1
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Kai H, Takada N, Thomson V, Suzuki H. Region-Specific Genetic Diversity of Black Rats ( Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events. Zoolog Sci 2024; 41:290-301. [PMID: 38809868 DOI: 10.2108/zs230065] [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: 07/03/2023] [Accepted: 12/27/2023] [Indexed: 05/31/2024]
Abstract
Among the six mitochondrial DNA lineages of the black rat (Rattus rattus Complex; RrC), lineages II and IV are widespread in Southeast and East Asia. This study explored their demographic history using 17 new sequences from the Miyako Islands in the Ryukyu archipelago, together with 178 publicly available cytochrome b sequences. We defined six and two haplotype groups showing rapid population expansion signals in Lineages II and IV, respectively. The six haplotype groups of Lineage II were represented by haplotypes from 1) Myanmar/Bangladesh/Northeast India, 2) Laos, 3) Thailand, 4) Indonesia/Philippines, 5) Vietnam/southern China, and 6) the Ryukyu archipelago. These expansion times were estimated using time-dependent evolutionary rates to be 115,300 years ago (ya), 128,500 ya, 9600 ya, 10,600 ya, 7200 ya, and 1400 ya, respectively, although all had large confidence intervals. The two groups of Lineage IV were recovered from the mainland and islands of Southeast Asia with predicted expansion times of 197,000 ya and 5800 ya, respectively. These results suggest that climatic fluctuations during the last 200,000 years of the Quaternary, affected the population dynamics in subtropical areas at different times. Furthermore, the results of the younger rapid expansion events of RrC suggest the possibility of agricultural advancement and dispersal of Neolithic farmers to different areas within the mainland and islands of Southeast Asia during the Holocene. A subset of rats from the Miyako Islands were found to have the same lineage IV haplotypes as those in Southeast Asia, suggesting a recent introduction of these new lineages.
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Affiliation(s)
- Hajime Kai
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Nobuhiro Takada
- Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Vicki Thomson
- Centre for Conservation Ecology and Genomics, University of Canberra, Bruce, ACT 2617, Australia
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan,
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2
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Ohdachi SD, Fujiwara K, Shekhar C, Sơn NT, Suzuki H, Osada N. Phylogenetics and Population Genetics of the Asian House Shrew, Suncus murinus-S. montanus Species Complex, Inferred From Whole-Genome and Mitochondrial DNA Sequences, with Special Reference to the Ryukyu Archipelago, Japan. Zoolog Sci 2024; 41:216-229. [PMID: 38587917 DOI: 10.2108/zs230030] [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: 04/06/2023] [Accepted: 11/09/2023] [Indexed: 04/10/2024]
Abstract
The house shrew (Suncus murinus-S. montanus species complex) colonized regions across southern Asia and the Indian Ocean following human activity. The house shrew is distributed on islands of the Ryukyu Archipelago, the southernmost part of Japan, but the evolutionary history of the shrew on those islands and possible associations between these populations and humans remain unknown. In this study, we conducted phylogenetic and population genetic analyses based on both nuclear and mitochondrial genome sequences of house shrews. Phylogenetic analyses based on mitochondrial cytochrome b (cytb) sequences revealed that shrews from the Ryukyu Archipelago showed strong genetic affinity to Vietnamese and southern Chinese shrews. Demographic analyses of cytb sequences indicated a rapid population expansion event affecting the haplotype group in Vietnam, southern China, and the Ryukyu Archipelago 3300-7900 years ago. Furthermore, gene flow between Ryukyu (Yonaguni Island) and Taiwan and between Ryukyu and Vietnam inferred from f4 statistics of the nuclear genomes suggested repeated immigration to Ryukyu in recent years. The present study demonstrates that the Nagasaki population has a different origin from the Ryukyu population. These findings elucidate the complex pattern of genetic admixture in house shrews and provide insights into their evolutionary history.
