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Huang L, Feng G, Li D, Shang W, Zhang L, Yan R, Jiang Y, Li S. Genetic variation of endangered Jankowski’s Bunting (Emberiza jankowskii): High connectivity and a moderate history of demographic decline. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.996617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
IntroductionContinued discovery of “mismatch” patterns between population size and genetic diversity, involving wild species such as insects, amphibians, birds, mammals, and others, has raised issues about how population history, especially recent dynamics under human disturbance, affects currently standing genetic variation. Previous studies have revealed high genetic diversity in endangered Jankowski’s Bunting. However, it is unclear how the demographic history and recent habitat changes shape the genetic variation of Jankowski’s Bunting.MethodsTo explore the formation and maintenance of high genetic diversity in endangered Jankowski’s Bunting, we used a mitochondrial control region (partial mtDNA CR) and 15 nuclear microsatellite markers to explore the recent demographic history of Jankowski’s Bunting, and we compared the historical and contemporary gene flows between populations to reveal the impact of habitat change on population connectivity. Specifically, we aimed to test the following hypotheses: (1) Jankowski’s Bunting has a large historical Ne and a moderate demographic history; and (2) recent habitat change might have no significant impact on the species’ population connectivity.ResultsThe results suggested that large historical effective population size, as well as severe but slow population decline, may partially explain the high observable genetic diversity. Comparison of historical (over the past 4Ne generations) and contemporary (1–3 generations) gene flow indicated that the connectivity between five local populations was only marginally affected by landscape changes.DiscussionOur results suggest that high population connectivity and a moderate history of demographic decline are powerful explanations for the rich genetic variation in Jankowski’s Bunting. Although there is no evidence that the genetic health of Jankowski’s Bunting is threatened, the time-lag effects on the genetic response to recent environmental changes is a reminder to be cautious about the current genetic characteristics of this species. Where possible, factors influencing genetic variation should be integrated into a systematic framework for conducting robust population health assessments. Given the small contemporary population size, inbreeding, and ecological specialization, we recommend that habitat protection be maintained to maximize the genetic diversity and population connectivity of Jankowski’s Bunting.
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Ikeda Y, Motokawa M. Phylogeography of the Japanese greater horseshoe bat Rhinolophus nippon (Mammalia: Chiroptera) in Northeast Asia: New insight into the monophyly of the Japanese populations. Ecol Evol 2021; 11:18181-18195. [PMID: 35003666 PMCID: PMC8717313 DOI: 10.1002/ece3.8414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022] Open
Abstract
The Japanese greater horseshoe bat (Rhinolophus nippon) is distributed widely in East Asia. Within the species, R. nippon in Northeast Asia is regarded as the lineage that diverged most recently. However, the monophyly of the Japanese populations is unclear due to insufficient data about phylogenetic relationship of the western Japanese populations. To test the monophyly of the Japanese populations of R. nippon, we sampled R. nippon from western Japan and performed a phylogeographic analysis based on mitochondrial DNA cytochrome b and the D-loop. The Northeast Asian lineage consisted of three main clades in eastern Japan (clade I), western Japan (clade II), and the continent as well as the Kumamoto population in westernmost Japan (clade III). The results of this study do not support the monophyly of the Japanese population. The findings suggest the "reverse colonization" of R. nippon from the Japanese Archipelago to the Eurasian continent, and provide important insight into the role of the island system in creation and supply of diversity to the continent.
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Affiliation(s)
- Yugo Ikeda
- Graduate School of ScienceKyoto UniversitySakyoKyotoJapan
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Kimprasit T, Nunome M, Iida K, Murakami Y, Wong ML, Wu CH, Kobayashi R, Hengjan Y, Takemae H, Yonemitsu K, Kuwata R, Shimoda H, Si L, Sohn JH, Asakawa S, Ichiyanagi K, Maeda K, Oh HS, Mizutani T, Kimura J, Iida A, Hondo E. Dispersal history of Miniopterus fuliginosus bats and their associated viruses in east Asia. PLoS One 2021; 16:e0244006. [PMID: 33444317 PMCID: PMC7808576 DOI: 10.1371/journal.pone.0244006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/02/2020] [Indexed: 12/23/2022] Open
Abstract
In this study, we examined the role of the eastern bent-winged bat (Miniopterus fuliginosus) in the dispersion of bat adenovirus and bat alphacoronavirus in east Asia, considering their gene flows and divergence times (based on deep-sequencing data), using bat fecal guano samples. Bats in China moved to Jeju Island and/or Taiwan in the last 20,000 years via the Korean Peninsula and/or Japan. The phylogenies of host mitochondrial D-loop DNA was not significantly congruent with those of bat adenovirus (m2XY = 0.07, p = 0.08), and bat alphacoronavirus (m2XY = 0.48, p = 0.20). We estimate that the first divergence time of bats carrying bat adenovirus in five caves studied (designated as K1, K2, JJ, N2, and F3) occurred approximately 3.17 million years ago. In contrast, the first divergence time of bat adenovirus among bats in the 5 caves was estimated to be approximately 224.32 years ago. The first divergence time of bats in caves CH, JJ, WY, N2, F1, F2, and F3 harboring bat alphacoronavirus was estimated to be 1.59 million years ago. The first divergence time of bat alphacoronavirus among the 7 caves was estimated to be approximately 2,596.92 years ago. The origin of bat adenovirus remains unclear, whereas our findings suggest that bat alphacoronavirus originated in Japan. Surprisingly, bat adenovirus and bat alphacoronavirus appeared to diverge substantially over the last 100 years, even though our gene-flow data indicate that the eastern bent-winged bat serves as an important natural reservoir of both viruses.
