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Claerhout S, Noppe H, Cohn B, Borry P. Opt-in or out? Public perspectives on forensic DNA kinship investigations within the Dutch-speaking community. Heliyon 2024; 10:e30074. [PMID: 38720757 PMCID: PMC11076844 DOI: 10.1016/j.heliyon.2024.e30074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Forensic DNA kinship investigation involves analyzing genetic relationships between individuals to offer new leads for solving (cold) cases. Familial DNA matching has become a valuable asset in criminal case investigations, especially when traditional DNA methods hit dead ends. However, concerns surrounding ethical and privacy implications raised questions about its implementation and acceptance among the general public. The present study investigated the public perspectives regarding forensic DNA kinship investigations among 1710 Dutch-speaking Belgians using an online cross-sectional survey. The questionnaire consisted of three categories, including personal information, DNA knowledge, and their opinion on several familial DNA searching and investigative genetic genealogy related questions. The participants' average DNA knowledge score was 71 %, indicating a relatively high level of understanding of DNA-related concepts. Remarkably, the study revealed that 92 % of the participants expressed willingness to cooperate as a volunteer in a forensic DNA kinship investigation, irrespective of their scientific background or educational level. Key factors influencing participation included assurance of painless sampling and robust privacy safeguards. Participants lacking familiarity with DNA hesitated more towards participating in forensic DNA analysis, referring to "the fear of the unknown". Despite ethical and privacy concerns, the highly positive attitude towards forensic DNA analysis reflects a level of empathy and willingness to contribute to the pursuit of justice. Nearly all participants (95 %) agreed to use online DNA databases for resolving violent crimes with forensic genetic genealogy, but half emphasized the need for prior informed consent, referring to the current "opt-in" system. The results underscore the need for stringent regulations and ethical oversight to ensure the responsible use of genetic data while striking a balance between public safety and the protection of individuals' privacy rights. These findings add to the growing body of evidence regarding the potential benefits of forensic DNA kinship matching as a tool in criminal investigations, suggesting its potential future utilization and legalization.
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Affiliation(s)
- Sofie Claerhout
- Laboratory for Forensic Genetics, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium
- Interdisciplinary Research Facility, KU Leuven Kulak, Kortrijk, Belgium
- Centre for Sociological Research, KU Leuven, Leuven, Belgium
| | - Hanna Noppe
- Biomedical Forensic Sciences, KU Leuven, Leuven, Belgium
| | - Betty Cohn
- Institute of Public Health Genetics, University of Washington, Seattle, USA
| | - Pascal Borry
- Center of Biomedical Ethics and Law, Department of Public Health, KU Leuven, Leuven, Belgium
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Lee JE, Park SU, So MH, Lee HY. Age prediction using DNA methylation of Y-chromosomal CpGs in semen samples. Forensic Sci Int Genet 2024; 69:103007. [PMID: 38217952 DOI: 10.1016/j.fsigen.2024.103007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
In cases of sexual assault, the evidence often exists as a mixture of female and male body fluids, and in many cases, contains a higher proportion of female body fluids than males. In these cases, Y-STR, rather than autosomal STRs, can provide useful information. It becomes very difficult to identify the true suspect if there is no match among known suspects or if a match exists for two or more suspects, e.g. two suspects from the same paternal lineage. However, age prediction using the DNA methylation of Y-chromosomal CpGs can help narrow the search for unknown suspects and discriminate between older and younger suspects. Therefore, the DNA methylation profiles of semen samples from 56 healthy Korean males were generated using Illumina's Infinium MethylationEPIC BeadChip Array. Among the ten identified age-associated CpG markers located in the Y-chromosome, nine were used to construct age prediction models. The identified markers were further investigated in the MPS analysis of 147 semen samples, and the multiplex assay was validated with the reliability, reproducibility and sensitivity tests. Several age prediction models were constructed using the MPS data with the multiple linear regression, stepwise linear regression, ridge linear regression, lasso regression, elastic net linear regression and support vector machine analyses, and all showed MAEs of 5 to 7 years in the test set samples. Six single-source female samples were also subjected to MPS analysis but showed very low coverage that could not affect the analysis of the mixed samples. Therefore, the age prediction models of the present study are expected to provide useful investigative leads, especially in mixed male and female samples from sexual assault cases.
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Affiliation(s)
- Ji Eun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, the Republic of Korea
| | - Sang Un Park
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, the Republic of Korea
| | - Moon Hyun So
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, the Republic of Korea
| | - Hwan Young Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, the Republic of Korea; Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, the Republic of Korea.
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Schurr TG, Shengelia R, Shamoon-Pour M, Chitanava D, Laliashvili S, Laliashvili I, Kibret R, Kume-Kangkolo Y, Akhvlediani I, Bitadze L, Mathieson I, Yardumian A. Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus). Genome Biol Evol 2023; 15:evad198. [PMID: 37935112 PMCID: PMC10665041 DOI: 10.1093/gbe/evad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/09/2023] Open
Abstract
To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian speaking. From these DNA samples, we generated mitochondrial DNA (mtDNA) control region sequences for all 485 participants (female and male), Y-short tandem repeat haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal single nucleotide polymorphisms (SNPs) plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, and W. X2) and low frequencies of East Eurasian haplogroups (A, C, D, F, and G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared with ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community.
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Affiliation(s)
- Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ramaz Shengelia
- Department of the History of Medicine, Tbilisi State Medical University, Tbilisi, Georgia
| | - Michel Shamoon-Pour
- First-year Research Immersion, Binghamton University, Binghamton, New York, USA
| | - David Chitanava
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Shorena Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Irma Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Redate Kibret
- Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA
| | - Yanu Kume-Kangkolo
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Lia Bitadze
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Aram Yardumian
- Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA
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Zhao GB, Miao L, Wang M, Yuan JH, Wei LH, Feng YS, Zhao J, Kang KL, Zhang C, Ji AQ, He G, Wang L. Developmental validation of a high-resolution panel genotyping 639 Y-chromosome SNP and InDel markers and its evolutionary features in Chinese populations. BMC Genomics 2023; 24:611. [PMID: 37828453 PMCID: PMC10568895 DOI: 10.1186/s12864-023-09709-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
Uniparental-inherited haploid genetic marker of Y-chromosome single nucleotide polymorphisms (Y-SNP) have the power to provide a deep understanding of the human evolutionary past, forensic pedigree, and bio-geographical ancestry information. Several international cross-continental or regional Y-panels instead of Y-whole sequencing have recently been developed to promote Y-tools in forensic practice. However, panels based on next-generation sequencing (NGS) explicitly developed for Chinese populations are insufficient to represent the Chinese Y-chromosome genetic diversity and complex population structures, especially for Chinese-predominant haplogroup O. We developed and validated a 639-plex panel including 633 Y-SNPs and 6 Y-Insertion/deletions, which covered 573 Y haplogroups on the Y-DNA haplogroup tree. In this panel, subgroups from haplogroup O accounted for 64.4% of total inferable haplogroups. We reported the sequencing metrics of 354 libraries sequenced with this panel, with the average sequencing depth among 226 individuals being 3,741×. We illuminated the high level of concordance, accuracy, reproducibility, and specificity of the 639-plex panel and found that 610 loci were genotyped with as little as 0.03 ng of genomic DNA in the sensitivity test. 94.05% of the 639 loci were detectable in male-female mixed DNA samples with a mix ratio of 1:500. Nearly all of the loci were genotyped correctly when no more than 25 ng/μL tannic acid, 20 ng/μL humic acid, or 37.5 μM hematin was added to the amplification mixture. More than 80% of genotypes were obtained from degraded DNA samples with a degradation index of 11.76. Individuals from the same pedigree shared identical genotypes in 11 male pedigrees. Finally, we presented the complex evolutionary history of 183 northern Chinese Hans and six other Chinese populations, and found multiple founding lineages that contributed to the northern Han Chinese gene pool. The 639-plex panel proved an efficient tool for Chinese paternal studies and forensic applications.
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Affiliation(s)
- Guang-Bin Zhao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Lei Miao
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Mengge Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jia-Hui Yuan
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Lan-Hai Wei
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Inner Mongolia, 010028, China
| | - Yao-Sen Feng
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Jie Zhao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Ke-Lai Kang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Chi Zhang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - An-Quan Ji
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China.
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China.
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Zhang H, Huang X, Jin X, Ren Z, Wang Q, Yang M, Xu R, Yuan X, Yang D, Liu H, Shen W, Zhang H, Que Y, Huang J. Comprehensive analyses of genetic diversities and population structure of the Guizhou Dong group based on 44 Y-markers. PeerJ 2023; 11:e16183. [PMID: 37780380 PMCID: PMC10538297 DOI: 10.7717/peerj.16183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023] Open
Abstract
Background The non-recombining region of the human Y chromosome (NRY) is a strictly paternally inherited genetic marker and the best material to trace the paternal lineages of populations. Y chromosomal short tandem repeat (Y-STR) is characterized by high polymorphism and paternal inheritance pattern, so it has been widely used in forensic medicine and population genetic research. This study aims to understand the genetic distribution of Y-STRs in the Guizhou Dong population, provide reference data for forensic application, and explore the phylogenetic relationships between the Guizhou Dong population and other comparison populations. Methods Based on the allele profile of 44 Y-markers in the Guizhou Dong group, we estimate their allele frequencies and haplotype frequencies. In addition, we also compare the forensic application efficiency of different Y-STR sets in the Guizhou Dong group. Finally, genetic relationships among Guizhou Dong and other reference populations are dissected by the multi-dimensional scaling and the phylogenetic tree. Results A total of 393 alleles are observed in 312 Guizhou Dong individuals for these Y-markers, with allele frequencies ranging from 0.0032 to 0.9679. The haplotype diversity and discriminatory capacity for these Y-markers in the Guizhou Dong population are 0.99984 and 0.97440, respectively. The population genetic analyses of the Guizhou Dong group and other reference populations show that the Guizhou Dong group has the closest genetic relationship with the Hunan Dong population, and followed by the Guizhou Tujia population. Conclusions In conclusion, these 44 Y-markers can be used as an effective tool for male differentiation in the Guizhou Dong group. The haplotype data in this study not only enrich the Y-STR data of different ethnic groups in China, but also have important significance for population genetics and forensic research.
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Affiliation(s)
- Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaolan Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Ronglan Xu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiang Yuan
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Daiquan Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongyan Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Wanyi Shen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Huiying Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yangjie Que
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
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Agdzhoyan A, Iskandarov N, Ponomarev G, Pylev V, Koshel S, Salaev V, Pocheshkhova E, Kagazezheva Z, Balanovska E. Origins of East Caucasus Gene Pool: Contributions of Autochthonous Bronze Age Populations and Migrations from West Asia Estimated from Y-Chromosome Data. Genes (Basel) 2023; 14:1780. [PMID: 37761920 PMCID: PMC10530682 DOI: 10.3390/genes14091780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The gene pool of the East Caucasus, encompassing modern-day Azerbaijan and Dagestan populations, was studied alongside adjacent populations using 83 Y-chromosome SNP markers. The analysis of genetic distances among 18 populations (N = 2216) representing Nakh-Dagestani, Altaic, and Indo-European language families revealed the presence of three components (Steppe, Iranian, and Dagestani) that emerged in different historical periods. The Steppe component occurs only in Karanogais, indicating a recent medieval migration of Turkic-speaking nomads from the Eurasian steppe. The Iranian component is observed in Azerbaijanis, Dagestani Tabasarans, and all Iranian-speaking peoples of the Caucasus. The Dagestani component predominates in Dagestani-speaking populations, except for Tabasarans, and in Turkic-speaking Kumyks. Each component is associated with distinct Y-chromosome haplogroup complexes: the Steppe includes C-M217, N-LLY22g, R1b-M73, and R1a-M198; the Iranian includes J2-M172(×M67, M12) and R1b-M269; the Dagestani includes J1-Y3495 lineages. We propose J1-Y3495 haplogroup's most common lineage originated in an autochthonous ancestral population in central Dagestan and splits up ~6 kya into J1-ZS3114 (Dargins, Laks, Lezgi-speaking populations) and J1-CTS1460 (Avar-Andi-Tsez linguistic group). Based on the archeological finds and DNA data, the analysis of J1-Y3495 phylogeography suggests the growth of the population in the territory of modern-day Dagestan that started in the Bronze Age, its further dispersal, and the microevolution of the diverged population.
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Affiliation(s)
| | - Nasib Iskandarov
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
| | - Georgy Ponomarev
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
| | - Vladimir Pylev
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
- Biobank of Northern Eurasia, 115201 Moscow, Russia
| | - Sergey Koshel
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
- Department of Cartography and Geoinformatics, Faculty of Geography, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vugar Salaev
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
| | - Elvira Pocheshkhova
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
- Department of Biology with Course in Medical Genetics, Faculty of Pharmacy, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Zhaneta Kagazezheva
- Department of Biology with Course in Medical Genetics, Faculty of Pharmacy, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Elena Balanovska
- Research Centre for Medical Genetics, 115522 Moscow, Russia (V.P.); (E.P.)