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Affiliation(s)
- Satoshi D Ohdachi
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan,
| | - Kazumichi Fujiwara
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Chandra Shekhar
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
| | - Nguyn Trưng Sơn
- Institute of Ecology and Biological Resources and Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo 060-0814, Japan
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Saitoh T, Murakami S, de Guia APO, Ohnishi N, Kawai K. Estimation of Evolutionary Rates for Mitochondrial Control Region in Sibling Species of Myodes (Rodentia) by Calibrations Based on Island Formation. MAMMAL STUDY 2022. [DOI: 10.3106/ms2022-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Takashi Saitoh
- Field Science Center, Hokkaido University, Kita 11, Nishi 10, Sapporo 060-0811, Japan
| | - Shota Murakami
- Department of General Systems Studies, Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
| | - Anna Pauline O. de Guia
- Animal Biology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, College, Laguna 4031, Philippines
| | - Naoki Ohnishi
- Tohoku Research Center, Forestry and Forest Products Research Institute, Nabeyashiki, Morioka 020-0123, Japan
| | - Kuniko Kawai
- School of Biological Sciences, Tokai University, Minamisawa, Sapporo 005-0825, Japan
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Inoue Y, Suzuki Y, Hanazaki K, Suzuki H. Quaternary Environmental Changes Shaped Mitochondrial DNA Diversity in the Large Japanese Wood Mouse Apodemus speciosus in Hokkaido, Japan. MAMMAL STUDY 2022. [DOI: 10.3106/ms2021-0050] [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)
- Yuta Inoue
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yutaro Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kaori Hanazaki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
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Inoue Y, Suzuki H. Temporal dynamics of mildly deleterious nonsynonymous substitutions in mitochondrial gene sequences in rodents and moles. Gene 2022; 97:111-121. [PMID: 35753758 DOI: 10.1266/ggs.21-00079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We have previously estimated the evolutionary rate (number of substitutions/site/million years) of mitochondrial cytochrome b gene (Cytb) sequences in rodents and moles to be about 0.11 at more recent divergence times of tens of thousands of years, and to decrease rapidly to about 0.03 at more distant divergence times. Because this time dependency is thought to be caused by the removal of mildly deleterious substitutions in later generations, we focused in this study on the abundance of nonsynonymous substitutions. We collected 23 haplogroups of Cytb with signals of late Quaternary population expansion events from rodents and moles and categorized them into three groups for comparison based on predicted expansion start time: 5,000-15,000 years ago (Group I), ca. 53,000 years ago (Group II) and 130,000-230,000 years ago (Group III). We counted the numbers of nonsynonymous and synonymous substitutions in all haplogroups. The rates of nonsynonymous substitutions were lowest in Groups II and III (0.08-0.22), whereas those in Group I varied markedly. We further classified Group I into two subgroups based on high (0.29-0.43) and low (0.09-0.20) nonsynonymous substitution rates, which were likely to be associated with the start of the expansion within 10,000 years and at around 15,000 years ago, respectively. The Group II and III networks had two- or three-step star-shaped structures and tended to exhibit frequent and less frequent nonsynonymous substitutions on exterior and interior branches, respectively. Based on temporal dynamics, nonsynonymous mitochondrial DNA (mtDNA) substitutions in small mammals accounted for at most 40% of all substitutions during the early evolutionary stage and then rapidly declined, dropping to approximately 15%. The results of this study provide a good explanation of the time-dependent trend in the mtDNA evolution rate predicted in previous work.
