551
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Khodjet el Khil H, Marrakchi RT, Loueslati BY, Langaney A, Fellous M, BenAmmar Elgaaied A. Distribution of Y chromosome lineages in Jerba island population. Forensic Sci Int 2005; 148:211-8. [PMID: 15639616 DOI: 10.1016/j.forsciint.2004.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Revised: 05/14/2004] [Accepted: 05/18/2004] [Indexed: 11/22/2022]
Abstract
We have analysed Y chromosome polymorphism on six STR markers (DYS19, DYS389I, DYS390, DYS391, DYS392, and DYS393) and eight classical UEP markers (SRY10831a, YAP, SRY4064, M2, 92R7, M9, SRY2627 and 12f2) in three distinct ethnical, linguistic and cultural groups of Jerba island (Berbers, Arabs and a Jerban group of Sub-Saharan origin). Fst genetic distance and principal co-ordinate analysis based on STR haplotype frequencies, showed a genetic differentiation between the three Jerban groups and a genetic relationship between Jerban Berbers and Mozabites (a well defined Berber group in Algeria). Compound use of UEP and STR markers have increased discriminatory capacity. The detection of the most common haplotype (H9) in both Berbers and Mozabites may be useful in forensic special cases.
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Affiliation(s)
- Houssein Khodjet el Khil
- Laboratoire de Génétique moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Campus Universitaire 2092 Manar II, Tunisia.
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552
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Hurles ME, Sykes BC, Jobling MA, Forster P. The dual origin of the Malagasy in Island Southeast Asia and East Africa: evidence from maternal and paternal lineages. Am J Hum Genet 2005; 76:894-901. [PMID: 15793703 PMCID: PMC1199379 DOI: 10.1086/430051] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2005] [Accepted: 03/01/2005] [Indexed: 11/03/2022] Open
Abstract
Linguistic and archaeological evidence about the origins of the Malagasy, the indigenous peoples of Madagascar, points to mixed African and Indonesian ancestry. By contrast, genetic evidence about the origins of the Malagasy has hitherto remained partial and imprecise. We defined 26 Y-chromosomal lineages by typing 44 Y-chromosomal polymorphisms in 362 males from four different ethnic groups from Madagascar and 10 potential ancestral populations in Island Southeast Asia and the Pacific. We also compared mitochondrial sequence diversity in the Malagasy with a manually curated database of 19,371 hypervariable segment I sequences, incorporating both published and unpublished data. We could attribute every maternal and paternal lineage found in the Malagasy to a likely geographic origin. Here, we demonstrate approximately equal African and Indonesian contributions to both paternal and maternal Malagasy lineages. The most likely origin of the Asia-derived paternal lineages found in the Malagasy is Borneo. This agrees strikingly with the linguistic evidence that the languages spoken around the Barito River in southern Borneo are the closest extant relatives of Malagasy languages. As a result of their equally balanced admixed ancestry, the Malagasy may represent an ideal population in which to identify loci underlying complex traits of both anthropological and medical interest.
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Affiliation(s)
- Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
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553
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Kwak KD, Jin HJ, Shin DJ, Kim JM, Roewer L, Krawczak M, Tyler-Smith C, Kim W. Y-chromosomal STR haplotypes and their applications to forensic and population studies in east Asia. Int J Legal Med 2005; 119:195-201. [PMID: 15856270 DOI: 10.1007/s00414-004-0518-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Accepted: 12/08/2004] [Indexed: 11/26/2022]
Abstract
We have analyzed 11 Y-STR loci (DYS19, the two DYS385 loci, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DXYS156Y) in 700 males from ten ethnic groups in east Asia in order to evaluate their usefulness for forensic and population genetic studies. A total of 644 different haplotypes were identified, among which 603 (86.14%) were individual-specific. The haplotype diversity averaged over all populations was 0.9997; using only the nine Y-STRs comprising the "minimal haplotype" (excluding DYS388 and DXYS156Y) it was 0.9996, a value similar to that found in 1924 samples from other Asian populations (0.9996; Lessig et al. Legal Medicine 5(2003) 160-163), and slightly higher than in European populations (0.9976; n=11,610; Roewer et al. For Sci International (2001) 118:103-111). All of the individual east Asian populations examined here had high haplotype diversity (> or =0.997), except for the Mongolians (0.992) and Manchurians (0.960). The most frequent haplotype identified by the nine markers was present at only 1% (7/700). Population comparisons based on Phi(ST) or rho genetic distance measures revealed clustering according to the traditional northeast-southeast distinction, but with exceptions. For example, the Yunnan population from southern China lay among the northern populations, possibly reflecting recent migration, while the Korean population, traditionally considered northern, lay at the boundary between northern and southern populations. An admixture estimate suggested 55(51-59)% northern, 45(41-49)% southern contribution to the Koreans, illustrating the complexity of the genetic history of this region.
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Affiliation(s)
- Kyoung Don Kwak
- Department of Biological Sciences, Dankook University, Cheonan, 330-714, South Korea
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554
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Berger B, Lindinger A, Niederstätter H, Grubwieser P, Parson W. Y-STR typing of an Austrian population sample using a 17-loci multiplex PCR assay. Int J Legal Med 2005; 119:241-6. [PMID: 15843993 DOI: 10.1007/s00414-005-0546-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Accepted: 03/23/2005] [Indexed: 11/26/2022]
Abstract
Y-chromosomal STR haplotypes were determined from a sample of 135 unrelated men and 70 sons from Tirol (Austria) using the AmpFlSTR Yfiler PCR amplification kit (Applied Biosystems) that coamplifies 17 Y-STRs. The panel of markers includes the 9-loci European minimal haplotype (minHt) and, in addition, the markers DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 (Y GATA C4) and Y GATA H4. A total of 130 different haplotypes (125 were unique) were identified by the 17 Y-STR markers, an increase of 19 compared with the minHt. The gene diversity of DYS635, DYS456 and DYS458 exceeded 0.75 and only that of the duplicated marker DYS385 (0.86) was higher. Consistently high haplotype diversity values were found in all tested Y-SNP haplogroups. Because the simultaneous analysis of 17 Y-STR systems offers a high power of discrimination at minimum sample consumption, the Yfiler kit is a promising tool for forensic applications.
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Affiliation(s)
- Burkhard Berger
- Institute of Legal Medicine, Innsbruck Medical University, Müllerstrasse 44, 6020, Innsbruck, Austria
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555
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Goodacre S, Helgason A, Nicholson J, Southam L, Ferguson L, Hickey E, Vega E, Stefánsson K, Ward R, Sykes B. Genetic evidence for a family-based Scandinavian settlement of Shetland and Orkney during the Viking periods. Heredity (Edinb) 2005; 95:129-35. [PMID: 15815712 DOI: 10.1038/sj.hdy.6800661] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The Viking age witnessed the expansion of Scandinavian invaders across much of northwestern Europe. While Scandinavian settlements had an enduring cultural impact on North Atlantic populations, the nature and extent of their genetic legacy in places such as Shetland and Orkney is not clear. In order to explore this question further, we have made an extensive survey of both Y-chromosomal and mitochondrial DNA (mtDNA) variation in the North Atlantic region. Our findings indicate an overall Scandinavian ancestry of approximately 44% for Shetland and approximately 30% for Orkney, with approximately equal contributions from Scandinavian male and female subjects in both cases. This contrasts with the situation for the Western Isles, where the overall Scandinavian ancestry is less ( approximately 15%) and where there is a disproportionately high contribution from Scandinavian males. In line with previous studies, we find that Iceland exhibits both the greatest overall amount of Scandinavian ancestry (55%) and the greatest discrepancy between Scandinavian male and female components. Our results suggest that while areas close to Scandinavia, such as Orkney and Shetland, may have been settled primarily by Scandinavian family groups, lone Scandinavian males, who later established families with female subjects from the British Isles, may have been prominent in areas more distant from their homeland.
