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Srivastava AK, Chopra R, Ali S, Aggarwal S, Vig L, Bamezai RNK. Inferring population structure and relationship using minimal independent evolutionary markers in Y-chromosome: a hybrid approach of recursive feature selection for hierarchical clustering. Nucleic Acids Res 2014; 42:e122. [PMID: 25030906 PMCID: PMC4150763 DOI: 10.1093/nar/gku585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Inundation of evolutionary markers expedited in Human Genome Project and 1000 Genome Consortium has necessitated pruning of redundant and dependent variables. Various computational tools based on machine-learning and data-mining methods like feature selection/extraction have been proposed to escape the curse of dimensionality in large datasets. Incidentally, evolutionary studies, primarily based on sequentially evolved variations have remained un-facilitated by such advances till date. Here, we present a novel approach of recursive feature selection for hierarchical clustering of Y-chromosomal SNPs/haplogroups to select a minimal set of independent markers, sufficient to infer population structure as precisely as deduced by a larger number of evolutionary markers. To validate the applicability of our approach, we optimally designed MALDI-TOF mass spectrometry-based multiplex to accommodate independent Y-chromosomal markers in a single multiplex and genotyped two geographically distinct Indian populations. An analysis of 105 world-wide populations reflected that 15 independent variations/markers were optimal in defining population structure parameters, such as FST, molecular variance and correlation-based relationship. A subsequent addition of randomly selected markers had a negligible effect (close to zero, i.e. 1 × 10−3) on these parameters. The study proves efficient in tracing complex population structures and deriving relationships among world-wide populations in a cost-effective and expedient manner.
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Affiliation(s)
- Amit Kumar Srivastava
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rupali Chopra
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shafat Ali
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shweta Aggarwal
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Lovekesh Vig
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rameshwar Nath Koul Bamezai
- National Centre of Applied Human Genetics, School of Life Sciences, and School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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van Oven M, Toscani K, van den Tempel N, Ralf A, Kayser M. Multiplex genotyping assays for fine-resolution subtyping of the major human Y-chromosome haplogroups E, G, I, J, and R in anthropological, genealogical, and forensic investigations. Electrophoresis 2013; 34:3029-38. [PMID: 23893838 DOI: 10.1002/elps.201300210] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 06/17/2013] [Accepted: 06/26/2013] [Indexed: 12/20/2022]
Abstract
Inherited DNA polymorphisms located within the nonrecombing portion of the human Y chromosome provide a powerful means of tracking the patrilineal ancestry of male individuals. Recently, we introduced an efficient genotyping method for the detection of the basal Y-chromosome haplogroups A to T, as well as an additional method for the dissection of haplogroup O into its sublineages. To further extend the use of the Y chromosome as an evolutionary marker, we here introduce a set of genotyping assays for fine-resolution subtyping of haplogroups E, G, I, J, and R, which make up the bulk of Western Eurasian and African Y chromosomes. The marker selection includes a total of 107 carefully selected bi-allelic polymorphisms that were divided into eight hierarchically organized multiplex assays (two for haplogroup E, one for I, one for J, one for G, and three for R) based on the single-base primer extension (SNaPshot) technology. Not only does our method allow for enhanced Y-chromosome lineage discrimination, the more restricted geographic distribution of the subhaplogroups covered also enables more fine-scaled estimations of patrilineal bio-geographic origin. Supplementing our previous method for basal Y-haplogroup detection, the currently introduced assays are thus expected to be of major relevance for future DNA studies targeting male-specific ancestry for forensic, anthropological, and genealogical purposes.
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Affiliation(s)
- Mannis van Oven
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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Cortellini V, Verzeletti A, Cerri N, Marino A, De Ferrari F. Y-chromosome polymorphisms and ethnic group - a combined STR and SNP approach in a population sample from northern Italy. Croat Med J 2013; 54:279-85. [PMID: 23771759 PMCID: PMC3692336 DOI: 10.3325/cmj.2013.54.279] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 06/01/2013] [Indexed: 11/16/2022] Open
Abstract
AIM To find an association between Y chromosome polymorphisms and some ethnic groups. METHODS Short tandem repeats (STR) and single-nucleotide polymorphisms (SNP) on the Y chromosome were typed in 311 unrelated men from four different ethnic groups - Italians from northern Italy, Albanians, Africans from the Maghreb region, and Indo-Pakistanis, using the AmpFlSTR® Yfiler PCR Amplification Kit and the SNaPshot Multiplex Kit. RESULTS STRs analysis found 299 different haplotypes and SNPs analysis 11 different haplogroups. Haplotypes and haplogroups were analyzed and compared between different ethnic groups. Significant differences were found among all the population groups, except between Italians and Indo-Pakistanis and between Albanians and Indo-Pakistanis. CONCLUSIONS Typing both STRs and SNPs on the Y chromosome could become useful in determining ethnic origin of a potential suspect.
