindner I, Büttner A, Wichmann HE, Siváková D, Soták M, Quintana-Murci L, Szczerkowska Z, Comas D. Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements. Eur J Hum Genet 2012; 21:415-22. [PMID: 22968131 DOI: 10.1038/ejhg.2012.190] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Homogeneous Proto-Slavic genetic substrate and/or extensive mixing after World War II were suggested to explain homogeneity of contemporary Polish paternal lineages. Alternatively, Polish local populations might have displayed pre-war genetic heterogeneity owing to genetic drift and/or gene flow with neighbouring populations. Although sharp genetic discontinuity along the political border between Poland and Germany indisputably results from war-mediated resettlements and homogenisation, it remained unknown whether Y-chromosomal diversity in ethnically/linguistically defined populations was clinal or discontinuous before the war. In order to answer these questions and elucidate early Slavic migrations, 1156 individuals from several Slavic and German populations were analysed, including Polish pre-war regional populations and an autochthonous Slavic population from Germany. Y chromosomes were assigned to 39 haplogroups and genotyped for 19 STRs. Genetic distances revealed similar degree of differentiation of Slavic-speaking pre-war populations from German populations irrespective of duration and intensity of contacts with German speakers. Admixture estimates showed minor Slavic paternal ancestry (~20%) in modern eastern Germans and hardly detectable German paternal ancestry in Slavs neighbouring German populations for centuries. BATWING analysis of isolated Slavic populations revealed that their divergence was preceded by rapid demographic growth, undermining theory that Slavic expansion was primarily linguistic rather than population spread. Polish pre-war regional populations showed within-group heterogeneity and lower STR variation within R-M17 subclades compared with modern populations, which might have been homogenised by war resettlements. Our results suggest that genetic studies on early human history in the Vistula and Oder basins should rely on reconstructed pre-war rather than modern populations.
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Affiliation(s)
- Krzysztof Rębała
- Institut de Biologia Evolutiva, CSIC-UPF, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
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Whole genome amplification of degraded and nondegraded DNA for forensic purposes. Int J Legal Med 2012; 127:309-19. [PMID: 22940764 PMCID: PMC3578730 DOI: 10.1007/s00414-012-0764-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 08/14/2012] [Indexed: 11/06/2022]
Abstract
Degraded DNA is often analyzed in forensic genetics laboratories. Reliable analysis of degraded DNA is of great importance, since its results impact the quality and reliability of expert testimonies. Recently, a number of whole genome amplification (WGA) methods have been proposed as preamplification tools. They work on the premise of being able to generate microgram quantities of DNA from as little as the quantity of DNA from a single cell. We chose, investigated, and compared seven WGA methods to evaluate their ability to “recover” degraded and nondegraded DNA: degenerate oligonucleotide-primed PCR, primer extension preamplification PCR, GenomePlex™ WGA commercial kit (Sigma), multiple displacement amplification, GenomiPhi™ Amplification kit (Amersham Biosciences), restriction and circularization-aided rolling circle amplification, and blunt-end ligation-mediated WGA. The efficiency and reliability of those methods were analyzed and compared using SGMPlus, YFiler, mtDNA, and Y-chromosome SNP typing. The best results for nondegraded DNA were obtained with GenomiPhi and PEP methods. In the case of degraded DNA (200 bp), the best results were obtained with GenomePlex which successfully amplified also severely degraded DNA (100 bp), thus enabling correct typing of mtDNA and Y-SNP loci. WGA may be very useful in analysis of low copy number DNA or degraded DNA in forensic genetics, especially after introduction of some improvements (sample pooling and replicate DNA typing).
