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Yagi G, Qi H, Arai K, Kita YF, Kogi K, Morisaka T, Yoshioka M, Inoue-Murayama M. Non-invasive age estimation based on faecal DNA using methylation-sensitive high-resolution melting for Indo-Pacific bottlenose dolphins. Mol Ecol Resour 2024; 24:e13906. [PMID: 38041546 DOI: 10.1111/1755-0998.13906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023]
Abstract
Age is necessary information for the study of life history of wild animals. A general method to estimate the age of odontocetes is counting dental growth layer groups (GLGs). However, this method is highly invasive as it requires the capture and handling of individuals to collect their teeth. Recently, the development of DNA-based age estimation methods has been actively studied as an alternative to such invasive methods, of which many have relied on used biopsy samples. However, if DNA-based age estimation can be developed from faecal samples, age estimation can be performed entirely non-invasively. We developed an age estimation model using the methylation rate of two gene regions, GRIA2 and CDKN2A, measured through methylation-sensitive high-resolution melting (MS-HRM) from faecal samples of wild Indo-Pacific bottlenose dolphins (Tursiops aduncus). The age of individuals was known through conducting longitudinal individual identification surveys underwater. Methylation rates were quantified from 36 samples collected from 30 individuals. Both gene regions showed a significant correlation between age and methylation rate. The age estimation model was constructed based on the methylation rates of both genes which achieved sufficient accuracy (after LOOCV: MAE = 5.08, R2 = 0.33) for the ecological studies of the Indo-Pacific bottlenose dolphins, with a lifespan of 40-50 years. This is the first study to report the use of non-invasive faecal samples to estimate the age of marine mammals.
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Affiliation(s)
- Genfu Yagi
- Graduate School of Bioresources, Mie University, Tsu, Mie, Japan
| | - Huiyuan Qi
- Wildlife Research Center, Kyoto University, Kyoto, Kyoto, Japan
| | - Kana Arai
- Wildlife Research Center, Kyoto University, Kyoto, Kyoto, Japan
| | - Yuki F Kita
- Department of Marine Biology and Sciences, School of Biological Sciences, Tokai University, Sapporo, Hokkaido, Japan
| | | | | | - Motoi Yoshioka
- Graduate School of Bioresources, Mie University, Tsu, Mie, Japan
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Inamori D, Kita YF, Funasaka N. External Morphological and Molecular Evidence of Natural Intrageneric Hybridization between Common and Indo-Pacific Bottlenose Dolphins (Tursiops truncatus × T. aduncus) from Japanese Waters. Mammal Study 2021. [DOI: 10.3106/ms2021-0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Daiki Inamori
- Taiji Whale Museum, Taiji, Higashimuro, Wakayama 649-5171, Japan
| | - Yuki F. Kita
- Department of Marine Biology and Sciences, School of Biological Sciences, Tokai University, Minami-ku, Sapporo, Hokkaido 005-8601, Japan
| | - Noriko Funasaka
- Cetacean Research Center, Graduate School of Bioresources, Mie University, Kurimamachiya, Tsu, Mie 514-8507, Japan
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Jimbo M, Kita YF, Kobayashi M, Mitani Y. Intraspecific differences in the diet of Kuril harbor seals (Phoca vitulina stejnegeri) in Erimo, Hokkaido, using DNA barcoding diet analysis. MAMMAL RES 2021. [DOI: 10.1007/s13364-021-00586-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Mitani Y, Kita YF, Saino S, Yoshioka M, Ohizumi H, Nakahara F. Mitochondrial DNA Haplotypes of Killer Whales around Hokkaido, Japan. Mammal Study 2021. [DOI: 10.3106/ms2020-0072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Yoko Mitani
- Field Science Center for Northern Biosphere, Hokkaido University, 20-5 Benten-cho, Hakodate, Hokkaido 040-0051, Japan
| | - Yuki F. Kita
- Department of Marine Biology and Sciences, School of Biological Sciences, Tokai University, Minami-ku, Sapporo, Hokkaido 005-8601, Japan
| | - Shigeo Saino
- Kobe Animals-and-Plants Environmental College, Higashinada-ku, Kobe, Hyogo 658-0032, Japan
| | - Motoi Yoshioka
- Graduate School of Bioresources, Mie University, Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Hiroshi Ohizumi
- Department of Marine Biology, School of Marin Science and Technology, Tokai University, Shimizu-ku, Shizuoka 424-8610, Japan
| | - Fumio Nakahara
