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Derbala MK, Sargious MAN, Hagag NM, Pycock JF, Abu-Seida AM. A case of a twin surviving to term following the abortion of its co-twin at 9 months in an Arabian mare. J Equine Vet Sci 2024; 139:105132. [PMID: 38897332 DOI: 10.1016/j.jevs.2024.105132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 06/10/2024] [Accepted: 06/16/2024] [Indexed: 06/21/2024]
Abstract
Twin pregnancy in mares is one of the leading causes of abortions. Abortion invariably impacts both fetuses. This report describes an unusual case of a twin surviving to term following the abortion of its co-twin at 9 months in a 7-year-old Egyptian Arabian mare. At the time of abortion at 9 months of gestation, the size of the aborted fetus was equivalent to one of approximately 5 months of age while the age of the live co-twin was 9 months. Both fetuses were males. A skin sample was collected from the aborted fetus and hair samples were collected from the dam, sire and live foal for parentage analysis. The parentage analysis confirmed that both fetuses were by the same dam and sire stallion. The authors suggest several scenarios to explain this condition. This report describes a unique case of a twin surviving to term following the abortion of its co-twin at 9 months in a mare.
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Affiliation(s)
- M K Derbala
- Animal Reproduction Research Institute, Diagnostic Imaging and Endoscopy Unit, ARC, Giza, Egypt
| | - M A N Sargious
- Animal Health Research Institute, Genome Research Unit, ARC, Giza, Egypt
| | - N M Hagag
- Animal Health Research Institute, Genome Research Unit, ARC, Giza, Egypt
| | - J F Pycock
- Diplomate in Equine Stud Medicine, Messenger Farm, United Kingdom
| | - A M Abu-Seida
- Department of Surgery, Anesthesiology and Radiology, Faculty of Veterinary Medicine, Cairo University, Giza, PO: 12211, Egypt..
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2
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Della Rocca C, Cannone F, D'Atanasio E, Bonito M, Anagnostou P, Russo G, Barni F, Alladio E, Destro-Bisol G, Trombetta B, Berti A, Cruciani F. Ethnic fragmentation and degree of urbanization strongly affect the discrimination power of Y-STR haplotypes in central Sahel. Forensic Sci Int Genet 2020; 49:102374. [PMID: 32890883 DOI: 10.1016/j.fsigen.2020.102374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/06/2020] [Accepted: 08/16/2020] [Indexed: 10/23/2022]
Abstract
Y chromosome short tandem repeats (Y-STRs) are commonly used to identify male lineages for investigative and judicial purposes and could represent the only source of male-specific genetic information from unbalanced female-male mixtures. The Yfiler Plus multiplex, which includes twenty conventional and seven rapidly-mutating Y-STRs, represents the most discriminating patrilineal system commercially available to date. Over the past five years, this multiplex has been used to analyze several Eurasian populations, with a reported discrimination capacity (DC) approaching or corresponding to the highest possible value. However, despite the inclusion of rapidly mutating Y-STRs, extensive haplotype sharing was still reported for some African populations due to a number of different factors affecting the effective population size. In the present study, we analyzed 27 Y-STRs included in the Yfiler Plus multiplex and 82 Y-SNPs in central Sahel (northern Cameroon and western Chad), an African region characterized by a strong ethnic fragmentation and linguistic diversity. We evaluated the effects of population sub-structuring on genetic diversity by stratifying a sample composed of 431 males according to their ethnicity (44 different ethnic groups) and urbanization degree (four villages and four towns). Overall, we observed a low discrimination capacity (DC = 0.90), with 71 subjects (16.5 %) sharing 27 Y-STR haplotypes. Haplotype sharing was essentially limited to subjects with the same binary haplogroup, coming from the same location and belonging to the same ethnic group. Haplotype sharing was much higher in rural areas (average DC = 0.83) than urban settlements (average DC = 0.96) with a significant correlation between DC and census size (r = 0.89; p = 0.003). Notably, we found that genetic differentiation between villages from the same country (ΦST = 0.14) largely exceeded that found among countries (ΦST = 0.02). These findings have important implications for the choice of the appropriate reference population database to evaluate the statistical relevance of forensic Y-haplotype matches.
