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Modina SA, Kusliy MA, Malikov DG, Molodtseva AS. Phylogeography of the woolly mammoth (Mammuthus primigenius) in the Minusinsk Depression of southern Siberia in the Late Pleistocene. Vavilovskii Zhurnal Genet Selektsii 2024; 28:571-577. [PMID: 39280844 PMCID: PMC11393653 DOI: 10.18699/vjgb-24-63] [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: 12/06/2023] [Revised: 04/12/2024] [Accepted: 05/13/2024] [Indexed: 09/18/2024] Open
Abstract
To date, a number of studies have been published on the phylogenetics of woolly mammoths (Mammuthus primigenius), ranging from analyses of parts of the mitochondrial genome to studies of complete nuclear genomes. However, until recently nothing was known about the genetic diversity of woolly mammoths in southern Siberia, in the Minusinsk Depression in particular. Within the framework of this effort, libraries for high-throughput sequencing of seven bone samples of woolly mammoths were obtained, two-round enrichment using biotinylated probes of modern mtDNA of Elephas maximus immobilised on magnetic microspheres and sequencing with subsequent bioinformatic analysis were carried out. Phylogenetic reconstructions showed the presence of all studied mammoths in clade I, which expanded its range. The assignment of mammoth mitotypes in the Minusinsk Depression to different clusters within clade I may indicate a sufficiently high diversity of their gene pool. Phylogeographic reconstructions revealed a genetic proximity of mitochondrial lineages of Late Pleistocene mammoths of the Minusinsk Depression and other regions of eastern Siberia and estimated their divergence time in the range of 100-150 thousand years ago, which indicates active migrations of woolly mammoths over vast territories of eastern Siberia in the late Middle Pleistoceneearly Late Pleistocene.
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Affiliation(s)
- S A Modina
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - M A Kusliy
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D G Malikov
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia V.S. Sobolev Institute of Geology and Mineralogy of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A S Molodtseva
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Chen J, Wang H, Li J, Liu S, Li B, Sun Y, Wang H, Manglai D. CKM intron: an appropriate marker for the determination of the genetic relationships among horse populations and breeds. Anim Biotechnol 2023; 34:3962-3970. [PMID: 37593944 DOI: 10.1080/10495398.2023.2247445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
To date, the origins, domestication, and genetic structure of Chinese Mongolian horses (CMH) are poorly understood. Furthermore, there have been sparse reports on the genetic differences between CMH and Thoroughbred. In order to determine their genetic structure, understand their genetic relationships, and explore their domestication processes, we performed an extensive survey of creatine kinase (muscle isoenzyme; CKM) variations among six populations of indigenous CMH, cultivated Sanhe horses, and imported Thoroughbred. Twenty-three single-nucleotide polymorphisms were found among the 343 horse sequences. From these, 40 haplotypes were inferred. Haplotype diversity (H) values differed from 0.6424 to 0.7881 and nucleotide diversity (π) values ranged from 0.00150 to 0.00211. The differences between Thoroughbred population and other Chinese horse populations were large, but only small differences were observed among Chinese horse populations with respect to CKM intron sequences suggesting that the domestication history, breeding measures, and origins of these horse populations are completely different. Results suggest that Sanhe and CMH are very closely related and the introgression (interbreeding) between them is serious. Our results suggest that Sanhe and Wushen require prompt and powerful protection. Overall, CKM intron was an appropriate marker for the determination of genetic relationships among horse populations and breeds.