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Y-SNP miniplexes for East Asian Y-chromosomal haplogroup determination in degraded DNA. Forensic Sci Int Genet 2013; 7:75-81. [DOI: 10.1016/j.fsigen.2012.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 05/14/2012] [Accepted: 06/26/2012] [Indexed: 11/18/2022]
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Simms TM, Martinez E, Herrera KJ, Wright MR, Perez OA, Hernandez M, Ramirez EC, McCartney Q, Herrera RJ. Paternal lineages signal distinct genetic contributions from British Loyalists and continental Africans among different Bahamian islands. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:594-608. [DOI: 10.1002/ajpa.21616] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 08/05/2011] [Indexed: 02/02/2023]
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van Oven M, Ralf A, Kayser M. An efficient multiplex genotyping approach for detecting the major worldwide human Y-chromosome haplogroups. Int J Legal Med 2011; 125:879-85. [PMID: 21785904 PMCID: PMC3192277 DOI: 10.1007/s00414-011-0605-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 07/13/2011] [Indexed: 01/07/2023]
Abstract
The Y chromosome is paternally inherited and therefore serves as an evolutionary marker of patrilineal descent. Worldwide DNA variation within the non-recombining portion of the Y chromosome can be represented as a monophyletic phylogenetic tree in which the branches (haplogroups) are defined by at least one SNP. Previous human population genetics research has produced a wealth of knowledge about the worldwide distribution of Y-SNP haplogroups. Here, we apply previous and very recent knowledge on the Y-SNP phylogeny and Y-haplogroup distribution by introducing two multiplex genotyping assays that allow for the hierarchical detection of 28 Y-SNPs defining the major worldwide Y haplogroups. PCR amplicons were kept small to make the method sensitive and thereby applicable to DNA of limited amount and/or quality such as in forensic settings. These Y-SNP assays thus form a valuable tool for researchers in the fields of forensic genetics and genetic anthropology to infer a man's patrilineal bio-geographic ancestry from DNA.
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Affiliation(s)
- Mannis van Oven
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
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Martínez-Cruz B, Ziegle J, Sanz P, Sotelo G, Anglada R, Plaza S, Comas D. Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes. INVESTIGATIVE GENETICS 2011; 2:13. [PMID: 21627798 PMCID: PMC3130649 DOI: 10.1186/2041-2223-2-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 05/31/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND The analysis of human Y-chromosome variation in the context of population genetics and forensics requires the genotyping of dozens to hundreds of selected single-nucleotide polymorphisms (SNPs). In the present study, we developed a 121-plex (121 SNPs in a single array) TaqMan array capable of distinguishing most haplogroups and subhaplogroups on the Y-chromosome human phylogeny in Europe. RESULTS We present data from 264 samples from several European areas and ethnic groups. The array developed in this study shows >99% accuracy of assignation to the Y human phylogeny (with an average call rate of genotypes >96%). CONCLUSIONS We have created and evaluated a robust and accurate Y-chromosome multiplex which minimises the possible errors due to mixup when typing the same sample in several independent reactions.
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Affiliation(s)
- Begoña Martínez-Cruz
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, E-08003 Barcelona, Spain.
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Berniell-Lee G, Calafell F, Bosch E, Heyer E, Sica L, Mouguiama-Daouda P, van der Veen L, Hombert JM, Quintana-Murci L, Comas D. Genetic and demographic implications of the Bantu expansion: insights from human paternal lineages. Mol Biol Evol 2009; 26:1581-9. [PMID: 19369595 DOI: 10.1093/molbev/msp069] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The expansion of Bantu languages, which started around 5,000 years before present in west/central Africa and spread all throughout sub-Saharan Africa, may represent one of the major and most rapid demographic movements in the history of the human species. Although the genetic footprints of this expansion have been unmasked through the analyses of the maternally inherited mitochondrial DNA lineages, information on the genetic impact of this massive movement and on the genetic composition of pre-Bantu populations is still scarce. Here, we analyze an extensive collection of Y-chromosome markers--41 single nucleotide polymorphisms and 18 short tandem repeats--in 883 individuals from 22 Bantu-speaking agriculturalist populations and 3 Pygmy hunter-gatherer populations from Gabon and Cameroon. Our data reveal a recent origin for most paternal lineages in west Central African populations most likely resulting from the expansion of Bantu-speaking farmers that erased the more ancient Y-chromosome diversity found in this area. However, some traces of ancient paternal lineages are observed in these populations, mainly among hunter-gatherers. These results are at odds with those obtained from mtDNA analyses, where high frequencies of ancient maternal lineages are observed, and substantial maternal gene flow from hunter-gatherers to Bantu farmers has been suggested. These differences are most likely explained by sociocultural factors such as patrilocality. We also find the intriguing presence of paternal lineages belonging to Eurasian haplogroup R1b1*, which might represent footprints of demographic expansions in central Africa not directly related to the Bantu expansion.