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Affiliation(s)
- Chiara Della Rocca
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Cannone
- Reparto Carabinieri Investigazioni Scientifiche di Roma - Sezione di Biologia, Viale Tor di Quinto 119, 00191, Rome, Italy
| | | | - Maria Bonito
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Paolo Anagnostou
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 - Rome, Italy; Istituto Italiano di Antropologia, Rome, Italy
| | - Gianluca Russo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Filippo Barni
- Reparto Carabinieri Investigazioni Scientifiche di Roma - Sezione di Biologia, Viale Tor di Quinto 119, 00191, Rome, Italy
| | - Eugenio Alladio
- Reparto Carabinieri Investigazioni Scientifiche di Roma - Sezione di Biologia, Viale Tor di Quinto 119, 00191, Rome, Italy
| | - Giovanni Destro-Bisol
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 - Rome, Italy; Istituto Italiano di Antropologia, Rome, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Berti
- Reparto Carabinieri Investigazioni Scientifiche di Roma - Sezione di Biologia, Viale Tor di Quinto 119, 00191, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy; Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy.
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3
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Zieger M, Utz S. The Y-chromosomal haplotype and haplogroup distribution of modern Switzerland still reflects the alpine divide as a geographical barrier for human migration. Forensic Sci Int Genet 2020; 48:102345. [PMID: 32622325 DOI: 10.1016/j.fsigen.2020.102345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/09/2022]
Abstract
A sample of 606 Swiss individuals has been characterized for 27 Y-STR and 34 Y-SNPs, defining major European haplogroups. For the first time, a subsample from the southernmost part of Switzerland, the Italian speaking canton Ticino, has been included. The data reveals significant intra-national differences in the distribution of haplogroups R1b-U106, R1b-U152, I1 and J2a north and south of the alpine divide, with R1b-U152 being the most frequent haplogroup among all Swiss subpopulations, reaching 26 % in average and 53 % in the Ticino sample. In addition, a high percentage of haplogroup E1b1b-M35 in Eastern Switzerland corresponds well with data reported from Western Austria. In general, we detected a low level of differentiation between the subgroups north of the alpine divide. The dataset also revealed a variety of microvariants. Some of them were previously known to be associated with particular haplogroups. However, we discovered one microvariant in DYS533 that seems to be closely associated with haplogroup I2-P215 (xM223). This association had not yet been reported to date. The concordance study with two STR-kits suggests that the DYS533 microvariant is due to an InDel in the flanking regions of the marker. One individual carried a large deletion, frequently detected in people of East Asian ancestry, encompassing the amelogenin locus. To our knowledge, this is the first time that such a deletion has been observed within European haplogroup R1b-U152. This is the first comprehensive Y chromosomal dataset for Switzerland, demonstrating significant population substructure due to an intra-national geographical barrier.
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Affiliation(s)
- Martin Zieger
- Institute of Forensic Medicine, Forensic Molecular BiologyDpt., University of Bern, Sulgenauweg 40, 3007, Bern, Switzerland.
| | - Silvia Utz
- Institute of Forensic Medicine, Forensic Molecular BiologyDpt., University of Bern, Sulgenauweg 40, 3007, Bern, Switzerland.