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Niederstätter H, Rampl G, Erhart D, Pitterl F, Oberacher H, Neuhuber F, Hausner I, Gassner C, Schennach H, Berger B, Parson W. Pasture names with Romance and Slavic roots facilitate dissection of Y chromosome variation in an exclusively German-speaking alpine region. PLoS One 2012; 7:e41885. [PMID: 22848647 PMCID: PMC3407130 DOI: 10.1371/journal.pone.0041885] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 06/28/2012] [Indexed: 01/04/2023] Open
Abstract
The small alpine district of East Tyrol (Austria) has an exceptional demographic history. It was contemporaneously inhabited by members of the Romance, the Slavic and the Germanic language groups for centuries. Since the Late Middle Ages, however, the population of the principally agrarian-oriented area is solely Germanic speaking. Historic facts about East Tyrol's colonization are rare, but spatial density-distribution analysis based on the etymology of place-names has facilitated accurate spatial mapping of the various language groups' former settlement regions. To test for present-day Y chromosome population substructure, molecular genetic data were compared to the information attained by the linguistic analysis of pasture names. The linguistic data were used for subdividing East Tyrol into two regions of former Romance (A) and Slavic (B) settlement. Samples from 270 East Tyrolean men were genotyped for 17 Y-chromosomal microsatellites (Y-STRs) and 27 single nucleotide polymorphisms (Y-SNPs). Analysis of the probands' surnames revealed no evidence for spatial genetic structuring. Also, spatial autocorrelation analysis did not indicate significant correlation between genetic (Y-STR haplotypes) and geographic distance. Haplogroup R-M17 chromosomes, however, were absent in region A, but constituted one of the most frequent haplogroups in region B. The R-M343 (R1b) clade showed a marked and complementary frequency distribution pattern in these two regions. To further test East Tyrol's modern Y-chromosomal landscape for geographic patterning attributable to the early history of settlement in this alpine area, principal coordinates analysis was performed. The Y-STR haplotypes from region A clearly clustered with those of Romance reference populations and the samples from region B matched best with Germanic speaking reference populations. The combined use of onomastic and molecular genetic data revealed and mapped the marked structuring of the distribution of Y chromosomes in an alpine region that has been culturally homogeneous for centuries.
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Affiliation(s)
| | - Gerhard Rampl
- Institute of Lexicography of Austrian Dialects and Names, Austrian Academy of Sciences, Vienna, Austria
| | - Daniel Erhart
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Florian Pitterl
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Franz Neuhuber
- Institute of Legal Medicine, University of Salzburg, Salzburg, Austria
| | - Isolde Hausner
- Institute of Lexicography of Austrian Dialects and Names, Austrian Academy of Sciences, Vienna, Austria
| | - Christoph Gassner
- Central Institute for Blood Transfusion & Immunological Department, Innsbruck, Austria
- Blood Transfusion Service Zürich, SRC, Schlieren, Switzerland
| | - Harald Schennach
- Central Institute for Blood Transfusion & Immunological Department, Innsbruck, Austria
| | - Burkhard Berger
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
- * E-mail:
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
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Khusnutdinova EK, Litvinov SS, Kutuev IA, Yunusbayev BB, Khusainova RI, Ahmetova VL, Ahatova FS, Metspalu E, Rootsi S, Villems R. Gene pool of ethnic groups of the Caucasus: Results of integrated study of the Y chromosome and mitochondrial DNA and genome-wide data. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412060063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Structural drift: the population dynamics of sequential learning. PLoS Comput Biol 2012; 8:e1002510. [PMID: 22685387 PMCID: PMC3369870 DOI: 10.1371/journal.pcbi.1002510] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 03/22/2012] [Indexed: 11/19/2022] Open
Abstract
We introduce a theory of sequential causal inference in which learners in a chain estimate a structural model from their upstream “teacher” and then pass samples from the model to their downstream “student”. It extends the population dynamics of genetic drift, recasting Kimura's selectively neutral theory as a special case of a generalized drift process using structured populations with memory. We examine the diffusion and fixation properties of several drift processes and propose applications to learning, inference, and evolution. We also demonstrate how the organization of drift process space controls fidelity, facilitates innovations, and leads to information loss in sequential learning with and without memory. Human knowledge is often transmitted orally within a group via a sequence of communications between individuals. The children's game of Telephone is a familiar, simplified version. A phrase is uttered, understood, and then transmitted to another. Genetic information is communicated in an analogous sequential communication chain via replication. We show that the evolutionary dynamics of both problems is a form of genetic drift which accounts for memory in the communication chain. Using this, one can predict the mechanisms that lead to variations in fidelity and to structural innovation.
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Adler G, Clark JSC, Loniewska B, Czerska E, Salkic NN, Ciechanowicz A. Prevalence of 1691G>A FV mutation in Poland compared with that in other Central, Eastern and South-Eastern European countries. Bosn J Basic Med Sci 2012; 12:82-7. [PMID: 22642591 DOI: 10.17305/bjbms.2012.2500] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The 1691G>A FV variant has been described as a common genetic risk factor in venous thromboembolism. The purpose of this study was to provide a further frequency value for 1691G>A FV in Poland and to collate summary data from Central (Poland, Czech, Slovakia), Eastern (Russia, Belarus, Ukraine) and South-Eastern (Slovenia, Croatia, Bosnia and Herzegovina, Serbia, Montenegro, Macedonia, Bulgaria) European countries. For this purpose in 2007 the 1691G>A FV variant was analyzed by polymerase chain reaction-restriction fragment length polymorphism from DNA collected in 2005-2006. We studied 650 subjects: 400 newborns and 250 older individuals (mean age 46.1 y) from Poland and compared results with reports from other countries, as well as with the frequency trend of 845G>A HFE across South-Eastern European countries using centroid cities. From our 1691G>A FV study we identified 626 GG homozygotes, 23 GA heterozygotes, and 1 AA homozygote (n = 650), giving an A allele frequency of 1.9%, and a summed frequency value for Poland of 2.0% (n = 1588); the frequency in Central European countries was 3.9% (n = 4559), mostly due to the high value in the Czech Republic: 5.1% (n = 2819); the South-Eastern European countries had 2.5% (n = 2410). Among the Eastern European countries the 1691G>A FV allele frequency was 1.9% (n=791), between the South-Eastern and Eastern European countries there was no significant difference (p=0.17). We confirm that the 1691G>A FV allele frequency in Poland, as well as other countries compared, is significantly lower than that in Czech.
