Population genomics of sika deer reveals recent speciation and genetic selective signatures during evolution and domestication
Abstract Background Population genomic analysis can reconstruct the phylogenetic relationship and demographic history, and identify genomic selective signatures of a species. To date, fundamental aspects of population genomic analyses, such as intraspecies taxonomy, evolutionary history, and adaptiv...
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2025-04-01
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| author | Huamiao Liu Bo Zhu Tianjiao Wang Yimeng Dong Yan Ju Yang Li Weilin Su Ranran Zhang Shiwu Dong Hongliang Wang Yongna Zhou Yanmin Zhu Lei Wang Zhengyi Zhang Pei Zhao Shuyan Zhang Rui Guo E. A Yuwen Zhang Xin Liu Hidetoshi B. Tamate Qiqi Liang De Ma Xiumei Xing |
| author_facet | Huamiao Liu Bo Zhu Tianjiao Wang Yimeng Dong Yan Ju Yang Li Weilin Su Ranran Zhang Shiwu Dong Hongliang Wang Yongna Zhou Yanmin Zhu Lei Wang Zhengyi Zhang Pei Zhao Shuyan Zhang Rui Guo E. A Yuwen Zhang Xin Liu Hidetoshi B. Tamate Qiqi Liang De Ma Xiumei Xing |
| author_sort | Huamiao Liu |
| collection | DOAJ |
| description | Abstract Background Population genomic analysis can reconstruct the phylogenetic relationship and demographic history, and identify genomic selective signatures of a species. To date, fundamental aspects of population genomic analyses, such as intraspecies taxonomy, evolutionary history, and adaptive evolution, of sika deer have not been systematically investigated. Furthermore, accumulating lines of evidences have illustrated that incorrect species delimitation will mislead conservation decisions, and even lead to irreversible mistakes in threatened species. Results In this study, we resequenced 81 wild and 71 domesticated sika deer representing 10 main geographic populations and two farms to clarify the species delimitation, demographic and divergence histories, and adaptive evolution of this species. First, our analyses of whole genomes, Y chromosomes and mitochondrial genomes revealed substantial genetic differentiation between the continental and Japanese lineages of sika deer, representing two phylogenetically distinct species. Second, sika deer in Japan were inferred to have experienced a “divergence-mixing-isolation” evolutionary scenario. Third, we identified four candidate genes (XKR4, NPAS3, CTNNA3, and CNTNAP5) possibly involved in body size regulation of sika deer by selective sweep analysis. Furthermore, we also detected two candidate genes (NRP2 and EDIL3) that may be associated with an important economic trait (antler weight) were under selection during the process of domestication. Conclusion Population genomic analyses revealed that the continental and Japanese lineages represent distinct phylogenetic species. Moreover, our results provide insights into the genetic selection signatures related to body size differences and a valuable genomic resource for future genetic studies and genomics-informed breeding of sika deer. |
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| institution | OA Journals |
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| language | English |
| publishDate | 2025-04-01 |
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| series | BMC Genomics |
| spelling | doaj-art-50cc2e486c7a437c9262257eec991e222025-08-20T02:11:51ZengBMCBMC Genomics1471-21642025-04-0126111910.1186/s12864-025-11541-wPopulation genomics of sika deer reveals recent speciation and genetic selective signatures during evolution and domesticationHuamiao Liu0Bo Zhu1Tianjiao Wang2Yimeng Dong3Yan Ju4Yang Li5Weilin Su6Ranran Zhang7Shiwu Dong8Hongliang Wang9Yongna Zhou10Yanmin Zhu11Lei Wang12Zhengyi Zhang13Pei Zhao14Shuyan Zhang15Rui Guo16E. A17Yuwen Zhang18Xin Liu19Hidetoshi B. Tamate20Qiqi Liang21De Ma22Xiumei Xing23State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesNovogene Bioinformatics InstituteState Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesState Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesState Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesState Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesState Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesState Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesState Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesState Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesState Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesState Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesState Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesState Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesState Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesAdministration of Zhejiang Qingliangfeng National Nature ReserveAdministration of Zhejiang Qingliangfeng National Nature ReserveSichuan Tiebu Sika Deer Nature ReserveAdministrative Office of Liugong Island National Forest ParkNortheast Forestry UniversityFaculty of Science, Yamagata UniversityGlbizzia Bioinformatics InstituteNovogene Bioinformatics InstituteState Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural SciencesAbstract Background Population genomic analysis can reconstruct the phylogenetic relationship and demographic history, and identify genomic selective signatures of a species. To date, fundamental aspects of population genomic analyses, such as intraspecies taxonomy, evolutionary history, and adaptive evolution, of sika deer have not been systematically investigated. Furthermore, accumulating lines of evidences have illustrated that incorrect species delimitation will mislead conservation decisions, and even lead to irreversible mistakes in threatened species. Results In this study, we resequenced 81 wild and 71 domesticated sika deer representing 10 main geographic populations and two farms to clarify the species delimitation, demographic and divergence histories, and adaptive evolution of this species. First, our analyses of whole genomes, Y chromosomes and mitochondrial genomes revealed substantial genetic differentiation between the continental and Japanese lineages of sika deer, representing two phylogenetically distinct species. Second, sika deer in Japan were inferred to have experienced a “divergence-mixing-isolation” evolutionary scenario. Third, we identified four candidate genes (XKR4, NPAS3, CTNNA3, and CNTNAP5) possibly involved in body size regulation of sika deer by selective sweep analysis. Furthermore, we also detected two candidate genes (NRP2 and EDIL3) that may be associated with an important economic trait (antler weight) were under selection during the process of domestication. Conclusion Population genomic analyses revealed that the continental and Japanese lineages represent distinct phylogenetic species. Moreover, our results provide insights into the genetic selection signatures related to body size differences and a valuable genomic resource for future genetic studies and genomics-informed breeding of sika deer.https://doi.org/10.1186/s12864-025-11541-wSika deerCervus nipponPopulation genomicsSpecies delimitationGenetic selective signatureDomestication |
| spellingShingle | Huamiao Liu Bo Zhu Tianjiao Wang Yimeng Dong Yan Ju Yang Li Weilin Su Ranran Zhang Shiwu Dong Hongliang Wang Yongna Zhou Yanmin Zhu Lei Wang Zhengyi Zhang Pei Zhao Shuyan Zhang Rui Guo E. A Yuwen Zhang Xin Liu Hidetoshi B. Tamate Qiqi Liang De Ma Xiumei Xing Population genomics of sika deer reveals recent speciation and genetic selective signatures during evolution and domestication BMC Genomics Sika deer Cervus nippon Population genomics Species delimitation Genetic selective signature Domestication |
| title | Population genomics of sika deer reveals recent speciation and genetic selective signatures during evolution and domestication |
| title_full | Population genomics of sika deer reveals recent speciation and genetic selective signatures during evolution and domestication |
| title_fullStr | Population genomics of sika deer reveals recent speciation and genetic selective signatures during evolution and domestication |
| title_full_unstemmed | Population genomics of sika deer reveals recent speciation and genetic selective signatures during evolution and domestication |
| title_short | Population genomics of sika deer reveals recent speciation and genetic selective signatures during evolution and domestication |
| title_sort | population genomics of sika deer reveals recent speciation and genetic selective signatures during evolution and domestication |
| topic | Sika deer Cervus nippon Population genomics Species delimitation Genetic selective signature Domestication |
| url | https://doi.org/10.1186/s12864-025-11541-w |
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