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Affiliation(s)
- Gemma Berniell-Lee
- Institute of Evolutionary Biology, Consejo Superior de Investigaciones Cientificas-UPF, CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
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Mendizabal I, Sandoval K, Berniell-Lee G, Calafell F, Salas A, Martínez-Fuentes A, Comas D. Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba. BMC Evol Biol 2008; 8:213. [PMID: 18644108 PMCID: PMC2492877 DOI: 10.1186/1471-2148-8-213] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 07/21/2008] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Before the arrival of Europeans to Cuba, the island was inhabited by two Native American groups, the Tainos and the Ciboneys. Most of the present archaeological, linguistic and ancient DNA evidence indicates a South American origin for these populations. In colonial times, Cuban Native American people were replaced by European settlers and slaves from Africa. It is still unknown however, to what extent their genetic pool intermingled with and was 'diluted' by the arrival of newcomers. In order to investigate the demographic processes that gave rise to the current Cuban population, we analyzed the hypervariable region I (HVS-I) and five single nucleotide polymorphisms (SNPs) in the mitochondrial DNA (mtDNA) coding region in 245 individuals, and 40 Y-chromosome SNPs in 132 male individuals. RESULTS The Native American contribution to present-day Cubans accounted for 33% of the maternal lineages, whereas Africa and Eurasia contributed 45% and 22% of the lineages, respectively. This Native American substrate in Cuba cannot be traced back to a single origin within the American continent, as previously suggested by ancient DNA analyses. Strikingly, no Native American lineages were found for the Y-chromosome, for which the Eurasian and African contributions were around 80% and 20%, respectively. CONCLUSION While the ancestral Native American substrate is still appreciable in the maternal lineages, the extensive process of population admixture in Cuba has left no trace of the paternal Native American lineages, mirroring the strong sexual bias in the admixture processes taking place during colonial times.
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Affiliation(s)
- Isabel Mendizabal
- Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Karla Sandoval
- Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Gemma Berniell-Lee
- Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Francesc Calafell
- Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, and Grupo de Medicina Xenómica, Hospital Clínico Universitario, Santiago de Compostela, Galicia, Spain
| | - Antonio Martínez-Fuentes
- Departamento de Biología Animal y Humana. Facultad de Biología, Universidad de la Habana, Ciudad de la Habana, Cuba
| | - David Comas
- Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Spain
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Berniell-Lee G, Plaza S, Bosch E, Calafell F, Jourdan E, Césari M, Lefranc G, Comas D. Admixture and sexual bias in the population settlement of La Réunion Island (Indian Ocean). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2008; 136:100-7. [PMID: 18186507 DOI: 10.1002/ajpa.20783] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
La Réunion, one of the three Mascarene islands located in the Indian Ocean, remained devoid of inhabitants until it was first colonized by the French in the middle of the 17th century. The continuous flow of foreign-born slaves and immigrant workers from Africa, India, Southeast Asia, and China to work on coffee and sugar cane plantations led to the island becoming a melting pot of people of multiple ethnic origins. To establish the impact of the different incoming ethnic groups on the present Reunionese gene pool, we have sequenced both hypervariable regions I and II of the mitochondrial DNA molecule, the 9 bp COII/tRNA(Lys) deletion, and four SNPs located in the coding region in a total of 41 samples of the general population, and a further 18 STRs and 35 SNPs on the Y chromosome in 26 of these samples. Our results show that there was a strong sexual bias (asymmetrical gene flow) in the peopling of La Réunion, where admixture events were mainly between male settlers and females from the incoming slave groups. Most of the Y-chromosome gene pool is of European/Middle Eastern ancestry (85%), whereas the mtDNA gene pool is mainly of Indian and East Asian ancestry (70%). The absence of genetic diversity within these two major components of the mtDNA gene pool suggests these populations may have witnessed strong founder effects during the colonization process.
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Affiliation(s)
- Gemma Berniell-Lee
- Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
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