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Zakoh K, Fujiwara K, Takada T, Osada N, Suzuki H. Genealogical characterization of regional populations and dorsal coat color variation in the house mouse Mus musculus from Asia based on haplotype structure analysis of a gene-rich region harboring Mc1r. Genes Genet Syst 2023; 98:73-87. [PMID: 37558462 DOI: 10.1266/ggs.22-00157] [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: 08/11/2023] Open
Abstract
We analyzed 196 haplotype sequences from a gene-rich region (250 kb) that includes Mc1r, a gene involved in coat color regulation, to gain insight into the evolution of coat color variation in subspecies of the house mouse Mus musculus. Phylogenetic networks revealed haplotype groups from the major subspecies of M. m. castaneus (CAS), M. m. domesticus (DOM), and M. m. musculus (MUS). Using haplotype sequences assigned to each of CAS and MUS through phylogenetic analysis, we proposed migration routes associated with prehistoric humans from west to east across Eurasia. Comparing nucleotide diversity among subspecies-specific haplotypes in different geographic areas showed a marked reduction during migration, particularly in MUS-derived haplotypes from Korea and Japan, suggesting intensive population bottlenecks during migration. We found that a C>T polymorphism at site 302 (c.302C>T) in the Mc1r coding region correlated with a darkening of dorsal fur color in both CAS and MUS. However, C/C homozygous mice in MUS showed marked variation in lightness, indicating the possibility of another genetic determinant that affects the lightness of dorsal fur color. Detailed sequence comparisons of haplotypes revealed that short fragments assigned to DOM were embedded in CAS-assigned fragments, indicating ancient introgression between subspecies. The estimated age of c.302C>T also supports the hypothesis that genetic interaction between subspecies occurred in ancient times. This suggests that the genome of M. musculus evolved through gene flow between subspecies over an extended period before the movement of the species in conjunction with prehistoric humans.
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Affiliation(s)
- Kazuhiro Zakoh
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University
| | - Kazumichi Fujiwara
- Graduate School of Information Science and Technology, Hokkaido University
| | - Toyoyuki Takada
- Integrated Bioresource Information Division, RIKEN BioResource Research Center
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University
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Epidemiology of Group A rotavirus in rodents and shrews in Bangladesh. Vet Res Commun 2023; 47:29-38. [PMID: 35380357 PMCID: PMC8980207 DOI: 10.1007/s11259-022-09923-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 03/29/2022] [Indexed: 01/27/2023]
Abstract
Rodents and shrews live in close proximity to humans and have been identified as important hosts of zoonotic pathogens. This study aimed to detect Group A rotavirus (RVA) and its potential risk factors in rodents and shrews in Bangladesh. We captured 417 small mammals from 10 districts with a high degree of contact between people and domestic animals and collected rectal swab samples between June 2011 and October 2013. We tested the swab samples for RVA RNA, targeting the NSP3 gene segment using real-time reverse transcription-polymerase chain reaction (rRT-PCR). Overall, RVA prevalence was the same (6.7%) in both rodents and shrews. We detected RVA RNA in 5.3% of Bandicota bengalensis (4/76; 95% CI: 1.4-12.9), 5.1% of B. indica (4/79; 95% CI: 1.4-12.4), 18.2% of Mus musculus (4/22; 95% CI: 5.2-40.3), 6.7% of Rattus rattus (6/90; 95% CI: 2.5-13.9), and 6.7% of Suncus murinus (10/150; 95% CI: 3.2-11.9). We found significantly more RVA in males (10.4%; OR: 3.4; P = 0.007), animals with a poor body condition score (13.9%; OR: 2.7; P = 0.05), during wet season (8.3%; OR: 4.1; P = 0.032), and in urban land gradients (10.04%; OR: 2.9; P = 0.056). These findings form a basis for understanding the prevalence of rotaviruses circulating among rodents and shrews in this region. We recommend additional molecular studies to ascertain the genotype and zoonotic potential of RVA circulating in rodents and shrews in Bangladesh.
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Lawal RA, Mathis VL, Barter ME, Charette JR, Garretson A, Dumont BL. Taxonomic assessment of two wild house mouse subspecies using whole-genome sequencing. Sci Rep 2022; 12:20866. [PMID: 36460842 PMCID: PMC9718808 DOI: 10.1038/s41598-022-25420-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
The house mouse species complex (Mus musculus) is comprised of three primary subspecies. A large number of secondary subspecies have also been suggested on the basis of divergent morphology and molecular variation at limited numbers of markers. While the phylogenetic relationships among the primary M. musculus subspecies are well-defined, relationships among secondary subspecies and between secondary and primary subspecies remain less clear. Here, we integrate de novo genome sequencing of museum-stored specimens of house mice from one secondary subspecies (M. m. bactrianus) and publicly available genome sequences of house mice previously characterized as M. m. helgolandicus, with whole genome sequences from diverse representatives of the three primary house mouse subspecies. We show that mice assigned to the secondary M. m. bactrianus and M. m. helgolandicus subspecies are not genetically differentiated from M. m. castaneus and M. m. domesticus, respectively. Overall, our work suggests that the M. m. bactrianus and M. m. helgolandicus subspecies are not well-justified taxonomic entities, emphasizing the importance of leveraging whole-genome sequence data to inform subspecies designations. Additionally, our investigation provides tailored experimental procedures for generating whole genome sequences from air-dried mouse skins, along with key genomic resources to inform future genomic studies of wild mouse diversity.