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Kharkov VN, Kolesnikov NA, Valikhova LV, Zarubin AA, Svarovskaya MG, Marusin AV, Khitrinskaya IY, Stepanov VA. Relationship of the gene pool of the Khants with the peoples of Western Siberia, Cis-Urals and the Altai-Sayan Region according to the data on the polymorphism of autosomic locus and the Y-chromosome. Vavilovskii Zhurnal Genet Selektsii 2023; 27:46-54. [PMID: 36923476 PMCID: PMC10009483 DOI: 10.18699/vjgb-23-07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/23/2022] [Accepted: 11/27/2022] [Indexed: 03/18/2023] Open
Abstract
Khanty are indigenous Siberian people living on the territory of Western Siberia, mainly on the territory of the Khanty-Mansiysk and Yamalo-Nenets Autonomous Okrugs. The present study is aimed at a comprehensive analysis of the structure of the Khanty gene pool and their comparison with other populations of the indigenous population of Southern and Western Siberia. To address the issues of genetic proximity of the Khanty with other indigenous peoples, we performed genotyping of a wide genomic set of autosomal markers using high-density biochips, as well as an expanded set of SNP and STR markers of the Y-chromosome in various ethnic groups: Khakas, Tuvans, Southern Altaians, Siberian Tatars, Chulyms (Turkic language family) and Kets (Yeniseian language family). The structure of the gene pool of the Khanty and other West Siberian and South Siberian populations was studied using a genome-wide panel of autosomal single nucleotide polymorphic markers and Y-chromosome markers. The results of the analysis of autosomal SNPs frequencies by various methods, the similarities in the composition of the Y-chromosome haplogroups and YSTR haplotypes indicate that the Khanty gene pool is quite specific. When analyzing autosomal SNPs, the Ugrian genetic component completely dominates in both samples (up to 99-100 %). The samples of the Khanty showed the maximum match in IBD blocks with each other, with a sample of the Kets, Chulyms, Tuvans, Tomsk Tatars, Khakas, Kachins, and Southern Altaians. The degree of coincidence of IBD blocks between the Khanty, Kets, and Tomsk Tatars is consistent with the results of the distribution of allele frequencies and common genetic components in these populations. According to the composition of the Y-chromosome haplogroups, the two samples of the Khanty differ significantly from each other. A detailed phylogenetic analysis of various Y-chromosome haplogroups made it possible to describe and clarify the differences in the phylogeny and structure of individual ethnospecific sublines, to determine their relationship, traces of population expansion in the Khanty gene pool. Variants of different haplogroups of the Y-chromosome in the Khanty, Khakas and Tuvans go back to their common ancestral lines. The results of a comparative analysis of male samples indicate a close genetic relationship between the Khanty and Nenets, Komi, Udmurts and Kets. The specificity of haplotypes, the discovery of various terminal SNPs confirms that the Khanty did not come into contact with other ethnic groups for a long time, except for the Nenets, which included many Khanty clans.
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Affiliation(s)
- V N Kharkov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - N A Kolesnikov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - L V Valikhova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - A A Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - M G Svarovskaya
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - A V Marusin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - I Yu Khitrinskaya
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - V A Stepanov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
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8
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Stepanov VA, Kolesnikov NA, Valikhova LV, Zarubin AA, Khitrinskaya IY, Kharkov VN. Structure and origin of Tuvan gene pool according to autosome SNP and Y-chromosome haplogroups. Vavilovskii Zhurnal Genet Selektsii 2023; 27:36-45. [PMID: 36923480 PMCID: PMC10009474 DOI: 10.18699/vjgb-23-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 03/11/2023] Open
Abstract
Tuvans are one of the most compactly living peoples of Southern Siberia, settled mainly in the territory of Tuva. The gene pool of the Tuvans is quite isolated, due to endogamy and a very low frequency of interethnic marriages. The structure of the gene pool of the Tuvans and other Siberian populations was studied using a genome-wide panel of autosomal single nucleotide polymorphic markers and Y-chromosome markers. The results of the analysis of the frequencies of autosomal SNPs by various methods, the similarities in the composition of the Y-chromosome haplogroups and YSTR haplotypes show that the gene pool of the Tuvans is very heterogeneous in terms of the composition of genetic components. It includes the ancient autochthonous Yeniseian component, which dominates among the Chulym Turks and Kets, the East Siberian component, which prevails among the Yakuts and Evenks, and the Far Eastern component, the frequency of which is maximum among the Nivkhs and Udeges. Analysis of the composition of IBD-blocks on autosomes shows the maximum genetic relationship of the Tuvans with the Southern Altaians, Khakas and Shors, who were formed during the settlement of the Turkic groups of populations on the territory of the Altai-Sayan region. A very diverse composition of the Tuvan gene pool is shown for various sublines of Y-chromosomal haplogroups, most of which show strong ethnic specificity. Phylogenetic analysis of individual Y-chromosome haplogroups demonstrates the maximum proximity of the gene pool of the Tuvans with the Altaians, Khakas and Shors. Differences in frequencies of Y-chromosome haplogroups between the Todzhans and Tuvans and a change in the frequencies of haplogroups from south to north associated with the East Asian component were found. The majority of the most frequent Y-chromosome haplogroups in the Tuvans demonstrate the founder effect, the formation age of which is fully consistent with the data on their ethnogenesis.
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Affiliation(s)
- V A Stepanov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - N A Kolesnikov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - L V Valikhova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - A A Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - I Yu Khitrinskaya
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - V N Kharkov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
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Andersen MM, Eriksen PS, Morling N. Weight of evidence of Y-STR matches computed with the discrete Laplace method: Impact of adding a suspect's profile to a reference database. Forensic Sci Int Genet 2023; 64:102839. [PMID: 36731195 DOI: 10.1016/j.fsigen.2023.102839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023]
Abstract
The discrete Laplace method is recommended by multiple parties (including the International Society for Forensic Genetics, ISFG) to estimate the weight of evidence in criminal cases when a suspect's Y-STR profile matches the crime scene Y-STR profile. Unfortunately, modelling the distribution of Y-STR profiles in the population reference database is time-consuming and requires expert knowledge. When the suspect's Y-STR profile is added to the database, as would be the protocol in many cases, the parameters of the discrete Laplace model must be re-estimated. We found that the likelihood ratios with and without adding the suspect's Y-STR profile were almost identical with 1,000 or more Y-STR profiles in the database for Y-STR profiles with 8, 12, and 17 loci. Thus, likelihood ratio calculations can be performed in seconds if an established discrete Laplace model based on at least 1,000 Y-STR profiles is used. A match in a population reference database with 17 Y-STR loci from at least 1,000 male individuals results in a likelihood ratio above 10,000 in approximately 94% of the cases, and above 100,000 in approximately 82% of the cases. We offer free software accessible without restrictions to estimate a discrete Laplace model using a Y-STR reference database and subsequently to calculate likelihood ratios.
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10
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Borbély N, Székely O, Szeifert B, Gerber D, Máthé I, Benkő E, Mende BG, Egyed B, Pamjav H, Szécsényi-Nagy A. High Coverage Mitogenomes and Y-Chromosomal Typing Reveal Ancient Lineages in the Modern-Day Székely Population in Romania. Genes (Basel) 2023; 14:genes14010133. [PMID: 36672874 PMCID: PMC9858685 DOI: 10.3390/genes14010133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/05/2023] Open
Abstract
Here we present 115 whole mitogenomes and 92 Y-chromosomal Short Tandem Repeat (STR) and Single Nucleotide Polymorphism (SNP) profiles from a Hungarian ethnic group, the Székelys (in Romanian: Secuii, in German: Sekler), living in southeast Transylvania (Romania). The Székelys can be traced back to the 12th century in the region, and numerous scientific theories exist as to their origin. We carefully selected sample providers that had local ancestors inhabiting small villages in the area of Odorheiu Secuiesc/Székelyudvarhely in Romania. The results of our research and the reported data signify a qualitative leap compared to previous studies since it presents the first complete mitochondrial DNA sequences and Y-chromosomal profiles of 23 STRs from the region. We evaluated the results with population genetic and phylogenetic methods in the context of the modern and ancient populations that are either geographically or historically related to the Székelys. Our results demonstrate a predominantly local uniparental make-up of the population that also indicates limited admixture with neighboring populations. Phylogenetic analyses confirmed the presumed eastern origin of certain maternal (A, C, D) and paternal (Q, R1a) lineages, and, in some cases, they could also be linked to ancient DNA data from the Migration Period (5th-9th centuries AD) and Hungarian Conquest Period (10th century AD) populations.
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Affiliation(s)
- Noémi Borbély
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Tóth Kálmán Street 4, 1097 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
- Correspondence: (N.B.); (A.S.-N.)
| | - Orsolya Székely
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Tóth Kálmán Street 4, 1097 Budapest, Hungary
| | - Bea Szeifert
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Tóth Kálmán Street 4, 1097 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Dániel Gerber
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Tóth Kálmán Street 4, 1097 Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - István Máthé
- Department of Bioengineering, Socio-Human Sciences and Engineering, Faculty of Economics, Sapientia Hungarian University of Transylvania (Cluj-Napoca), Piața Libertății 1, 530104 Miercurea-Ciuc, Romania
| | - Elek Benkő
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Tóth Kálmán Street 4, 1097 Budapest, Hungary
| | - Balázs Gusztáv Mende
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Tóth Kálmán Street 4, 1097 Budapest, Hungary
| | - Balázs Egyed
- Department of Genetics, Faculty of Natural Sciences, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Horolma Pamjav
- Department of Reference Sample Analysis, Institute of Forensic Genetics, Hungarian Institutes for Forensic Sciences, Mosonyi Street 9, 1087 Budapest, Hungary
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Tóth Kálmán Street 4, 1097 Budapest, Hungary
- Correspondence: (N.B.); (A.S.-N.)
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11
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Sharif MB, Fitak RR, Wallner B, Orozco-terWengel P, Frewin S, Fremaux M, Mohandesan E. Reconstruction of the Major Maternal and Paternal Lineages in the Feral New Zealand Kaimanawa Horses. Animals (Basel) 2022; 12:ani12243508. [PMID: 36552427 PMCID: PMC9774138 DOI: 10.3390/ani12243508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/29/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
New Zealand has the fourth largest feral horse population in the world. The Kaimanawas (KHs) are feral horses descended from various domestic horse breeds released into the Kaimanawa ranges in the 19th and 20th centuries. Over time, the population size has fluctuated dramatically due to hunting, large-scale farming and forestry. Currently, the herd is managed by an annual round-up, limiting the number to 300 individuals to protect the native ecosystem. Here, we genotyped 96 KHs for uniparental markers (mitochondrial DNA, Y-chromosome) and assessed their genetic similarity with respect to other domestic horses. We show that at least six maternal and six paternal lineages contributed unequally to the KH gene pool, and today's KH population possibly represents two sub-populations. Our results indicate that three horse breeds, namely Welsh ponies, Thoroughbreds and Arabian horses had a major influence in the genetic-makeup of the extant KH population. We show that mitochondrial genetic diversity in KHs (π = 0.00687 ± 0.00355) is closer to that of the Sable Island horses (π = 0.0034 ± 0.00301), and less than other feral horse populations around the world. Our current findings, combined with ongoing genomic research, will provide insight into the population-specific genetic variation and inbreeding among KHs. This will largely advance equine research and improve the management of future breeding programs of these treasured New Zealand horse.
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Affiliation(s)
- Muhammad Bilal Sharif
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
| | - Robert Rodgers Fitak
- Department of Biology, Genomics and Bioinformatics Cluster, University of Central Florida, 4110 Libra Dr, Orlando, FL 32816, USA
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, Veterinary University of Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Pablo Orozco-terWengel
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK
| | - Simone Frewin
- Feed2U Ltd., 19 Wairere Valley Road, Paparoa 0571, New Zealand
| | - Michelle Fremaux
- InfogeneNZ (EPAGSC), School of Agriculture and Environment, Massey University, 1 Drysdale Drive, Palmerston North 4410, New Zealand
| | - Elmira Mohandesan
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Djerassiplatz 1, A-1030 Vienna, Austria
- Correspondence:
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12
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Abur U, Gunes S, Hekim N, Akar OS, Altundag E, Asci R. Clinical, cytogenomic, and molecular characterization of isodicentric Y-chromosome and prediction of testicular sperm retrieval outcomes in azoospermic and severe oligozoospermic infertile men. J Assist Reprod Genet 2022; 39:2799-2810. [PMID: 36251127 PMCID: PMC9790839 DOI: 10.1007/s10815-022-02632-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 09/29/2022] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Sex chromosome abnormalities are associated with male infertility. The aim of this study was to characterize the clinical, cytogenetic, and molecular findings of 12 infertile men with isodicentric Y-chromosome [idic(Y)] abnormalities diagnosed over a period of 13 years. MATERIALS AND METHODS Chromosomal analyses of peripheral blood samples were done using standard procedures. Fluorescence in situ hybridization (FISH) analysis was performed on metaphase spreads of the patients. Multiplex polymerase chain reaction (PCR) using several sequence-tagged site (STS) primer sets within the long arm of Y-chromosome was used to detect AZF deletions.The breakpoints and copy number variations (CNV) were identified by array comparative genomic hybridization analysis (aCGH) analysis.The short-stature homeobox (SHOX) gene deletions were verified using multiplex ligation-dependent probe amplification (MLPA) analysis. RESULTS Twelve infertile men were diagnosed cytogenetically with idic(Y). The karyotypes of two of the patients were non-mosaic, and the remaining karyotypes showed various degrees of mosaicism. SHOX gene deletion was found in two of the four patients with short stature, and the remaining two patients had shown a 45,X dominant cell line (33.3%). The most common breakpoints for idic(Yq) and idic(Yp) were found to be in Yq11.222 and Yp11.32, respectively. Semen analysis of ten patients (83.3%) demonstrated azoospermia, and the remaining two patients (16.7%) showed severe oligoasthenoteratozoospermia (OAT). In total, 33% (4/12) of idic(Y) patients with or without microsurgical testicular sperm extraction (microTESE) had sperm retrieval. CONCLUSIONS Twelve patients with idic(Y) and different breakpoints of Y-chromosome were characterized using multiple detection strategies. Sperm retrieval outcomes of patients either with idic(Yp) or idic(Yq) showed the possibility to find sperm by microTESE.
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Affiliation(s)
- Ummet Abur
- Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
- Department of Molecular Medicine, Graduate Institute, Ondokuz Mayis University, Samsun, Turkey
| | - Sezgin Gunes
- Department of Molecular Medicine, Graduate Institute, Ondokuz Mayis University, Samsun, Turkey.