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Affiliation(s)
- Yuta Inoue
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University
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Imai H, Kano K, Kusakabe KT. Histological analysis of implanted embryos in large Japanese field mouse (Apodemus speciosus) and estimation of developmental stage. J Vet Med Sci 2021; 83:1178-1181. [PMID: 34148913 PMCID: PMC8437710 DOI: 10.1292/jvms.21-0197] [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] [Indexed: 11/25/2022] Open
Abstract
The large Japanese field mouse (Apodemus speciosus) is a small rodent
species endemic to Japan. The genetic characteristics of A. speciosus
include different chromosome numbers within the same species. Furthermore, A.
speciosus has been used in radiation and genetic research. In the present
study, a pregnant A. speciosus was obtained, and histochemical analysis
of the implanted embryos was performed and compared with the developmental stages of the
mouse (Mus musculus). Although there were some differences, the
structures of the implanted embryos, including the primitive streak and placenta of
A. speciosus were similar to those of mouse. Our study will be
important for the construction of a developmental atlas of A.
speciosus.
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Affiliation(s)
- Hiroyuki Imai
- Laboratory of Veterinary Anatomy, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Kiyoshi Kano
- Laboratory of Veterinary Embryology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Ken Takeshi Kusakabe
- Laboratory of Veterinary Anatomy, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi 753-8515, Japan
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Late Pleistocene Expansion of Small Murid Rodents across the Palearctic in Relation to the Past Environmental Changes. Genes (Basel) 2021; 12:genes12050642. [PMID: 33925980 PMCID: PMC8145813 DOI: 10.3390/genes12050642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022] Open
Abstract
We investigated the evolutionary history of the striped field mouse to identify factors that initiated its past demographic changes and to shed light on the causes of its current genetic structure and trans-Eurasian distribution. We sequenced mitochondrial cyt b from 184 individuals, obtained from 35 sites in central Europe and eastern Mongolia. We compared genetic analyses with previously published historical distribution models and data on environmental and climatic changes. The past demographic changes displayed similar population trends in the case of recently expanded clades C1 and C3, with the glacial (MIS 3–4) expansion and postglacial bottleneck preceding the recent expansion initiated in the late Holocene and were related to environmental changes during the upper Pleistocene and Holocene. The past demographic trends of the eastern Asian clade C3 were correlated with changes in sea level and the formation of new land bridges formed by the exposed sea shelf during the glaciations. These data were supported by reconstructed historical distribution models. The results of our genetic analyses, supported by the reconstruction of the historical spatial distributions of the distinct clades, confirm that over time the local populations mixed as a consequence of environmental and climatic changes resulting from cyclical glaciation and the interglacial period during the Pleistocene.
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Nakamoto A, Harada M, Mitsuhashi R, Tsuchiya K, Kryukov AP, Shinohara A, Suzuki H. Influence of Quaternary environmental changes on mole populations inferred from mitochondrial sequences and evolutionary rate estimation. ZOOLOGICAL LETTERS 2021; 7:2. [PMID: 33588942 PMCID: PMC7885446 DOI: 10.1186/s40851-021-00169-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
Quaternary environmental changes fundamentally influenced the genetic diversity of temperate-zone terrestrial animals, including those in the Japanese Archipelago. The genetic diversity of present-day populations is taxon- and region-specific, but its determinants are poorly understood. Here, we analyzed cytochrome b gene (Cytb) sequences (1140 bp) of mitochondrial DNA (mtDNA) to elucidate the factors determining the genetic variation in three species of large moles: Mogera imaizumii and Mogera wogura, which occur in central and southern mainland Japan (Honshu, Shikoku, and Kyushu), and Mogera robusta, which occurs on the nearby Asian continent. Network construction with the Cytb sequences revealed 10 star-shaped clusters with apparent geographic affinity. Mismatch distribution analysis showed that modes of pairwise nucleotide differences (τ values) were grouped into five classes in terms of the level, implying the occurrence of five stages for rapid expansion. It is conceivable that severe cold periods and subsequent warm periods during the late Quaternary were responsible for the population expansion events. The first and third oldest events included island-derived haplotypes, indicative of the involvement of land bridge formation between remote islands, hence suggesting an association of the ends of the penultimate (PGM, ca. 130,000 years ago) and last (LGM, ca. 15,000 years ago) glacial maxima, respectively. Since the third event was followed by the fourth, it is plausible that the termination of the Younger Dryas and subsequent abrupt warming ca. 11,500 years ago facilitated the fourth expansion event. The second event most likely corresponded to early marine isotope stage (MIS) 3 (ca. 53,000 years ago) when the glaciation and subsequent warming period were predicted to have influenced biodiversity. Utilization of the critical times of 130,000, 53,000, 15,000, and 11,500 years ago as calibration points yielded evolutionary rates of 0.03, 0.045, 0.10 and 0.10 substitutions/site/million years, respectively, showing a time-dependent manner whose pattern was similar to that seen in small rodents reported in our previous studies. The age of the fifth expansion event was calculated to be 5800 years ago with a rate of 0.10 substitutions/site/million years ago during the mid-Holocene, suggestive of the influence of humans or other unspecified reasons, such as the Jomon marine transgression.
