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Pathak AK, Simonian H, Ibrahim IAA, Hrechdakian P, Behar DM, Ayub Q, Arsanov P, Metspalu E, Yepiskoposyan L, Rootsi S, Endicott P, Villems R, Sahakyan H. Human Y chromosome haplogroup L1-M22 traces Neolithic expansion in West Asia and supports the Elamite and Dravidian connection. iScience 2024; 27:110016. [PMID: 38883810 PMCID: PMC11177204 DOI: 10.1016/j.isci.2024.110016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/06/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024] Open
Abstract
West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.6 thousand years ago (kya). Moreover, this haplogroup parallels the genome-wide genetic ancestry of hunter-gatherers from the Iranian Plateau and the Caucasus. We characterized two L1-M22 harboring population groups during the Early Holocene. One expanded with the West Asian Neolithic transition. The other moved to South Asia ∼8-6 kya but showed no expansion. This group likely participated in the spread of Dravidian languages. These South Asian L1-M22 lineages expanded ∼4-3 kya, coinciding with the Steppe ancestry introduction. Our findings advance the current understanding of Eurasian historical dynamics, emphasizing L1-M22's West Asian origin, associated population movements, and possible linguistic impacts.
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Affiliation(s)
- Ajai Kumar Pathak
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Hovann Simonian
- Armenian DNA Project at Family Tree DNA, Houston, TX 77008, USA
| | - Ibrahim Abdel Aziz Ibrahim
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | | | - Doron M Behar
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Qasim Ayub
- Monash University Malaysia Genomics Platform, School of Science, Monash University, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
| | - Pakhrudin Arsanov
- Chechen-Noahcho DNA Project at Family Tree DNA, Kostanay 110008, Kazakhstan
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Levon Yepiskoposyan
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Phillip Endicott
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- Department of Archaeology and Anthropology, Bournemouth University, Fern Barrow, Poole, Dorset BH12 5BB, UK
- Department of Linguistics, University of Hawai'i at Mānoa, Honolulu, Hawai'i 96822, USA
- DFG Center for Advanced Studies, University of Tübingen, 72074 Tübingen, Germany
| | - Richard Villems
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia
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Castaneda C, Radović L, Felkel S, Juras R, Davis BW, Cothran EG, Wallner B, Raudsepp T. Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups. G3 (BETHESDA, MD.) 2022; 12:jkac278. [PMID: 36227030 PMCID: PMC9713435 DOI: 10.1093/g3journal/jkac278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/08/2022] [Indexed: 11/03/2023]
Abstract
Structural rearrangements like copy number variations in the male-specific Y chromosome have been associated with male fertility phenotypes in human and mouse but have been sparsely studied in other mammalian species. Here, we designed digital droplet PCR assays for 7 horse male-specific Y chromosome multicopy genes and SRY and evaluated their absolute copy numbers in 209 normal male horses of 22 breeds, 73 XY horses with disorders of sex development and/or infertility, 5 Przewalski's horses and 2 kulans. This established baseline copy number for these genes in horses. The TSPY gene showed the highest copy number and was the most copy number variable between individuals and breeds. SRY was a single-copy gene in most horses but had 2-3 copies in some indigenous breeds. Since SRY is flanked by 2 copies of RBMY, their copy number variations were interrelated and may lead to SRY-negative XY disorders of sex development. The Przewalski's horse and kulan had 1 copy of SRY and RBMY. TSPY and ETSTY2 showed significant copy number variations between cryptorchid and normal males (P < 0.05). No significant copy number variations were observed in subfertile/infertile males. Notably, copy number of TSPY and ETSTY5 differed between successive male generations and between cloned horses, indicating germline and somatic mechanisms for copy number variations. We observed no correlation between male-specific Y chromosome gene copy number variations and male-specific Y chromosome haplotypes. We conclude that the ampliconic male-specific Y chromosome reference assembly has deficiencies and further studies with an improved male-specific Y chromosome assembly are needed to determine selective constraints over horse male-specific Y chromosome gene copy number and their relation to stallion reproduction and male biology.
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Affiliation(s)
- Caitlin Castaneda
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Lara Radović
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Sabine Felkel
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Department of Biotechnology, Institute of Computational Biology, BOKU University of Life Sciences and Natural Resources, Vienna 1190, Austria
| | - Rytis Juras
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Ernest Gus Cothran
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Barbara Wallner
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
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