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Takagi T, Murakami R, Takano A, Torii H, Kaneko S, Tamate HB. A historic religious sanctuary may have preserved ancestral genetics of Japanese sika deer ( Cervus nippon). J Mammal 2023; 104:303-315. [PMID: 37032702 PMCID: PMC10075338 DOI: 10.1093/jmammal/gyac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/10/2022] [Indexed: 01/31/2023] Open
Abstract
Abstract
Deer have been a major resource for human populations for thousands of years. Anthropogenic activities, such as hunting, have influenced the genetic structure and distribution of deer populations. In Japan, wild Japanese sika deer (Cervus nippon) have been hunted since ancient times but have also been historically protected as sacred animals in several sanctuaries. Sika deer have been protected for over a thousand years in the religious sanctuary around the Kasuga Taisha Shrine on the Kii Peninsula, located in the center of Japan. Here, we used short sequence repeats (SSR) and mitochondrial DNA (mtDNA) to investigate the genetic diversity, population structure, and demography of Japanese sika deer inhabiting the Kii Peninsula, Japan, and discuss possible anthropogenic influences. Using SSR, three distinct genetic groups were distinguished on the Kii Peninsula: an Eastern genetic group, a Western genetic group, and an isolated genetic group with individuals in the religious sanctuary of Kasuga Taisha Shrine in Nara city. The isolated genetic sanctuary group had only the mtDNA haplotype S4. The SSR genotype data suggested a newer divergence time of the genetic groups of the religious sanctuary than would have occurred as a result of Late Quaternary climate change. This time scale coincided with the establishment of the sanctuary with Kasuga Taisha Shrine. Thus, the religious protection conserved genetic variation over a thousand years.
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Affiliation(s)
- Toshihito Takagi
- Fukushima University, Graduate School of Symbiotic Systems Science and Technology , Fukushima 960-1296 , Japan
| | - Ryoko Murakami
- Yamagata University, Faculty of Medicine , Yamagata 990-9585 , Japan
| | - Ayako Takano
- Nara University of Education, Center for Natural Environment Education , Nara 630-8528 , Japan
| | - Harumi Torii
- Nara University of Education, Center for Natural Environment Education , Nara 630-8528 , Japan
| | - Shingo Kaneko
- Fukushima University, Faculty of Symbiotic Systems Science , Fukushima 960-1296 , Japan
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Takagi T, Tsuda Y, Torii H, Tamate HB, Kaneko S, Nagata J. Development of paternally‐inherited Y chromosome simple sequence repeats of sika deer and their application in genetic structure, artificial introduction, and interspecific hybridization analyses. POPUL ECOL 2022. [DOI: 10.1002/1438-390x.12109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Toshihito Takagi
- Graduate School of Symbiotic Systems Science and Technology Fukushima University Kanayagawa Fukushima Japan
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center (MSC) University of Tsukuba Ueda Nagano Japan
| | - Harumi Torii
- Center for Natural Environment Education Nara University of Education Takahata‐cho Nara Japan
| | | | - Shingo Kaneko
- Faculty of Symbiotic Systems Science Fukushima University Kanayagawa Fukushima Japan
| | - Junco Nagata
- Forestry and Forest Products Research Institute (FFPRI) Tsukuba Ibaraki Japan
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Tanaka K, Hoshi A, Nojima R, Suzuki K, Takiguchi H, Takatsuki S, Takizawa T, Hosoi E, Tamate HB, Hayashida M, Anezaki T, Fukue Y, Minami M. Genetic Variation in Y-Chromosome Genes of Sika Deer ( Cervus nippon) in Japan. Zoolog Sci 2021; 37:411-416. [PMID: 32972081 DOI: 10.2108/zs200043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/21/2020] [Indexed: 11/17/2022]
Abstract
Sika deer (Cervus nippon) in Japan are classified into southern and northern groups. However, previous studies primarily relied on maternally inherited mitochondrial DNA (mtDNA). The paternally inherited Y-chromosome is useful for analyzing the contribution of males to the population genetic history of sika deer. In total, approximately 16 kb of partial sequences of four Y-chromosomal genes, Y-linked, sex-determining region Y, DEAD-box helicase 3 Y-linked, and Zinc finger protein Y-linked, were sequenced to investigate intraspecific variation. As a result, we identified nine intronic single nucleotide polymorphisms (SNPs) in 478 sika deer samples collected over the entire Japanese archipelago from Hokkaido to Kyushu. SNP genotyping revealed 10 distinct haplotypes (SYH1-SYH10). The most common haplotype (SYH1) was present in all populations and was the most abundant haplotype, identified in 80.3% of the sampled individuals. The remaining haplotypes were unique to a single locality. SYH1 was also central to all other haplotypes that diverged by a SNP, resulting in this haplotype being the core of a star-like cluster topography. We found that contrary to mtDNA patterns, there was no clear differentiation of Y-chromosome markers between the southern and the northern populations. Due to the female philopatry of sika deer, mtDNA may provide a highly structured differentiation of populations. On the other hand, the male-biased gene flow may provide a reduced differentiation of populations. Our findings revealed that the genetic structure of the Japanese sika deer is more complex than previously thought based on mtDNA-based phylogeographic studies.
