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Richdon S, Menchaca Rodriguez A, Price E, Wormell D, McCabe G, Jones G. Thirty years of conservation breeding: Assessing the genetic diversity of captive Livingstone's fruit bats. Zoo Biol 2024. [PMID: 38837463 DOI: 10.1002/zoo.21845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/18/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024]
Abstract
Fruit bats (genus Pteropus) are typically island-endemic species important in seed dispersal and reforestation that are vulnerable to increased extinction risk. An effective method of reducing extinction risk in vulnerable species that cannot be conserved in their native habitat is establishing an ex-situ captive breeding programme. Due to anthropogenic threats and low population numbers, in the early 1990s, a captive breeding programme was established at Jersey Zoo, British Isles, for Critically Endangered Livingstone's fruit bats (Pteropus livingstonii). Here we use six polymorphic microsatellite loci to assess genetic diversity in the captive breeding population of Livingstone's fruit bats (P. livingstonii), 30 years after the programme's establishment, investigating change over generations and comparing our findings with published data from the wild population. We found no significant difference between the genetic diversity in the captive and wild populations of Livingstone's fruit bats (P. livingstonii), in both expected heterozygosity and allelic richness. The captive population has retained a comparable level of genetic diversity to that documented in the wild, and there has been no significant decline in genetic diversity over the last 30 years. We advise that a full pedigree of the paternal lineage is created to improve the management of the captive breeding programme and further reduce the possibility of inbreeding. However, it appears that the captive breeding programme is currently effective at maintaining genetic diversity at levels comparable to those seen in the wild population, which suggests reintroductions could be viable if genetic diversity remains stable in captivity.
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Affiliation(s)
- Sarah Richdon
- School of Biological Sciences, University of Bristol, Bristol, UK
- Bristol Zoological Society, Clifton, Bristol, UK
| | | | - Eluned Price
- Durrell Wildlife Conservation Trust, La Profonde Rue, Jersey, UK
| | - Dominic Wormell
- Durrell Wildlife Conservation Trust, La Profonde Rue, Jersey, UK
| | | | - Gareth Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
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2
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Zink RM, Klicka LB. The taxonomic basis of subspecies listed as threatened and endangered under the endangered species act. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.971280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
More than 170 subspecies are listed as threatened or endangered under the US Endangered Species Act. Most of these subspecies were described decades ago on the basis of geographical variation in morphology using relatively primitive taxonomic methods. The US Fish and Wildlife Service defaults to subspecies descriptions by taxonomists working with specific groups of organisms, but there is no single definition of subspecies across plants and animals. Valid tests today usually entail molecular analyses of variation within and among populations, although there is no reason that behavioral, ecological or molecular characters could not be used, and include tests for significant differences between samples of the putative endangered subspecies and its nearest geographic relatives. We evaluated data gathered since subspecies listed under the ESA were described finding about one-third are valid (distinct evolutionary taxa), one-third are not, and one-third have not been tested. Therefore, it should not be assumed that because a subspecies occurs in a checklist, it is taxonomically valid. If the US Fish and Wildlife Service intends to continue listing subspecies, we suggest that they convene taxonomic experts representing various groups of organisms to provide a minimal set of criteria for a subspecies to be listed under the ESA.
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3
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Lin KP, Chaw SM, Lo YH, Kinjo T, Tung CY, Cheng HC, Liu Q, Satta Y, Izawa M, Chen SF, Ko WY. Genetic Differentiation and Demographic Trajectory of the Insular Formosan and Orii's Flying Foxes. J Hered 2021; 112:192-203. [PMID: 33675222 PMCID: PMC8006818 DOI: 10.1093/jhered/esab007] [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: 12/07/2020] [Accepted: 02/24/2021] [Indexed: 12/04/2022] Open
Abstract
Insular flying foxes are keystone species in island ecosystems due to their critical roles in plant pollination and seed dispersal. These species are vulnerable to population decline because of their small populations and low reproductive rates. The Formosan flying fox (Pteropus dasymallus formosus) is one of the 5 subspecies of the Ryukyu flying fox. Pteropus dasymallus formosus has suffered from a severe decline and is currently recognized as a critically endangered population in Taiwan. On the contrary, the Orii's flying fox (Pteropus dasymallus inopinatus) is a relatively stable population inhabiting Okinawa Island. Here, we applied a genomic approach called double digest restriction-site associated DNA sequencing to study these 2 subspecies for a total of 7 individuals. We detected significant genetic structure between the 2 populations. Despite their contrasting contemporary population sizes, both populations harbor very low degrees of genetic diversity. We further inferred their demographic history based on the joint folded site frequency spectrum and revealed that both P. d. formosus and P. d. inopinatus had maintained small population sizes for a long period of time after their divergence. Recently, these populations experienced distinct trajectories of demographic changes. While P. d. formosus suffered from a drastic ~10-fold population decline not long ago, P. d. inopinatus underwent a ~4.5-fold population expansion. Our results suggest separate conservation management for the 2 populations-population recovery is urgently needed for P. d. formosus while long-term monitoring for adverse genetic effects should be considered for P. d. inopinatus.