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Affiliation(s)
- Azusa Nakamoto
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Sapporo, 060-0810 Japan
| | - Masashi Harada
- Laboratory Animal Center, Osaka City University Graduate School of Medical School, Osaka, 545-8585 Japan
| | - Reiko Mitsuhashi
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Sapporo, 060-0810 Japan
| | - Kimiyuki Tsuchiya
- Oyo-seibutsu Co. Ltd., 4-12-3, Minami-Aoyama, Minato-ku, Tokyo, 107-0062 Japan
| | - Alexey P. Kryukov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022 Russia
| | - Akio Shinohara
- Frontier Science Research Center, University of Miyazaki, Kihara 5200, Miyazaki, 889-1692 Japan
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Sapporo, 060-0810 Japan
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Harigai W, Saito A, Suzuki H, Yamamoto M. Genetic Diversity of Ligidium Isopods in Hokkaido and Niigata, Northern Japan, Based on Mitochondrial DNA Analysis. Zoolog Sci 2021; 37:417-428. [PMID: 32972082 DOI: 10.2108/zs200017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/24/2020] [Indexed: 11/17/2022]
Abstract
The genetic diversity of the genus Ligidium in Hokkaido and Niigata, northern Japan, was investigated by analyzing the cytochrome c oxidase subunit 1 (CO1) region in the mitochondrial DNA (mtDNA). The genetic diversity in Hokkaido was much lower than that in Niigata. Nine different operational taxonomic units (OTUs) were identified. Only a single OTU, most likely Ligidium japonicum, was found in Hokkaido, whereas all nine OTUs were found in Niigata. Using the mtDNA evolutionary rate determined for the marine invertebrate Haptosquilla pulchella (Miers, 1880), population expansion for OTU1 in Hokkaido was estimated to have occurred at 12,600 years BP, suggesting that Ligidium underwent a bottleneck due to glacial cooling, and the population then expanded after postglacial warming. Assuming that the expansion of the OTU1 population occurred at 9600 years BP, when the sea surface temperature rose offshore of Tokachi in the Northwestern Pacific, the evolutionary rate (µ) of the mtDNA CO1 region in Ligidium is calculated as: 0.087 (95% confidence intervals: min: 0.042-max: 0.12) (substitutions/site/million years). The presence of a haplotype common to Hokkaido and Niigata implies that the haplotype migrated across the Tsugaru Strait. Considering that geological evidence indicates that the Tsugaru Strait was continuously present even during the last glacial maximum when the sea level was at its lowest, accidental transport by human beings or animals might have been critical to the migration of Ligidium.