- Department of Medical Biology, Faculty of Medicine, Ondokuz Mayis University, Samsun, 55139, Turkey.
| | - Neslihan Hekim
- Department of Medical Biology, Faculty of Medicine, Ondokuz Mayis University, Samsun, 55139, Turkey
| | - Omer Salih Akar
- Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
- Department of Molecular Medicine, Graduate Institute, Ondokuz Mayis University, Samsun, Turkey
| | - Engin Altundag
- Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
- Department of Molecular Medicine, Graduate Institute, Ondokuz Mayis University, Samsun, Turkey
| | - Ramazan Asci
- Department of Molecular Medicine, Graduate Institute, Ondokuz Mayis University, Samsun, Turkey
- Department of Urology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
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13
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Zhabagin M, Wei LH, Sabitov Z, Ma PC, Sun J, Dyussenova Z, Balanovska E, Li H, Ramankulov Y. Ancient Components and Recent Expansion in the Eurasian Heartland: Insights into the Revised Phylogeny of Y-Chromosomes from Central Asia. Genes (Basel) 2022; 13:1776. [PMID: 36292661 DOI: 10.3390/genes13101776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 11/04/2022] Open
Abstract
In the past two decades, studies of Y chromosomal single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) have shed light on the demographic history of Central Asia, the heartland of Eurasia. However, complex patterns of migration and admixture have complicated population genetic studies in Central Asia. Here, we sequenced and analyzed the Y-chromosomes of 187 male individuals from Kazakh, Kyrgyz, Uzbek, Karakalpak, Hazara, Karluk, Tajik, Uyghur, Dungan, and Turkmen populations. High diversity and admixture from peripheral areas of Eurasia were observed among the paternal gene pool of these populations. This general pattern can be largely attributed to the activities of ancient people in four periods, including the Neolithic farmers, Indo-Europeans, Turks, and Mongols. Most importantly, we detected the consistent expansion of many minor lineages over the past thousand years, which may correspond directly to the formation of modern populations in these regions. The newly discovered sub-lineages and variants provide a basis for further studies of the contributions of minor lineages to the formation of modern populations in Central Asia.
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14
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Doniec A, Januła M, Grzmil P, Kupiec T. Assessing the utility of quantitative and qualitative metrics in the DNA quantification process of skeletal remains for autosomal and Y-chromosome STR amplification purposes. Forensic Sci Int Genet 2022; 60:102751. [PMID: 35914369 DOI: 10.1016/j.fsigen.2022.102751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/30/2022] [Accepted: 07/25/2022] [Indexed: 11/20/2022]
Abstract
In historical cases, ancient DNA investigations and missing persons identification, teeth or bone samples are often the only and almost always the best biological material available for DNA typing. On the other hand, DNA obtained from bone material may be characterized by a high degradation index (DI) or its low content, or DNA tests cannot be repeated due to bone piece size limitation. That is often the effect of the environment in which the material was placed and the time during which exposure to unfavorable environmental factors took place. Therefore, it is very important to use appropriate procedures related to STR analysis. For our study, we selected 80 challenging bone samples. The amount of DNA was compared in qPCR using Quantifiler™ Trio DNA Quantification Kit and Investigator® Quantiplex® Pro RGQ. All qPCR results were confirmed by PCR-CE. The results of DNA concentrations and the assigned degradation index (DI) differed significantly within analyzed samples (~10%). Additionally, the Y-chromosome DI also differed from the autosomal DI in the samples. The difference in degradation indexes could explain the lower Y-chromosome amplification success rate compared to autosomal e.g. during human identification process. The results indicate that performing two DNA quantifications with the use of two different kits (primers sets) allows for a much more precise evaluation of the DNA quality and quantity in the isolate. We suggest that at least one of two suggested DNA concentration measurements should be based on an additional determination of the Y chromosome degradation index. Altogether, it allows for rational isolate management, especially when the volume is limited and the sample is unique.
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Affiliation(s)
- Andrzej Doniec
- Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31-033 Kraków, Poland; Laboratory of Genetics and Evolutionism, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland.
| | - Miłosz Januła
- Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31-033 Kraków, Poland
| | - Paweł Grzmil
- Laboratory of Genetics and Evolutionism, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
| | - Tomasz Kupiec
- Forensic Genetics Section, Institute of Forensic Research, Westerplatte 9, 31-033 Kraków, Poland.
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15
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Consortium VG, Nijman IJ, Rosen BD, Bardou P, Faraut T, Cumer T, Daly KG, Zheng Z, Cai Y, Asadollahpour H, Kul BÇ, Zhang WY, Guangxin E, Ayin A, Baird H, Bakhtin M, Bâlteanu VA, Barfield D, Berger B, Blichfeldt T, Boink G, Bugiwati SRA, Cai Z, Carolan S, Clark E, Cubric-Curik V, Dagong MIA, Dorji T, Drew L, Guo J, Hallsson J, Horvat S, Kantanen J, Kawaguchi F, Kazymbet P, Khayatzadeh N, Kim N, Shah MK, Liao Y, Martínez A, Masangkay JS, Masaoka M, Mazza R, McEwan J, Milanesi M, Faruque MO, Nomura Y, Ouchene-Khelifi NA, Pereira F, Sahana G, Salavati M, Sasazaki S, Da Silva A, Simčič M, Sölkner J, Sutherland A, Tigchelaar J, Zhang H, Consortium E, Ajmone-Marsan P, Bradley DG, Colli L, Drögemüller C, Jiang Y, Lei C, Mannen H, Pompanon F, Tosser-Klopp G, Lenstra JA. Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions. Mol Ecol 2022; 31:4364-4380. [PMID: 35751552 DOI: 10.1111/mec.16579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/12/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022]
Abstract
By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and 7 wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during the migrations into northern Europe, eastern and southern Asia and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographic range.
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Affiliation(s)
| | - Isaäc J Nijman
- Utrecht Univ., Netherlands.,Univ. Medical Center Utrecht, Utrecht Univ, The Netherlands
| | | | - Philippe Bardou
- GenPhySE, Univ. Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Thomas Faraut
- GenPhySE, Univ. Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Tristan Cumer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | | | - Zhuqing Zheng
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | - Yudong Cai
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | | | | | | | | | | | - Hayley Baird
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | - Valentin A Bâlteanu
- Inst. of Life SciencesUniv. Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | | | - Beate Berger
- Univ. Natural Resources and Life Sciences Vienna (BOKU)
| | - Thor Blichfeldt
- Norwegian Association of Sheep and Goat Breeders, Aas, Norway
| | - Geert Boink
- Stichting Zeldzame Huisdierrassen, Wageningen, The Netherlands
| | | | | | | | | | | | | | - Tashi Dorji
- International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | | | | | | | - Simon Horvat
- Univ. Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | | | | | | | - Namshin Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | | | - Yuying Liao
- Guangxi Key Laboratory of Livestock Genetic Improvement, Guangxi, China
| | | | | | | | - Raffaele Mazza
- Laboratorio Genetica e Servizi, Agrotis srl, Cremona, Italy
| | - John McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | | | | | | | - Filipe Pereira
- IDENTIFICA Genetic Testing Maia & Centre for Functional Ecology, Porto, Portugal
| | | | | | | | | | - Mojca Simčič
- Univ. Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | | | | | | | | | | | - Paolo Ajmone-Marsan
- Univ. Cattolica del S. Cuore di Piacenza and BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy.,UCSC PRONUTRIGEN Nutrigenomics Res. Centre, Piacenza, Italy
| | | | - Licia Colli
- Univ. Cattolica del S. Cuore di Piacenza and BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy.,UCSC BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy
| | | | - Yu Jiang
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | - Chuzhao Lei
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | | | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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16
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Olsen SDH, Kolte AM, Bang N, Krog MC, Steffensen R, Nielsen HS, Jakobsen MA. The development of an indel panel for microchimerism detection. Exp Mol Pathol 2022; 127:104804. [PMID: 35718190 DOI: 10.1016/j.yexmp.2022.104804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 05/17/2022] [Accepted: 06/11/2022] [Indexed: 11/04/2022]
Abstract
OBJECTIVES The aim of the study was to create a simple assay for microchimerism detection independent of sex and without HLA genotyping. METHODS The method is based on detection of insertion or deletions utilizing a multiplex PCR followed by fragment analysis by capillary electrophoresis, and probe-based qPCR assays. A total of 192 samples, taken either before pregnancy, during 1st trimester, or either during 2nd trimester or at miscarriage, obtained from a cohort of 97 female patients with either primary or secondary recurrent pregnancy loss, were screened for fetal microchimerism by the indel panel as well as an existing assay based on detection of the Y-chromosome marker; DYS14. RESULTS The overall prevalence of DYS14 positive samples was 29% (55/192) whereas 32% (61/192) tested positive by the indel method. There was an overall agreement of 64% (122/192) between the results obtained by the two methods. A Fisher's Exact test showed no statistic significant difference in the prevalence of microchimerism detected by the two methods at any of the three times of sampling. The distribution of the number of positive wells detected by both methods were compared by a Mann-Whitney U test, which showed no statistically significant difference at any of the three times of sampling. CONCLUSION The data indicates that microchimerism can be detected efficiently by the indel method. This makes it possible to detect both female and male cells without the need of HLA-genotyping. Furthermore, the indel method has potential to be implemented as a routine analysis. This will remove the sex bias in future explorations of the role microchimerism plays in health and disease.
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Affiliation(s)
- Sofie D H Olsen
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark.
| | - Astrid M Kolte
- The Recurrent Pregnancy Loss Unit, The Capital Region, Copenhagen University Hospitals, Hvidovre Hospital, DK-2650, Hvidovre & Rigshospitalet, DK-2100 Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Denmark
| | - Nina Bang
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Maria Christine Krog
- The Recurrent Pregnancy Loss Unit, The Capital Region, Copenhagen University Hospitals, Hvidovre Hospital, DK-2650, Hvidovre & Rigshospitalet, DK-2100 Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Denmark
| | - Rudi Steffensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Henriette S Nielsen
- The Recurrent Pregnancy Loss Unit, The Capital Region, Copenhagen University Hospitals, Hvidovre Hospital, DK-2650, Hvidovre & Rigshospitalet, DK-2100 Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Denmark; Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
| | - Marianne A Jakobsen
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
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17
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Khussainova E, Kisselev I, Iksan O, Bekmanov B, Skvortsova L, Garshin A, Kuzovleva E, Zhaniyazov Z, Zhunussova G, Musralina L, Kahbatkyzy N, Amirgaliyeva A, Begmanova M, Seisenbayeva A, Bespalova K, Perfilyeva A, Abylkassymova G, Farkhatuly A, Good SV, Djansugurova L. Genetic Relationship Among the Kazakh People Based on Y-STR Markers Reveals Evidence of Genetic Variation Among Tribes and Zhuz. Front Genet 2022; 12:801295. [PMID: 35069700 PMCID: PMC8777105 DOI: 10.3389/fgene.2021.801295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/10/2021] [Indexed: 11/21/2022] Open
Abstract
Ethnogenesis of Kazakhs took place in Central Asia, a region of high genetic and cultural diversity. Even though archaeological and historical studies have shed some light on the formation of modern Kazakhs, the process of establishment of hierarchical socioeconomic structure in the Steppe remains contentious. In this study, we analyzed haplotype variation at 15 Y-chromosomal short-tandem-repeats obtained from 1171 individuals from 24 tribes representing the three socio-territorial subdivisions (Senior, Middle and Junior zhuz) in Kazakhstan to comprehensively characterize the patrilineal genetic architecture of the Kazakh Steppe. In total, 577 distinct haplotypes were identified belonging to one of 20 haplogroups; 16 predominant haplogroups were confirmed by SNP-genotyping. The haplogroup distribution was skewed towards C2-M217, present in all tribes at a global frequency of 51.9%. Despite signatures of spatial differences in haplotype frequencies, a Mantel test failed to detect a statistically significant correlation between genetic and geographic distance between individuals. An analysis of molecular variance found that ∼8.9% of the genetic variance among individuals was attributable to differences among zhuzes and ∼20% to differences among tribes within zhuzes. The STRUCTURE analysis of the 1164 individuals indicated the presence of 20 ancestral groups and a complex three-subclade organization of the C2-M217 haplogroup in Kazakhs, a result supported by the multidimensional scaling analysis. Additionally, while the majority of the haplotypes and tribes overlapped, a distinct cluster of the O2 haplogroup, mostly of the Naiman tribe, was observed. Thus, firstly, our analysis indicated that the majority of Kazakh tribes share deep heterogeneous patrilineal ancestries, while a smaller fraction of them are descendants of a founder paternal ancestor. Secondly, we observed a high frequency of the C2-M217 haplogroups along the southern border of Kazakhstan, broadly corresponding to both the path of the Mongolian invasion and the ancient Silk Road. Interestingly, we detected three subclades of the C2-M217 haplogroup that broadly exhibits zhuz-specific clustering. Further study of Kazakh haplotypes variation within a Central Asian context is required to untwist this complex process of ethnogenesis.