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4
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Lang M, Song F, Ye Y, Xie M, Zhu H, Wang Z, Hou Y. Sequence characterization of microvariant alleles at DYS627 and DYS458. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Y-STRs’ genetic profiling of 1953 individuals from two Chinese Han populations (Guizhou and Shanxi). Forensic Sci Int Genet 2019; 38:e8-e10. [DOI: 10.1016/j.fsigen.2018.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/20/2018] [Accepted: 10/19/2018] [Indexed: 01/07/2023]
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6
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Rapidly mutating Y-STRs in rapidly expanding populations: Discrimination power of the Yfiler Plus multiplex in northern Africa. Forensic Sci Int Genet 2019; 38:185-194. [DOI: 10.1016/j.fsigen.2018.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/02/2018] [Accepted: 11/02/2018] [Indexed: 11/18/2022]
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7
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Forensic data and microvariant sequence characterization of 27 Y-STR loci analyzed in four Eastern African countries. Forensic Sci Int Genet 2017; 27:123-131. [DOI: 10.1016/j.fsigen.2016.12.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/19/2016] [Accepted: 12/29/2016] [Indexed: 11/17/2022]
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8
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Warshauer DH, Churchill JD, Novroski N, King JL, Budowle B. Novel Y-chromosome Short Tandem Repeat Variants Detected Through the Use of Massively Parallel Sequencing. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:250-7. [PMID: 26391384 PMCID: PMC4610967 DOI: 10.1016/j.gpb.2015.08.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/28/2015] [Accepted: 08/19/2015] [Indexed: 02/01/2023]
Abstract
Massively parallel sequencing (MPS) technology is capable of determining the sizes of short tandem repeat (STR) alleles as well as their individual nucleotide sequences. Thus, single nucleotide polymorphisms (SNPs) within the repeat regions of STRs and variations in the pattern of repeat units in a given repeat motif can be used to differentiate alleles of the same length. In this study, MPS was used to sequence 28 forensically-relevant Y-chromosome STRs in a set of 41 DNA samples from the 3 major U.S. population groups (African Americans, Caucasians, and Hispanics). The resulting sequence data, which were analyzed with STRait Razor v2.0, revealed 37 unique allele sequence variants that have not been previously reported. Of these, 19 sequences were variations of documented sequences resulting from the presence of intra-repeat SNPs or alternative repeat unit patterns. Despite a limited sampling, two of the most frequently-observed variants were found only in African American samples. The remaining 18 variants represented allele sequences for which there were no published data with which to compare. These findings illustrate the great potential of MPS with regard to increasing the resolving power of STR typing and emphasize the need for sample population characterization of STR alleles.
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Affiliation(s)
- David H Warshauer
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Jennifer D Churchill
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Nicole Novroski
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Jonathan L King
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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9
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Larmuseau MHD, Vanderheyden N, Van Geystelen A, Oven M, Knijff P, Decorte R. Recent Radiation within Y‐chromosomal Haplogroup R‐M269 Resulted in High Y‐STR Haplotype Resemblance. Ann Hum Genet 2014; 78:92-103. [DOI: 10.1111/ahg.12050] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/07/2013] [Indexed: 01/18/2023]
Affiliation(s)
- Maarten H. D. Larmuseau
- Laboratory of Forensic Genetics and Molecular ArchaeologyUZ Leuven Leuven Belgium
- Department of Imaging & PathologyBiomedical Forensic SciencesKU Leuven Leuven Belgium
- Laboratory of Biodiversity and Evolutionary GenomicsDepartment of BiologyKU Leuven Leuven Belgium
| | - Nancy Vanderheyden
- Laboratory of Forensic Genetics and Molecular ArchaeologyUZ Leuven Leuven Belgium
| | - Anneleen Van Geystelen
- Laboratory of Socioecology and Social EvolutionDepartment of BiologyKU Leuven Leuven Belgium
| | - Mannis Oven
- Department of Forensic Molecular BiologyErasmus MC – University Medical Center Rotterdam Rotterdam The Netherlands
| | - Peter Knijff
- Department of Human GeneticsLeiden University Medical Center Leiden The Netherlands