- Department of Psychology, Faculty of Human Science, Tokiwa University, Miwa, Mito, Ibaraki 310-8585, Japan
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Sakai M, Kita YF, Kogi K, Shinohara M, Morisaka T, Shiina T, Inoue-Murayama M. A wild Indo-Pacific bottlenose dolphin adopts a socially and genetically distant neonate. Sci Rep 2016; 6:23902. [PMID: 27049937 PMCID: PMC4822121 DOI: 10.1038/srep23902] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 03/16/2016] [Indexed: 11/08/2022] Open
Abstract
Alloparental behaviour and adoption have been reported in many mammals and birds. Such behaviours are energetically costly, and their causes and functions remain unclear. We observed the adoption behaviour of a wild Indo-Pacific bottlenose dolphin (Tursiops aduncus) near Mikura Island, Japan. A calf was seen with its mother on six observation days. Following the mother's death, the calf was observed with a sub-adult female on all 18 observation days from May to September 2012. On three days, the calf was observed swimming with this female in the suckling position and milk was seen leaking from the female's mammary slit. A five-year dataset revealed no significant social or kin relationships between the biological mother and allomother, indicating that kinship and social relationships did not play an important role in the observed adoption.
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Affiliation(s)
- Mai Sakai
- Department of Fisheries, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | - Yuki F. Kita
- Department of Marine Biology and Sciences School of Biological Sciences, Tokai University, 5-1-1 Minamisawa, Minami-ku, Sapporo-shi, Hokkaido 005-8601, Japan
| | - Kazunobu Kogi
- Mikura Island Tourist Information Centre, Mikurajima-mura, Tokyo 100-1301, Japan
| | - Masanori Shinohara
- Faculty of Life and Environmental Sciences, Teikyo University of Science, 2525 Yatsusawa, Uenohara-shi, Yamanashi 409-0193, Japan
| | - Tadamichi Morisaka
- Institute of Innovative Science and Technology, Tokai University, 3-20-1 Orido, Shimizu-ku, Shizuoka-shi, Shizuoka 424-8610, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara-shi, Kanagawa 259-1143, Japan
| | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, 2-24 Tanaka-sekiden-cho, Sakyo-ku, Kyoto-shi, Kyoto 606-8203, Japan
- Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba-shi, Ibaraki 305-8506, Japan
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Shiina T, Kono A, Westphal N, Suzuki S, Hosomichi K, Kita YF, Roos C, Inoko H, Walter L. Comparative genome analysis of the major histocompatibility complex (MHC) class I B/C segments in primates elucidated by genomic sequencing in common marmoset (Callithrix jacchus). Immunogenetics 2011; 63:485-99. [PMID: 21505866 DOI: 10.1007/s00251-011-0526-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 04/07/2011] [Indexed: 01/20/2023]
Abstract
Common marmoset monkeys (Callithrix jacchus) have emerged as important animal models for biomedical research, necessitating a more extensive characterization of their major histocompatibility complex (MHC) region. However, the genomic information of the marmoset MHC (Caja) is still lacking. The MHC-B/C segment represents the most diverse MHC region among primates. Therefore, in this paper, to elucidate the detailed gene organization and evolutionary processes of the Caja class I B (Caja-B) segment, we determined two parts of the Caja-B sequences with 1,079 kb in total, ranging from H6orf15 to BAT1 and compared the structure and phylogeny with that of other primates. This segment contains 54 genes in total, nine Caja-B genes (Caja-B1 to Caja-B9), two MIC genes (MIC1 and MIC2), eight non-MHC genes, two non-coding genes, and 33 non-MHC pseudogenes that have not been observed in other primate MHC-B/C segments. Caja-B3, Caja-B4, and Caja-B7 encode proper MHC class I proteins according to amino acid structural characteristics. Phylogenetic relationships based on 48 MHC-I nucleotide sequences in primates suggested (1) species-specific divergence for Caja, Mamu, and HLA/Patr/Gogo lineages, (2) independent generation of the "seven coding exon" type MHC-B genes in Mamu and HLA/Patr/Gogo lineages from an ancestral "eight coding exon" type MHC-I gene, (3) parallel correlation with the long and short segmental duplication unit length in Caja and Mamu lineages. These findings indicate that the MHC-B/C segment has been under permanent selective pressure in the evolution of primates.