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Affiliation(s)
- S Goodacre
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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556
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Sanchez JJ, Hallenberg C, Børsting C, Hernandez A, Morling N. High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males. Eur J Hum Genet 2005; 13:856-66. [PMID: 15756297 DOI: 10.1038/sj.ejhg.5201390] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
We genotyped 45 biallelic markers and 11 STR systems on the Y chromosome in 201 male Somalis. In addition, 65 sub-Saharan Western Africans, 59 Turks and 64 Iraqis were typed for the biallelic Y chromosome markers. In Somalis, 14 Y chromosome haplogroups were identified including E3b1 (77.6%) and K2 (10.4%). The haplogroup E3b1 with the rare DYS19-11 allele (also called the E3b1 cluster gamma) was found in 75.1% of male Somalis, and 70.6% of Somali Y chromosomes were E3b1, DYS19-11, DYS392-12, DYS437-14, DYS438-11 and DYS393-13. The haplotype diversity of eight Y-STRs ('minimal haplotype') was 0.9575 compared to an average of 0.9974 and 0.9996 in European and Asian populations. In sub-Saharan Western Africans, only four haplogroups were identified. The West African clade E3a was found in 89.2% of the samples and the haplogroup E3b1 was not observed. In Turks, 12 haplogroups were found including J2*(xJ2f2) (27.1%), R1b3*(xR1b3d, R1b3f) (20.3%), E3b3 and R1a1*(xR1a1b) (both 11.9%). In Iraqis, 12 haplogroups were identified including J2*(xJ2f2) (29.7%) and J*(xJ2) (26.6%). The data suggest that the male Somali population is a branch of the East African population - closely related to the Oromos in Ethiopia and North Kenya - with predominant E3b1 cluster gamma lineages that were introduced into the Somali population 4000-5000 years ago, and that the Somali male population has approximately 15% Y chromosomes from Eurasia and approximately 5% from sub-Saharan Africa.
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Affiliation(s)
- Juan J Sanchez
- Department of Forensic Genetics, Institute of Forensic Medicine, University of Copenhagen, Denmark.
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557
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Roewer L, Croucher PJP, Willuweit S, Lu TT, Kayser M, Lessig R, de Knijff P, Jobling MA, Tyler-Smith C, Krawczak M. Signature of recent historical events in the European Y-chromosomal STR haplotype distribution. Hum Genet 2005; 116:279-91. [PMID: 15660227 DOI: 10.1007/s00439-004-1201-z] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2004] [Accepted: 09/13/2004] [Indexed: 10/25/2022]
Abstract
Previous studies of human Y-chromosomal single-nucleotide polymorphisms (Y-SNPs) established a link between the extant Y-SNP haplogroup distribution and the prehistoric demography of Europe. By contrast, our analysis of seven rapidly evolving Y-chromosomal short tandem repeat loci (Y-STRs) in over 12,700 samples from 91 different locations in Europe reveals a signature of more recent historic events, not previously detected by other genetic markers. Cluster analysis based upon molecular variance yields two clearly identifiable sub-clusters of Western and Eastern European Y-STR haplotypes, and a diverse transition zone in central Europe, where haplotype spectra change more rapidly with longitude than with latitude. This and other observed patterns of Y-STR similarity may plausibly be related to particular historical incidents, including, for example, the expansion of the Franconian and Ottoman Empires. We conclude that Y-STRs may be capable of resolving male genealogies to an unparalleled degree and could therefore provide a useful means to study local population structure and recent demographic history.
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Affiliation(s)
- Lutz Roewer
- Institute of Legal Medicine, Humboldt-University, Berlin, Germany
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558
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Marrero AR, Das Neves Leite FP, De Almeida Carvalho B, Peres LM, Kommers TC, Da Cruz IM, Salzano FM, Ruiz-Linares A, Da Silva Júnior WA, Bortolini MC. Heterogeneity of the genome ancestry of individuals classified as White in the State of Rio Grande do Sul, Brazil. Am J Hum Biol 2005; 17:496-506. [PMID: 15981186 DOI: 10.1002/ajhb.20404] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
One hundred nineteen individuals classified as White, living in different localities of the Brazilian state of Rio Grande do Sul, were studied in relation to the HVS-I region of the mitochondrial DNA (mtDNA). The male fraction of the sample (N = 74) was also tested for seven Y-chromosome polymorphisms. In a specific population (Veranópolis), a city characterized by a large influence of the Italian immigration of the 19th century, the results from the maternal and paternal sides indicated almost complete European ancestry. However, another sample identified as White, from different localities of Rio Grande do Sul, presented significant fractions of Native American (36%) and African (16%) mtDNA haplogroups. These results indicate that Brazilian populations are remarkably heterogeneous; while some present an overwhelming majority of transplanted European genomes, with a complete correspondence between physical appearance and ancestry, others reflect a history of extensive admixture with dissociation between physical appearance and ancestry.
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Affiliation(s)
- Andrea Rita Marrero
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil
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559
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Cox MP, Mirazón Lahr M. Y-chromosome diversity is inversely associated with language affiliation in paired Austronesian- and Papuan-speaking communities from Solomon Islands. Am J Hum Biol 2005; 18:35-50. [PMID: 16378340 DOI: 10.1002/ajhb.20459] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Solomon Islands lie in the center of Island Melanesia, bordered to the north by the Bismarck Archipelago and to the south by Vanuatu. The nation's half-million inhabitants speak around 70 languages from two unrelated language groups: Austronesian, a language family widespread in the Pacific and closely related to languages spoken in Island Southeast Asia, and "East Papuan", generally defined as non-Austronesian and distantly related to the extremely diverse Papuan languages of New Guinea. Despite the archipelago's presumed role as a staging post for the settlement of Remote Oceania, genetic research on Solomon Island populations is sparse. We collected paired samples from two regions that have populations speaking Austronesian and Papuan languages, respectively. Here we present Y-chromosome data from these samples, the first from Solomon Islands. We detected five Y-chromosome lineages: M-M106, O-M175, K-M9*, K-M230, and the extremely rare clade, K1-M177. Y-chromosome lineages from Solomon Islands fall within the range of other Island Melanesian populations but display markedly lower haplogroup diversity. From a broad Indo-Pacific perspective, Y-chromosome lineages show partial association with the distribution of language groups: O-M175 is associated spatially with Austronesian-speaking areas, whereas M-M106 broadly correlates with the distribution of Papuan languages. However, no relationship between Y-chromosome lineages and language affiliation was observed on a small scale within Solomon Islands. This pattern may result from a sampling strategy that targeted small communities, where individual Y-chromosome lineages can be fixed or swept to extinction by genetic drift or favored paternal exogamy.
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Affiliation(s)
- Murray P Cox
- Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Downing Street, Cambridge, United Kingdom.
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560
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Bertoni B, Jin L, Chakraborty R, Sans M. Directional mating and a rapid male population expansion in a hybrid Uruguayan population. Am J Hum Biol 2005; 17:801-8. [PMID: 16254907 DOI: 10.1002/ajhb.20443] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The Uruguayan population has been considered as mainly European descent, with a negligible Native American or African contributions. Based on serological and molecular markers, recent studies demonstrate that these two populations had an important influence in the conformation of the present one. To the Northeastern region of Uruguay, a 20% Native American contribution was estimated using autosomal markers and a 62% Native American female origin based on mitochondrial markers. In this paper, we analyze four Y chromosome markers, two biallelic loci (M3 and YAP) and two microsatellites (DYS389I and DYS391), to characterize the male genetic contribution of a sample from the Northeastern city of Tacuarembó. We take different approaches to estimate the origin of male contributions to the population of Tacuarembó; Native American contribution ranges between 1.60% and 8.31%, confirming strong directional mating, which was also detected before with mitochondrial markers. Furthermore, the male population of Tacuarembó presents the characteristic of a population that suffered a bottleneck and a posterior expansion, confirmed using two microsatellite-based statistics to analyze the past population growth; patrilocality and migration could be responsible of those characteristics.
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Affiliation(s)
- Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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561
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Martinez L, Reategui EP, Fonseca LR, Sierra-Montes JM, Terreros MC, Pereira-Simon S, Herrera RJ. Superimposing Polymorphism: The Case of a Point Mutation within a Polymorphic Alu Insertion. Hum Hered 2005; 59:109-17. [PMID: 15838180 DOI: 10.1159/000085225] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2004] [Accepted: 01/25/2005] [Indexed: 11/19/2022] Open
Abstract
The COL3A1 Alu insertion is a member of the AluY subfamily. It has been found to be absent in non-human primates and polymorphic in worldwide human populations. The integration of the element into the human genome seems to have preceded the initial migration(s) of anatomically modern humans out of the African continent. Although the insertion has been detected in populations from all the continents, its highest frequency values are located within sub-Saharan Africa. The sequence alignment of the COL3A1 insertion from several African individuals revealed a bi-allelic single nucleotide polymorphism (SNP) at the downstream terminus of the element's poly-A tract. Once discovered, a selective PCR procedure was designed to determine the frequency of both alleles in 19 worldwide populations. The A-allele in this binary SNP experiences a clinal increase in the eastward direction from Africa to Southeast Asia and Mongolia, reaching fixation in the two latter regions. The T variant, on the other hand, exhibits a westward clinal increase outside of Africa, with its lowest frequency in Asia and achieving fixation in northern Europe. The presence of this internal SNP extends the usefulness provided by the polymorphic Alu insertion (PAI). It is possible that superimposing polymorphisms like this one found in the COL3A1 locus may accentuate signals from genetic drift events allowing for visualization of recent dispersal patterns.
