Article
Biochemistry & Molecular Biology
Qiliang Ding, Ya Hu, Amnon Koren, Andrew G. Clark
Summary: This study found significant variation in Y-chromosome mutation rates among different haplogroups, which may be a likely cause of branch length heterogeneity in phylogenetic trees.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Zhihan Zhou, Zhimin Li, Yining Yao, Jinglei Qian, Qiqi Ji, Chengchen Shao, Jianhui Xie
Summary: The Y-chromosomal haplogroup tree has various applications in anthropology, archaeology, and population genetics. This study identified a group of potential phylogenetic informative Y-InDels in the dominant East Asian haplogroup O-M175, which provides a supplement for updating and applying Y-chromosomal markers.
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Isaac J. Nijman, Benjamin D. Rosen, Philippe Bardou, Thomas Faraut, Tristan Cumer, Kevin G. Daly, Zhuqing Zheng, Yudong Cai, Hojjat Asadollahpour, Bengi Cinar Kul, Wei-Yi Zhang, Guangxin E, A. Ayin, Hayley Baird, Meirat Bakhtin, Valentin A. Balteanu, Diana Barfield, Beate Berger, Thor Blichfeldt, Geert Boink, Sri R. A. Bugiwati, Zexi Cai, Sean Carolan, Emily Clark, Vlatka Cubric-Curik, Muhammad I. A. Dagong, Tashi Dorji, Louise Drew, Jiazhong Guo, Jon Hallsson, Simon Horvat, Juha Kantanen, Fuki Kawaguchi, Polat Kazymbet, Negar Khayatzadeh, Namshin Kim, Manoj Kumar Shah, Yuying Liao, Amparo Martinez, Joseph S. Masangkay, Maho Masaoka, Raffaele Mazza, John McEwan, Marco Milanesi, Faruque Md Omar, Yuto Nomura, Nadjet-Amina Ouchene-Khelifi, Filipe Pereira, Goutam Sahana, Mazdak Salavati, Shinji Sasazaki, Anne Da Silva, Mojca Simcic, Johann Solkner, Alison Sutherland, Johannes Tigchelaar, Hongpin Zhang, Paolo Ajmone-Marsan, Daniel G. Bradley, Licia Colli, Cord Drogemuller, Yu Jiang, Chuzhao Lei, Hideyuki Mannen, Francois Pompanon, Gwenola Tosser-Klopp, Johannes A. Lenstra
Summary: This study analyzed the Y-chromosomal variants in domestic and wild goats, revealing the importance of paternal population history and male-mediated introgression. The findings provide insights into the evolution of goat species and the influence of migrations and crossbreeding on their genetic diversity.
Article
Biochemical Research Methods
Hao Chen, Yan Lu, Dongsheng Lu, Shuhua Xu
Summary: Y-LineageTracker is a high-throughput analysis framework for analyzing Y-DNA data, providing various functions at both NRY haplogroup and Y-STR level. The tool outperforms existing tools, supports various input data formats, and generates high-quality figures.
BMC BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Sofie Claerhout, Paulien Verstraete, Liesbeth Warnez, Simon Vanpaemel, Maarten Larmuseau, Ronny Decorte
Summary: The study highlights the limitations in chrY research due to the lack of a comprehensive sequencing panel and introduces the CSYseq as the first extensive chrY-specific sequencing panel. It successfully targets both slow mutating Y-SNPs for evolutionary ancestry and rapid mutating Y-STRs for patrilineage identification, making it a valuable tool for genetic-genealogical applications in various research fields.
Article
Medicine, Legal
Zhihan Zhou, Yuxiang Zhou, Zhimin Li, Yining Yao, Qinrui Yang, Jinglei Qian, Chengchen Shao, Xiaoqin Qian, Kuan Sun, Qiqun Tang, Jianhui Xie
Summary: Y-chromosomal single nucleotide polymorphisms (Y-SNPs) play an important role in forensic practice by providing additional information beyond the limitations of Y-chromosomal STR (Y-STR) haplotypes and helping to distinguish different paternal pedigrees.
FORENSIC SCIENCE INTERNATIONAL
(2022)
Article
Biochemistry & Molecular Biology
David G. Mahal
Summary: This study revealed the genetic affinities of Brahmins with foreign populations as well as with domestic non-Brahmin groups in India. By tracing Y-chromosome haplogroups and genetic markers, the deep ancient origins of Brahmins were identified, with their progenitors emerging from at least 12 different geographic regions worldwide. Additionally, the study found that 83% of Brahmins in the dataset belonged to four major haplogroups, two from Central Asia, one from the Fertile Crescent, and one of indigenous Indian origin.