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Affiliation(s)
| | - Ilya Kisselev
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- The University of Winnipeg, Winnipeg, MB, Canada
| | - Olzhas Iksan
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Bakhytzhan Bekmanov
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | - Alexander Garshin
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | | | | | - Lyazzat Musralina
- Institute of Genetics and Physiology, Almaty, Kazakhstan
- Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | | | | | | | - Kira Bespalova
- Institute of Genetics and Physiology, Almaty, Kazakhstan
| | | | | | | | - Sara V. Good
- The University of Winnipeg, Winnipeg, MB, Canada
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18
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Calafell F. Uniparental markers and their role in the future of Molecular Anthropology. J Anthropol Sci 2021; 99:183-185. [PMID: 34569944 DOI: 10.4436/jass.99005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Francesc Calafell
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain,
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19
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Boattini A, Bortolini E, Bauer R, Ottone M, Miglio R, Gueresi P, Pettener D. The surname structure of Trentino (Italy) and its relationship with dialects and genes. Ann Hum Biol 2021; 48:260-269. [PMID: 34459343 DOI: 10.1080/03014460.2021.1936635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Thanks to the availability of rich surname, linguistic and genetic information, together with its geographic and cultural complexity, Trentino (North-Eastern Italy) is an ideal place to test the relationships between genetic and cultural traits. AIM We provide a comprehensive study of population structures based on surname and dialect variability and evaluate their relationships with genetic diversity in Trentino. SUBJECTS AND METHODS Surname data were collected for 363 parishes, linguistic data for 57 dialects and genetic data for different sets of molecular markers (Y-chromosome, mtDNA, autosomal) in 10 populations. Analyses relied on different multivariate methods and correlation tests. RESULTS Besides the expected isolation-by-distance-like patterns (with few local exceptions, likely related to sociocultural instances), we detected a significant and geography-independent association between dialects and surnames. As for molecular markers, only Y-chromosomal STRs seem to be associated with the dialects, although no significant result was obtained. No evidence for correlation between molecular markers and surnames was observed. CONCLUSION Surnames act as cultural markers as do other words, although in this context they cannot be used as reliable proxies for genetic variability at a local scale.
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Affiliation(s)
- Alessio Boattini
- Department of Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, Bologna, Italy
| | - Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Roland Bauer
- Fachbereich Romanistik, Universität Salzburg, Austria
| | - Marta Ottone
- Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Rossella Miglio
- Department of Statistical Sciences, University of Bologna, Italy
| | - Paola Gueresi
- Department of Statistical Sciences, University of Bologna, Italy
| | - Davide Pettener
- Department of Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, Bologna, Italy
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20
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Claerhout S, Vanpaemel S, Gill MS, Antiga LG, Baele G, Decorte R. YMrCA: Improving Y-chromosomal ancestor time estimation for DNA kinship research. Hum Mutat 2021; 42:1307-1320. [PMID: 34265144 DOI: 10.1002/humu.24259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022]
Abstract
The Y-chromosome is a valuable kinship indicator in family history and forensic research. To reconstruct genealogies, the time to the most recent common ancestor (tMRCA) between paternal relatives can be estimated through Y-STR analysis. Existing models are the stepwise mutation model (SMM, only one-step Y-STR changes) and the infinite allele model (IAM, new allele per Y-STR change). In this study, these mutation models and all existing tMRCA calculators were validated through a genetic-genealogy database containing 1,120 biologically related genealogical pairs confirmed by 46 Y-STRs with known tMRCA (18,109 generations). Consistent under- and overestimation and broad confidence intervals were observed, leading to dubious tMRCA estimates. This is because they do not include individual mutation rates or multi-step changes and ignore hidden multiple, back, or parallel modifications. To improve tMRCA estimation, we developed a user-friendly calculator, the "YMrCA", including all previously mentioned mutation characteristics. After extensive validation, we observed that the YMrCA calculator demonstrated a promising performance. The YMrCA yields a significantly higher tMRCA success rate (96%; +20%) and a lower tMRCA error (7; -3) compared to the mutation models and all online tMRCA calculators. Therefore, YMrCA offers the next step towards more objective tMRCA estimation for DNA kinship research.
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Affiliation(s)
- Sofie Claerhout
- Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium
| | - Simon Vanpaemel
- Department of Mechanical Engineering, KU Leuven, Noise and Vibration Engineering, Heverlee, Belgium.,DMMS Lab, Flanders Make, Heverlee, Belgium
| | - Mandev S Gill
- Department of Microbiology, KU Leuven, Immunology and Transplantation, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | - Laura G Antiga
- Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium.,Bioinformatics for Health Science, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guy Baele
- Department of Microbiology, KU Leuven, Immunology and Transplantation, Rega Institute, Laboratory of Evolutionary and Computational Virology, Leuven, Belgium
| | - Ronny Decorte
- Department of Imaging & Pathology, KU Leuven, Forensic Biomedical Sciences, Leuven, Belgium.,Laboratory of Forensic Genetics, Department of Forensic Medicine, UZ Leuven, Leuven, Belgium
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21
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Bisso-Machado R, Fagundes NJR. Uniparental genetic markers in Native Americans: A summary of all available data from ancient and contemporary populations. Am J Phys Anthropol 2021; 176:445-458. [PMID: 34184252 DOI: 10.1002/ajpa.24357] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 05/26/2021] [Accepted: 06/16/2021] [Indexed: 01/01/2023]
Abstract
OBJECTIVES The aim of this study was to create a comprehensive summary of available mtDNA and Y-chromosome data for Native Americans from North, Central, and South America, including both modern and ancient DNA. To illustrate the usefulness of this dataset we present a broad picture of the genetic variation for both markers across the Americas. METHODS We searched PubMed, ResearchGate, Google Scholar for studies about mtDNA or Y-chromosome variation in Native American populations, including geographic, linguistic, ecological (ecoregion), archeological and chronological information. We used AMOVA to estimate the genetic structure associated with language and ecoregion grouping and Mantel tests to evaluate the correlation between genetic and geographic distances. RESULTS Genetic data were obtained from 321 primary sources, including 22,569 individuals from 298 contemporary populations, and 3628 individuals from 202 archeological populations. MtDNA lineages of probable non-Amerindian origin were rare, in contrast with Y-chromosome lineages. Mantel tests showed a statistically significant correlation for the whole continent considering mtDNA but not the Y-chromosome. Genetic structure between groups was always stronger for mtDNA than for the Y-chromosome. CONCLUSIONS This study summarizes decades of research conducted in Native American populations for both mtDNA and the Y-chromosome. Continental or sub-continental patterns of variation reveal that most of the genetic variation occurs within populations rather than among linguistic or ecoregional groups, and that isolation by distance is barely detectable in most population sets. The genetic structure among groups was always larger for mtDNA than for the Y-chromosome, suggesting between-sex differences in gene flow.
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Affiliation(s)
- Rafael Bisso-Machado
- Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Nelson J R Fagundes
- Programa de Pós-Graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Programa de Pós-Graduação em Biologia Animal, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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22
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Escouflaire C, Capitan A. Analysis of pedigree data and whole-genome sequences in 12 cattle breeds reveals extremely low within-breed Y-chromosome diversity. Anim Genet 2021; 52:725-729. [PMID: 34157133 PMCID: PMC8518513 DOI: 10.1111/age.13104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2021] [Indexed: 01/07/2023]
Abstract
In this article, we analyzed pedigree information on males from 12 bovine breeds born in France between 2015 and 2019. We report an overall small number of paternal lineages with, for example, a minimal number of ancestors accounting for 95% of the Y‐chromosome pool of their breed ranging from only 2 to 15 individuals. Then, we mined whole‐genome sequence data from 811 sires (2 ≤ n ≤ 510 per breed) and built a median‐joining network using 1411 SNPs. Most branches were breed‐specific and in agreement with the geographic and genetic relatedness of these populations. The within‐breed haplotype diversity was lower than expected based on genealogical information, which supports the existence of major male founder effects predating pedigree recording. In addition, we observed de novo mutation events among the descendants of the same ancestors, which are of interest to define paternal sub‐lineages. Our results pave the way to future studies on the estimation of the effects of Y‐chromosome haplotypes on male reproductive performances and on the conservation of Y‐chromosome diversity.
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Affiliation(s)
- C Escouflaire
- ALLICE, Paris, 75012, France.,Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - A Capitan
- ALLICE, Paris, 75012, France.,Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
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23
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Sarno S, Boscolo Agostini R, De Fanti S, Ferri G, Ghirotto S, Modenini G, Pettener D, Boattini A. Y-chromosome variability and genetic history of Commons from Northern Italy. Am J Phys Anthropol 2021; 175:665-679. [PMID: 33969895 PMCID: PMC8360088 DOI: 10.1002/ajpa.24302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/19/2021] [Accepted: 04/17/2021] [Indexed: 12/31/2022]
Abstract
Objectives Genetic drift and admixture are driving forces in human evolution, but their concerted impact to population evolution in historical times and at a micro‐geographic scale is poorly assessed. In this study we test a demographic model encompassing both admixture and drift to the case of social‐cultural isolates such as the so‐called “Commons.” Materials and methods Commons are peculiar institutions of medieval origins whose key feature is the tight relationship between population and territory, mediated by the collective property of shared resources. Here, we analyze the Y‐chromosomal genetic structure of four Commons (for a total of 366 samples) from the Central and Eastern Padana plain in Northern Italy. Results Our results reveal that all these groups exhibit patterns of significant diversity reduction, peripheral/outlier position within the Italian/European genetic space and high frequency of Common‐specific haplogroups. By explicitly testing different drift‐admixture models, we show that a drift‐only model is more probable for Central Padana Commons, while additional admixture (~20%) from external population around the same time of their foundation cannot be excluded for the Eastern ones. Discussion Building on these results, we suggest central Middle Ages as the most probable age of foundation for three of the considered Commons, the remaining one pointing to late antiquity. We conclude that an admixture‐drift model is particularly useful for interpreting the genetic structure and recent demographic history of small‐scale populations in which social‐cultural features play a significant role.
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Affiliation(s)
- Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | | | - Sara De Fanti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
| | - Gianmarco Ferri
- Department of Diagnostic and Clinical Medicine and Public Health, University of Modena and Reggio Emilia, Modena, Italy
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Giorgia Modenini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Davide Pettener
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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24
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Vidaki A, Montiel González D, Planterose Jiménez B, Kayser M. Male-specific age estimation based on Y-chromosomal DNA methylation. Aging (Albany NY) 2021; 13:6442-6458. [PMID: 33744870 PMCID: PMC7993701 DOI: 10.18632/aging.202775] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 02/25/2021] [Indexed: 11/29/2022]
Abstract
Although DNA methylation variation of autosomal CpGs provides robust age predictive biomarkers, no male-specific age predictor exists based on Y-CpGs yet. Since sex chromosomes play an important role in aging, a Y-chromosome-based age predictor would allow studying male-specific aging effects and would also be useful in forensics. Here, we used blood-based DNA methylation microarray data of 1,057 males from six cohorts aged 15-87 and identified 75 Y-CpGs with an interquartile range of ≥0.1. Of these, 22 and six were significantly hyper- and hypomethylated with age (p(cor)<0.05, Bonferroni), respectively. Amongst several machine learning algorithms, a model based on support vector machines with radial kernel performed best in male-specific age prediction. We achieved a mean absolute deviation (MAD) between true and predicted age of 7.54 years (cor=0.81, validation) when using all 75 Y-CpGs, and a MAD of 8.46 years (cor=0.73, validation) based on the most predictive 19 Y-CpGs. The accuracies of both age predictors did not worsen with increased age, in contrast to autosomal CpG-based age predictors that are known to predict age with reduced accuracy in the elderly. Overall, we introduce the first-of-its-kind male-specific epigenetic age predictor for future applications in aging research and forensics.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
| | - Benjamin Planterose Jiménez
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
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25
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Mauki DH, Adeola AC, Ng’ang’a SI, Tijjani A, Akanbi IM, Sanke OJ, Abdussamad AM, Olaogun SC, Ibrahim J, Dawuda PM, Mangbon GF, Gwakisa PS, Yin TT, Peng MS, Zhang YP. Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers. PeerJ 2021; 9:e10607. [PMID: 33717663 PMCID: PMC7938780 DOI: 10.7717/peerj.10607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/29/2020] [Indexed: 01/29/2023] Open
Abstract
The African cattle provide unique genetic resources shaped up by both diverse tropical environmental conditions and human activities, the assessment of their genetic diversity will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the genetic diversity of cattle samples from Nigeria using both maternal and paternal DNA markers. Nigerian cattle can be assigned to 80 haplotypes based on the mitochondrial DNA (mtDNA) D-loop sequences and haplotype diversity was 0.985 + 0.005. The network showed two major matrilineal clustering: the dominant cluster constituting the Nigerian cattle together with other African cattle while the other clustered Eurasian cattle. Paternal analysis indicates only zebu haplogroup in Nigerian cattle with high genetic diversity 1.000 ± 0.016 compared to other cattle. There was no signal of maternal genetic structure in Nigerian cattle population, which may suggest an extensive genetic intermixing within the country. The absence of Bos indicus maternal signal in Nigerian cattle is attributable to vulnerability bottleneck of mtDNA lineages and concordance with the view of male zebu genetic introgression in African cattle. Our study shades light on the current genetic diversity in Nigerian cattle and population history in West Africa.
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Affiliation(s)
- David H. Mauki
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | - Adeniyi C. Adeola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
| | - Said I. Ng’ang’a
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | | | - Ibikunle Mark Akanbi
- Ministry of Agriculture and Rural Development, Secretariat, Ibadan, Oyo, Nigeria
| | - Oscar J. Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Taraba, Nigeria
| | | | - Sunday C. Olaogun
- Department of Veterinary Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Jebi Ibrahim
- College of veterinary medicine, department of theriogenology, University of agriculture, Makurdi, Makurdi, Benue, Nigeria
| | - Philip M. Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Benue, Nigeria
| | | | - Paul S. Gwakisa
- Department of Microbiology, Parasitology and Biotechnology/ Genome Science Center, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Chinese Academy of Sciences, Sino-Africa Joint Research Center, Kunming, Yunnan, China
- University of Academy of Sciences, Kunming College of Life Science, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
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26
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Albujja MH, Vasudevan R, Alghamdi S, Pei CP, Bin Mohd Ghani KA, Ranneh Y, Ismail PB. A review of studies examining the association between genetic biomarkers (short tandem repeats and single-nucleotide polymorphisms) and risk of prostate cancer: the need for valid predictive biomarkers. Prostate Int 2020; 8:135-145. [PMID: 33425790 PMCID: PMC7767939 DOI: 10.1016/j.prnil.2019.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/22/2019] [Accepted: 11/08/2019] [Indexed: 01/22/2023] Open
Abstract
Prostate cancer (PCa) is a challenging polygenic disease because the genes that cause PCa remain largely elusive and are affected by several causal factors. Consequently, research continuously strives to identify a genetic marker which could be used as an indicator to predict the most vulnerable (i.e., predisposed) segments of the population to the disease or for the gene which may be directly responsible for PCa. To enhance the genetic etiology of PCa, this research sought to discover the key studies conducted in this field using data from the main journal publication search engines, as it was hoped that this could shed light on the main research findings from these studies, which in turn could assist in determining these genes or markers. From the research highlighted, the studies primarily used two kinds of markers: short tandem repeats or single-nucleotide polymorphisms. These markers were found to be quite prevalent in all the chromosomes within the research carried out. It also became apparent that the studies differed in both quantity and quality, as well as being conducted in a variety of societies. Links were also determined between the degree and strength of the relationship between these markers and the occurrence of the disease. From the studies identified, most recommended a larger and more diverse survey for the parameters which had not been studied before, as well as an increase in the size of the community (i.e., the population) being studied. This is an indication that work in this field is far from complete, and thus, current research remains committed toward finding genetic markers that can be used clinically for the diagnosis and screening of patients with PCa.