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Affiliation(s)
- Kazuaki Tanaka
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan,
| | - Asuka Hoshi
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan
| | - Rai Nojima
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan
| | - Kaho Suzuki
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan
| | - Harutaka Takiguchi
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan
| | - Seiki Takatsuki
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan
| | - Tatsuya Takizawa
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan
| | - Eiji Hosoi
- Faculty of Agriculture, Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Hidetoshi B Tamate
- Department of Biology, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Maki Hayashida
- Department of Animal Science Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Kanagawa 243-0034, Japan
| | - Tomoko Anezaki
- Gunma Museum of Natural History, Tomioka, Gunma 370-2345, Japan
| | - Yuko Fukue
- NPO Institute for Biodiversity Research and Education "Earthworm," Karuizawa, Nagano 389-0115, Japan
| | - Masato Minami
- School of Veterinary Medicine, Azabu University, Chuo-Ku, Sagamihara 252-5201, Japan
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Genome-Wide SNP Discovery and Analysis of Genetic Diversity in Farmed Sika Deer ( Cervus nippon) in Northeast China Using Double-Digest Restriction Site-Associated DNA Sequencing. G3-GENES GENOMES GENETICS 2017; 7:3169-3176. [PMID: 28751500 PMCID: PMC5592941 DOI: 10.1534/g3.117.300082] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Sika deer are an economically valuable species owing to their use in traditional Chinese medicine, particularly their velvet antlers. Sika deer in northeast China are mostly farmed in enclosure. Therefore, genetic management of farmed sika deer would benefit from detailed knowledge of their genetic diversity. In this study, we generated over 1.45 billion high-quality paired-end reads (288 Gbp) across 42 unrelated individuals using double-digest restriction site-associated DNA sequencing (ddRAD-seq). A total of 96,188 (29.63%) putative biallelic SNP loci were identified with an average sequencing depth of 23×. Based on the analysis, we found that the majority of the loci had a deficit of heterozygotes (FIS >0) and low values of Hobs, which could be due to inbreeding and Wahlund effects. We also developed a collection of high-quality SNP probes that will likely be useful in a variety of applications in genotyping for cervid species in the future.
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Konishi S, Hata S, Matsuda S, Arai K, Mizoguchi Y. Evaluation of the genetic structure of sika deer (Cervus nippon
) in Japan's Kanto and Tanzawa mountain areas, based on microsatellite markers. Anim Sci J 2017. [DOI: 10.1111/asj.12844] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sayaka Konishi
- Graduate School of Agriculture; Meiji University; Tama-ku Kawasaki Kanagawa Japan
| | - Shoko Hata
- Tokyo Metropolitan Agriculture and Forestry Research Center; Fujimi-cho Tachikawa Tokyo Japan
| | - Sayumi Matsuda
- School of Agriculture; Meiji University; Tama-ku Kawasaki Kanagawa Japan
| | - Kazushi Arai
- Tokyo Metropolitan Agriculture and Forestry Research Center; Fujimi-cho Tachikawa Tokyo Japan
| | - Yasushi Mizoguchi
- School of Agriculture; Meiji University; Tama-ku Kawasaki Kanagawa Japan
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Krojerová-Prokešová J, Barančeková M, Kawata Y, Oshida T, Igota H, Koubek P. Genetic differentiation between introduced Central European sika and source populations in Japan: effects of isolation and demographic events. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1424-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Rivals F, Takatsuki S, Albert RM, Macià L. Bamboo feeding and tooth wear of three sika deer (Cervus nippon) populations from northern Japan. J Mammal 2014. [DOI: 10.1644/14-mamm-a-097] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Kubo MO, Minami M, Higuchi N, Ohnishi N, Okada A, Kaji K, Ohba T, Hosoi E, Koizumi T, Takatsuki S. Female sika deer have evolved larger incisors than males under relaxed selection against rapid tooth wear. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mugino O. Kubo
- The University Museum; The University of Tokyo; 7-3-1 Hongo; Bunkyo-ku; Tokyo; 113-0033; Japan
| | - Masato Minami
- Laboratory of Wildlife Ecology; Azabu University; 1-17-71 Fuchinobe; Sagamihara; Kanagawa; 229-8501; Japan
| | - Naoko Higuchi
- NPO Earthworm for Bio-Diversity; 1549-3-1 Oiwake; Karuizawa; Nagano; 389-0115; Japan
| | - Nobumasa Ohnishi
- Eco-Planning Research Co. Ltd; 2-28-5 Sakae-cho; Higashimarayama; Tokyo; 189-0013; Japan
| | - Ayumi Okada
- Department of Environmental Bioscience; School of Veterinary Medicine; Kitasato University; 23-35-1 Higashi; Towada; Aomori; 034-8628; Japan
| | - Koichi Kaji
- Department of Ecoregion Science; Laboratory of Wildlife Conservation; Tokyo University of Agriculture and Technology; 3-5-8 Saiwaicho; Fuchu; Tokyo; 183-8509; Japan
| | - Takahiro Ohba
- Forestry and Forest Products Research Center; Shizuoka Research Institute of Agriculture and Forestry; 2542-8 Negata, Hamakita-ku; Hamamatsu; Shizuoka; 434-0016; Japan
| | - Eiji Hosoi
- Department of Biological and Environmental Sciences; Faculty of Agriculture; Yamaguchi University; 1677-1 Yoshida; Yamaguchi; 753-8515; Japan
| | - Toru Koizumi
- Wildlife Ecology Laboratory; Forestry and Forest Products Research Institute; 1 Matsunosato; Tsukuba; Ibaraki; 305-8687; Japan
| | - Seiki Takatsuki
- Laboratory of Wildlife Ecology; Azabu University; 1-17-71 Fuchinobe; Sagamihara; Kanagawa; 229-8501; Japan
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