| | - Ronny Decorte
- Laboratory of Forensic Genetics and Molecular ArchaeologyUZ Leuven Leuven Belgium
- Department of Imaging & PathologyBiomedical Forensic SciencesKU Leuven Leuven Belgium
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Collins TE, Ottens R, Ballantyne KN, Nagle N, Henry J, Taylor D, Gardner MG, Fitch AJ, Goodman A, van Oorschot RAH, Mitchell RJ, Linacre A. Characterisation of novel and rare Y-chromosome short tandem repeat alleles in self-declared South Australian Aboriginal database. Int J Legal Med 2013; 128:27-31. [DOI: 10.1007/s00414-013-0911-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/03/2013] [Indexed: 10/26/2022]
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11
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Battaglia V, Grugni V, Perego UA, Angerhofer N, Gomez-Palmieri JE, Woodward SR, Achilli A, Myres N, Torroni A, Semino O. The first peopling of South America: new evidence from Y-chromosome haplogroup Q. PLoS One 2013; 8:e71390. [PMID: 23990949 PMCID: PMC3749222 DOI: 10.1371/journal.pone.0071390] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/03/2013] [Indexed: 01/13/2023] Open
Abstract
Recent progress in the phylogenetic resolution of the Y-chromosome phylogeny permits the male demographic dynamics and migratory events that occurred in Central and Southern America after the initial human spread into the Americas to be investigated at the regional level. To delve further into this issue, we examined more than 400 Native American Y chromosomes (collected in the region ranging from Mexico to South America) belonging to haplogroup Q – virtually the only branch of the Y phylogeny observed in modern-day Amerindians of Central and South America – together with 27 from Mongolia and Kamchatka. Two main founding lineages, Q1a3a1a-M3 and Q1a3a1-L54(xM3), were detected along with novel sub-clades of younger age and more restricted geographic distributions. The first was also observed in Far East Asia while no Q1a3a1-L54(xM3) Y chromosome was found in Asia except the southern Siberian-specific sub-clade Q1a3a1c-L330. Our data not only confirm a southern Siberian origin of ancestral populations that gave rise to Paleo-Indians and the differentiation of both Native American Q founding lineages in Beringia, but support their concomitant arrival in Mesoamerica, where Mexico acted as recipient for the first wave of migration, followed by a rapid southward migration, along the Pacific coast, into the Andean region. Although Q1a3a1a-M3 and Q1a3a1-L54(xM3) display overlapping general distributions, they show different patterns of evolution in the Mexican plateau and the Andean area, which can be explained by local differentiations due to demographic events triggered by the introduction of agriculture and associated with the flourishing of the Great Empires.
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Affiliation(s)
- Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
| | - Viola Grugni
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
| | - Ugo Alessandro Perego
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | - Norman Angerhofer
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | | | - Scott Ray Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- AncestryDNA, Provo, Utah, United States of America
| | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Natalie Myres
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- AncestryDNA, Provo, Utah, United States of America
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
- Centro Interdipartimentale “Studi di Genere”, Università di Pavia, Pavia, Italy
- * E-mail:
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Scozzari R, Massaia A, D’Atanasio E, Myres NM, Perego UA, Trombetta B, Cruciani F. Molecular dissection of the basal clades in the human Y chromosome phylogenetic tree. PLoS One 2012; 7:e49170. [PMID: 23145109 PMCID: PMC3492319 DOI: 10.1371/journal.pone.0049170] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 10/04/2012] [Indexed: 11/19/2022] Open
Abstract
One hundred and forty-six previously detected mutations were more precisely positioned in the human Y chromosome phylogeny by the analysis of 51 representative Y chromosome haplogroups and the use of 59 mutations from literature. Twenty-two new mutations were also described and incorporated in the revised phylogeny. This analysis made it possible to identify new haplogroups and to resolve a deep trifurcation within haplogroup B2. Our data provide a highly resolved branching in the African-specific portion of the Y tree and support the hypothesis of an origin in the north-western quadrant of the African continent for the human MSY diversity.