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Affiliation(s)
- Mohammed H. Albujja
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
- Department of Forensic Sciences, Faculty of Criminal Justice, Naif Arab University of Security Sciences, Riyadh, Saudi Arabia
| | - Ramachandran Vasudevan
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
- Malaysian Research Institute on Ageing (MYAGEING), Malaysia
| | - Saleh Alghamdi
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Chong P. Pei
- School of Biosciences, Faculty of Health & Medical Sciences, Taylors University, Malaysia
| | - Khairul A. Bin Mohd Ghani
- Department of Surgery, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Yazan Ranneh
- Department of Nutrition and Dietetics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Patimah B. Ismail
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
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27
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Dettori ML, Petretto E, Pazzola M, Vidal O, Amills M, Vacca GM. Assessing the Diversity and Population Substructure of Sarda Breed Bucks by Using Mtdna and Y-Chromosome Markers. Animals (Basel) 2020; 10:E2194. [PMID: 33255190 PMCID: PMC7761473 DOI: 10.3390/ani10122194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/21/2020] [Accepted: 11/22/2020] [Indexed: 11/16/2022] Open
Abstract
A sample of 146 Sarda bucks from eight subregions of Sardinia, Italy (Nuorese, Barbagia, Baronia, Ogliastra, Sarrabus, Guspinese, Iglesiente, Sulcis) were characterized for Y-chromosome and mtDNA markers to assess the levels of population substructure. Five polymorphic loci (SRY, AMELY, ZFY, and DDX3Y) on the Y-chromosome were genotyped. The control region of mtDNA was sequenced as a source of complementary information. Analysis of Y-chromosome data revealed the segregation of 5 haplotypes: Y1A (66.43%), Y2 (28.57%), Y1C (3.57%), Y1B1 (0.71%), and Y1B2 (0.71%). High levels of Y-chromosome diversity were observed in populations from Southwest Sardinia. The FST values based on Y-chromosome and mtDNA data were low, although a paternal genetic differentiation was observed when comparing the Nuorese and Barbagia populations (Central Sardinia) with the Sulcis, Iglesiente, and Sarrabus populations (Southern Sardinia). AMOVA analysis supported the lack of population substructure. These results suggest the occurrence of a historical and extensive gene flow between Sarda goat populations from different locations of Sardinia, despite the fact that this island is covered by several large mountain ranges. Introgression with foreign caprine breeds in order to improve milk production might have also contributed to avoiding the genetic differentiation amongst Sarda populations.
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Affiliation(s)
- Maria Luisa Dettori
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Elena Petretto
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
| | - Oriol Vidal
- Departament de Biologia, Universitat de Girona, 17003 Girona, Spain;
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Department of Animal Genetics, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain;
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Giuseppe Massimo Vacca
- Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy; (E.P.); (M.P.); (G.M.V.)
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28
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Ruiz CA, Chaney ME, Imamura M, Imai H, Tosi AJ. Predicted structural differences of four fertility-related Y-chromosome proteins in Macaca mulatta, M. fascicularis, and their Indochinese hybrids. Proteins 2020; 89:361-370. [PMID: 33146441 DOI: 10.1002/prot.26021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 11/10/2022]
Abstract
Species in the genus Macaca typically live in multimale-multifemale social groups with male macaques exhibiting some of the largest testis: body weight ratios among primates. Males are believed to experience intense levels of sperm competition. Several spermatogenesis genes are located on the Y-chromosome and, interestingly, occasional hybridization between two species has led to the introgression of the rhesus macaque (Macaca mulatta) Y-chromosome deep into the range of the long-tailed macaque (M. fascicularis). These observations have led to the prediction that the successful introgression of the rhesus Y-haplotype is due to functional differences in spermatogenesis genes compared to those of the native long-tailed Y-haplotype. We examine here four Y-chromosomal loci-RBMY, XKRY, and two nearly identical copies of CDY-and their corresponding protein sequences. The genes were surveyed in representative animals from north of, south of, and within the rhesus x long-tailed introgression zone. Our results show a series of non-synonymous amino acid substitutions present between the two Y-haplotypes. Protein structure modeling via I-TASSER revealed different folding patterns between the two species' Y-proteins, and functional predictions via TreeSAAP further reveal physicochemical differences as a result of non-synonymous substitutions. These differences inform our understanding of the evolution of primate Y-proteins involved in spermatogenesis and, in turn, have biomedical implications for human male fertility.
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Affiliation(s)
- Cody A Ruiz
- Department of Anthropology, Kent State University, Kent, Ohio, USA.,School of Biomedical Sciences, Kent State University, Kent, Ohio, USA
| | - Morgan E Chaney
- Department of Anthropology, Kent State University, Kent, Ohio, USA.,School of Biomedical Sciences, Kent State University, Kent, Ohio, USA
| | - Masanori Imamura
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Hiroo Imai
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Anthony J Tosi
- Department of Anthropology, Kent State University, Kent, Ohio, USA.,School of Biomedical Sciences, Kent State University, Kent, Ohio, USA
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29
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Grochowalski Ł, Jarczak J, Urbanowicz M, Słomka M, Szargut M, Borówka P, Sobalska-Kwapis M, Marciniak B, Ossowski A, Lorkiewicz W, Strapagiel D. Y-Chromosome Genetic Analysis of Modern Polish Population. Front Genet 2020; 11:567309. [PMID: 33193657 PMCID: PMC7644898 DOI: 10.3389/fgene.2020.567309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/27/2020] [Indexed: 01/11/2023] Open
Abstract
The study presents a full analysis of the Y-chromosome variability of the modern male Polish population. It is the first study of the Polish population to be conducted with such a large set of data (2,705 individuals), which includes genetic information from inhabitants of all voivodeships, i.e., the first administrative level, in the country and the vast majority of its counties, i.e., the second level. In addition, the available data were divided into clusters corresponding to more natural geographic regions. Genetic analysis included the estimation of FST distances, the visualization with the use of multidimensional scaling plots and analysis of molecular variance. Y-chromosome binary haplogroups were classified and visualized with the use of interpolation maps. Results showed that the level of differentiation within Polish population is quite low, but some differences were indicated. It was confirmed that the Polish population is characterized by a high degree of homogeneity, with only slight genetic differences being observed at the regional level. The use of regional clustering as an alternative to counties and voivodeships provided a more detailed view of the genetic structure of the population. Those regional differences identified in the present study highlighted the need for additional division of the population by cultural and ethnic criteria in such studies rather than just by geographical or administrative regionalization.
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Affiliation(s)
- Łukasz Grochowalski
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Justyna Jarczak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Maria Urbanowicz
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Marcin Słomka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Maria Szargut
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland.,The Polish Genetic Database of Totalitarianism Victims, Szczecin, Poland
| | - Paulina Borówka
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Błażej Marciniak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Andrzej Ossowski
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland.,The Polish Genetic Database of Totalitarianism Victims, Szczecin, Poland
| | - Wiesław Lorkiewicz
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
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30
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Zhabagin M, Sabitov Z, Tarlykov P, Tazhigulova I, Junissova Z, Yerezhepov D, Akilzhanov R, Zholdybayeva E, Wei LH, Akilzhanova A, Balanovsky O, Balanovska E. The medieval Mongolian roots of Y-chromosomal lineages from South Kazakhstan. BMC Genet 2020; 21:87. [PMID: 33092538 PMCID: PMC7583311 DOI: 10.1186/s12863-020-00897-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/05/2020] [Indexed: 12/02/2022] Open
Abstract
Background The majority of the Kazakhs from South Kazakhstan belongs to the 12 clans of the Senior Zhuz. According to traditional genealogy, nine of these clans have a common ancestor and constitute the Uissun tribe. There are three main hypotheses of the clans’ origin, namely, origin from early Wusuns, from Niru’un Mongols, or from Darligin Mongols. We genotyped 490 samples of South Kazakhs by 35 Y-chromosomal SNPs (single nucleotide polymorphism) and 17 STRs (short tandem repeat). Additionally, 133 samples from citizen science projects were included into the study. Results We found that three Uissun clans have unique Y-chromosomal profiles, but the remaining six Uissun clans and one non-Uissun clan share a common paternal gene pool. They share a high frequency (> 40%) of the C2*-ST haplogroup (marked by the SNP F3796), which is associated with the early Niru’un Mongols. Phylogenetic analysis of this haplogroup carried out on 743 individuals from 25 populations of Eurasia has revealed a set of haplotype clusters, three of which contain the Uissun haplotypes. The demographic expansion of these clusters dates back to the 13-fourteenth century, coinciding with the time of the Uissun’s ancestor Maiky-biy known from historical sources. In addition, it coincides with the expansion period of the Mongol Empire in the Late Middle Ages. A comparison of the results with published aDNA (ancient deoxyribonucleic acid) data and modern Y haplogroups frequencies suggest an origin of Uissuns from Niru’un Mongols rather than from Wusuns or Darligin Mongols. Conclusions The Y-chromosomal variation in South Kazakh clans indicates their common origin in 13th–14th centuries AD, in agreement with the traditional genealogy. Though genetically there were at least three ancestral lineages instead of the traditional single ancestor. The majority of the Y-chromosomal lineages of South Kazakhstan was brought by the migration of the population related to the medieval Niru’un Mongols.
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Affiliation(s)
- Maxat Zhabagin
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan. .,National Center for Biotechnology, Nur-Sultan, Kazakhstan.
| | - Zhaxylyk Sabitov
- L.N. Gumilyov Eurasian National University, Nur-Sultan, Kazakhstan.,Young Researchers Alliance, Nur-Sultan, Republic of Kazakhstan
| | - Pavel Tarlykov
- National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Inkar Tazhigulova
- Forensic Science Center of the Ministry of Justice of the Republic of Kazakhstan, Nur-Sultan, Kazakhstan
| | - Zukhra Junissova
- Research Institute of Archeology named after K.A. Akishev, Nur-Sultan, Republic of Kazakhstan
| | - Dauren Yerezhepov
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | | | - Lan-Hai Wei
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China.,Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Ainur Akilzhanova
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Oleg Balanovsky
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
| | - Elena Balanovska
- Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia
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31
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Mahal DG. Y-DNA genetic evidence reveals several different ancient origins in the Brahmin population. Mol Genet Genomics 2020; 296:67-78. [PMID: 32978661 DOI: 10.1007/s00438-020-01725-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/09/2020] [Indexed: 10/23/2022]
Abstract
The ancient geographical origins of Brahmins-a prominent ethnic group in the Indian subcontinent-have remained controversial for a long time. This study employed the AMOVA (analysis of molecular variance) test to evaluate genetic affinities of this group with thirty populations of Central Asia and Europe. A domestic comparison was performed with fifty non-Brahmin groups in India. The results showed that Brahmins had genetic affinities with several foreign populations and also shared their genetic heritage with several domestic non-Brahmin groups. The study identified the deep ancient origins of Brahmins by tracing their Y-chromosome haplogroups and genetic markers on the Y-DNA phylogenetic tree. It was confirmed that the progenitors of this group emerged from at least 12 different geographic regions of the world. The study concluded that about 83% of the Brahmins in the dataset belonged to four major haplogroups, of which two emerged from Central Asia, one from the Fertile Crescent, and one was of an indigenous Indian origin.
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Affiliation(s)
- David G Mahal
- DGM Associates, Pacific Palisades, CA, USA. .,Institut Avrio de Geneve, Geneva, Switzerland.
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32
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Hu X, Kueppers ST, Kooreman NG, Gravina A, Wang D, Tediashvili G, Schlickeiser S, Frentsch M, Nikolaou C, Thiel A, Marcus S, Fuchs S, Velden J, Reichenspurner H, Volk HD, Deuse T, Schrepfer S. The H-Y Antigen in Embryonic Stem Cells Causes Rejection in Syngeneic Female Recipients. Stem Cells Dev 2020; 29:1179-1189. [PMID: 32723003 DOI: 10.1089/scd.2019.0299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pluripotent stem cells are promising candidates for cell-based regenerative therapies. To avoid rejection of transplanted cells, several approaches are being pursued to reduce immunogenicity of the cells or modulate the recipient's immune response. These include gene editing to reduce the antigenicity of cell products, immunosuppression of the host, or using major histocompatibility complex-matched cells from cell banks. In this context, we have investigated the antigenicity of H-Y antigens, a class of minor histocompatibility antigens encoded by the Y chromosome, to assess whether the gender of the donor affects the cell's antigenicity. In a murine transplant model, we show that the H-Y antigen in undifferentiated embryonic stem cells (ESCs), as well as ESC-derived endothelial cells, provokes T- and B cell responses in female recipients.