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Affiliation(s)
- Kung-Ping Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yun-Hwa Lo
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | | | - Chien-Yi Tung
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | | | - Quintin Liu
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Masako Izawa
- Kitakyushu Museum of Natural History and Human History, Fukuoka, Japan
| | - Shiang-Fan Chen
- Center for General Education, National Taipei University, New Taipei City, Taiwan
| | - Wen-Ya Ko
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
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4
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Taki Y, Vincenot CE, Sato Y, Inoue-Murayama M. Genetic diversity and population structure in the Ryukyu flying fox inferred from remote sampling in the Yaeyama archipelago. PLoS One 2021; 16:e0248672. [PMID: 33735322 PMCID: PMC7971866 DOI: 10.1371/journal.pone.0248672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/04/2021] [Indexed: 11/26/2022] Open
Abstract
The Ryukyu flying fox (Pteropus dasymallus) is distributed throughout the island chain spanning across southern Japan, Taiwan, and possibly the Philippines. Although P. dasymallus is listed as VU (vulnerable) in the IUCN Red List, only few genetic works have been conducted to support its conservation. In this study we analyzed 19 markers (mtDNA haplotypes and 18 microsatellite markers) to evaluate genetic diversity and investigate the genetic structure of this species. mtDNA analysis was conducted with 142 DNA remote samples, mostly from faeces, and wing tissues collected on eight islands (Miyako, Ishigaki, Kohama, Kuroshima, Hateruma, Taketomi, Iriomote, Yonaguni). 39 haplotypes were identified in 526bp of the control region, and haplotype network showed no clear genetic structure. Microsatellite analysis was also conducted with 155 samples collected on six islands (Miyako, Ishigaki, Kohama, Taketomi, Iriomote, Yonaguni). It showed that the Yonaguni population exhibits low genetic diversity, high inbreeding, and clear genetic differentiation from other populations. Gene flow between Ishigaki and Miyako through small stepstone islands might be preventing inbreeding of the Miyako population. We provide for the first time indirect proof of long-distance inter-island dispersal in the Ryukyu flying fox and revealed genetic diversity, gene flow and genetic differentiation among the archipelago’s populations. These results will be useful for delineating conservation units and designing specific conservation policies for each island based on metapopulation genetic structure.
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Affiliation(s)
- Yuto Taki
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Island Bat Research Group (IBRG), Yoshida-honmachi, Sakyo-ku, Kyoto, Japan
| | - Christian E. Vincenot
- Island Bat Research Group (IBRG), Yoshida-honmachi, Sakyo-ku, Kyoto, Japan
- Department of Social Informatics, Kyoto University, Kyoto, Japan
- * E-mail: (MIM); (CEV)
| | - Yu Sato
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Tsukuba, Japan
- * E-mail: (MIM); (CEV)
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Chen S, Juan C, Rossiter SJ, Kinjo T, Fukui D, Kawai K, Tsang SM, Veluz MJ, Sakurai H, Lin H, Jang‐Liaw N, Osawa K, Ko W, Izawa M. Population genetic structure of the insular Ryukyu flying fox
Pteropus dasymallus. Biotropica 2021. [DOI: 10.1111/btp.12897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shiang‐Fan Chen
- Center for General Education National Taipei University New Taipei City Taiwan
| | - Chung‐Hao Juan
- Center for General Education National Taipei University New Taipei City Taiwan
| | | | | | - Dai Fukui
- The University of Tokyo Hokkaido Forest The University of Tokyo Hokkaido Japan
| | - Kuniko Kawai
- Department of Biology Tokai University Hokkaido Japan
| | - Susan M. Tsang
- Department of Mammalogy American Museum of Natural History New York NY USA
- Mammalogy Section National Museum of Natural History Manila Philippines
| | | | | | - Hua‐Ching Lin
- Forestry Bureau Council of Agriculture Taipei Taiwan
| | | | | | - Wen‐Ya Ko
- Department of Life Sciences and Institute of Genome Sciences National Yang‐Ming University Taipei Taiwan
| | - Masako Izawa
- Biology Program Faculty of Science University of the Ryukyus Okinawa Japan