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Affiliation(s)
- Wakana Harigai
- Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan,
| | - Aya Saito
- Department of Earth and Planetary Sciences, School of Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Masanobu Yamamoto
- Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
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SUZUKI HITOSHI. The time-dependent evolutionary rate of mitochondrial DNA in small mammals inferred from biogeographic calibration points with reference to the late Quaternary environmental changes in the Japanese archipelago. ANTHROPOL SCI 2021. [DOI: 10.1537/ase.201201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- HITOSHI SUZUKI
- Graduate School of Environmental Science, Hokkaido University, Sapporo
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Li Y, Fujiwara K, Osada N, Kawai Y, Takada T, Kryukov AP, Abe K, Yonekawa H, Shiroishi T, Moriwaki K, Saitou N, Suzuki H. House mouse Mus musculus dispersal in East Eurasia inferred from 98 newly determined complete mitochondrial genome sequences. Heredity (Edinb) 2021; 126:132-147. [PMID: 32934361 PMCID: PMC7852662 DOI: 10.1038/s41437-020-00364-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 11/09/2022] Open
Abstract
The Eurasian house mouse Mus musculus is useful for tracing prehistorical human movement related to the spread of farming. We determined whole mitochondrial DNA (mtDNA) sequences (ca. 16,000 bp) of 98 wild-derived individuals of two subspecies, M. m. musculus (MUS) and M. m. castaneus (CAS). We revealed directional dispersals reaching as far as the Japanese Archipelago from their homelands. Our phylogenetic analysis indicated that the eastward movement of MUS was characterised by five step-wise regional extension events: (1) broad spatial expansion into eastern Europe and the western part of western China, (2) dispersal to the eastern part of western China, (3) dispersal to northern China, (4) dispersal to the Korean Peninsula and (5) colonisation and expansion in the Japanese Archipelago. These events were estimated to have occurred during the last 2000-18,000 years. The dispersal of CAS was characterised by three events: initial divergences (ca. 7000-9000 years ago) of haplogroups in northernmost China and the eastern coast of India, followed by two population expansion events that likely originated from the Yangtze River basin to broad areas of South and Southeast Asia, including Sri Lanka, Bangladesh and Indonesia (ca. 4000-6000 years ago) and to Yunnan, southern China and the Japanese Archipelago (ca. 2000-3500). This study provides a solid framework for the spatiotemporal movement of the human-associated organisms in Holocene Eastern Eurasia using whole mtDNA sequences, reliable evolutionary rates and accurate branching patterns. The information obtained here contributes to the analysis of a variety of animals and plants associated with prehistoric human migration.
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Affiliation(s)
- Yue Li
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Kita-ku, Sapporo, 060-0810, Japan
| | - Kazumichi Fujiwara
- Graduate School of Information Science and Technology, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
| | - Naoki Osada
- Graduate School of Information Science and Technology, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
- Global Station for Big Data and Cybersecurity, GI-CoRE, Hokkaido University, North 14, West 9, Kita-ku, Sapporo, 060-0814, Japan
| | - Yosuke Kawai
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine, 1-21-1, Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Toyoyuki Takada
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, 305-0074, Japan
| | - Alexey P Kryukov
- Far Eastern Branch of the Russian Academy of Sciences, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Vladivostok, 690022, Russia
| | - Kuniya Abe
- Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, 305-0074, Japan
| | - Hiromichi Yonekawa
- Laboratory for Transgenic Technology, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kami-kitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | | | - Kazuo Moriwaki
- RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, 305-0074, Japan
- National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
- School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara-cho, 903-0215, Japan
| | - Hitoshi Suzuki
- Graduate School of Environmental Science, Hokkaido University, North 10, West 5, Kita-ku, Sapporo, 060-0810, Japan.