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Affiliation(s)
- Rosaria Scozzari
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Andrea Massaia
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Eugenia D’Atanasio
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Natalie M. Myres
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- AncestryDNA, Provo, Utah, United States of America
| | - Ugo A. Perego
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- Dipartimento di Biologia e Biotecnologie “Lazzaro Spallanzani”, Università di Pavia, Pavia, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
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13
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Understanding the Y chromosome variation in Korea—relevance of combined haplogroup and haplotype analyses. Int J Legal Med 2012; 126:589-99. [DOI: 10.1007/s00414-012-0703-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 04/26/2012] [Indexed: 11/26/2022]
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14
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Croatian national reference Y-STR haplotype database. Mol Biol Rep 2012; 39:7727-41. [PMID: 22391654 DOI: 10.1007/s11033-012-1610-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 02/07/2012] [Indexed: 10/28/2022]
Abstract
A reference Y-chromosome short tandem repeat (STR) haplotype database is needed for Y-STR match interpretation as well as for national and regional characterization of populations. The aim of this study was to create a comprehensive Y-STR haplotype database of the Croatian contemporary population and to analyze substructure between the five Croatian regions. We carried out a statistical analysis of the data from previously performed genetic analyses collected during routine forensic work by the Forensic Science Centre "Ivan Vučetić". A total of 1,100 unrelated men from eastern, western, northern, southern and central Croatia were selected for the purpose of this study. Y-STRs were typed using the AmpFISTR Yfiler PCR amplification kit. Analysis of molecular variance calculated with the Y chromosome haplotype reference database online analysis tool included 16 population samples with 20,247 haplotypes. A total of 947 haplotypes were recorded, 848 of which were unique (89.5%). Haplotype diversity was 0.998, with the most frequent haplotype found in 9 of 1,100 men (0.82%). Locus diversity varied from 0.266 for DYS392 to 0.868 for DYS385. Discrimination capacity was 86.1%. Our results suggested high level of similarity among regional subpopulations within Croatia, except for mildly different southern Croatia. Relative resemblance was found with Bosnia and Herzegovina and Serbia. Whit Atheys' Haplogroup Predictor was used to estimate the frequencies of Y-chromosome haplogroups. I2a, R1a, E1b1b and R1b haplogroups were most frequent in all Croatian regions. These results are important in forensics and contribute to the population genetics and genetic background of the contemporary Croatian population.
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Temporal differentiation across a West-European Y-chromosomal cline: genealogy as a tool in human population genetics. Eur J Hum Genet 2011; 20:434-40. [PMID: 22126748 DOI: 10.1038/ejhg.2011.218] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The pattern of population genetic variation and allele frequencies within a species are unstable and are changing over time according to different evolutionary factors. For humans, it is possible to combine detailed patrilineal genealogical records with deep Y-chromosome (Y-chr) genotyping to disentangle signals of historical population genetic structures because of the exponential increase in genetic genealogical data. To test this approach, we studied the temporal pattern of the 'autochthonous' micro-geographical genetic structure in the region of Brabant in Belgium and the Netherlands (Northwest Europe). Genealogical data of 881 individuals from Northwest Europe were collected, from which 634 family trees showed a residence within Brabant for at least one generation. The Y-chr genetic variation of the 634 participants was investigated using 110 Y-SNPs and 38 Y-STRs and linked to particular locations within Brabant on specific time periods based on genealogical records. Significant temporal variation in the Y-chr distribution was detected through a north-south gradient in the frequencies distribution of sub-haplogroup R1b1b2a1 (R-U106), next to an opposite trend for R1b1b2a2g (R-U152). The gradient on R-U106 faded in time and even became totally invisible during the Industrial Revolution in the first half of the nineteenth century. Therefore, genealogical data for at least 200 years are required to study small-scale 'autochthonous' population structure in Western Europe.