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Affiliation(s)
- Laisel Martinez
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
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562
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Chaix R, Austerlitz F, Khegay T, Jacquesson S, Hammer MF, Heyer E, Quintana-Murci L. The genetic or mythical ancestry of descent groups: lessons from the Y chromosome. Am J Hum Genet 2004; 75:1113-6. [PMID: 15467979 PMCID: PMC1182146 DOI: 10.1086/425938] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Accepted: 09/09/2004] [Indexed: 11/03/2022] Open
Abstract
Traditional societies are often organized into descent groups called "lineages," "clans," and "tribes." Each of these descent groups claims to have a common ancestor, and this ancestry distinguishes the group's members from the rest of the population. To test the hypothesis of common ancestry within these groups, we compared ethnological and genetic data from five Central Asian populations. We show that, although people from the same lineage and clan share generally a recent common ancestor, no such common ancestry is observed at the tribal level. Thus, a tribe might be a conglomerate of clans who subsequently invented a mythical ancestor to strengthen group unity.
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Affiliation(s)
- Raphaëlle Chaix
- Unité d’Eco-Anthropologie, Centre National de la Recherche Scientifique (CNRS) UMR 5145/Université Paris 7, Musée de l'Homme, and CNRS URA 1961, Unit of Molecular Prevention and Therapy of Human Diseases, Institut Pasteur, Paris; Laboratoire Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France; Institute of Immunology, Academy of Sciences, and Institut Français d’Etudes sur l’Asie Centrale, Tashkent, Uzbekistan; and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson
| | - Frédéric Austerlitz
- Unité d’Eco-Anthropologie, Centre National de la Recherche Scientifique (CNRS) UMR 5145/Université Paris 7, Musée de l'Homme, and CNRS URA 1961, Unit of Molecular Prevention and Therapy of Human Diseases, Institut Pasteur, Paris; Laboratoire Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France; Institute of Immunology, Academy of Sciences, and Institut Français d’Etudes sur l’Asie Centrale, Tashkent, Uzbekistan; and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson
| | - Tatyana Khegay
- Unité d’Eco-Anthropologie, Centre National de la Recherche Scientifique (CNRS) UMR 5145/Université Paris 7, Musée de l'Homme, and CNRS URA 1961, Unit of Molecular Prevention and Therapy of Human Diseases, Institut Pasteur, Paris; Laboratoire Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France; Institute of Immunology, Academy of Sciences, and Institut Français d’Etudes sur l’Asie Centrale, Tashkent, Uzbekistan; and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson
| | - Svetlana Jacquesson
- Unité d’Eco-Anthropologie, Centre National de la Recherche Scientifique (CNRS) UMR 5145/Université Paris 7, Musée de l'Homme, and CNRS URA 1961, Unit of Molecular Prevention and Therapy of Human Diseases, Institut Pasteur, Paris; Laboratoire Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France; Institute of Immunology, Academy of Sciences, and Institut Français d’Etudes sur l’Asie Centrale, Tashkent, Uzbekistan; and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson
| | - Michael F. Hammer
- Unité d’Eco-Anthropologie, Centre National de la Recherche Scientifique (CNRS) UMR 5145/Université Paris 7, Musée de l'Homme, and CNRS URA 1961, Unit of Molecular Prevention and Therapy of Human Diseases, Institut Pasteur, Paris; Laboratoire Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France; Institute of Immunology, Academy of Sciences, and Institut Français d’Etudes sur l’Asie Centrale, Tashkent, Uzbekistan; and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson
| | - Evelyne Heyer
- Unité d’Eco-Anthropologie, Centre National de la Recherche Scientifique (CNRS) UMR 5145/Université Paris 7, Musée de l'Homme, and CNRS URA 1961, Unit of Molecular Prevention and Therapy of Human Diseases, Institut Pasteur, Paris; Laboratoire Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France; Institute of Immunology, Academy of Sciences, and Institut Français d’Etudes sur l’Asie Centrale, Tashkent, Uzbekistan; and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson
| | - Lluís Quintana-Murci
- Unité d’Eco-Anthropologie, Centre National de la Recherche Scientifique (CNRS) UMR 5145/Université Paris 7, Musée de l'Homme, and CNRS URA 1961, Unit of Molecular Prevention and Therapy of Human Diseases, Institut Pasteur, Paris; Laboratoire Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France; Institute of Immunology, Academy of Sciences, and Institut Français d’Etudes sur l’Asie Centrale, Tashkent, Uzbekistan; and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson
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563
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Hucklenbroich K, Gromoll J, Heinrich M, Hohoff C, Nieschlag E, Simoni M. Partial deletions in the AZFc region of the Y chromosome occur in men with impaired as well as normal spermatogenesis. Hum Reprod 2004; 20:191-7. [PMID: 15498781 DOI: 10.1093/humrep/deh558] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Partial deletions of the AZFc region of the Y chromosome were reported to be a significant risk factor for oligo-/azoospermia. In this study, we assessed the occurrence and frequency of partial AZFc microdeletions in patients with spermatogenic failure and in controls with normal spermatogenesis. METHODS In a retrospective study design, gr/gr, b1/b3 and b2/b3 deletions were analysed by multiplex PCR in 170 men with normal spermatogenesis and 348 men with non-obstructive oligo-/azoospermia. RESULTS gr/gr deletions were found in 14 men with oligozoospermia or azoospermia (4.0%) and in three normozoospermic men (1.8%) (NS). b1/b3 deletions were found both in controls (n=1) and in patients (n=1). b2/b3 deletions were significantly more frequent in the normozoospermic (five out of 170) than in the oligo-/azoospermic men (two out of 348). Three novel partial AZFc deletion patterns were found in four oligo-/azoospermic men. No correlation with semen or other clinical parameters was found. CONCLUSIONS The frequency of gr/gr deletions is not significantly increased in men with oligo-/azoospermia, indicating that they are not sufficient per se to cause spermatogenetic impairment and infertility. b1/b3 and b2/b3 deletions are probably irrelevant for spermatogenesis. Novel deletion patterns found exclusively in infertile men suggest that other, still unexplored partial deletions might contribute to spermatogenic failure.
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Affiliation(s)
- K Hucklenbroich
- Institute of Reproductive Medicine and Institute of Legal Medicine, University of Münster, D-48149 Münster, Germany
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564
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Moran CN, Scott RA, Adams SM, Warrington SJ, Jobling MA, Wilson RH, Goodwin WH, Georgiades E, Wolde B, Pitsiladis YP. Y chromosome haplogroups of elite Ethiopian endurance runners. Hum Genet 2004; 115:492-7. [PMID: 15503146 DOI: 10.1007/s00439-004-1202-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2004] [Accepted: 09/14/2004] [Indexed: 10/26/2022]
Abstract
Favourable genetic endowment has been proposed as part of the explanation for the success of East African endurance athletes, but no evidence has yet been presented. The Y chromosome haplogroup distribution of elite Ethiopian athletes (n=62) was compared with that of the general Ethiopian population (n=95) and a control group from Arsi (a region producing a disproportionate number of athletes; n=85). Athletes belonged to three groups: marathon runners (M; n=23), 5-km to 10-km runners (5-10K; n=21) and other track and field athletes (TF; n=18). DNA was extracted from buccal swabs and haplogroups were assigned after the typing of binary markers in multiplexed minisequencing reactions. Frequency differences between groups were assessed by using contingency exact tests and showed that Y chromosome haplogroups are not distributed amongst elite Ethiopian endurance runners in the same proportions as in the general population, with statistically significant (P<0.05) differences being found in four of the individual haplogroups. The geographical origins and languages of the athletes and controls suggest that these differences are less likely to be a reflection of population structure and that Y chromosome haplogroups may play a significant role in determining Ethiopian endurance running success.