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Sato JJ, Aiba H, Ohtake K, Minato S. Evolutionary and Anthropogenic Factors Affecting the Mitochondrial D-loop Genetic Diversity of Apodemus and Myodes Rodents on the Northern Slope of Mt. Fuji. MAMMAL STUDY 2020. [DOI: 10.3106/ms2020-0033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Jun J. Sato
- Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
| | - Haruka Aiba
- Japanese Dormice Preservation & Research Group, Yamanashi 408-0015, Japan
| | - Kouichi Ohtake
- Japanese Dormice Preservation & Research Group, Yamanashi 408-0015, Japan
| | - Shusaku Minato
- Japanese Dormice Preservation & Research Group, Yamanashi 408-0015, Japan
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13
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Late Quaternary Environmental and Human Impacts on the Mitochondrial DNA Diversity of Four Commensal Rodents in Myanmar. J MAMM EVOL 2020. [DOI: 10.1007/s10914-020-09519-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AbstractWe addressed the spatiotemporal characteristics of four commensal rodent species occurring in Myanmar in comparison with other areas of the Indo-Malayan region. We examined sequence variations of the mitochondrial cytochrome b gene (Cytb) in the Pacific rat (Rattus exulans), roof rat (Rattus rattus complex, RrC), lesser bandicoot rat (Bandicota bengalensis), and house mouse (Mus musculus) using the recently developed time-dependent evolutionary rates of mtDNA. The Cytb sequences of RrC from Myanmar were shown to belong to RrC Lineage II, and their level of genetic diversity was relatively high compared to those of the other three species. RrC was found to have experienced bottleneck and rapid expansion events at least twice in the late Pleistocene period in Myanmar and a nearby region. Accordingly, paleoclimatic environmental fluctuations were shown to be an important factor affecting rodents in the subtropics of the Indo-Malayan region. Our results show that human activities during the last 10,000 years of the Holocene period affected the population dynamics of the rodent species examined, including introducing them to Myanmar from neighboring countries. Further study of these four commensal rodents in other geographic areas of the Indo-Malayan region would allow us to better understand the factors that drove their evolution and their ecological trends.
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14
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Species and genetic diversity of Bandicota (Murinae, Rodentia) from Myanmar based on mitochondrial and nuclear gene sequences. MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00491-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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15
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Myat Zaw KM, Thwe T, Shimada T, Maung Theint SM, Saing KM, Bawm S, Katakura K, Suzuki H. Molecular Characterization of Species of the Subgenus Mus from Myanmar. Zoolog Sci 2019; 36:299-305. [PMID: 34664900 DOI: 10.2108/zs180161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/05/2019] [Indexed: 11/17/2022]
Abstract
The species composition and genetic diversity of the subgenus Mus in Myanmar are not yet fully understood. In this study, mice were trapped in rural areas near the Ayeyarwady River basin, spanning five Myanmar cities from north to south: Mandalay, Bagan, Magway, Pyay, and Yangon. Mitochondrial cytochrome b (Cytb) and nuclear melanocortin 1 receptor (Mc1r) gene sequences were determined for mice sampled and revealed a widespread occurrence of Mus nitidulus in central Myanmar in addition to its previously known occurrence in the Yangon district of southern Myanmar. Analyses of Cytb revealed two haplogroups with a genetic distance of 2.0%, suggestive of divergence several hundred thousand years ago. Mus caroli and M. musculus were confined to Yangon and Mandalay/Bagan/Magway, respectively. Mice collected from a locality on the eastern side of the Ayeyarwady River in Pyay were identified using Cytb and Mc1r sequences as M. fragilicauda, which was previously identified only in Laos and Thailand. The species M. booduga and M. cervicolor previously predicted to be common in the study area were not found. These findings elucidate the species and genetic diversity of the subgenus Mus in the Indo-Malayan Region.