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Affiliation(s)
- Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Shimokasuya, Isehara, Kanagawa, Japan,
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Aarnink A, Estrade L, Apoil PA, Kita YF, Saitou N, Shiina T, Blancher A. Study of cynomolgus monkey (Macaca fascicularis) DRA polymorphism in four populations. Immunogenetics 2010; 62:123-36. [PMID: 20094710 DOI: 10.1007/s00251-009-0421-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2009] [Accepted: 12/21/2009] [Indexed: 12/11/2022]
Abstract
To describe the polymorphism of the DRA gene in Macaca fascicularis, we have studied 141 animals either at cDNA level (78 animals from Mauritius, the Philippines, and Vietnam) or genomic level (63 animals from the Philippines, Indonesia, and Vietnam). In total, we characterized 22 cDNA DRA alleles, 13 of which had not been described until now. In the Mauritius population, we confirmed the presence of three DRA alleles. In the Philippine and Vietnam populations, we observed 11 and 14 DRA alleles, respectively. Only two alleles were present in all three populations. All DRA alleles but one differ from the consensus sequence by one to three mutations, most being synonymous; so, only seven DR alpha proteins were deduced from the 22 cDNA alleles. One DRA cDNA allele, Mafa-DRA*02010101, differs from all other alleles by 11 to 14 mutations of which only four are non-synonymous. The two amino acid changes inside the peptide groove of Mafa-DRA*02010101 are highly conservative. The very low proportion of non-synonymous/synonymous mutations is compatible with a purifying selection which is comparable to all previous observations concerning the evolution of the DRA gene in mammals. Homologues of the allele Mafa-DRA*02010101 are also found in two other Asian macaques (Macaca mulatta and Macaca nemestrina). The forces able to maintain this highly divergent allele in three different macaque species remain hypothetical.
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Affiliation(s)
- Alice Aarnink
- Laboratoire d'immunogénétique moléculaire, EA3034, Faculté de Médecine Purpan, Toulouse 3, France
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Kita YF, Hosomichi K, Kohara S, Itoh Y, Ogasawara K, Tsuchiya H, Torii R, Inoko H, Blancher A, Kulski JK, Shiina T. MHC class I A loci polymorphism and diversity in three Southeast Asian populations of cynomolgus macaque. Immunogenetics 2009; 61:635-48. [PMID: 19649628 DOI: 10.1007/s00251-009-0390-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Accepted: 07/22/2009] [Indexed: 11/26/2022]
Abstract
Cynomolgus macaques (Macaca fascicularis, Mafa) have emerged as important animal models for biomedical research, necessitating a more extensive characterization of their major histocompatibility complex polymorphic regions. The current information on the polymorphism or diversity of the polygenetic Mafa class I A loci is limited in comparison to the more commonly studied rhesus macaque Mafa class I A loci. Therefore, in this paper, to better elucidate the degree and types of polymorphisms and genetic differences of Mafa-A1 among three native Southeast Asian populations (Indonesian, Vietnamese, and Filipino) and to investigate how the allele differences between macaques and humans might have evolved to affect their respective immune responses, we identified 83 Mafa-A loci-derived alleles by DNA sequencing of which 66 are newly described. Most alleles are unique to each population, but seven of the most frequent alleles were identical in sequence to some alleles in other macaque species. We also revealed (1) the large and dynamic genetic and structural differences and similarities in allelic variation by analyzing the population allele frequencies, Hardy-Weinberg's equilibrium, heterozygosity, nucleotide diversity profiles, and phylogeny, (2) the difference in genetic structure of populations by Wright's FST statistic and hierarchical analysis of molecular variance, and (3) the different demographic and selection pressures on the three populations by performing Tajima's D test of neutrality. The large level of diversity and polymorphism at the Mafa-A1 was less evident in the Filipino than in the Vietnam or the Indonesian populations, which may have important implications in animal capture, selection, and breeding for medical research.