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Affiliation(s)
- Colin N Moran
- International Centre for East African Running Science (ICEARS), Institute of Biomedical and Life Sciences, University of Glasgow, West Medical Building, Glasgow, G12 8QQ, UK
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565
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Wen B, Li H, Lu D, Song X, Zhang F, He Y, Li F, Gao Y, Mao X, Zhang L, Qian J, Tan J, Jin J, Huang W, Deka R, Su B, Chakraborty R, Jin L. Genetic evidence supports demic diffusion of Han culture. Nature 2004; 431:302-5. [PMID: 15372031 DOI: 10.1038/nature02878] [Citation(s) in RCA: 268] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2004] [Accepted: 07/20/2004] [Indexed: 11/09/2022]
Abstract
The spread of culture and language in human populations is explained by two alternative models: the demic diffusion model, which involves mass movement of people; and the cultural diffusion model, which refers to cultural impact between populations and involves limited genetic exchange between them. The mechanism of the peopling of Europe has long been debated, a key issue being whether the diffusion of agriculture and language from the Near East was concomitant with a large movement of farmers. Here we show, by systematically analysing Y-chromosome and mitochondrial DNA variation in Han populations, that the pattern of the southward expansion of Han culture is consistent with the demic diffusion model, and that males played a larger role than females in this expansion. The Han people, who all share the same culture and language, exceed 1.16 billion (2000 census), and are by far the largest ethnic group in the world. The expansion process of Han culture is thus of great interest to researchers in many fields.
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Affiliation(s)
- Bo Wen
- State Key Laboratory of Genetic Engineering and Center for Anthropological Studies, School of Life Sciences and Morgan-Tan International Center for Life Sciences, Fudan University, Shanghai 200433, China
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566
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Abstract
Sherlock Holmes said "it has long been an axiom of mine that the little things are infinitely the most important", but never imagined that such a little thing, the DNA molecule, could become perhaps the most powerful single tool in the multifaceted fight against crime. Twenty years after the development of DNA fingerprinting, forensic DNA analysis is key to the conviction or exoneration of suspects and the identification of victims of crimes, accidents and disasters, driving the development of innovative methods in molecular genetics, statistics and the use of massive intelligence databases.
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Affiliation(s)
- Mark A Jobling
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom.
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567
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Vogt PH. Genomic heterogeneity and instability of the AZF locus on the human Y chromosome. Mol Cell Endocrinol 2004; 224:1-9. [PMID: 15353175 DOI: 10.1016/j.mce.2004.06.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2004] [Revised: 06/04/2004] [Accepted: 06/11/2004] [Indexed: 12/30/2022]
Abstract
The spermatogenesis locus azoospermia factor (AZF) in Yq11 has been mapped to three microdeletion intervals designated as AZFa, AZFb, and AZFc. They are caused by intrachromosomal recombination events between large homologous repetitive sequence blocks, and AZFc microdeletions are now recognised as the most frequent known genetic lesion causing male infertility. However, in the same Y-region, large genomic heterogeneities are also observed in fertile men, and only complete AZFa and AZFb deletions are associated with a specific testicular pathology. Partial AZF deletions are associated with variable pathologies and partial AZFc deletions may even have no impact on male fertility. This suggests a genetic redundancy of the multi-copy genes in AZFb and AZFc and a causative relationship between the occurrence of first microdeletions then macrodeletions in the repetitive structure of Yq11 where large palindromes are probably promoting multiple gene conversions and AZF rearrangements.
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Affiliation(s)
- Peter H Vogt
- Section of Molecular Genetics and Infertility, Department of Gynecological Endocrinology and Reproductive Medicine, University of Heidelberg, Vossstrasse 9, D-69115 Heidelberg, FRG, Heidelberg, Germany.
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568
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Craig IW, Harper E, Loat CS. The genetic basis for sex differences in human behaviour: role of the sex chromosomes. Ann Hum Genet 2004; 68:269-84. [PMID: 15180708 DOI: 10.1046/j.1529-8817.2004.00098.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The nature of the mechanisms underlying observed sex differences in human behaviour continues to be debated. This review concentrates on the thesis that genes on the sex chromosomes other than those directly controlling sex determination, and whose functions are, at least in part, independent from hormonal influences, play a significant role in determining gender differences in behaviour. To provide an adequate basis for examining this issue, the current understanding of the nature of sex determination, differences in behaviour and the influences of sex hormones are evaluated. The possible contribution to behavioural differences of those X-linked genes which escape inactivation, or which may be subjected to imprinting, is discussed. The review concludes with a summary of the genetic basis for two sexually disparate types of behaviour.
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Affiliation(s)
- Ian W Craig
- SGDP Centre, Box PO 82, Institute of Psychiatry, Denmark Hill, London SE5, UK.
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569
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Fernandes S, Paracchini S, Meyer L, Floridia G, Tyler-Smith C, Vogt PH. Reply to Repping et al. Am J Hum Genet 2004. [DOI: 10.1086/423395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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570
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Maca-Meyer N, Villar J, Pérez-Méndez L, Cabrera de León A, Flores C. A Tale of Aborigines, Conquerors and Slaves: Alu Insertion Polymorphisms and the Peopling of Canary Islands. Ann Hum Genet 2004; 68:600-5. [PMID: 15598218 DOI: 10.1046/j.1529-8817.2003.00125.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Classical, mitochondrial DNA (mtDNA) and Y chromosome markers have been used to examine the genetic admixture in present day inhabitants of the Canary Islands. In this study, we report the analysis of ten autosomal Alu insertion polymorphisms in 364 samples from the seven main islands of the Archipelago, and their comparison to continental samples. The detection of population-specific alleles from the Iberian Peninsula and Northwest Africa, as well as their affinities on the basis of genetic distances and principal component analysis, support a clear link between these populations. Coincident with previous results, the Canarian gene pool can be distinguished as being halfway between those of its putative parents, although with a major Iberian contribution (62-78%). Both the substantial Northwest African contribution (23-38%), and the minor sub-Saharan African input (3%), suggest that the genetic legacy from the aborigines and slaves still persists in the Canary Islanders.
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Affiliation(s)
- N Maca-Meyer
- Unidad de Investigación, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
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571
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Di Giacomo F, Luca F, Popa LO, Akar N, Anagnou N, Banyko J, Brdicka R, Barbujani G, Papola F, Ciavarella G, Cucci F, Di Stasi L, Gavrila L, Kerimova MG, Kovatchev D, Kozlov AI, Loutradis A, Mandarino V, Mammi' C, Michalodimitrakis EN, Paoli G, Pappa KI, Pedicini G, Terrenato L, Tofanelli S, Malaspina P, Novelletto A. Y chromosomal haplogroup J as a signature of the post-neolithic colonization of Europe. Hum Genet 2004; 115:357-71. [PMID: 15322918 DOI: 10.1007/s00439-004-1168-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2004] [Accepted: 06/21/2004] [Indexed: 10/26/2022]
Abstract
In order to attain a finer reconstruction of the peopling of southern and central-eastern Europe from the Levant, we determined the frequencies of eight lineages internal to the Y chromosomal haplogroup J, defined by biallelic markers, in 22 population samples obtained with a fine-grained sampling scheme. Our results partially resolve a major multifurcation of lineages within the haplogroup. Analyses of molecular variance show that the area covered by haplogroup J dispersal is characterized by a significant degree of molecular radiation for unique event polymorphisms within the haplogroup, with a higher incidence of the most derived sub-haplogroups on the northern Mediterranean coast, from Turkey westward; here, J diversity is not simply a subset of that present in the area in which this haplogroup first originated. Dating estimates, based on simple tandem repeat loci (STR) diversity within each lineage, confirmed the presence of a major population structuring at the time of spread of haplogroup J in Europe and a punctuation in the peopling of this continent in the post-Neolithic, compatible with the expansion of the Greek world. We also present here, for the first time, a novel method for comparative dating of lineages, free of assumptions of STR mutation rates.