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Affiliation(s)
| | - Thidalay Thwe
- Department of Zoology, University of Yangon, Yangon 11041, Myanmar,
| | | | | | - Khin Maung Saing
- Department of Zoology, University of Yangon, Yangon 11041, Myanmar
| | - Saw Bawm
- Department of Pharmacology and Parasitology, University of Veterinary Science, Yezin, Nay Pyi Taw 15013, Myanmar
| | - Ken Katakura
- Graduate School of Infectious Diseases, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan
| | - Hitoshi Suzuki
- Graduate School of Environmental Earth Science, Hokkaido University, Sapporo 060-0810, Japan,
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Honda A, Murakami S, Harada M, Tsuchiya K, Kinoshita G, Suzuki H. Late Pleistocene climate change and population dynamics of Japanese Myodes voles inferred from mitochondrial cytochrome b sequences. J Mammal 2019; 100:1156-1168. [PMID: 31379389 PMCID: PMC6660811 DOI: 10.1093/jmammal/gyz093] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The Japanese archipelago is comprised of four main islands—Hokkaido, Honshu, Shikoku, and Kyushu—which contain high mountainous areas that likely allowed for lineage differentiation and population genetic structuring during the climatic changes of the late Pleistocene. Here, we assess the historical background of the evolutionary dynamics of herbivorous red-backed voles (Myodes) in Japan, examining the evolutionary trends of mitochondrial cytochrome b gene (Cytb) sequence variation. Four apparent signals from rapid expansion events were detected in three species, M. rufocanus and M. rutilus from Hokkaido and M. smithii from central Honshu. Taken together with results from previous studies on Japanese wood mice (Apodemus spp.), three of the expansion events were considered to be associated with predicted bottleneck events at the marine isotope stage (MIS) 4 period, in which glaciers are thought to have expanded extensively, especially at higher elevations. In the late Pleistocene, the possible candidates are transitions MIS 6/5, MIS 4/3, and MIS 2/1, which can be characterized by the cold periods of the penultimate glacial maximum, MIS 4, and the last glacial maximum, respectively. Our data further reveal the genetic footprints of repeated range expansion and contraction in the northern and southern lineages of the vole species currently found in central Honshu, namely M. andersoni and M. smithii, in response to climatic oscillation during the late Pleistocene. The time-dependent evolutionary rates of the mitochondrial Cytb presented here would provide a possible way for assessing population dynamics of cricetid rodents responding to the late Pleistocene environmental fluctuation.
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Affiliation(s)
- Asuka Honda
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Shota Murakami
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Masashi Harada
- Laboratory Animal Center, Osaka City University Graduate School of Medical School, Osaka, Japan (MH)
| | | | - Gohta Kinoshita
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, Japan
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, Japan
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17
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Kinoshita G, Nunome M, Kryukov AP, Kartavtseva IV, Han SH, Yamada F, Suzuki H. Contrasting phylogeographic histories between the continent and islands of East Asia: Massive mitochondrial introgression and long-term isolation of hares (Lagomorpha: Lepus). Mol Phylogenet Evol 2019; 136:65-75. [PMID: 30951923 DOI: 10.1016/j.ympev.2019.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 03/19/2019] [Accepted: 04/01/2019] [Indexed: 01/16/2023]
Abstract
Hares of the genus Lepus are distributed worldwide, and introgressive hybridization is thought to be pervasive among species, leading to reticulate evolution and taxonomic confusion. Here, we performed phylogeographic analyses of the following species of hare across East Asia: L. timidus, L. mandshuricus, L. coreanus, and L. brachyurus collected from far-eastern Russia, South Korea, and Japan. Nucleotide sequences of one mitochondrial DNA and eight nuclear gene loci were examined, adding sequences of hares in China from databases. All nuclear DNA analyses supported the clear separation of three phylogroups: L. timidus, L. brachyurus, and the L. mandshuricus complex containing L. coreanus. On the other hand, massive mitochondrial introgression from two L. timidus lineages to the L. mandshuricus complex was suggested in continental East Asia. The northern population of the L. mandshuricus complex was mainly associated with introgression from the continental lineage of L. timidus, possibly since the last glacial period, whereas the southern population of the L. mandshuricus complex experienced introgression from another L. timidus lineage related to the Hokkaido population, possibly before the last glacial period. In contrast to continental hares, no evidence of introgression was found in L. brachyurus in the Japanese Archipelago, which showed the oldest divergence amongst East Asian hare lineages. Our findings suggest that glacial-interglacial climate changes in the circum-Japan Sea region promoted distribution shifts and introgressive hybridization among continental hare species, while the geographic structure of the region contributed to long-term isolation of hares on the islands, preventing inter-species gene flow.