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Affiliation(s)
- Yuki F Kita
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1143, Japan
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Sumiyama D, Kikkawa EF, Kita YF, Shinagawa H, Mabuchi T, Ozawa A, Inoko H. HLA alleles are associated with postherpetic neuralgia but not with herpes zoster. Tokai J Exp Clin Med 2008; 33:150-153. [PMID: 21318987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 11/04/2008] [Indexed: 05/30/2023]
Abstract
OBJECTIVE In some herpes zoster (HZ) patients, one symptom is problematic; postherpetic neuralgia (PHN), a persistence of pain such as spontaneous pain and stimulus-evoked pain, allodynia or hyperpathia, for more than 6 months after healing of the vesicular eruptions. In our previous study, we reported the association between HLA alleles, HLA-A*33 and B*44, and PHN patients. In this study, we aim to refine the association of these alleles with PHN or HZ using higher-resolution HLA typing technique with an increased sample size. METHODS HLA allele frequencies were compared in 70 PHN patients, 80 HZ patients, 52 HZ(-) patients, and 140 Japanese controls using HLA typing kits of SSOP protocols. RESULT AND CONCLUSION The allele frequencies of HLA-A*3303, B*4403, and DRB1*1302 in PHN(+) patients were significantly higher than those in Japanese controls (P=0.00007, P=0.000002, and P=0.0003, respectively). The frequencies of above alleles in PHN(+) patients were also significantly higher than those in PHN(-) patients (P=0.03, P=0.006 and P=0.03, respectively). However, no association was found in comparison of HZ(+) patients and HZ(-). And the frequency of HLA-B*5101 in HZ(-) patients was significantly higher than those in HZ(+) and PHN(+) patients (P=0.003 and P=0.009, respectively) indicating that HLA-B*5101 functions as a protective allele to HZ.
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Affiliation(s)
- Daisuke Sumiyama
- Depertment of Molecular Life Science, Tokai University, School of Medicine, Shimokasuya 143, Isehara, Kanagawa, Japan.
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Watanabe A, Shiina T, Shimizu S, Hosomichi K, Yanagiya K, Kita YF, Kimura T, Soeda E, Torii R, Ogasawara K, Kulski JK, Inoko H. A BAC-based contig map of the cynomolgus macaque (Macaca fascicularis) major histocompatibility complex genomic region. Genomics 2006; 89:402-12. [PMID: 17174065 DOI: 10.1016/j.ygeno.2006.11.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Revised: 09/12/2006] [Accepted: 11/01/2006] [Indexed: 11/18/2022]
Abstract
The construction of a cynomolgus macaque (Macaca fascicularis, Mafa) BAC library for genomic comparison between rhesus and cynomolgus macaques is necessary to promote the cynomolgus macaque as one of the important experimental animals for future medical and biological research. In this paper, we constructed a cynomolgus macaque BAC library and a map of the MHC (Mafa) genomic region for comparison of the genomic organization and nucleotide similarities between the human, the chimpanzee, and the rhesus macaque. The BAC library consists of 221,184 clones with an average insert size of 83 kb, providing a sixfold coverage of the haploid genome. A total of 114 BAC clones and 54 PCR primer sets were used to construct a 4.3-Mb contig of the MHC region. Diversity analysis of genomic sequence from selected subregions of the MHC revealed that the cynomolgus sequence varied compared to rhesus macaque, human, and chimpanzee sequences by 0.48, 4.15, and 4.10%, respectively. From these findings, we conclude that the BAC library and Mafa genomic map are useful tools for genome analysis and will have important applications for comparative genomics and identifying regions of consequence in medical research.
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Affiliation(s)
- Atsushi Watanabe
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1143, Japan
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