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Xu W, Zhou X, Fang W, Chen X. Primer development of toll-like receptor genes in the vulnerable Chinese egret (Egretta eulophotes) and its applicability in Ardeidae. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01179-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zuercher ME, Monson TA, Dvoretzky RR, Ravindramurthy S, Hlusko LJ. Dental Variation in Megabats (Chiroptera: Pteropodidae): Tooth Metrics Correlate with Body Size and Tooth Proportions Reflect Phylogeny. J MAMM EVOL 2020. [DOI: 10.1007/s10914-020-09508-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Xu W, Zhou X, Fang W, Chen X. Genetic diversity of toll-like receptor genes in the vulnerable Chinese egret (Egretta eulophotes). PLoS One 2020; 15:e0233714. [PMID: 32469968 PMCID: PMC7259618 DOI: 10.1371/journal.pone.0233714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/11/2020] [Indexed: 01/15/2023] Open
Abstract
Toll-like receptor (TLR) genes have recently been employed to assess genetic diversity, as they can be used to infer both demographic history and adaptation to environments with different pathogen pressure. Here, we sampled 120 individuals of the Chinese egret (Egretta eulophotes), a globally vulnerable species, from four breeding populations across China. We assessed the levels of genetic diversity, selection pressure, and population differentiation at seven TLR loci (TLR1LB, TLR2A, TLR3, TLR4, TLR5, TLR7, and TLR15). Using a variety of metrics (SNPs, heterozygosity, nucleotides, haplotypes), our analyses showed that genetic diversity was lower at 4 of the 7 TLR loci in the vulnerable Chinese egret compared to the more common little egret (Egretta garzetta). The selection test indicated TLRs, except for TLR5, were under purifying selection in TLR evolution, suggesting that low TLR genetic diversity in the Chinese egret may be caused by purifying selection. Moreover, analysis of molecular variance indicated low but significant population differentiation among four populations at all of the TLR loci in this egret. However, some comparisons based on fixation index analyses did not show significant population differentiation, and Bayesian clustering showed admixture. Our finding suggested that these four populations of the Chinese egret in China may be considered a single unit for conservation planning. These results, the new report of TLR genetic diversity in a long-distance migratory vulnerable Ardeid species, will provide fundamental TLR information for further studies on the conservation genetics of the Chinese egret and other Ardeids.
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Affiliation(s)
- Wei Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Xiaoping Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Wenzhen Fang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
| | - Xiaolin Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, People’s Republic of China
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Tsang SM, Wiantoro S, Veluz MJ, Sugita N, Nguyen YL, Simmons NB, Lohman DJ. Dispersal out of Wallacea spurs diversification of Pteropus flying foxes, the world's largest bats (Mammalia: Chiroptera). JOURNAL OF BIOGEOGRAPHY 2020; 47:527-537. [PMID: 33041434 PMCID: PMC7546435 DOI: 10.1111/jbi.13750] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 10/04/2019] [Indexed: 05/25/2023]
Abstract
AIM Islands provide opportunities for isolation and speciation. Many landmasses in the Indo-Australian Archipelago (IAA) are oceanic islands, and founder-event speciation is expected to be the predominant form of speciation of volant taxa on these islands. We studied the biogeographic history of flying foxes, a group with many endemic species and a predilection for islands, to test this hypothesis and infer the biogeographic origin of the group. LOCATION Australasia, Indo-Australian Archipelago, Madagascar, Pacific Islands. TAXON Pteropus (Pteropodidae). METHODS To infer the biogeographic history of Pteropus, we sequenced up to 6169 bp of genetic data from 10 markers and reconstructed a multilocus species tree of 34 currently recognized Pteropus species and subspecies with 3 Acerodon outgroups using BEAST and subsequently estimated ancestral areas using models implemented in BioGeoBEARS. RESULTS Species-level resolution was occasionally low because of slow rates of molecular evolution and/or recent divergences. Older divergences, however, were more strongly supported and allow the evolutionary history of the group to be inferred. The genus diverged in Wallacea from its common ancestor with Acerodon; founder-event speciation out of Wallacea was a common inference. Pteropus species in Micronesia and the western Indian Ocean were also inferred to result from founder-event speciation. MAIN CONCLUSIONS Dispersal between regions of the IAA and the islands found therein fostered diversification of Pteropus throughout the IAA and beyond. Dispersal in Pteropus is far higher than in most other volant taxa studied to date, highlighting the importance of inter-island movement in the biogeographic history of this large clade of large bats.