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Affiliation(s)
- F Di Giacomo
- Department of Biology, University Tor Vergata, Rome, Italy
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572
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Lopes AM, Calafell F, Amorim A. Microsatellite variation and evolutionary history of PCDHX/Y gene pair within the Xq21.3/Yp11.2 hominid-specific homology block. Mol Biol Evol 2004; 21:2092-101. [PMID: 15297598 DOI: 10.1093/molbev/msh218] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To better understand the evolutionary dynamics of repetitive sequences in human sex chromosomes, we have analyzed seven new X/Y homologous microsatellites located within PCDHX/Y, one of the two recently described gene pairs in the Xq21.3/Yp11.2 hominid-specific homology block, in samples from Portugal and Mozambique. Sharp differences were observed on X/Y allele distributions, concerning both the presence of private alleles and a different modal repeat length for X-linked and Y-linked markers, and this difference was statistically significant. Higher diversity was found in X-linked microsatellites than in their Y chromosome counterparts; when comparing populations, Mozambicans showed more allele diversity for the X chromosome, but the contrary was true for the Y chromosome microsatellites. Evolutionary patterns, relying on intragenic PCDHX/Y SNPs, also revealed distinct scenarios for X and Y chromosomes. Greater microsatellite diversity was displayed by African X chromosomes within the most common haplotypes shared by both populations, whereas higher microsatellite diversity was found in Portugal for the ancestral Y chromosome haplotype. The most frequent PCDHY haplotype in Portuguese was the derived one, and it was not found in Mozambicans. TMRCA estimated by the rho parameter resulted in 13,700 years (7,500-20,000 years), which is consistent with a recent, post-Out-of-Africa origin for this haplotype. In conclusion, the newly described microsatellite loci generally displayed greater X-linked to Y-linked diversity and this pattern was also detected with slower evolving markers, with a remarkable differentiation between populations observed for Y chromosome haplotypes and, thus, greater divergence among Y chromosomes in human populations.
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Affiliation(s)
- Alexandra M Lopes
- IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal.
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573
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Arredi B, Poloni ES, Paracchini S, Zerjal T, Fathallah DM, Makrelouf M, Pascali VL, Novelletto A, Tyler-Smith C. A predominantly neolithic origin for Y-chromosomal DNA variation in North Africa. Am J Hum Genet 2004; 75:338-45. [PMID: 15202071 PMCID: PMC1216069 DOI: 10.1086/423147] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2004] [Accepted: 06/07/2004] [Indexed: 11/04/2022] Open
Abstract
We have typed 275 men from five populations in Algeria, Tunisia, and Egypt with a set of 119 binary markers and 15 microsatellites from the Y chromosome, and we have analyzed the results together with published data from Moroccan populations. North African Y-chromosomal diversity is geographically structured and fits the pattern expected under an isolation-by-distance model. Autocorrelation analyses reveal an east-west cline of genetic variation that extends into the Middle East and is compatible with a hypothesis of demic expansion. This expansion must have involved relatively small numbers of Y chromosomes to account for the reduction in gene diversity towards the West that accompanied the frequency increase of Y haplogroup E3b2, but gene flow must have been maintained to explain the observed pattern of isolation-by-distance. Since the estimates of the times to the most recent common ancestor (TMRCAs) of the most common haplogroups are quite recent, we suggest that the North African pattern of Y-chromosomal variation is largely of Neolithic origin. Thus, we propose that the Neolithic transition in this part of the world was accompanied by demic diffusion of Afro-Asiatic-speaking pastoralists from the Middle East.
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Affiliation(s)
- Barbara Arredi
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Estella S. Poloni
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Silvia Paracchini
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Tatiana Zerjal
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Dahmani M. Fathallah
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Mohamed Makrelouf
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Vincenzo L. Pascali
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Andrea Novelletto
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Chris Tyler-Smith
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore di Roma, Rome; Department of Biochemistry, University of Oxford, Oxford, United Kingdom; Department of Anthropology, University of Geneva, Geneva; Institut Pasteur de Tunis, Tunis, Tunisia; Laboratoire Central, Chu Bab El Oued, Alger, Algeria; Department of Cell Biology, University of Calabria, Rende, Italy; and The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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574
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Shriver MD, Kittles RA. Genetic ancestry and the search for personalized genetic histories. Nat Rev Genet 2004; 5:611-8. [PMID: 15266343 DOI: 10.1038/nrg1405] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mark D Shriver
- Department of Anthropology, Penn State University, University Park, Pennsylvania 16802, USA.
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575
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Flores C, Maca-Meyer N, González AM, Oefner PJ, Shen P, Pérez JA, Rojas A, Larruga JM, Underhill PA. Reduced genetic structure of the Iberian peninsula revealed by Y-chromosome analysis: implications for population demography. Eur J Hum Genet 2004; 12:855-63. [PMID: 15280900 DOI: 10.1038/sj.ejhg.5201225] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Europe has been influenced by both intra- and intercontinental migrations. Since the Iberian peninsula was a refuge during the Last Glacial Maximum, demographic factors associated with contraction, isolation, subsequent expansion and gene flow episodes have contributed complexity to its population history. In this work, we analysed 26 Y-chromosome biallelic markers in 568 chromosomes from 11 different Iberian population groups and compared them to published data on the Basques and Catalans to gain insight into the paternal gene pool of these populations and find out to what extent major demographic processes account for their genetic structure. Our results reveal a reduced, although geographically correlated, Y-chromosomal interpopulation variance (1.2%), which points to a limited heterogeneity in the region. Coincidentally, spatial analysis of genetic distances points to a focal distribution of Y-chromosome haplogroups in this area. These results indicate that neither old or recent Levantine expansions nor North African contacts have influenced the current Iberian Y-chromosome diversity so that geographical patterns can be identified.
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Affiliation(s)
- Carlos Flores
- Departamento de Genética, Universidad de La Laguna, Tenerife E-38271, Spain.
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576
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Rootsi S, Magri C, Kivisild T, Benuzzi G, Help H, Bermisheva M, Kutuev I, Barać L, Pericić M, Balanovsky O, Pshenichnov A, Dion D, Grobei M, Zhivotovsky LA, Battaglia V, Achilli A, Al-Zahery N, Parik J, King R, Cinnioğlu C, Khusnutdinova E, Rudan P, Balanovska E, Scheffrahn W, Simonescu M, Brehm A, Goncalves R, Rosa A, Moisan JP, Chaventre A, Ferak V, Füredi S, Oefner PJ, Shen P, Beckman L, Mikerezi I, Terzić R, Primorac D, Cambon-Thomsen A, Krumina A, Torroni A, Underhill PA, Santachiara-Benerecetti AS, Villems R, Semino O. Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in europe. Am J Hum Genet 2004; 75:128-37. [PMID: 15162323 PMCID: PMC1181996 DOI: 10.1086/422196] [Citation(s) in RCA: 184] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2004] [Accepted: 04/26/2004] [Indexed: 11/03/2022] Open
Abstract
To investigate which aspects of contemporary human Y-chromosome variation in Europe are characteristic of primary colonization, late-glacial expansions from refuge areas, Neolithic dispersals, or more recent events of gene flow, we have analyzed, in detail, haplogroup I (Hg I), the only major clade of the Y phylogeny that is widespread over Europe but virtually absent elsewhere. The analysis of 1,104 Hg I Y chromosomes, which were identified in the survey of 7,574 males from 60 population samples, revealed several subclades with distinct geographic distributions. Subclade I1a accounts for most of Hg I in Scandinavia, with a rapidly decreasing frequency toward both the East European Plain and the Atlantic fringe, but microsatellite diversity reveals that France could be the source region of the early spread of both I1a and the less common I1c. Also, I1b*, which extends from the eastern Adriatic to eastern Europe and declines noticeably toward the southern Balkans and abruptly toward the periphery of northern Italy, probably diffused after the Last Glacial Maximum from a homeland in eastern Europe or the Balkans. In contrast, I1b2 most likely arose in southern France/Iberia. Similarly to the other subclades, it underwent a postglacial expansion and marked the human colonization of Sardinia approximately 9,000 years ago.
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Affiliation(s)
- Siiri Rootsi
- Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Riia, Tartu, Estonia.