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Affiliation(s)
- Xiaomeng Hu
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA.,Cardiovascular Research Center Hamburg (CVRC) and DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Luebeck, Hamburg, Germany.,University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Simon T Kueppers
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA.,Cardiovascular Research Center Hamburg (CVRC) and DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Luebeck, Hamburg, Germany.,University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Nigel G Kooreman
- Stanford Cardiovascular Institute, Stanford University, Stanford, California, USA.,Department of Medicine, Stanford University, Stanford, California, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA.,Department of Vascular Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Alessia Gravina
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA.,Cardiovascular Research Center Hamburg (CVRC) and DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Luebeck, Hamburg, Germany
| | - Dong Wang
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA.,Cardiovascular Research Center Hamburg (CVRC) and DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Luebeck, Hamburg, Germany.,University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Grigol Tediashvili
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA.,Cardiovascular Research Center Hamburg (CVRC) and DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Luebeck, Hamburg, Germany.,University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Stephan Schlickeiser
- BIH-Center for Regenerative Therapies (BCRT), Charité University Medicine and Berlin Institute of Health (BIH), Berlin, Germany.,Institute of Medical Immunology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, BIH, Berlin, Germany
| | - Marco Frentsch
- BIH-Center for Regenerative Therapies (BCRT), Charité University Medicine and Berlin Institute of Health (BIH), Berlin, Germany
| | - Christos Nikolaou
- BIH-Center for Regenerative Therapies (BCRT), Charité University Medicine and Berlin Institute of Health (BIH), Berlin, Germany
| | - Andreas Thiel
- BIH-Center for Regenerative Therapies (BCRT), Charité University Medicine and Berlin Institute of Health (BIH), Berlin, Germany
| | - Sivan Marcus
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA
| | - Sigrid Fuchs
- Institute of Human Genetics, University Medical Center Hamburg, Hamburg, Germany
| | - Joachim Velden
- Evotec AG, Histopathology and In Vivo Pharmacology, Hamburg, Germany
| | - Hermann Reichenspurner
- Cardiovascular Research Center Hamburg (CVRC) and DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Luebeck, Hamburg, Germany.,University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Hans-Dieter Volk
- BIH-Center for Regenerative Therapies (BCRT), Charité University Medicine and Berlin Institute of Health (BIH), Berlin, Germany.,Institute of Medical Immunology, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, BIH, Berlin, Germany
| | - Tobias Deuse
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA
| | - Sonja Schrepfer
- Transplant and Stem Cell Immunobiology Lab, Department of Surgery, University of California, San Francisco, California, USA.,Cardiovascular Research Center Hamburg (CVRC) and DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Luebeck, Hamburg, Germany.,University Heart & Vascular Center Hamburg, Hamburg, Germany
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33
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Triay C, Conte MA, Baroiller JF, Bezault E, Clark FE, Penman DJ, Kocher TD, D'Cotta H. Structure and Sequence of the Sex Determining Locus in Two Wild Populations of Nile Tilapia. Genes (Basel) 2020; 11:E1017. [PMID: 32872430 DOI: 10.3390/genes11091017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/15/2020] [Accepted: 08/27/2020] [Indexed: 12/30/2022] Open
Abstract
In domesticated strains of the Nile tilapia, phenotypic sex has been linked to genetic variants on linkage groups 1, 20 and 23. This diversity of sex-loci might reflect a naturally polymorphic sex determination system in Nile tilapia, or it might be an artefact arising from the process of domestication. Here, we searched for sex-determiners in wild populations from Kpandu, Lake Volta (Ghana-West Africa), and from Lake Koka (Ethiopia-East Africa) that have not been subjected to any genetic manipulation. We analysed lab-reared families using double-digest Restriction Associated DNA sequencing (ddRAD) and analysed wild-caught males and females with pooled whole-genome sequencing (WGS). Strong sex-linked signals were found on LG23 in both populations, and sex-linked signals with LG3 were observed in Kpandu samples. WGS uncovered blocks of high sequence coverage, suggesting the presence of B chromosomes. We confirmed the existence of a tandem amh duplication in LG23 in both populations and determined its breakpoints between the oaz1 and dot1l genes. We found two common deletions of ~5 kb in males and confirmed the presence of both amhY and amh∆Y genes. Males from Lake Koka lack both the previously reported 234 bp deletion and the 5 bp frameshift-insertion that creates a premature stop codon in amh∆Y.
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34
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Deng J, Xie XL, Wang DF, Zhao C, Lv FH, Li X, Yang J, Yu JL, Shen M, Gao L, Yang JQ, Liu MJ, Li WR, Wang YT, Wang F, Li JQ, Hehua EE, Liu YG, Shen ZQ, Ren YL, Liu GJ, Chen ZH, Gorkhali NA, Rushdi HE, Salehian-Dehkordi H, Esmailizadeh A, Nosrati M, Paiva SR, Caetano AR, Štěpánek O, Olsaker I, Weimann C, Erhardt G, Curik I, Kantanen J, Mwacharo JM, Hanotte O, Bruford MW, Ciani E, Periasamy K, Amills M, Lenstra JA, Han JL, Zhang HP, Li L, Li MH. Paternal Origins and Migratory Episodes of Domestic Sheep. Curr Biol 2020; 30:4085-4095.e6. [PMID: 32822607 DOI: 10.1016/j.cub.2020.07.077] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/14/2020] [Accepted: 07/27/2020] [Indexed: 01/22/2023]
Abstract
The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred ∼11,800-9,000 years BP and ∼5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution.
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Affiliation(s)
- Juan Deng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Life Science, Hebei University, Baoding 071002, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xin Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jia-Lin Yu
- Station for Breeding and Improvement of Animal and Poultry of Changshou District, Chongqing 401220, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China; State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China; State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China; State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi 830001, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi 830001, China
| | - Yu-Tao Wang
- College of Life and Geographic Sciences, Kashi University, Kashi 844000, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010000, China
| | - EEr Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750000, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650000, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou 256600, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou 256600, China
| | - Guang-Jian Liu
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Neena A Gorkhali
- Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council (NARC), Kathmandu, Nepal
| | - Hossam E Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Samuel R Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Avenida W5 Norte (Final), Caixa Postal 02372, CEP 70770-917 Brasília, DF, Brazil
| | - Alexandre R Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, PqEB, Avenida W5 Norte (Final), Caixa Postal 02372, CEP 70770-917 Brasília, DF, Brazil
| | - Ondřej Štěpánek
- Department of Virology, State Veterinary Institute Jihlava, Rantirovska 93, 58601, Jihlava, Czech Republic
| | - Ingrid Olsaker
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Christina Weimann
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Georg Erhardt
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - Joram M Mwacharo
- International Center for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, Addis Ababa, Ethiopia; CTLGH and SRUC, the Roslin Institute Building, Easter Bush Campus, Edinburgh EH25 9RG, UK
| | - Olivier Hanotte
- LiveGene, International Livestock Research Institute (ILRI), P.O. Box 5689, Addis Ababa, Ethiopia; School of Life Sciences, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff CF10 3AX, Wales, United Kingdom; Sustainable Places Research Institute, Cardiff University CF10 3BA, Wales, United Kingdom
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo 24 Moro, Bari, Italy
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency (IAEA), Vienna, Austria
| | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Hong-Ping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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Wang K, Tomura R, Chen W, Kiyooka M, Ishizaki H, Aizu T, Minakuchi Y, Seki M, Suzuki Y, Omotezako T, Suyama R, Masunaga A, Plessy C, Luscombe NM, Dantec C, Lemaire P, Itoh T, Toyoda A, Nishida H, Onuma TA. A genome database for a Japanese population of the larvacean Oikopleura dioica. Dev Growth Differ 2020; 62:450-461. [PMID: 32677034 DOI: 10.1111/dgd.12689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 06/10/2020] [Accepted: 06/10/2020] [Indexed: 01/01/2023]
Abstract
The larvacean Oikopleura dioica is a planktonic chordate and is a tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of 5 days make it a promising model organism for the study of developmental biology. The genome browser OikoBase was established in 2013 using Norwegian O. dioica. However, genome information for other populations is not available, even though many researchers have studied local populations. In the present study, we sequenced using Illumina and PacBio RSII technologies the genome of O. dioica from a southwestern Japanese population that was cultured in our laboratory for 3 years. The genome of Japanese O. dioica was assembled into 576 scaffold sequences with a total length and N50 length of 56.6 and 1.5 Mb, respectively. A total of 18,743 gene models (transcript models) were predicted in the genome assembly, named OSKA2016. In addition, 19,277 non-redundant transcripts were assembled using RNA-seq data. The OSKA2016 has global sequence similarity of only 86.5% when compared with the OikoBase, highlighting the sequence difference between the two far distant O. dioica populations on the globe. The genome assembly, transcript assembly, and transcript models were incorporated into ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and BLAST searches. Mapping of reads obtained from male- or female-specific genome libraries yielded male-specific scaffolds in the OSKA2016 and revealed that over 2.6 Mb of sequence were included in the male-specific Y-region. The genome and transcriptome resources from two distinct populations will be useful datasets for developmental biology, evolutionary biology, and molecular ecology using this model organism.
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Affiliation(s)
- Kai Wang
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Ryo Tomura
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Wei Chen
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Miho Kiyooka
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hinako Ishizaki
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tomoyuki Aizu
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yohei Minakuchi
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masahide Seki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Tatsuya Omotezako
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Ritsuko Suyama
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Aki Masunaga
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Charles Plessy
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Nicholas M Luscombe
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Kunigami-gun, Okinawa, Japan
| | - Christelle Dantec
- Centre de Recherches de Biochimie Macromoleculaire (CRBM), UMR5237, CNRS-Universite de Montpellier, Montpellier, France
| | - Patrick Lemaire
- Centre de Recherches de Biochimie Macromoleculaire (CRBM), UMR5237, CNRS-Universite de Montpellier, Montpellier, France
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
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36
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Nakamura Y, Samejima M, Minaguchi K, Nambiar P, Hashimoto M. Population Genetics in Malaysia and Japanese Populations Using Power Plex Y23 System. Bull Tokyo Dent Coll 2020; 61:83-94. [PMID: 32522936 DOI: 10.2209/tdcpublication.2019-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Population flow between Southeast Asian countries and Japan continues to gather pace. Accordingly, the number of foreigners involved in incidents in Japan has markedly increased, which means that forensic dentistry is now increasingly being faced with the need to analyze DNA from persons of non-Japanese extraction. The DNA test currently used for personal identification mainly utilizes short tandem repeats (STRs) on autosomal chromosomes and the Y-chromosome. This test was developed for use in personal identification, not for distinguishing among races; nonetheless, the standard method for personal identification is often used because the procedure has been established. To determine the degree to which racial differences can be distinguished by standard DNA analysis, 23 STRs located on the Y chromosome were investigated in 218 Malay and 426 Japanese males. The frequencies of each STR were calculated in the two populations. The difference in the power of discrimination between the Malay and Japanese populations ranged from a minimum of 0.01 to a maximum of 0.27; the difference in polymorphic information content ranged from 0.01 (minimum) to 0.23 (maximum). No major differences were noted in the polymorphisms in these two Mongoloid populations, but the distributions of the 17 STRs differed significantly. Short tandem repeat types demonstrating a likelihood of racial differences were identified in 14 of the STRs. Race-specific STR types were identified in 10 STRs. These results suggest that the likelihood of Malay or Japanese genetic background can be judged based on Y-chromosome STR test results.
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Affiliation(s)
- Yasutaka Nakamura
- Department of Forensic Odontology and Forensic Anthropology, Tokyo Dental College
| | | | - Kiyoshi Minaguchi
- Department of Forensic Medicine, Tokai University School of Medicine
| | | | - Masatsugu Hashimoto
- Department of Forensic Odontology and Forensic Anthropology, Tokyo Dental College
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37
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Liu S, Yang Y, Pan Q, Sun Y, Ma H, Liu Y, Wang M, Zhao C, Wu C. Ancient Patrilineal Lines and Relatively High ECAY Diversity Preserved in Indigenous Horses Revealed With Novel Y-Chromosome Markers. Front Genet 2020; 11:467. [PMID: 32508879 PMCID: PMC7253630 DOI: 10.3389/fgene.2020.00467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 04/15/2020] [Indexed: 02/06/2023] Open
Abstract
Extremely low nucleotide diversity of modern horse Y-chromosome has been reported, and only poor phylogenetic resolution could be resulted from limited Y-chromosome markers. In this study, three types of horse Y-chromosome markers, including Single-nucleotide polymorphisms (SNPs), copy number variants (CNVs), and allele-specific CNVs, were developed by screening more than 300 male horses from 23 indigenous Chinese horse populations and 4 imported horse breeds. Fourteen segregating sites including a novel SNP in the AMELY gene were found in approximately 53 kb of male-specific Y-chromosome sequences. CNVs were detected at 11 of 14 sites, while allele-specific CNVs at 6 polymorphic sites in repeated fragments were also determined. The phylogenetic analyses with the SNPs identified in this study and previously published 51 SNPs obtained mainly from European horses showed that indigenous Chinese horses exhibit much deeper divergence than European and Middle Eastern horses, while individuals of Chinese horses with the C allele of the AMELY gene constituted the most ancient group. Via SNPs, CNVs, and allele-specific CNVs, much higher diversity of paternal lines can be detected than those identified with merely SNPs. Our results indicated that there are ancient paternal horse lines preserved in southwestern China, which sheds new light on the domestication and immigration of horses, and suggest that the priorities of the conservation should be given to the ancient and rare paternal lines. These three marker types provided finer phylogenetic resolution of horse patrilineal lines, and the strategies used in the present study also provide valuable reference for the genetic studies of other mammalian patrilineages.