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Affiliation(s)
- Thachawech Kimprasit
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Keisuke Iida
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | | | - Min-Liang Wong
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Hsin Wu
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ryosuke Kobayashi
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yupadee Hengjan
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hitoshi Takemae
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenzo Yonemitsu
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Ryusei Kuwata
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hiroshi Shimoda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Lifan Si
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan, China
| | - Joon-Hyuk Sohn
- Laboratory of Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Susumu Asakawa
- Laboratory of Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Ken Maeda
- Laboratory of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Hong-Shik Oh
- Institute of Science Education, Jeju National University, Jeju, Korea
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Junpei Kimura
- Laboratory of Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Atsuo Iida
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Eiichi Hondo
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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Liu T, Zhang K, Dai W, Jin L, Sun K, Feng J. Evolutionary insights into
Rhinolophus episcopus
(Chiroptera, Rhinolophidae) in China: Isolation by distance, environment, or sensory system? J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Kangkang Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- Key Laboratory of Vegetation Ecology Ministry of Education Changchun China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- College of Life Science Jilin Agricultural University Changchun China
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Kafaei S, Sharifi M, Akmali V. Population Genetic Structure and Phylogeography of the Small Mouse-Tailed Bat, Rhinopoma muscatellum Thomas, 1903 (Chiroptera: Rhinopomatidae) in Iran Inferred from Mitochondrial DNA. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2020.22.1.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Sasan Kafaei
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Mozafar Sharifi
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Vahid Akmali
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
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Ikeda Y, Jiang T, Oh H, Csorba G, Motokawa M. Geographic variations of skull morphology in the Rhinolophus ferrumequinum species complex (Mammalia: Chiroptera). ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Mehdizadeh R, Akmali V, Sharifi M. Population genetic structure and phylogeography of the greater horseshoe bat ( Rhinolophus ferrumequinum) along Alborz and Zagros Mts. in Iran. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:87-97. [PMID: 32202175 DOI: 10.1080/24701394.2020.1741562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In this paper, we investigate the genetic structure and phylogeography of Rhinolophus ferrumequinum, using the mitochondrial cytochrome b gene (1017 bp) in Iran and adjacent regions. The total haplotype and nucleotide diversity are 0.63 ± 0.055 and 0.0021 ± 0.00017, respectively which suggest that R. ferrumequinum exhibits low genetic diversity. AMOVA analysis shows that more variation of genetic differentiation is present among populations of phylogenetic groupings than within populations. Our phylogenetic results support the monophyly of R. ferrumequinum and suggest this taxon comprises three allopatric/parapatric phylogroups that are distributed in Europe-western Turkey, eastern Turkey-northern Iran, and southern Iran. The Europe-western Turkey lineage (clade 2) split from the eastern Turkey-Iran lineage (clade 1) during the middle Pleistocene (0.8534 (ca.I)-0.6454 (ca.II) Ma). The divergence time among subclades A and B occurred during the mid-Pleistocene (0.4849 (ca.I)-0.369 (ca.II) Ma). All phylogenetic analyses also indicate that the Iranian and eastern Turkey R. ferrumequinum diverged from Europe and western Turkey R. ferrumequinum, with the mean percentage sequence differences ranging from 0.92%-0.75% between them. We infer that long-term isolation of R. ferrumequinum in spatially distinct refugia in parts of southwestern and northeastern Iran has promoted distinct phylogeographic lineages during the Pleistocene.