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577
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Kayser M, Kittler R, Erler A, Hedman M, Lee AC, Mohyuddin A, Mehdi SQ, Rosser Z, Stoneking M, Jobling MA, Sajantila A, Tyler-Smith C. A comprehensive survey of human Y-chromosomal microsatellites. Am J Hum Genet 2004; 74:1183-97. [PMID: 15195656 PMCID: PMC1182082 DOI: 10.1086/421531] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2004] [Accepted: 03/17/2004] [Indexed: 11/03/2022] Open
Abstract
We have screened the nearly complete DNA sequence of the human Y chromosome for microsatellites (short tandem repeats) that meet the criteria of having a repeat-unit size of > or = 3 and a repeat count of > or = 8 and thus are likely to be easy to genotype accurately and to be polymorphic. Candidate loci were tested in silico for novelty and for probable Y specificity, and then they were tested experimentally to identify Y-specific loci and to assess their polymorphism. This yielded 166 useful new Y-chromosomal microsatellites, 139 of which were polymorphic, in a sample of eight diverse Y chromosomes representing eight Y-SNP haplogroups. This large sample of microsatellites, together with 28 previously known markers analyzed here--all sharing a common evolutionary history--allowed us to investigate the factors influencing their variation. For simple microsatellites, the average repeat count accounted for the highest proportion of repeat variance (approximately 34%). For complex microsatellites, the largest proportion of the variance (again, approximately 34%) was explained by the average repeat count of the longest homogeneous array, which normally is variable. In these complex microsatellites, the additional repeats outside the longest homogeneous array significantly increased the variance, but this was lower than the variance of a simple microsatellite with the same total repeat count. As a result of this work, a large number of new, highly polymorphic Y-chromosomal microsatellites are now available for population-genetic, evolutionary, genealogical, and forensic investigations.
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Affiliation(s)
- Manfred Kayser
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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578
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Bosch E, Hurles ME, Navarro A, Jobling MA. Dynamics of a human interparalog gene conversion hotspot. Genome Res 2004; 14:835-44. [PMID: 15123583 PMCID: PMC479110 DOI: 10.1101/gr.2177404] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Accepted: 02/16/2004] [Indexed: 11/25/2022]
Abstract
Gene conversion between paralogs can alter their patterns of sequence identity, thus obscuring their evolutionary relationships and affecting their propensity to sponsor genomic rearrangements. The details of this important process are poorly understood in the human genome because allelic diversity complicates the interpretation of interparalog sequence differences. Here we exploit the haploid nature of the Y chromosome, which obviates complicating interallelic processes, together with its known phylogeny, to understand the dynamics of conversion between two directly repeated HERVs flanking the 780-kb AZFa region on Yq. Sequence analysis of a 787-bp segment of each of the HERVs in 36 Y chromosomes revealed one of the highest nucleotide diversities in the human genome, as well as evidence of a complex patchwork of highly directional gene conversion events. The rate of proximal-to-distal conversion events was estimated as 2.4 x 10(-4) to 1.2 x 10(-3) per generation (3.9 x 10(-7) to 1.9 x 10(-6) per base per generation), and the distal-to-proximal rate as about one-twentieth of this. Minimum observed conversion tract lengths ranged from 1 to 158 bp and maximum lengths from 19 to 1365 bp, with an estimated mean of 31 bp. Analysis of great ape homologs shows that conversion in this hotspot has a deep evolutionary history.
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Affiliation(s)
- Elena Bosch
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
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Cruciani F, La Fratta R, Santolamazza P, Sellitto D, Pascone R, Moral P, Watson E, Guida V, Colomb EB, Zaharova B, Lavinha J, Vona G, Aman R, Calì F, Akar N, Richards M, Torroni A, Novelletto A, Scozzari R. Phylogeographic analysis of haplogroup E3b (E-M215) y chromosomes reveals multiple migratory events within and out of Africa. Am J Hum Genet 2004; 74:1014-22. [PMID: 15042509 PMCID: PMC1181964 DOI: 10.1086/386294] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Accepted: 02/06/2004] [Indexed: 11/04/2022] Open
Abstract
We explored the phylogeography of human Y-chromosomal haplogroup E3b by analyzing 3401 individuals from five continents. Our data refine the phylogeny of the entire haplogroup, which appears as a collection of lineages with very different evolutionary histories, and reveal signatures of several distinct processes of migrations and/or recurrent gene flow that occurred in Africa and western Eurasia over the past 25000 years. In Europe, the overall frequency pattern of haplogroup E-M78 does not support the hypothesis of a uniform spread of people from a single parental Near Eastern population. The distribution of E-M81 chromosomes in Africa closely matches the present area of distribution of Berber-speaking populations on the continent, suggesting a close haplogroup-ethnic group parallelism. E-M34 chromosomes were more likely introduced in Ethiopia from the Near East. In conclusion, the present study shows that earlier work based on fewer Y-chromosome markers led to rather simple historical interpretations and highlights the fact that many population-genetic analyses are not robust to a poorly resolved phylogeny.
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Affiliation(s)
- Fulvio Cruciani
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Roberta La Fratta
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Piero Santolamazza
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Daniele Sellitto
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Roberto Pascone
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Pedro Moral
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Elizabeth Watson
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Valentina Guida
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Eliane Beraud Colomb
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Boriana Zaharova
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - João Lavinha
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Giuseppe Vona
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Rashid Aman
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Francesco Calì
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Nejat Akar
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Martin Richards
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Antonio Torroni
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Andrea Novelletto
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
| | - Rosaria Scozzari
- Dipartimento di Genetica e Biologia Molecolare and Dipartimento di Scienze Ginecologiche Perinatologia e Puericultura, Università “La Sapienza,” Istituto di Biologia e Patologia Molecolare del Consiglio Nazionale delle Ricerche, and Istituto Casa Sollievo della Sofferenza-Mendel, Rome; Departament de Biologia Animal, Universitat de Barcelona, Barcelona; The Swedish Museum of Natural History, Stockholm; Laboratoire d’Immunologie, Hôpital de Sainte-Marguerite, Marseille; Laboratory of Molecular Pathology, University Hospital of Obstetrics and Gynecology, Sofia, Bulgaria; Centro de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal; Dipartimento di Biologia Sperimentale, Università di Cagliari, Cagliari, Italy; Department of Molecular Genetics, National Museums of Kenya, and African Centre for Clinical Trials, Nairobi; Laboratorio di Genetica Molecolare, Istituto per la Ricerca sul Ritardo Mentale e l'Involuzione Cerebrale, Associazione Oasi Maria SS, Troina, Italy; Pediatrics Department, Ankara University, Ankara, Turkey; Schools of Biology and Computing, University of Leeds, Leeds, United Kingdom; Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; and Dipartimento di Biologia Cellulare, Università della Calabria, Rende, Italy
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Zheng HY, Zhao P, Suganami H, Ohasi Y, Ikegaya H, Kim JC, Sugimoto C, Takasaka T, Kitamura T, Yogo Y. Regional distribution of two related Northeast Asian genotypes of JC virus, CY-a and -b: implications for the dispersal of Northeast Asians. Microbes Infect 2004; 6:596-603. [PMID: 15158194 DOI: 10.1016/j.micinf.2004.02.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2003] [Accepted: 02/20/2004] [Indexed: 11/24/2022]
Abstract
JC virus (JCV) is a useful marker to trace human dispersal. Two genotypes of JCV (MY and CY) are mainly distributed in Northeast Asia. The population history of people carrying MY has been studied in some detail but that of people carrying CY remains poorly understood. To gain insights into the population history of Northeast Asians carrying CY we analyzed the genetic variation in CY isolates. We constructed a neighbor-joining phylogenetic tree from 28 complete CY DNA sequences: on the resultant tree the CY DNA sequences diverged into two clades, designated CY-a and -b, each clustered with a high bootstrap probability. The split into CY-a and -b was estimated to have occurred about 10 000 years ago, based on K(s) values (synonymous substitutions per synonymous site) and the suggested rate of synonymous nucleotide substitutions. Comparison of the 28 complete CY sequences revealed six nucleotide mismatches between CY-a and -b, one of which showed a restriction fragment length polymorphism (RFLP). We then PCR-amplified a region of the genome containing this polymorphic site from many CY isolates in various Northeast Asian populations and classified the isolates into CY-a or -b according to the RFLP analysis. CY-a was more abundant than CY-b in various Chinese and Japanese populations but CY-b was more abundant than CY-a in South Koreans. On the basis of the present findings we inferred the population history in East Asians carrying CY.
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Affiliation(s)
- Huai-Ying Zheng
- Department of Urology, Faculty of Medicine, The University of Tokyo, Hongo 7-3-1, Tokyo 113-8655, Japan.