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Gršković B, Mršić G, Polašek O, Vrdoljak A, Merkaš S, Anđelinović S. Genetic polymorphisms of 17 short tandem repeat loci on Y chromosome in central Croatian population. Forensic Sci Med Pathol 2011; 7:155-61. [PMID: 21279707 DOI: 10.1007/s12024-010-9216-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2010] [Indexed: 11/25/2022]
Abstract
In forensic casework, Y-chromosome short tandem repeat (STR) haplotyping is used in human identification, paternity testing and sexual assault cases where Y-STRs provide a male-specific DNA profile. The aim of this study was to describe the genetic structure of Y chromosome in a central Croatian population. We carried out a statistical analysis of the data from previously performed genetic analyses collected during routine forensic work by the Forensic Science Centre "Ivan Vučetić". A total of 220 unrelated healthy men from central Croatia were selected for the purpose of this study. Genomic DNA was extracted using a Chelex procedure from FTA(®) cards. Y-chromosomal STRs were determined using the AmpFISTR Yfiler PCR amplification kit. The haplotype frequencies were determined by direct counting and analyzed using Arlequin 3.1 and analysis of molecular variance calculated with the Y chromosome haplotype reference database online analysis tool. A total of 212 haplotypes were identified, 204 of which were unique. Total haplotype diversity was 0.993. Locus diversity varied from 0.325 for DYS392 to 0.786 for DYS385. Discrimination capacity was 92.7%. Allele frequencies diversity was 0.615. Intermediate alleles 17.2, 18.2 and 19.2 were found at DYS458 locus. A comparison with published data for the European minimal haplotype set showed the closest relationship to the Croatian capital of Zagreb and Bosnia and Herzegovina with significant genetic distance from Slovenia and Austria. The central Croatian population is now well characterized in terms of Y-chromosome STRs, thus providing a solid basis for further forensic and genetic epidemiology studies.
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Affiliation(s)
- Branka Gršković
- Department of Biology and Fibers, Division of Biology, Forensic Science Centre Ivan Vučetić, General Police Directorate, Ministry of Interior, Ilica Zagreb, Croatia.
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17
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Gršković B, Mršić G, Polašek O, Vrdoljak A, Merkaš S, Anđelinović S. Population data for 17 short tandem repeat loci on Y chromosome in northern Croatia. Mol Biol Rep 2010; 38:2203-9. [PMID: 20859689 DOI: 10.1007/s11033-010-0349-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 09/06/2010] [Indexed: 11/30/2022]
Abstract
Human Y-short tandem repeats (STRs) are tandem repeat arrays of two to seven base pair units on non-recombining region (NRY) of the human Y chromosome. Studies on Y-STR are interesting in both population genetics and forensics. The aim of this study was to investigate the population genetic properties of 17 STR loci on Y chromosome in the northern Croatia region. We carried out a statistical analysis of the data from previously performed genetic analysis collected during routine forensic work by the Forensic Science Centre "Ivan Vučetić". A total of 220 unrelated healthy men from northern Croatia were selected for the purpose of this study. Genomic DNA was extracted using Chelex procedure from FTA(®) cards. Y-chromosomal STRs were determined using the AmpFISTR Yfiler PCR amplification kit. The haplotype frequencies were determined by direct counting and analyzed using Arlequin 3.1 and analysis of molecular variance calculated with the Y chromosome haplotype reference database online analysis tool. A total of 210 haplotypes were identified, 200 of which were unique. Total haplotype diversity was 0.995. Locus diversity varied from 0.331 for DYS392 to 0.783 for DYS385 locus. Allele frequencies diversity was 0.662. Discrimination capacity was 95.7%. The use of European minimal haplotype set indicated the most resemblance of this population to the Croatian capital of Zagreb, with modest resemblance to Bosnia and Herzegovina, Serbia and Hungary. This article provides the first overview of the Y chromosome STR variability in northern Croatia, thus providing the referent point for any future forensic and genetic epidemiology efforts in this region.
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Affiliation(s)
- Branka Gršković
- Department of Biology and Fibers, Divison of Biology, Forensic Science Centre Ivan Vučetić, General Police Directorate, Ministry of Interior, Ilica 335, 10000 Zagreb, Croatia.
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Cruciani F, Trombetta B, Antonelli C, Pascone R, Valesini G, Scalzi V, Vona G, Melegh B, Zagradisnik B, Assum G, Efremov GD, Sellitto D, Scozzari R. Strong intra- and inter-continental differentiation revealed by Y chromosome SNPs M269, U106 and U152. Forensic Sci Int Genet 2010; 5:e49-52. [PMID: 20732840 DOI: 10.1016/j.fsigen.2010.07.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 07/23/2010] [Accepted: 07/28/2010] [Indexed: 12/01/2022]
Abstract
More than 2700 unrelated individuals from Europe, northern Africa and western Asia were analyzed for the marker M269, which defines the Y chromosome haplogroup R1b1b2. A total of 593 subjects belonging to this haplogroup were identified and further analyzed for two SNPs, U106 and U152, which define haplogroups R1b1b2g and R1b1b2h, respectively. These haplogroups showed quite different frequency distribution patterns within Europe, with frequency peaks in northern Europe (R1b1b2g) and northern Italy/France (R1b1b2h).