MOLECULAR GENETICS AND GENOMICS
(2021)
Article
Genetics & Heredity
Hyung Jun Kim, Han Jun Jin
Summary: This study analyzed the genetic correlation between Y chromosome haplogroups and ADHD in Korean boys and found a lack of association.
Article
Genetics & Heredity
Naida Babic Jordamovic, Tamara Kojovic, Serkan Dogan, Larisa Besic, Lana Salihefendic, Rijad Konjhodzic, Vedrana Skaro, Petar Projic, Vesna Hadziavdic, Adna Asic, Damir Marjanovic
Summary: This study analyzed Y-chromosomal haplogroups of adult males from Bosnia and Herzegovina, identifying 14 different haplogroups with I2a, R1a, and E1b1b being the most prevalent. Compared to previous studies, this research had a significantly larger sample size, providing more accurate results and a higher likelihood of detecting rare haplogroups.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Victor Garcia-Olivares, Adrian Munoz-Barrera, Luis A. Rubio-Rodriguez, David Jaspez, Ana Diaz-de Usera, Antonio Inigo-Campos, Krishna R. Veeramah, Santos Alonso, Mark G. Thomas, Jose M. Lorenzo-Salazar, Rafaela Gonzalez-Montelongo, Carlos Flores
Summary: This study evaluates command-line tools for NRY haplogroup classification using high-throughput sequencing data. The results show that WES is an effective method for determining the NRY haplogroup, with Yleaf performing the best in WES data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Genetics & Heredity
Zehra Koeksal, Claus Borsting, Leonor Gusmao, Vania Pereira
Summary: SNPtotree v1.0 is a software that can uniquely determine the hierarchical order of variants on non-recombining DNA without the need for manual sorting. The software infers the relationships between variants using pairwise comparisons and integrates the combined information into a phylogenetic tree. In benchmark testing, SNPtotree outperforms traditional methods in the accuracy of phylogenetic trees for sequencing data with high amounts of missing information.
Article
Genetics & Heredity
Caiyong Yin, Ziwei He, Yi Wang, Xi He, Xiao Zhang, Mingying Xia, Dian Zhai, Kaichuang Chang, Xueyun Chen, Xingneng Chen, Feng Chen, Li Jin, Shilin Li
Summary: This study focused on improving the resolution of the Y-STR dataset by utilizing a Y-SNP Pedigree Tagging System in a regional Y-DNA database. Results indicated the critical role of haplogroups in enhancing regional Y-STR haplotype resolution and the ability of Y-SNPs to correct misclassifications from Y-STRs, ultimately improving prediction accuracy.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2022)
Article
Genetics & Heredity
Jing Liu, Lirong Jiang, Mengyao Zhao, Weian Du, Yufeng Wen, Suyu Li, Shuyuan Zhang, Fengfei Fang, Jian Shen, Guanglin He, Mengge Wang, Hao Dai, Yiping Hou, Zheng Wang
Summary: A highly reliable and sensitive Y-SNP analysis method specific to the Chinese population has been developed, allowing for the determination of male paternal lineage and biogeographic ancestry. This method has demonstrated excellent performance and can be widely used for Y-chromosomal haplogroup analysis in China.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Balnd M. Albarzinji, Farhad M. Abdulkarim, Shaho A. Hussein, Dlshad Rashid, Hayder Lazim
Summary: This study investigates the population relationship of the Sorani Kurdish population in Sulaymaniyah province using DNA samples. The results show that the J2 subclade predominates in this population, and they cluster with Asian populations while being furthest from European and African populations.
Article
Biotechnology & Applied Microbiology
Guang-Bin Zhao, Lei Miao, Mengge Wang, Jia-Hui Yuan, Lan-Hai Wei, Yao-Sen Feng, Jie Zhao, Ke-Lai Kang, Chi Zhang, An-Quan Ji, Guanglin He, Le Wang
Summary: This article introduces a 639-plex panel including 633 Y-SNPs and 6 Y-Insertion/deletions for paternal studies and forensic applications in Chinese populations. The panel shows high concordance, accuracy, and reproducibility, and can represent the genetic diversity and complex population structures of the Chinese Y-chromosome.