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Semino O, Magri C, Benuzzi G, Lin AA, Al-Zahery N, Battaglia V, Maccioni L, Triantaphyllidis C, Shen P, Oefner PJ, Zhivotovsky LA, King R, Torroni A, Cavalli-Sforza LL, Underhill PA, Santachiara-Benerecetti AS. Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area. Am J Hum Genet 2004; 74:1023-34. [PMID: 15069642 PMCID: PMC1181965 DOI: 10.1086/386295] [Citation(s) in RCA: 265] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Accepted: 02/06/2004] [Indexed: 11/03/2022] Open
Abstract
The phylogeography of Y-chromosome haplogroups E (Hg E) and J (Hg J) was investigated in >2400 subjects from 29 populations, mainly from Europe and the Mediterranean area but also from Africa and Asia. The observed 501 Hg E and 445 Hg J samples were subtyped using 36 binary markers and eight microsatellite loci. Spatial patterns reveal that (1). the two sister clades, J-M267 and J-M172, are distributed differentially within the Near East, North Africa, and Europe; (2). J-M267 was spread by two temporally distinct migratory episodes, the most recent one probably associated with the diffusion of Arab people; (3). E-M81 is typical of Berbers, and its presence in Iberia and Sicily is due to recent gene flow from North Africa; (4). J-M172(xM12) distribution is consistent with a Levantine/Anatolian dispersal route to southeastern Europe and may reflect the spread of Anatolian farmers; and (5). E-M78 (for which microsatellite data suggest an eastern African origin) and, to a lesser extent, J-M12(M102) lineages would trace the subsequent diffusion of people from the southern Balkans to the west. A 7%-22% contribution of Y chromosomes from Greece to southern Italy was estimated by admixture analysis.
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Affiliation(s)
- Ornella Semino
- Dipartimento di Genetica e Microbiologia, Universita di Pavia, 27100 Pavia, Italy.
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582
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Brion M, Sobrino B, Blanco-Verea A, Lareu MV, Carracedo A. Hierarchical analysis of 30 Y-chromosome SNPs in European populations. Int J Legal Med 2004; 119:10-5. [PMID: 15095093 DOI: 10.1007/s00414-004-0439-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2003] [Accepted: 03/02/2004] [Indexed: 10/26/2022]
Abstract
Analysis of Y-chromosome haplogroups defined by binary polymorphisms, has became a standard approach for studying the origin of modern human populations and for measuring the variability between them. Furthermore, the simplicity and population specificity of binary polymorphisms allows inferences to be drawn about the population origin of any male sample of interest for forensic purposes. From the 245 binary polymorphisms that can be analysed by PCR described in the Y Chromosome Consortium tree, we have selected 30 markers. The set of 30 has been grouped into 4 multiplexes in order to determine the most frequent haplogroups in Europe, using only 1 or 2 multiplexes. In this way, we avoid typing unnecessary SNPs to define the final haplogroup saving effort and cost, since we only need to type 9 SNPs in the best case and in the worst case, no more than 17 SNPs to define the haplogroup. The selected method for allele discrimination was a single base extension reaction using the SNaPshot multiplex kit. A total of 292 samples from 8 different districts of Galicia (northwest Spain) were analysed with this strategy. No significant differences were detected among the different districts, except for the population from Marina Lucense, which showed a distant haplogroup frequency but not higher Phi(st) values.
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Affiliation(s)
- M Brion
- Institute of Legal Medicine, University of Santiago de Compostela, San Francisco s/n, 15782 Santiago de Compostela, Spain.
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583
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Niederstätter H, Berger B, Oberacher H, Brandstätter A, Huber CG, Parson W. Separate analysis of DYS385a and b versus conventional DYS385 typing: is there forensic relevance? Int J Legal Med 2004; 119:1-9. [PMID: 15071745 DOI: 10.1007/s00414-004-0437-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2003] [Accepted: 03/03/2004] [Indexed: 11/30/2022]
Abstract
In order to determine to what extent the separate analysis of both copies of DYS385 improves Y-chromosomal short tandem repeat (Y-STR) haplotyping, we followed a recently published protocol for the separate amplification of DYS385a and DYS385b with modifications and compared the results with those obtained by conventional analysis in a population sample comprising 133 unrelated Caucasian males from Austria. Additionally, we typed all markers of the minimal haplotype (minHT) and a set of Y-chromosomal single nucleotide polymorphisms (Y-SNPs) in order to interpret the STR data depending on the Y-SNP haplogroup structure. The separate amplification of DYS385a and b improved the power of discrimination of this marker when compared to the results obtained with the conventional non-locus-discriminating amplification strategy. However, the degree of this improvement varied greatly between different haplogroups and was found to be highest in clade K. In the forensically relevant context of the minHT, the separate analysis of the DYS385 alleles had no effect on the differentiation of paternal lineages in our study. Furthermore, the amplicon lengths of 700-780 base pairs obtained in the course of the locus-discriminating approach restrict the applicability of this amplification strategy to high quality DNA samples.
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Affiliation(s)
- Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstrasse 44, 6020 Innsbruck, Austria
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584
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Sanchez JJ, Brión M, Parson W, Blanco-Verea AJ, Børsting C, Lareu M, Niederstätter H, Oberacher H, Morling N, Carracedo A. Duplications of the Y-chromosome specific loci P25 and 92R7 and forensic implications. Forensic Sci Int 2004; 140:241-50. [PMID: 15036445 DOI: 10.1016/j.forsciint.2003.11.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2003] [Revised: 10/11/2003] [Accepted: 11/20/2003] [Indexed: 11/23/2022]
Abstract
In the present study, we demonstrate that two commonly used Y-chromosome single nucleotide polymorphisms (SNPs), P25 and 92R7, are paralogous sequence variants (PSVs) originating from segmental duplications and that at least one of the sequence variants in each group of loci is polymorphic. Several methodologies were used in order to detect the SNP alleles and the PSVs of the loci. All results obtained with the various typing techniques supported the conclusion. The allele distributions of the binary markers were analysed in more than 600 males with seven different haplogroups. For P25, the ancestral allele C was found in several samples from different haplogroups. The derived allele A was always present with an additional C variant. Haplogroup P was defined by the derived allele A at the 92R7 locus. However, the ancestral allele G was always associated with an A variant due to the duplication.
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Affiliation(s)
- Juan J Sanchez
- Department of Forensic Genetics, Institute of Forensic Medicine, University of Copenhagen, 11 Frederik V's Vej, DK-2100 Copenhagen, Denmark.
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585
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Butler JM, Schoske R. Duplication of DYS19 flanking regions in other parts of the Y chromosome. Int J Legal Med 2004; 118:178-83. [PMID: 15069570 DOI: 10.1007/s00414-004-0436-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2003] [Accepted: 03/02/2004] [Indexed: 10/26/2022]
Abstract
During the testing of alternative primers for the Y chromosome short tandem repeat marker DYS19, a duplicated region of the Y chromosome was discovered. The duplicated sequence is contained within GenBank accession AC006335 and has a high degree of homology with the DYS19 flanking region (GenBank accession AC017019) but without the polymorphic TAGA repeat. Bioinformatic approaches have been taken to try and understand the implications of this homolog to enable improved primer design for DYS19. Sequence alignments and careful placement of primers in order to obtain specific amplification of the DYS19 locus are discussed in the context of all previously published primer sets. Since the DYS19 locus is part of the widely used minimal haplotype, its robust amplification is highly desirable particularly in multiplex reactions. The discovery of this duplicated region of the Y chromosome shows the value of newly available human genome sequence information for assay design and the importance of using sequence queries and alignments in the primer design process.
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Affiliation(s)
- John M Butler
- Biotechnology Division, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 8311, Gaithersburg, MD 20899, USA.