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Affiliation(s)
- Fulvio Cruciani
- Dipartimento di Genetica e Biologia Molecolare, Sapienza Università di Roma, Rome, Italy
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Ehler E, Marvan R, Vanek D. Evaluation of 14 Y-chromosomal short tandem repeat haplotype with focus on DYS449, DYS456, and DYS458: Czech population sample. Croat Med J 2010; 51:54-60. [PMID: 20162746 DOI: 10.3325/cmj.2010.51.54] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
AIM To evaluate the novel triplex polymerase chain reaction (PCR) assay for the analysis of polymorphic Y-chromosomal short tandem repeat loci (Y-STR). METHODS A total of 14 Y-STR loci was analyzed. Allele frequencies for 3 tetrameric Y-STR loci (DYS449, DYS456, and DYS458) and extended haplotype loci typed by Y-PLEXTM 12 system were investigated in a sample of 50 unrelated healthy Czech male donors. We computed the relevant intra-population statistic parameters for our data (gene diversity, average gene diversity over loci, and mean number of pairwise differences) and compared our sample set with other Central European populations using RST pairwise genetic distance. RESULTS We focused on the comparison of genetic diversity between the Y-STR extended haplotype loci and that of the 3 additional loci, and on the benefit of using DYS449, DYS456, and DYS458 in forensic and population genetics applications. Total gene diversity in our sample set was 0.998367 when using all 14 loci. Our data analysis revealed very high genetic diversity at DYS449 locus (0.876735), which surpasses even the diversity at DYS385a/b (0.819592). Population comparison showed no difference between Czech, Bavarian, Austrian, and Saxon sample set. A minor difference was found between Czech and Polish sample set. CONCLUSION Typing of 3 Y-chromosomal microsatellite polymorphisms may provide a useful complement to already established sets of Y-STRs.
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Affiliation(s)
- Edvard Ehler
- Charles University in Prague, Faculty of Science, Department of Anthropology and Human Genetics, Vinicna 7, 12844 Praha 2, Czech Republic.
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Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages. Eur J Hum Genet 2010; 18:800-7. [PMID: 20051990 DOI: 10.1038/ejhg.2009.231] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Although human Y chromosomes belonging to haplogroup R1b are quite rare in Africa, being found mainly in Asia and Europe, a group of chromosomes within the paragroup R-P25(*) are found concentrated in the central-western part of the African continent, where they can be detected at frequencies as high as 95%. Phylogenetic evidence and coalescence time estimates suggest that R-P25(*) chromosomes (or their phylogenetic ancestor) may have been carried to Africa by an Asia-to-Africa back migration in prehistoric times. Here, we describe six new mutations that define the relationships among the African R-P25(*) Y chromosomes and between these African chromosomes and earlier reported R-P25 Eurasian sub-lineages. The incorporation of these new mutations into a phylogeny of the R1b haplogroup led to the identification of a new clade (R1b1a or R-V88) encompassing all the African R-P25(*) and about half of the few European/west Asian R-P25(*) chromosomes. A worldwide phylogeographic analysis of the R1b haplogroup provided strong support to the Asia-to-Africa back-migration hypothesis. The analysis of the distribution of the R-V88 haplogroup in >1800 males from 69 African populations revealed a striking genetic contiguity between the Chadic-speaking peoples from the central Sahel and several other Afroasiatic-speaking groups from North Africa. The R-V88 coalescence time was estimated at 9.2-5.6 [corrected] kya, in the early mid Holocene. We suggest that R-V88 is a paternal genetic record of the proposed mid-Holocene migration of proto-Chadic Afroasiatic speakers through the Central Sahara into the Lake Chad Basin, and geomorphological evidence is consistent with this view.
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