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Affiliation(s)
- Susan M. Tsang
- Biology Department, City College, City University of New York, NY 10031, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, NY 10034, USA
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, NY 10024, USA
- Mammalogy Section, National Museum of Natural History, Manila 1000, Philippines
| | - Sigit Wiantoro
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences-LIPI, Bogor 16911, Indonesia
| | - Maria Josefa Veluz
- Mammalogy Section, National Museum of Natural History, Manila 1000, Philippines
| | - Norimasa Sugita
- Department of Zoology, National Museum of Nature and Science, Tokyo, Tsukuba, Ibaraki 305-0005, Japan
- National Institute for Environmental Studies, Tokyo, Tsukuba, Ibaraki 305-8506, Japan
| | - Y-Lan Nguyen
- Biology Department, City College, City University of New York, NY 10031, USA
- Macaulay Honors College, City University of New York, NY 10021, USA
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, NY 10024, USA
| | - David J. Lohman
- Biology Department, City College, City University of New York, NY 10031, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, NY 10034, USA
- Entomology Section, National Museum of Natural History, Manila 1000, Philippines
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10
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Olival KJ, Latinne A, Islam A, Epstein JH, Hersch R, Engstrand RC, Gurley ES, Amato G, Luby SP, Daszak P. Population genetics of fruit bat reservoir informs the dynamics, distribution and diversity of Nipah virus. Mol Ecol 2019; 29:970-985. [PMID: 31652377 DOI: 10.1111/mec.15288] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 12/26/2022]
Abstract
The structure and connectivity of wildlife host populations may influence zoonotic disease dynamics, evolution and therefore spillover risk to people. Fruit bats in the genus Pteropus, or flying foxes, are the primary natural reservoir for henipaviruses-a group of emerging paramyxoviruses that threaten livestock and public health. In Bangladesh, Pteropus medius is the reservoir for Nipah virus-and viral spillover has led to human fatalities nearly every year since 2001. Here, we use mitochondrial DNA and nuclear microsatellite markers to measure the population structure, demographic history and phylogeography of P. medius in Bangladesh. We combine this with a phylogeographic analysis of all known Nipah virus sequences and strains currently available to better inform the dynamics, distribution and evolutionary history of Nipah virus. We show that P. medius is primarily panmictic, but combined analysis of microsatellite and morphological data shows evidence for differentiation of two populations in eastern Bangladesh, corresponding to a divergent strain of Nipah virus also found in bats from eastern Bangladesh. Our demographic analyses indicate that a large, expanding population of flying foxes has existed in Bangladesh since the Late Pleistocene, coinciding with human population expansion in South Asia, suggesting repeated historical spillover of Nipah virus likely occurred. We present the first evidence of mitochondrial introgression, or hybridization, between P. medius and flying fox species found in South-East Asia (P. vampyrus and P. hypomelanus), which may help to explain the distribution of Nipah virus strains across the region.
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Affiliation(s)
| | | | | | | | - Rebecca Hersch
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Rachel C Engstrand
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | | | - George Amato
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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11
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Li JY, Zeng C, Yan GY, He LS. Characterization of the mitochondrial genome of an ancient amphipod Halice sp. MT-2017 (Pardaliscidae) from 10,908 m in the Mariana Trench. Sci Rep 2019; 9:2610. [PMID: 30796230 PMCID: PMC6385184 DOI: 10.1038/s41598-019-38735-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 12/11/2018] [Indexed: 01/02/2023] Open
Abstract
Small amphipods (Halice sp. MT-2017) with body length <1 cm were collected from the Challenger Deep (~10,920 m below sea level). The divergence time of their lineage was approximately 109 Mya, making this group ancient compared to others under study. The mitochondrial genome of Halice sp. shared the usual gene components of metazoans, comprising 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), and 2 ribosomal RNAs (rRNAs). The arrangement of these genes, however, differed greatly from that of other amphipods. Of the 15 genes that were rearranged with respect to the pancrustacean gene pattern, 12 genes (2 PCGs, 2 rRNAs, and 8 tRNAs) were both translocated and strand-reversed. In contrast, the mitochondrial genomes in other amphipods never show so many reordered genes, and in most instances, only tRNAs were involved in strand-reversion-coupled translocation. Other characteristics, including reversed strand nucleotide composition bias, relatively higher composition of non-polar amino acids, and lower evolutionary rate, were also identified. Interestingly, the latter two features were shared with another hadal amphipod, Hirondellea gigas, suggesting their possible associations with the adaptation to deep-sea extreme habitats. Overall, our data provided a useful resource for future studies on the evolutionary and adaptive mechanisms of hadal faunas.