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Affiliation(s)
| | - Verity L Mathis
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL, 32611, USA
| | - Mary E Barter
- The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, USA
| | | | - Alexis Garretson
- The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, 136 Harrison Ave, Boston, MA, 02111, USA
| | - Beth L Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, 04609, USA.
- Graduate School of Biomedical Sciences, Tufts University, 136 Harrison Ave, Boston, MA, 02111, USA.
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Molecular Evidence Reveals the Sympatric Distribution of Cervus nippon yakushimae and Cervus nippon taiouanus on Jeju Island, South Korea. Animals (Basel) 2022; 12:ani12080998. [PMID: 35454244 PMCID: PMC9029077 DOI: 10.3390/ani12080998] [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: 03/29/2022] [Revised: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 11/17/2022] Open
Abstract
Non-native species threaten native ecosystems and species, particularly on islands where rates of endemism and vulnerability to threats are high. Understanding species invasion will aid in providing insights into ecological and evolutionary processes. To identify the non-native sika deer (Cervus nippon) population in Jeju, South Korea, and their phylogenetic affinities, we collected tissue samples from roadkill and the World Natural Heritage Headquarters in Jeju. Mitochondrial DNA cytochrome B (CytB) gene sequences were analyzed to determine two distinct CytB haplotypes. Phylogenetic analysis using maximum likelihood tree revealed two haplotypes of CytB clustered into two different groups representing two subspecies: C. n. yakushimae, native to Japan, and C. n. taiouanus, native to Taiwan. The tentative divergence time between the two subspecies was estimated at 1.81 million years. Our study confirmed that the two subspecies of sika deer are sympatric in the natural ecosystem of Jeju Island. This study provides valuable information to help government and conservation agencies understand alien species and determine control policies for conserving native biodiversity in South Korea.
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Kishimoto M, Kato M, Suzuki H. Morphological and Molecular Recharacterization of the Rodent Genus Mus from Nepal Based on Museum Specimens. MAMMAL STUDY 2021. [DOI: 10.3106/ms2020-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Makoto Kishimoto
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Sapporo 060-0810, Japan
| | - Masaru Kato
- Field Science Center for Northern Biosphere, Botanic Garden & Museum, Hokkaido University, North 3, West 8, Sapporo, 060-0003, Japan
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Sapporo 060-0810, Japan
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Adhikari P, Han SH, Kim YK, Kim TW, Thapa TB, Subedi N, Kunwar A, Banjade M, Oh HS. New record of the Oriental house rat, Rattus tanezumi, in Nepal inferred from mitochondrial Cytochrome B gene sequences. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:386-390. [PMID: 33474178 PMCID: PMC7800815 DOI: 10.1080/23802359.2018.1436991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This study determines the presence of R. tanezumi from in Nepal using morphological and molecular analyses. Morphologically, it is indistinguishable with R. rattus owing to similar fur colour and morphometric data. However, molecular identification and phylogenetic analysis using sequences of the mitochondrial DNA (mtDNA) Cytochrome B (CytB) gene revealed two different species R. rattus and R. tanezumi from collected specimens. The genetic distance between R. rattus and R. tanezumi was found 0.043. In phylogenetic tree, the clade of R. tanezumi is distinguished into two sub-clades, R. tanezumi found in Nepal, and East Asian countries, China, Laos, Thailand, Viet Nam, and South Korea have genetic distance 0.031, suggesting the different lineages of R. tanezumi. This study confirmed the R. tanezumi present in Nepal. Our findings suggest that morphological analysis and molecular study should be carried out simultaneously for accurate identification of small sized cryptic mammals like R. tanezumi and R. rattus.
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Affiliation(s)
- Pradeep Adhikari
- Faculty of Science Education, Jeju National University, Jeju, Republic of Korea.,National Institute of Ecology, Seocheon, Republic of Korea
| | - Sang-Hyun Han
- Educational Science Research Institute, Jeju National University, Jeju, Republic of Korea.,Species Restoration Technology Institute, Korea National Park Service, Yeongju, Republic of Korea
| | - Yoo-Kyung Kim
- Educational Science Research Institute, Jeju National University, Jeju, Republic of Korea
| | - Tae-Wook Kim
- Species Restoration Technology Institute, Korea National Park Service, Yeongju, Republic of Korea
| | - Tej Bahadur Thapa
- Central Department of Zoology, Tribhuvan University, Kathmandu, Nepal
| | - Naresh Subedi
- National Trust for Nature Conservation, Lalitpur, Nepal
| | - Amar Kunwar
- Small Mammals Conservation and Research Foundation, Kathmandu, Nepal
| | - Maniram Banjade
- Faculty of Science Education, Jeju National University, Jeju, Republic of Korea
| | - Hong-Shik Oh
- Faculty of Science Education, Jeju National University, Jeju, Republic of Korea
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Gertler C, Schlegel M, Linnenbrink M, Hutterer R, König P, Ehlers B, Fischer K, Ryll R, Lewitzki J, Sauer S, Baumann K, Breithaupt A, Faulde M, Teifke JP, Tautz D, Ulrich RG. Indigenous house mice dominate small mammal communities in northern Afghan military bases. BMC ZOOL 2017. [DOI: 10.1186/s40850-017-0024-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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