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Affiliation(s)
- Jianxing Chen
- The Research Institute for the Development Strategy of the Equine Industry, Chifeng University, Chifeng, China
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Huidong Wang
- The Research Institute for the Development Strategy of the Equine Industry, Chifeng University, Chifeng, China
- College of Chemistry and Life Science, Chifeng University, Chifeng, China
| | - Jing Li
- The Research Institute for the Development Strategy of the Equine Industry, Chifeng University, Chifeng, China
- College of Chemistry and Life Science, Chifeng University, Chifeng, China
| | - Shuqin Liu
- Gene Bank for Equine Genetic Resources of Shandong Province, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Benke Li
- Binzhou Refferral Center for Agricultural Technologies, Binzhou, China
| | - Yujiang Sun
- Gene Bank for Equine Genetic Resources of Shandong Province, College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
- Vocational College of Dongying, Dongying, China
| | - Huaidong Wang
- The Research Institute for the Development Strategy of the Equine Industry, Chifeng University, Chifeng, China
| | - Dugarjaviin Manglai
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
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Kang Z, Shi J, Liu T, Zhang Y, Zhang Q, Liu Z, Wang J, Cheng S. Genome-wide single-nucleotide polymorphism data and mitochondrial hypervariable region 1 nucleotide sequence reveal the origin of the Akhal-Teke horse. Anim Biosci 2023; 36:1499-1507. [PMID: 37170508 PMCID: PMC10475378 DOI: 10.5713/ab.23.0044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 04/10/2023] [Indexed: 05/13/2023] Open
Abstract
OBJECTIVE The study investigated the origin of the Akhal-Teke horse using genome-wide single-nucleotide polymorphism (SNP) data and mitochondrial hypervariable region 1 (HVR-1) nucleotide sequences. METHODS Genome-wide SNP data from 22 breeds (481 horses) and mitochondrial HVR-1 sequences from 24 breeds (544 sequences) worldwide to examine the origin of the Akhal- Teke horse. The data were analyzed using principal component analysis, linkage disequilibrium analysis, neighbor-joining dendrograms, and ancestry inference to determine the population relationships, ancestral source, genetic structure, and relationships with other varieties. RESULTS A close genetic relationship between the Akhal-Teke horse and horses from the Middle East was found. Analysis of mitochondrial HVR-1 sequences showed that there were no shared haplotypes between the Akhal-Teke and Tarpan horses, and the mitochondrial data indicated that the Akhal-Teke horse has not historically expanded its group. Ancestral inference suggested that Arabian and Caspian horses were the likely ancestors of the Akhal- Teke horse. CONCLUSION The Akhal-Teke horse originated in the Middle East.
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Affiliation(s)
- Zhoucairang Kang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070,
China
| | - Jinping Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070,
China
| | - Ting Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070,
China
| | - Yong Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070,
China
| | - Quanwei Zhang
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070,
China
| | - Zhe Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070,
China
| | - Jianfu Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070,
China
| | - Shuru Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070,
China
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Kusliy MA, Yurlova AA, Neumestova AI, Vorobieva NV, Gutorova NV, Molodtseva AS, Trifonov VA, Popova KO, Polosmak NV, Molodin VI, Vasiliev SK, Semibratov VP, Iderkhangai TO, Kovalev AA, Erdenebaatar D, Graphodatsky AS, Tishkin AA. Genetic History of the Altai Breed Horses: From Ancient Times to Modernity. Genes (Basel) 2023; 14:1523. [PMID: 37628575 PMCID: PMC10454587 DOI: 10.3390/genes14081523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/16/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, that the Altai horse is represented by two populations (Eastern and Southern) and that the Mongolian horse has a greater genetic proximity to Eastern Altai horses. Bone samples of ancient horses from different cultures of Altai were investigated to clarify the genetic history of this horse breed. As a genetic marker, we chose hypervariable region I of mitochondrial DNA. The results of the performed phylogenetic and population genetic analyses of our and previously published data confirmed the hypothesis stated above. As we found out, almost all the haplotypes of the ancient domesticated horses of Altai are widespread among modern Altai horses. The differences between the mitochondrial gene pools of the ancient horses of Altai and Mongolia are more significant than between those of modern horses of the respective regions, which is most likely due to an increase in migration processes between these regions after the Early Iron Age.