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Affiliation(s)
- Shuqin Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China
| | - Yunzhou Yang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China
| | - Qingjie Pan
- School of Animal Science and Technology, Qingdao Agricultural University, Shandong, China
| | - Yujiang Sun
- School of Animal Science and Technology, Qingdao Agricultural University, Shandong, China
| | - Hongying Ma
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China
| | - Yu Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China
| | - Min Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China
| | - Chunjiang Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China.,Beijing Key Laboratory for Animal Genetic Improvement, Beijing, China
| | - Changxin Wu
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Equine Center, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China.,Beijing Key Laboratory for Animal Genetic Improvement, Beijing, China
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38
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Lu Q, Cheng HZ, Li L, Yao HB, Ru K, Wen SQ, Shi MS, Zeng ZS, Wei LH. Paternal heritage of the Han Chinese in Henan province (Central China): high diversity and evidence of in situ Neolithic expansions. Ann Hum Biol 2020; 47:294-299. [PMID: 32281408 DOI: 10.1080/03014460.2020.1748226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Background: Due to their long history, complex admixture processes and large population sizes, more research is required to explore the fine genetic structure of Han populations from different geographic locations of China.Aim: To characterise the paternal genetic structure of the Han Chinese in Henan province, which was once the central living region of the ancient Huaxia population, the precursors of the Han Chinese.Subjects and methods: We sequenced Y chromosomes of 60 males from Zhengzhou, Henan Province, and reconstructed a phylogenetic tree for these samples with age estimation.Results: We observed high diversity of paternal lineages in our collection. We found that the in situ Neolithic expansion of the "Major lineages" contributed to a large portion of the paternal gene pool of the Han population in Henan Province. We also detected a large number of "Minor lineages" that diverged in the Palaeolithic Age.Conclusion: We suggest that the high genetic diversity in the paternal gene pool of modern Han populations is mainly attributed to the reservation of a larger number of lineages that diverged in the Palaeolithic Age, while the recent expansion of limited lineages contributed to the majority of the gene pool of modern Han populations. We propose that such a structure is a basal characteristic for the genetic structure of modern Han populations.
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Affiliation(s)
- Qi Lu
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Li Li
- Department of Obstetrics & Gynecology, Zhengzhou Central Hospital, Zhengzhou University, Zhengzhou, China
| | - Hong-Bin Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu University of Political Science and Law, Lanzhou, China
| | - Kai Ru
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Shao-Qing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China.,B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| | - Mei-Sen Shi
- Institute of the Investigation, School of Criminal Justice, China University of Political Science and Law, Beijing, China
| | - Zhao-Shu Zeng
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China.,B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
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Shonhai M, Nhiwatiwa T, Nangammbi T, Mazando S. Genetic analysis of 27 Y-chromosomal STR loci in a Zimbabwean Shona ethnic group. Leg Med (Tokyo) 2020; 43:101660. [PMID: 31911187 DOI: 10.1016/j.legalmed.2019.101660] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/28/2019] [Accepted: 12/05/2019] [Indexed: 01/09/2023]
Abstract
Buccal swabs from 200 unrelated Zimbabwean males were collected from voluntary participants located in Harare province. The 5-dye SureID® 27Y Human STR Identification Kit was used to perform multiplex polymerase chain reactions (PCR) and generate Y-chromosomal DNA profiles. This kit targets markers DYS456, DYS576, DYS570, DYS481, DYF387S1, DYS627, DYS393, DYS391, DYS390, DYS635, DYS449, DYS533, DYS438, DYS389I, DYS448, DYS389II, DYS19, GATA_H4, DYS518, DYS458, DYS460, DYS437, DYS439, DYS392, and DYS385, similar to the Yfiler® Plus Amplification Kit. A total of 161 haplotypes were generated with the PowerPlex® Y system, whereas 159 complete haplotypes were generated for the Yfiler® Plus system. Haplotype Discrimination Capacity (DC) with the Yfiler® Plus system was determined to be 0.9686, while the Genetic Diversity (GD) of the targeted loci ranged from 0.03748 at DYS392 to 0.867239 at DYS449. One haplotype contained the triallelic pattern 37, 38, and 39 at DYS387S1. In addition, marker DYS387S1 and marker DYS385 had 13 counts of microvariant alleles overall, while 9 null allele counts were noted at marker DYS448. Genetic distances between our population data and 22 other data sets from African countries and people of African descent were estimated and results showed significant genetic variation.
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40
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Choo A, Nguyen TNM, Ward CM, Chen IY, Sved J, Shearman D, Gilchrist AS, Crisp P, Baxter SW. Identification of Y-chromosome scaffolds of the Queensland fruit fly reveals a duplicated gyf gene paralogue common to many Bactrocera pest species. Insect Mol Biol 2019; 28:873-886. [PMID: 31150140 DOI: 10.1111/imb.12602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/22/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Bactrocera tryoni (Queensland fruit fly) are polyphagous horticultural pests of eastern Australia. Heterogametic males contain a sex-determining Y-chromosome thought to be gene poor and repetitive. Here, we report 39 Y-chromosome scaffolds (~700 kb) from B. tryoni identified using genotype-by-sequencing data and whole-genome resequencing. Male diagnostic PCR assays validated eight Y-scaffolds, and one (Btry4096) contained a novel gene with five exons that encode a predicted 575 amino acid protein. The Y-gene, referred to as typo-gyf, is a truncated Y-chromosome paralogue of X-chromosome gene gyf (1773 aa). The Y-chromosome contained ~41 copies of typo-gyf, and expression occurred in male flies and embryos. Analysis of 13 tephritid transcriptomes confirmed typo-gyf expression in six additional Bactrocera species, including Bactrocera latifrons, Bactrocera dorsalis and Bactrocera zonata. Molecular dating estimated typo-gyf evolved within the past 8.02 million years (95% highest posterior density 10.56-5.52 million years), after the split with Bactrocera oleae. Phylogenetic analysis also highlighted complex evolutionary histories among several Bactrocera species, as discordant nuclear (116 genes) and mitochondrial (13 genes) topologies were observed. B. tryoni Y-sequences may provide useful sites for future transgene insertions, and typo-gyf could act as a Y-chromosome diagnostic marker for many Bactrocera species, although its function is unknown.
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Affiliation(s)
- Amanda Choo
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Thu N M Nguyen
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Christopher M Ward
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Isabel Y Chen
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- South Australian Research and Development Institute, Adelaide, South Australia, Australia
| | - John Sved
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Deborah Shearman
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Anthony S Gilchrist
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Peter Crisp
- South Australian Research and Development Institute, Adelaide, South Australia, Australia
| | - Simon W Baxter
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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Claerhout S, Roelens J, Van der Haegen M, Verstraete P, Larmuseau MHD, Decorte R. Ysurnames? The patrilineal Y-chromosome and surname correlation for DNA kinship research. Forensic Sci Int Genet 2019; 44:102204. [PMID: 31760354 DOI: 10.1016/j.fsigen.2019.102204] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 11/30/2022]
Abstract
The Y-chromosome is a widely studied and useful small part of the genome providing different applications for interdisciplinary research. In many (Western) societies, the Y-chromosome and surnames are paternally co-inherited, suggesting a corresponding Y-haplotype for every namesake. While it has already been observed that this correlation may be disrupted by a false-paternity event, adoption, anonymous sperm donor or the co-founding of surnames, extensive information on the strength of the surname match frequency (SMF) with the Y-chromosome remains rather unknown. For the first time in Belgium and the Netherlands, we were able to study this correlation using 2,401 males genotyped for 46 Y-STRs and 183 Y-SNPs. The SMF was observed to be dependent on the number of Y-STRs analyzed, their mutation rates and the number of Y-STR differences allowed for a kinship. For a perfect match, the Yfiler® Plus and our in-house YForGen kit gave a similar high SMF of 98%, but for non-perfect matches, the latter could overall be identified as the best kit. The SMF generally increased due to less mismatches when encountering [1] deep Y-subhaplogroups, [2] less frequently occurring surnames, and [3] small geographical distances between relatives. This novel information enabled the design of a surname prediction model based on genetic and geographical distances of a kinship. The prediction model has an area under the curve (AUC) of 0.9 and is therefore useable for DNA kinship priority listing in estimation applications like forensic familial searching.
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Affiliation(s)
- Sofie Claerhout
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium.
| | - Jennifer Roelens
- Department of Earth and Environmental Sciences, KU Leuven, Leuven 3000, Belgium
| | - Michiel Van der Haegen
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Paulien Verstraete
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Maarten H D Larmuseau
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven 3000, Belgium; Histories vzw, Mechelen 2800, Belgium; Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Ronny Decorte
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium; Laboratory of Forensic genetics and Molecular Archaeology, UZ Leuven, Leuven 3000, Belgium
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42
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Sayyari M, Salehzadeh A, Tabatabaiefar MA, Abbasi A. Profiling of 17 Y-STR loci in Mazandaran and Gilan provinces of Iran. Turk J Med Sci 2019; 49:1277-1286. [PMID: 30893979 PMCID: PMC7018379 DOI: 10.3906/sag-1808-179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/20/2019] [Indexed: 11/19/2022] Open
Abstract
Background/aim The Y-chromosome mainly consists of heterochromatin regions that have a father-to-son inheritance. Short tandem repeat polymorphic (STRP) markers distributed all over the chromosome provide the opportunity for investigations in forensic medicine and ancestral lineage studies. Due to the existence of wide varieties of geographical and ethnic groups in Iran, studying Y-STRP markers is necessary for further applications. Here we investigated the provinces of Mazandaran and Gilan for the first time. Materials and methods Samples included 119 and 90 unrelated males from Mazandaran and Gilan, respectively. Using a PCR amplification kit, 17 Y-STRP markers were amplified and genotyping was conducted by capillary electrophoresis. Allele frequency, haplotype diversity (HD), and haplotype discrimination capacity (DC) were calculated. The populations were compared together and to neighboring countries including Afghanistan and Azerbaijan by FST index. Results A total of 204 unique haplotypes were observed. No uniqueness was observed between the two provinces. HD was 0.9993 and 0.9998 in Mazandaran and Gilan, respectively. DC was 0.9666 and 0.9888 for Mazandaran and Gilan, respectively. DYS385b and DYS391 had the most and least polymorphic content in both provinces, respectively. There was not a significant difference between these two provinces (FST = 0.0006 and P = 0.00) and neighboring countries. Conclusion The results highlight the effectiveness of these Y-STRP markers for male discrimination in the north of Iran. Using additional markers along with extended sample size would provide a better opportunity for removing matched haplotypes and introducing the best polymorphic markers in this specific population.
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Affiliation(s)
- Minoo Sayyari
- Department of Biology, Rasht Branch, Islamic Azad University, Rasht, Iran
| | - Ali Salehzadeh
- Department of Biology, Rasht Branch, Islamic Azad University, Rasht, Iran
| | - Mohamad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease,Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali Abbasi
- Iranian Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
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43
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Johansson MM, Pottmeier P, Suciu P, Ahmad T, Zaghlool A, Halvardson J, Darj E, Feuk L, Peuckert C, Jazin E. Novel Y-Chromosome Long Non-Coding RNAs Expressed in Human Male CNS During Early Development. Front Genet 2019; 10:891. [PMID: 31608120 PMCID: PMC6769107 DOI: 10.3389/fgene.2019.00891] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/23/2019] [Indexed: 01/01/2023] Open
Abstract
Global microarray gene expression analyses previously demonstrated differences in female and male embryos during neurodevelopment. In particular, before sexual maturation of the gonads, the differences seem to concentrate on the expression of genes encoded on the X- and Y-chromosomes. To investigate genome-wide differences in expression during this early developmental window, we combined high-resolution RNA sequencing with qPCR to analyze brain samples from human embryos during the first trimester of development. Our analysis was tailored for maximum sensitivity to discover Y-chromosome gene expression, but at the same time, it was underpowered to detect X-inactivation escapees. Using this approach, we found that 5 out of 13 expressed gametolog pairs showed unbalanced gene dosage, and as a consequence, a male-biased expression. In addition, we found six novel non-annotated long non-coding RNAs on the Y-chromosome with conserved expression patterns in newborn chimpanzee. The tissue specific and time-restricted expression of these long non-coding RNAs strongly suggests important functions during central nervous system development in human males.
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Affiliation(s)
- Martin M Johansson
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Philipp Pottmeier
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Pascalina Suciu
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Tauseef Ahmad
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Ammar Zaghlool
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Elisabeth Darj
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden.,Department of Public Health and General Practice, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Christiane Peuckert
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden.,Department of Molecular Biology, Stockholms University, Stockholm, Sweden
| | - Elena Jazin
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
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Sun N, Ma PC, Yan S, Wen SQ, Sun C, Du PX, Cheng HZ, Deng XH, Wang CC, Wei LH. Phylogeography of Y-chromosome haplogroup Q1a1a-M120, a paternal lineage connecting populations in Siberia and East Asia. Ann Hum Biol 2019; 46:261-266. [PMID: 31208219 DOI: 10.1080/03014460.2019.1632930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Background: Previous studies have suggested that the human Y-chromosome haplogroup Q1a1a-M120, a widespread paternal lineage in East Asian populations, originated in South Siberia. However, much uncertainty remains regarding the origin, diversification, and expansion of this paternal lineage.Aim: To explore the origin and diffusion of paternal Q-M120 lineages in East Asia.Subjects and methods: The authors generated 26 new Y chromosome sequences of Q-M120 males and co-analysed 45 Y chromosome sequences of this haplogroup. A highly-revised phylogenetic tree of haplogroup Q-M120 with age estimates was reconstructed. Additionally, a comprehensive phylogeographic analysis of this lineage was performed including 15,007 samples from 440 populations in eastern Eurasia.Results: An ancient connection of this lineage with populations in Siberia was revealed. However, this paternal lineage experienced an in-situ expansion between 5000 and 3000 years ago in northwestern China. Ancient populations with high frequencies of Q-M120 were involved in the formation of ancient Huaxia populations before 2000 years ago; this haplogroup eventually became one of the founding paternal lineages of modern Han populations.Conclusion: This study provides a clear pattern of the origin and diffusion process of haplogroup Q1a1a-M120, as well as the role of this paternal lineage during the formation of ancient Huaxia populations and modern Han populations.