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Affiliation(s)
- Robab Mehdizadeh
- Department of Biology, Faculty of Science, Razi University, Baghabrisham, Kermanshah, Iran
| | - Vahid Akmali
- Department of Biology, Faculty of Science, Razi University, Baghabrisham, Kermanshah, Iran
| | - Mozafar Sharifi
- Department of Biology, Faculty of Science, Razi University, Baghabrisham, Kermanshah, Iran
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Endo K, Iida K, Nunome M, Kim YK, Han SH, Sohn JH, Ohmori Y, Oh HS, Kimura J, Hondo E. Phylogeography of Miniopterus fuliginosus (Chiroptera) with special reference to Jeju Island, South Korea. MAMMALIA 2019. [DOI: 10.1515/mammalia-2018-0115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
To better understand the genetic relatedness of the eastern bent-wing bat Miniopterus fuliginosus across East Asia, mitochondrial D-loop sequences were analyzed from 39 M. fuliginosus individuals living on Jeju Island, South Korea. Seven different haplotypes were identified. Neighbor-joining analysis was performed and divergence time was calculated in combination with available online data on D-loop and ND2 sequences of M. fuliginosus in East Asia, respectively. Results suggest that M. fuliginosus populations living on Jeju Island and in Japan originated from China in the past 20,000 years.
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Affiliation(s)
- Kanako Endo
- Laboratory of Animal Morphology, Faculty of Agriculture, Nagoya University , Nagoya 464-8601 , Japan
| | - Keisuke Iida
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya , Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya , Japan
| | - Yoo-Kyung Kim
- Institute of Science Education, Jeju National University , Jeju , Korea
| | - Sang-Hyun Han
- Institute of Science Education, Jeju National University , Jeju , Korea
| | - Joon-Hyuk Sohn
- Laboratory of Veterinary Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University , Seoul , Korea
| | - Yasushige Ohmori
- Laboratory of Animal Morphology, Faculty of Agriculture, Nagoya University , Nagoya 464-8601 , Japan
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya , Japan
| | - Hong-Shik Oh
- Institute of Science Education, Jeju National University , Jeju , Korea
| | - Junpei Kimura
- Laboratory of Veterinary Anatomy and Cell Biology and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University , Seoul , Korea
| | - Eiichi Hondo
- Laboratory of Animal Morphology, Faculty of Agriculture, Nagoya University , Nagoya 464-8601 , Japan
- Laboratory of Animal Morphology, Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya , Japan
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Rakotoarivelo AR, Goodman SM, Schoeman MC, Willows-Munro S. Phylogeography and population genetics of the endemic Malagasy bat, Macronycteris commersoni s.s. (Chiroptera: Hipposideridae). PeerJ 2019; 7:e5866. [PMID: 30671293 PMCID: PMC6339777 DOI: 10.7717/peerj.5866] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
Macronycteris commersoni (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island and utilizes a range of habitat types including open woodland, degraded habitats, and forested areas from sea level to 1,325 m. Despite being widely distributed, there is evidence that M. commersoni exhibits morphological and bioacoustic variation across its geographical range. We investigated the fine-scale phylogeographic structure of populations in the western half of the island using extensive spatial sampling and sequence data from two mitochondrial DNA regions. Our results indicated several lineages within M. commersoni. Individuals collected from northern Madagascar formed a single monophyletic clade (clade C). A second clade (clade B) included individuals collected from the south-western portion of the island. This second clade displayed more phylogeographical partitioning with differences in mtDNA haplotypes frequency detected between populations collected in different bioclimatic regions. Lineage dispersal, genetic divergence, and timing of expansion events of M. commersoni were probably associated with Pleistocene climate fluctuations. Our data suggest that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.
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Affiliation(s)
- Andrinajoro R. Rakotoarivelo
- Department of Zoology, University of Venda, Thohoyandou, Limpopo, South Africa
- School of Life Sciences, University of Kwa-Zulu Natal, Pietermaritzburg, Kwa-Zulu Natal, South Africa
- Natiora Ahy, Antananarivo, Madagascar
| | - Steven M. Goodman
- Field Museum of Natural History, Chicago, IL, United States of America
- Association Vahatra, Antananarivo, Madagascar
| | - M. Corrie Schoeman
- School of Life Sciences, University of Kwa-Zulu Natal, Westville, Kwa-Zulu Natal, South Africa
| | - Sandi Willows-Munro
- School of Life Sciences, University of Kwa-Zulu Natal, Pietermaritzburg, Kwa-Zulu Natal, South Africa
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Shahabi S, Akmali V, Sharifi M. Taxonomic Evaluation of the Greater Horseshoe Bat Rhinolophus ferrumequinum (Chiroptera: Rhinolophidae) in Iran Inferred from the Mitochondrial D-Loop Gene. Zoolog Sci 2017; 34:361-367. [DOI: 10.2108/zs170001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Saeed Shahabi
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Vahid Akmali
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Mozafar Sharifi
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
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