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Affiliation(s)
- Mariya A Kusliy
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Anna A Yurlova
- Laboratory of Genomics, Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Alexandra I Neumestova
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Nadezhda V Vorobieva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Natalya V Gutorova
- Department of Human Molecular Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Anna S Molodtseva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Vladimir A Trifonov
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Kseniya O Popova
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Natalia V Polosmak
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, 630090 Novosibirsk, Russia
| | - Vyacheslav I Molodin
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, 630090 Novosibirsk, Russia
| | - Sergei K Vasiliev
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, 630090 Novosibirsk, Russia
| | - Vladimir P Semibratov
- Department of Archaeology, Ethnography and Museology, Altai State University, 656049 Barnaul, Russia
| | - Tumur-O Iderkhangai
- Department of Archaeology, Ulaanbaatar School, National University of Mongolia, 13343 Ulaanbaatar, Mongolia
| | - Alexey A Kovalev
- Department of Archaeological Heritage Preservation, Institute of Archaeology of the Russian Academy of Sciences, 117292 Moscow, Russia
| | - Diimaajav Erdenebaatar
- Department of Archaeology, Ulaanbaatar School, National University of Mongolia, 13343 Ulaanbaatar, Mongolia
| | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Alexey A Tishkin
- Department of Archaeology, Ethnography and Museology, Altai State University, 656049 Barnaul, Russia
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Ran B, Zhu W, Zhao X, Li L, Yi Z, Li M, Wang T, Li D. Studying Genetic Diversity and Relationships between Mountainous Meihua Chickens Using Mitochondrial DNA Control Region. Genes (Basel) 2023; 14:genes14050998. [PMID: 37239358 DOI: 10.3390/genes14050998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/18/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
The Mountainous Meihua chicken is a unique regional germplasm resource from Tongjiang County, Bazhong City, China, but its genetic structure and evolutionary relationships with other native chicken breeds in the Sichuan region remain unclear. Here, we analyzed a total of 469 sequences, including 199 Mountainous Meihua chicken sequences generated in this study, together with 30 sequences representing 13 clades and 240 sequences from seven different Sichuan local chicken breeds downloaded from NCBI. These sequences were further used to analyze genetic diversity, patterns of population differentiation, and phylogenetic relationships between groups. We show that Mountainous Meihua chicken mtDNA sequences have high haplotypic and nucleotide diversity (0.876 and 0.012, respectively) and with a T bias that is suggestive of good breeding potential. Phylogenetic analysis showed that Mountainous Meihua chickens belong to clades A, B, E, and G and have a low affinity to other chicken breeds, with a moderate degree of differentiation. A non-significant Tajima's D indicates that no demographic expansions occurred in the past. Finally, the four maternal lineages identified in Mountainous Meihua chicken showed unique genetic characteristics.
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Affiliation(s)
- Bo Ran
- School of Pharmacy, Chengdu University, Chengdu 610106, China
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Wei Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoling Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linxiang Li
- Bazhong Academy of Agricultural and Forestry Sciences, Bazhong 610066, China
| | - Zhixin Yi
- Bazhong Academy of Agricultural and Forestry Sciences, Bazhong 610066, China
| | - Miao Li
- Bazhong Academy of Agricultural and Forestry Sciences, Bazhong 610066, China
| | - Tao Wang
- School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu 610106, China
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Hong JH, Oh CS, Kim S, Kang IU, Shin DH. Genetic analysis of mitochondrial DNA from ancient <i>Equus caballus</i> bones found at archaeological site of Joseon dynasty period capital area. Anim Biosci 2022; 35:1141-1150. [PMID: 35240033 PMCID: PMC9262724 DOI: 10.5713/ab.21.0500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/28/2022] [Indexed: 11/27/2022] Open
Abstract
Objective To understand the domestication and spread of horses in history, genetic information is essential. However, mitogenetic traits of ancient or medieval horses have yet to be comprehensively revealed, especially for East Asia. This study thus set out to reveal the maternal lineage of skeletal horse remains retrieved from a 15th century archaeological site (Gongpyeongdong) at Old Seoul City in South Korea. Methods We extracted DNA from the femur of Equus caballus (SNU-A001) from Joseon period Gongpyeongdong site. Mitochondrial (mt) DNA (HRS 15128-16116) of E. caballus was amplified by polymerase chain reaction. Cloning and sequencing were conducted for the mtDNA amplicons. The sequencing results were analyzed by NCBI/BLAST and phylogenetic tool of MEGA7 software. Results By means of mtDNA cytochrome b and D-loop analysis, we found that the 15th century Korean horse belonged to haplogroup Q representing those horses that have historically been raised widely in East Asia. Conclusion The horse is unique among domesticated animals for the remarkable impact it has on human civilization in terms of transportation and trade. Utilizing the Joseon-period horse remains, we can obtain clues to reveal the genetic traits of Korean horse that existed before the introduction of Western horses.
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Ancient and Archaic Genomes. Genes (Basel) 2021; 12:genes12091411. [PMID: 34573393 PMCID: PMC8470403 DOI: 10.3390/genes12091411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 09/08/2021] [Indexed: 11/17/2022] Open
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