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586
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Sanchez J, Børsting C, Hernandez A, Mengel-Jørgensen J, Morling N. Y chromosome SNP haplogroups in Danes, Greenlanders and Somalis. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0531-5131(03)01635-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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587
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588
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Tambets K, Rootsi S, Kivisild T, Help H, Serk P, Loogväli EL, Tolk HV, Reidla M, Metspalu E, Pliss L, Balanovsky O, Pshenichnov A, Balanovska E, Gubina M, Zhadanov S, Osipova L, Damba L, Voevoda M, Kutuev I, Bermisheva M, Khusnutdinova E, Gusar V, Grechanina E, Parik J, Pennarun E, Richard C, Chaventre A, Moisan JP, Barác L, Pericić M, Rudan P, Terzić R, Mikerezi I, Krumina A, Baumanis V, Koziel S, Rickards O, De Stefano GF, Anagnou N, Pappa KI, Michalodimitrakis E, Ferák V, Füredi S, Komel R, Beckman L, Villems R. The western and eastern roots of the Saami--the story of genetic "outliers" told by mitochondrial DNA and Y chromosomes. Am J Hum Genet 2004; 74:661-82. [PMID: 15024688 PMCID: PMC1181943 DOI: 10.1086/383203] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2003] [Accepted: 01/16/2004] [Indexed: 11/03/2022] Open
Abstract
The Saami are regarded as extreme genetic outliers among European populations. In this study, a high-resolution phylogenetic analysis of Saami genetic heritage was undertaken in a comprehensive context, through use of maternally inherited mitochondrial DNA (mtDNA) and paternally inherited Y-chromosomal variation. DNA variants present in the Saami were compared with those found in Europe and Siberia, through use of both new and previously published data from 445 Saami and 17,096 western Eurasian and Siberian mtDNA samples, as well as 127 Saami and 2,840 western Eurasian and Siberian Y-chromosome samples. It was shown that the "Saami motif" variant of mtDNA haplogroup U5b is present in a large area outside Scandinavia. A detailed phylogeographic analysis of one of the predominant Saami mtDNA haplogroups, U5b1b, which also includes the lineages of the "Saami motif," was undertaken in 31 populations. The results indicate that the origin of U5b1b, as for the other predominant Saami haplogroup, V, is most likely in western, rather than eastern, Europe. Furthermore, an additional haplogroup (H1) spread among the Saami was virtually absent in 781 Samoyed and Ob-Ugric Siberians but was present in western and central European populations. The Y-chromosomal variety in the Saami is also consistent with their European ancestry. It suggests that the large genetic separation of the Saami from other Europeans is best explained by assuming that the Saami are descendants of a narrow, distinctive subset of Europeans. In particular, no evidence of a significant directional gene flow from extant aboriginal Siberian populations into the haploid gene pools of the Saami was found.
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Affiliation(s)
- Kristiina Tambets
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia.
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589
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Luis JR, Rowold DJ, Regueiro M, Caeiro B, Cinnioğlu C, Roseman C, Underhill PA, Cavalli-Sforza LL, Herrera RJ. The Levant versus the Horn of Africa: evidence for bidirectional corridors of human migrations. Am J Hum Genet 2004; 74:532-44. [PMID: 14973781 PMCID: PMC1182266 DOI: 10.1086/382286] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2003] [Accepted: 12/16/2003] [Indexed: 11/04/2022] Open
Abstract
Paleoanthropological evidence indicates that both the Levantine corridor and the Horn of Africa served, repeatedly, as migratory corridors between Africa and Eurasia. We have begun investigating the roles of these passageways in bidirectional migrations of anatomically modern humans, by analyzing 45 informative biallelic markers as well as 10 microsatellite loci on the nonrecombining region of the Y chromosome (NRY) in 121 and 147 extant males from Oman and northern Egypt, respectively. The present study uncovers three important points concerning these demic movements: (1) The E3b1-M78 and E3b3-M123 lineages, as well as the R1*-M173 lineages, mark gene flow between Egypt and the Levant during the Upper Paleolithic and Mesolithic. (2) In contrast, the Horn of Africa appears to be of minor importance in the human migratory movements between Africa and Eurasia represented by these chromosomes, an observation based on the frequency distributions of E3b*-M35 (no known downstream mutations) and M173. (3) The areal diffusion patterns of G-M201, J-12f2, the derivative M173 haplogroups, and M2 suggest more recent genetic associations between the Middle East and Africa, involving the Levantine corridor and/or Arab slave routes. Affinities to African groups were also evaluated by determining the NRY haplogroup composition in 434 samples from seven sub-Saharan African populations. Oman and Egypt's NRY frequency distributions appear to be much more similar to those of the Middle East than to any sub-Saharan African population, suggesting a much larger Eurasian genetic component. Finally, the overall phylogeographic profile reveals several clinal patterns and genetic partitions that may indicate source, direction, and relative timing of different waves of dispersals and expansions involving these nine populations.
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Affiliation(s)
- J R Luis
- Department of Biological Sciences, Florida International University, Miami, 33199, USA
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590
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Paracchini S, Pearce CL, Kolonel LN, Altshuler D, Henderson BE, Tyler-Smith C. A Y chromosomal influence on prostate cancer risk: the multi-ethnic cohort study. J Med Genet 2004; 40:815-9. [PMID: 14627670 PMCID: PMC1735314 DOI: 10.1136/jmg.40.11.815] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND A Y chromosomal role in prostate cancer has previously been suggested by both cytogenetic findings and patterns of Y chromosomal gene expression. We took advantage of the well established and stable phylogeny of the non-recombining segment of the Y chromosome to investigate the association between Y chromosomal DNA variation and prostate cancer risk. METHODS We examined the distribution of 116 Y lineages in 930 prostate cancer cases and 1208 controls from four ethnic groups from a cohort study in Hawaii and California. RESULTS One lineage, found only among the Japanese group in our study, was associated with a statistically significant predisposition to prostate cancer (odds ratio (OR) = 1.63; 95% confidence interval (CI) 1.07 to 2.47), and, in particular, to high severity disease in younger individuals (OR = 3.89; 95% CI 1.34 to 11.31). CONCLUSIONS This finding suggests that a Y chromosomal factor contributes significantly to the development of prostate cancer in Japanese men.
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Affiliation(s)
- S Paracchini
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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591
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Abstract
Ninety-five percent of the length of the human Y chromosome is inherited as a single block in linkage from father to male offspring as a haploid entity. Thus, the Y chromosome represents an invaluable record of all mutations that have occurred along male lineages throughout evolution. For this reason, Y chromosomal DNA variation has been mainly used for investigations on human evolution and for forensic purposes or paternity analysis. Recently, Y chromosomal polymorphisms have been applied in molecular medicine from the perspective of male-specific (spermatogenic failure, testis and prostate cancer) and prevalently male-associated (hypertension, autism) diseases. The absence of recombination on the MSY (male-specific Y) region means that polymorphisms, located in this region, are in tight association with potential functional variations associated with Y-linked phenotypes. Thus, an indirect way to explore if Y chromosome genes are involved in the etiology of a specific disease is the definition of Y chromosome haplogroups in patients versus disease-free and/or the general population. Data on patients with reduced sperm count and prostate cancer indicate that the 'at risk Y haplogroup' may be different in different populations. The situation is rather contradictory for other male-specific or male-associated diseases and further multicenter--possibly multiethnic--studies are needed.
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Affiliation(s)
- Csilla Krausz
- Department of Clinical Physiopathology, University of Florence, Florence, Italy.
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592
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Affiliation(s)
- Stephen F Schaffner
- Whitehead/MIT Center for Genome Research, Cambridge, Massachusetts 02139, USA.
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593
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594
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Repping S, Skaletsky H, Brown L, van Daalen SKM, Korver CM, Pyntikova T, Kuroda-Kawaguchi T, de Vries JWA, Oates RD, Silber S, van der Veen F, Page DC, Rozen S. Polymorphism for a 1.6-Mb deletion of the human Y chromosome persists through balance between recurrent mutation and haploid selection. Nat Genet 2003; 35:247-51. [PMID: 14528305 DOI: 10.1038/ng1250] [Citation(s) in RCA: 307] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2003] [Accepted: 09/16/2003] [Indexed: 11/09/2022]
Abstract
Many human Y-chromosomal deletions are thought to severely impair reproductive fitness, which precludes their transmission to the next generation and thus ensures their rarity in the population. Here we report a 1.6-Mb deletion that persists over generations and is sufficiently common to be considered a polymorphism. We hypothesized that this deletion might affect spermatogenesis because it removes almost half of the Y chromosome's AZFc region, a gene-rich segment that is critical for sperm production. An association study established that this deletion, called gr/gr, is a significant risk factor for spermatogenic failure. The gr/gr deletion has far lower penetrance with respect to spermatogenic failure than previously characterized Y-chromosomal deletions; it is often transmitted from father to son. By studying the distribution of gr/gr-deleted chromosomes across the branches of the Y chromosome's genealogical tree, we determined that this deletion arose independently at least 14 times in human history. We suggest that the existence of this deletion as a polymorphism reflects a balance between haploid selection, which culls gr/gr-deleted Y chromosomes from the population, and homologous recombination, which continues to generate new gr/gr deletions.
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Affiliation(s)
- Sjoerd Repping
- Howard Hughes Medical Institute, Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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