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Affiliation(s)
- Grażyna Adler
- Department of Medical Biology, Pomeranian Medical University, Powst.Wlkp. 72, 70-111 Szczecin, Poland
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Simms TM, Wright MR, Hernandez M, Perez OA, Ramirez EC, Martinez E, Herrera RJ. Y-chromosomal diversity in Haiti and Jamaica: Contrasting levels of sex-biased gene flow. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 148:618-31. [DOI: 10.1002/ajpa.22090] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 04/04/2012] [Indexed: 11/06/2022]
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Croatian national reference Y-STR haplotype database. Mol Biol Rep 2012; 39:7727-41. [PMID: 22391654 DOI: 10.1007/s11033-012-1610-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 02/07/2012] [Indexed: 10/28/2022]
Abstract
A reference Y-chromosome short tandem repeat (STR) haplotype database is needed for Y-STR match interpretation as well as for national and regional characterization of populations. The aim of this study was to create a comprehensive Y-STR haplotype database of the Croatian contemporary population and to analyze substructure between the five Croatian regions. We carried out a statistical analysis of the data from previously performed genetic analyses collected during routine forensic work by the Forensic Science Centre "Ivan Vučetić". A total of 1,100 unrelated men from eastern, western, northern, southern and central Croatia were selected for the purpose of this study. Y-STRs were typed using the AmpFISTR Yfiler PCR amplification kit. Analysis of molecular variance calculated with the Y chromosome haplotype reference database online analysis tool included 16 population samples with 20,247 haplotypes. A total of 947 haplotypes were recorded, 848 of which were unique (89.5%). Haplotype diversity was 0.998, with the most frequent haplotype found in 9 of 1,100 men (0.82%). Locus diversity varied from 0.266 for DYS392 to 0.868 for DYS385. Discrimination capacity was 86.1%. Our results suggested high level of similarity among regional subpopulations within Croatia, except for mildly different southern Croatia. Relative resemblance was found with Bosnia and Herzegovina and Serbia. Whit Atheys' Haplogroup Predictor was used to estimate the frequencies of Y-chromosome haplogroups. I2a, R1a, E1b1b and R1b haplogroups were most frequent in all Croatian regions. These results are important in forensics and contribute to the population genetics and genetic background of the contemporary Croatian population.
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50
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A comparative phylogenetic study of genetics and folk music. Mol Genet Genomics 2012; 287:337-49. [PMID: 22392540 DOI: 10.1007/s00438-012-0683-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 02/21/2012] [Indexed: 10/28/2022]
Abstract
Computer-aided comparison of folk music from different nations is one of the newest research areas. We were intrigued to have identified some important similarities between phylogenetic studies and modern folk music. First of all, both of them use similar concepts and representation tools such as multidimensional scaling for modelling relationship between populations. This gave us the idea to investigate whether these connections are merely accidental or if they mirror population migrations from the past. We raised the question; does the complex structure of musical connections display a clear picture and can this system be interpreted by the genetic analysis? This study is the first to systematically investigate the incidental genetic background of the folk music context between different populations. Paternal (42 populations) and maternal lineages (56 populations) were compared based on Fst genetic distances of the Y chromosomal and mtDNA haplogroup frequencies. To test this hypothesis, the corresponding musical cultures were also compared using an automatic overlap analysis of parallel melody styles for 31 Eurasian nations. We found that close musical relations of populations indicate close genetic distances (<0.05) with a probability of 82%. It was observed that there is a significant correlation between population genetics and folk music; maternal lineages have a more important role in folk music traditions than paternal lineages. Furthermore, the combination of these disciplines establishing a new interdisciplinary research field of "music-genetics" can be an efficient tool to get a more comprehensive picture on the complex behaviour of populations in prehistoric time.
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