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Affiliation(s)
- Gohta Kinoshita
- Course in Ecological Genetics, Graduate School of Environmental Science, Hokkaido University, N10W5, Kita-ku, Sapporo 060-0810, Japan; Laboratory of Forest Biology Division of Forest & Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake, Sakyoku, Kyoto 606-8502, Japan.
| | - Mitsuo Nunome
- Laboratory of Animal Genetics, Graduate School of Bioagricultural Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Alexey P Kryukov
- Laboratory of Evolutionary Zoology and Genetics, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Irina V Kartavtseva
- Laboratory of Evolutionary Zoology and Genetics, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch Russian Academy of Sciences, Vladivostok 690022, Russia
| | - San-Hoon Han
- Inter-Korea Wildlife Institute, Namtong-dong, Gumi-si, Kyeongsang-Bukdo 39301, Republic of Korea
| | - Fumio Yamada
- Laboratory of Wildlife Ecology, Forestry and Forest Products Research Institute (FFPRI), Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Hitoshi Suzuki
- Course in Ecological Genetics, Graduate School of Environmental Science, Hokkaido University, N10W5, Kita-ku, Sapporo 060-0810, Japan
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18
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Bibi S, Nadeem MS, Wiewel AS, Beg MA, Hameed K, Jabeen M, Raja GK. Mitochondrial Genetic Diversity and Phylogeography of Mus musculus castaneus in Northern Punjab, Pakistan. Zoolog Sci 2017; 34:490-497. [PMID: 29219045 DOI: 10.2108/zs170086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Regions of Iran, Afghanistan, Pakistan and northwestern India have been proposed as the place of origin of Mus musculus castaneus. But despite the fact that Pakistan encompasses an important part of its range, M. m. castaneus populations in Pakistan have not been the subject of intensive genetic and biogeographic studies, except for a very small number of samples included in past studies. We studied genetic variation in M. m. castaneus (CAS) from northern Punjab Province, Pakistan, by using cytochrome b (Cytb) analysis in a sample of 98 individuals. Median-joining network revealed four well differentiated CAS sub-lineages coexisting within a small geographical region; these had previously been thought to have largely non-overlapping geographic distributions. Moreover, haplotypes from Pakistan occupied a central position in the network and all identified global haplotypes were also present in Pakistan. All identified CAS sub-lineages proved to be highly diverse on the basis of haplotype and nucleotide diversity indices. Tajima's D test and Fu's Fs tests of neutrality suggest recent population expansions in all sub-lineages. Expansion times were estimated as 21,760-134,930, 10,800-64,400 and 4950-30,665 ybp using substitution rates of 2.5%, 5% and 11%, respectively. Our results support the hypothesis that northern Punjab Province in Pakistan is the most likely source area for M. m. castaneus, and that the CAS sub-lineages in this region have undergone rapid population expansion events at different time periods, which appear to have benefitted from human-mediated transport, although one of them clearly predates the establishment of human settlements in this region.
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Affiliation(s)
- Shahnaz Bibi
- 1 Zoology Department, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi 46300, Pakistan
| | - Muhammad Sajid Nadeem
- 1 Zoology Department, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi 46300, Pakistan
| | | | - Mirza Azhar Beg
- 1 Zoology Department, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi 46300, Pakistan
| | - Khalid Hameed
- 3 Mirpur University of Science and Technology, Mirpur Azad Jammu and Kashmir 10250, Pakistan
| | | | - Ghazala Kaukab Raja
- 5 Department of Biochemistry, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi 46300, Pakistan
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Kuwayama T, Nunome M, Kinoshita G, Abe K, Suzuki H. Heterogeneous genetic make-up of Japanese house mice (Mus musculus) created by multiple independent introductions and spatio-temporally diverse hybridization processes. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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