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Affiliation(s)
- Na Sun
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, PR China.,Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China
| | - Peng-Cheng Ma
- Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China
| | - Shi Yan
- Human Phenome Institute, Fudan University, Shanghai, PR China.,B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China
| | - Shao-Qing Wen
- B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China.,Institute of Archaeological Science, Fudan University, Shanghai, PR China
| | - Chang Sun
- B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China.,Institute of Archaeological Science, Fudan University, Shanghai, PR China
| | - Pan-Xin Du
- B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China
| | - Hui-Zhen Cheng
- Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China.,Culture Development Institute of Xiamen University, Xiamen, PR China
| | - Xiao-Hua Deng
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, PR China.,Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, PR China.,Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China.,Laboratory for Anthropology and Human Development, Xiamen University, Xiamen, PR China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Xiamen University, Xiamen, PR China.,Center for Anthropological Linguistics, Xiamen University, Xiamen, PR China.,B&R International Joint Laboratory for Eurasian Anthropology, MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, PR China.,Culture Development Institute of Xiamen University, Xiamen, PR China.,Laboratory for Anthropology and Human Development, Xiamen University, Xiamen, PR China
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Gegenschatz-Schmid K, Verkauskas G, Stadler MB, Hadziselimovic F. Genes located in Y-chromosomal regions important for male fertility show altered transcript levels in cryptorchidism and respond to curative hormone treatment. Basic Clin Androl 2019; 29:8. [PMID: 31171972 PMCID: PMC6545630 DOI: 10.1186/s12610-019-0089-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/24/2019] [Indexed: 01/27/2023] Open
Abstract
Background Undescended (cryptorchid) testes in patients with defective mini-puberty and low testosterone levels contain gonocytes that fail to differentiate normally, which impairs the development of Ad spermatogonia and ultimately leads to adult infertility. Treatment with the gonadotropin-releasing hormone agonist GnRHa increases luteinizing hormone and testosterone and rescues fertility in the majority of pathological cryptorchid testes. Several Y-chromosomal genes in the male-specific Y region (MSY) are essential for spermatogenesis, testis development and function, and are associated with azoospermia, infertility and cryptorchidism. In this study, we analyzed the expression of MSY genes in testes with Ad spermatogonia (low infertility risk patients) as compared to testes lacking Ad spermatogonia (high infertility risk) before and after curative GnRHa treatment, and in correlation to their location on the Y-chromosome. Results Twenty genes that are up- or down-regulated in the Ad- group are in the X-degenerate or the ampliconic region, respectively. GnRHa treatment increases mRNA levels of 14 genes in the ampliconic region and decreases mRNA levels of 10 genes in the X-degenerate region. Conclusion Our findings implicate Y-chromosomal genes, including USP9Y, UTY, TXLNGY, RBMY1B, RBMY1E, RBMY1J and TSPY4, some of which are known to be important for spermatogenesis, in the curative hormonal treatment of cryptorchidism-induced infertility.
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Affiliation(s)
| | - Gilvydas Verkauskas
- 2Children's Surgery Centre, Faculty of Medicine, Vilnius of University, 01513 Vilnius, Lithuania
| | - Michael B Stadler
- 3Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,4Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Faruk Hadziselimovic
- Cryptorchidism Research Institute, Kindermedizinisches Zentrum Liestal, 4410 Liestal, Switzerland
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Rando HM, Wadlington WH, Johnson JL, Stutchman JT, Trut LN, Farré M, Kukekova AV. The Red Fox Y-Chromosome in Comparative Context. Genes (Basel) 2019; 10:E409. [PMID: 31142040 PMCID: PMC6627929 DOI: 10.3390/genes10060409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/16/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022] Open
Abstract
While the number of mammalian genome assemblies has proliferated, Y-chromosome assemblies have lagged behind. This discrepancy is caused by biological features of the Y-chromosome, such as its high repeat content, that present challenges to assembly with short-read, next-generation sequencing technologies. Partial Y-chromosome assemblies have been developed for the cat (Feliscatus), dog (Canislupusfamiliaris), and grey wolf (Canislupuslupus), providing the opportunity to examine the red fox (Vulpesvulpes) Y-chromosome in the context of closely related species. Here we present a data-driven approach to identifying Y-chromosome sequence among the scaffolds that comprise the short-read assembled red fox genome. First, scaffolds containing genes found on the Y-chromosomes of cats, dogs, and wolves were identified. Next, analysis of the resequenced genomes of 15 male and 15 female foxes revealed scaffolds containing male-specific k-mers and patterns of inter-sex copy number variation consistent with the heterogametic chromosome. Analyzing variation across these two metrics revealed 171 scaffolds containing 3.37 Mbp of putative Y-chromosome sequence. The gene content of these scaffolds is consistent overall with that of the Y-chromosome in other carnivore species, though the red fox Y-chromosome carries more copies of BCORY2 and UBE1Y than has been reported in related species and fewer copies of SRY than in other canids. The assignment of these scaffolds to the Y-chromosome serves to further characterize the content of the red fox draft genome while providing resources for future analyses of canid Y-chromosome evolution.
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Affiliation(s)
- Halie M Rando
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - William H Wadlington
- Tropical Research and Education Center, Agronomy Department, University of Florida, Homestead, FL 33031, USA.
| | - Jennifer L Johnson
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Jeremy T Stutchman
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Lyudmila N Trut
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Marta Farré
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Anna V Kukekova
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Benn Torres J, Martucci V, Aldrich MC, Vilar MG, MacKinney T, Tariq M, Gaieski JB, Bharath Hernandez R, Browne ZE, Stevenson M, Walters W, Schurr TG. Analysis of biogeographic ancestry reveals complex genetic histories for indigenous communities of St. Vincent and Trinidad. Am J Phys Anthropol 2019; 169:482-497. [PMID: 31125126 DOI: 10.1002/ajpa.23859] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 11/07/2022]
Abstract
OBJECTIVES From a genetic perspective, relatively little is known about how mass emigrations of African, European, and Asian peoples beginning in the 16th century affected Indigenous Caribbean populations. Therefore, we explored the impact of serial colonization on the genetic variation of the first Caribbean islanders. MATERIALS AND METHODS Sixty-four members of St. Vincent's Garifuna Community and 36 members of Trinidad's Santa Rosa First People's Community (FPC) of Arima were characterized for mitochondrial DNA and Y-chromosome diversity via direct sequencing and targeted SNP and STR genotyping. A subset of 32 Garifuna and 18 FPC participants were genotyped using the GenoChip 2.0 microarray. The resulting data were used to examine genetic diversity, admixture, and sex biased gene flow in the study communities. RESULTS The Garifuna were most genetically comparable to African descendant populations, whereas the FPC were more similar to admixed American groups. Both communities also exhibited moderate frequencies of Indigenous American matrilines and patrilines. Autosomal SNP analysis indicated modest Indigenous American ancestry in these populations, while both showed varying degrees of African, European, South Asian, and East Asian ancestry, with patterns of sex-biased gene flow differing between the island communities. DISCUSSION These patterns of genetic variation are consistent with historical records of migration, forced, or voluntary, and suggest that different migration events shaped the genetic make-up of each island community. This genomic study is the highest resolution analysis yet conducted with these communities, and provides a fuller understanding of the complex bio-histories of Indigenous Caribbean peoples in the Lesser Antilles.
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Affiliation(s)
- Jada Benn Torres
- Department of Anthropology, Vanderbilt University, Nashville, Tennessee.,Department of Anthropology, University of Notre Dame, Notre Dame, Indiana
| | - Victoria Martucci
- Department of Thoracic Surgery and Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Melinda C Aldrich
- Department of Thoracic Surgery and Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Miguel G Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania.,Science and Exploration, National Geographic Society, Washington, District of Columbia
| | - Taryn MacKinney
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Muhammad Tariq
- Department of Anthropology, Vanderbilt University, Nashville, Tennessee.,Department of Genetics, Hazara University, Mansehra, KP, Pakistan
| | - Jill B Gaieski
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Zoila E Browne
- The Garifuna Heritage Foundation Inc., Kingstown, St. Vincent
| | | | - Wendell Walters
- The Garifuna Heritage Foundation Inc., Kingstown, St. Vincent.,Sandy Bay Village, St. Vincent
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania
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Abstract
Background: Aurès is a vast territory in the east of Algeria, characterised by its traditional Berber settlement which has preserved its language and its rich history; its name goes back to antiquity and before the Roman conquest it was part of the territory of ancient Numidia. The Chaoui people in this region are one of Algeria's largest Berber groups. Aim: The aims were to investigate the level of genetic diversity of the Berbers of Aurès through the analysis of the paternal gene pool and to estimate the percentage of genetic variation among different geographical regions and linguistic groups from Algeria. Subjects and methods: Twenty-three Y-STRs were genotyped in a sample of 218 unrelated males of the Berbers of Aurès. Algorithms were used to estimate the Y-chromosome haplogroups. Genetic distance, non-metric MDS and AMOVA were used to analyse the genetic relationships between sample groups. Results: The paternal lineage of this sample of the Aurès region did not exhibit strong signals of differentiation with other samples from North-central, Northwest, and South Algeria. However, significant differences were found within this sample, demonstrating a high degree of heterogeneity. Conclusion: The results demonstrate that Aurès people are isolated and closed, but nevertheless have quite different genetic profiles.
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Affiliation(s)
- Amine Abdeli
- a Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques , Université des Sciences et de la Technologie Houari Boumediene , Algiers , Algeria.,b Institut National de Criminalistique et de Criminologie de la Gendarmerie Nationale , Algiers , Algeria
| | - Traki Benhassine
- a Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques , Université des Sciences et de la Technologie Houari Boumediene , Algiers , Algeria
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Kido T, Lau YFC. The Y-linked proto-oncogene TSPY contributes to poor prognosis of the male hepatocellular carcinoma patients by promoting the pro-oncogenic and suppressing the anti-oncogenic gene expression. Cell Biosci 2019; 9:22. [PMID: 30867900 PMCID: PMC6399826 DOI: 10.1186/s13578-019-0287-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 02/27/2019] [Indexed: 12/15/2022] Open
Abstract
Background Liver cancer is one of the major causes of cancer death worldwide, with significantly higher incidence and mortality among the male patients. Although sex hormones and their receptors could contribute to such sex differences, the story is incomplete. Genes on the male-specific region of the Y chromosome could play a role(s) in this cancer. TSPY is the putative gene for the gonadoblastoma locus on the Y chromosome (GBY) that is ectopically expressed in a subset of male hepatocellular carcinomas (HCCs). Although various studies showed that TSPY expression is associated with poor prognosis in the patients and its overexpression promotes cell proliferation of various cancer cell lines, it remains unclear how TSPY contributes to the clinical outcomes of the HCC patients. Identifying the downstream genes and pathways of TSPY actions would provide novel insights on its contribution(s) to male predominance in this deadly cancer. Results To determine the effects of TSPY on HCC, a TSPY transgene was introduced to the HCC cell line, HuH-7, and studied with RNA-Seq transcriptome analysis. The results showed that TSPY upregulates various genes associated with cell-cycle and cell-viability, and suppresses cell-death related genes. To correlate the experimental observations with those of clinical specimens, transcriptomes of male HCCs with high TSPY expression were analyzed with reference to those with silent TSPY expression from the Cancer Genome Atlas (TCGA). The comparative analysis identified 49 genes, which showed parallel expression patterns between HuH-7 cells overexpressing TSPY and clinical specimens with high TSPY expression. Among these 49 genes, 16 likely downstream genes could be associated with survival rates in HCC patients. The major upregulated targets were cell-cycle related genes and growth factor receptor genes, including CDC25B and HMMR, whose expression levels are negatively correlated with the patient survival rates. In contrast, PPARGC1A, SLC25A25 and SOCS2 were downregulated with TSPY expression, and possess favorable prognoses for HCC patients. Conclusion We demonstrate that TSPY could exacerbate the oncogenesis of HCC by differentially upregulate the expression of pro-oncogenic genes and downregulate those of anti-oncogenic genes in male HCC patients, thereby contributing to the male predominance in this deadly cancer. Electronic supplementary material The online version of this article (10.1186/s13578-019-0287-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tatsuo Kido
- 1Division of Cell and Developmental Genetics, Department of Medicine, Veterans Affairs Medical Center, University of California, San Francisco, 4150 Clement Street, San Francisco, CA 94121 USA.,2Institute for Human Genetics, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143 USA
| | - Yun-Fai Chris Lau
- 1Division of Cell and Developmental Genetics, Department of Medicine, Veterans Affairs Medical Center, University of California, San Francisco, 4150 Clement Street, San Francisco, CA 94121 USA.,2Institute for Human Genetics, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143 USA
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50
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Abstract
Despite the importance of Y-chromosomes in evolution and sex determination, their heterochromatic, repeat-rich nature makes them difficult to sequence (due, in part, to ambiguities in sequence alignment and assembly) and to genetically manipulate. Therefore, they generally remain poorly understood. For example, the Drosophila melanogaster Y-chromosome, one of the most extensively studied Y-chromosomes, is widely heterochromatic and composed mainly of highly repetitive sequences, with only a handful of expressed genes scattered throughout its length. Efforts to insert transgenes on this chromosome have thus far relied on either random insertion of transposons (sometimes harbouring 'landing sites' for subsequent integrations) with limited success or on chromosomal translocations, thereby limiting the types of Y-chromosome-related questions that could be explored. Here, we describe a versatile approach to site-specifically insert transgenes on the Y-chromosome in D. melanogaster via CRISPR/Cas9-mediated homology-directed repair. We demonstrate the ability to insert, and detect expression from, fluorescently marked transgenes at two specific locations on the Y-chromosome, and we utilize these marked Y-chromosomes to detect and quantify rare chromosomal nondisjunction effects. Finally, we discuss how this Y-docking technique could be adapted to other insects to aid in the development of genetic control technologies for the management of insect disease vectors and pests.
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Affiliation(s)
- Anna Buchman
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, 92093, United States of America
| | - Omar S. Akbari
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, 92093, United States of America
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093, United States of America
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