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Affiliation(s)
- Jun-Yuan Li
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cong Zeng
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- Hunan Agricultural University, Changsha, Hunan, China
| | - Guo-Yong Yan
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Sheng He
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.
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12
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The contrasting genetic patterns of two sympatric flying fox species from the Comoros and the implications for conservation. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1111-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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13
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Tsang SM, Wiantoro S, Veluz MJ, Simmons NB, Lohman DJ. Low Levels of Population Structure among Geographically Distant Populations of Pteropus vampyrus (Chiroptera: Pteropodidae). ACTA CHIROPTEROLOGICA 2018. [DOI: 10.3161/15081109acc2018.20.1.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Susan M. Tsang
- Department of Biology, City College and the Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA
| | - Sigit Wiantoro
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Jl. Raya Jakarta-Bogor, Km. 46, Cibinong, 16911, Indonesia
| | - Maria Josefa Veluz
- Zoology Division, National Museum of the Philippines, Padres Burgos Ave, Ermita, Manila, 1000 Metro Manila, Philippines
| | - Nancy B. Simmons
- Department of Mammalogy, American Museum of Natural History, Central Park West and 79th Street, New York, NY, 10024, USA
| | - David J. Lohman
- Department of Biology, City College and the Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA
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14
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Unmasking the complexity of species identification in Australasian flying-foxes. PLoS One 2018; 13:e0194908. [PMID: 29634748 PMCID: PMC5892893 DOI: 10.1371/journal.pone.0194908] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/13/2018] [Indexed: 02/01/2023] Open
Abstract
Pteropus (flying-foxes) are a speciose group of non-echolocating large bats, with five extant Australian species and 24 additional species distributed amongst the Pacific Islands. In 2015, an injured flying-fox with unusual facial markings was found in Sydney, Australia, following severe and widespread storms. Based on an initial assessment, the individual belonged to Pteropus but could not be readily identified to species. As a consequence, four hypotheses for its identification/origin were posited: the specimen represented (1) an undescribed Australian species; or (2) a morphological variant of a recognised Australian species; or (3) a hybrid individual; or (4) a vagrant from the nearby Southwest Pacific Islands. We used a combination of morphological and both mitochondrial- and nuclear DNA-based identification methods to assess these hypotheses. Based on the results, we propose that this morphologically unique Pteropus most likely represents an unusual P. alecto (black flying-fox) potentially resulting from introgression from another Pteropus species. Unexpectedly, this individual, and the addition of reference sequence data from newly vouchered specimens, revealed a previously unreported P. alecto mitochondrial DNA lineage. This lineage was distinct from currently available haplotypes. It also suggests long-term hybridisation commonly occurs between P. alecto and P. conspicillatus (spectacled flying-fox). This highlights the importance of extensive reference data, and the inclusion of multiple vouchered specimens for each species to encompass both intraspecific and interspecific variation to provide accurate and robust species identification. Moreover, our additional reference data further demonstrates the complexity of Pteropus species relationships, including hybridisation, and potential intraspecific biogeographical structure that may impact on their management and conservation.
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15
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Zhang B, Zhang Y, Wang X, Zhang H, Lin Q. The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment. Ecol Evol 2017; 7:4951-4962. [PMID: 28690821 PMCID: PMC5496520 DOI: 10.1002/ece3.3067] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/13/2017] [Accepted: 04/24/2017] [Indexed: 01/14/2023] Open
Abstract
The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep‐sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein‐coding genes and two ribosomal RNAs. However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon‐like noncanonical open reading frames (ORFs), and a control region‐like (CR‐like) element. All of the mitochondrial genes were coded by the same strand (the H‐strand). The genetic order and orientation were identical to those of most sequenced actiniarians. Phylogenetic analyses showed that this species was closely related to Bolocera tuediae. Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp. were positively selected sites. By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes. This study may provide some clues regarding the adaptation of Bolocera sp. to the deep‐sea environment.
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Affiliation(s)
- Bo Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yan‐Hong Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hui‐Xian Zhang
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio‐Resources and EcologySouth China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
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Phalen DN, Hall J, Ganesh G, Hartigan A, Smith C, De Jong C, Field H, Rose K. Genetic diversity and phylogeny of the Christmas Island flying fox (Pteropus melanotus natalis). J Mammal 2017. [DOI: 10.1093/jmammal/gyx001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Russell AL, Brown VA, Utzurrum RCB, Brooke AP, Wolf LA, Mccracken GF. Comparative Phylogeography of Pteropus samoensis and P. tonganus (Pteropodidae: Chiroptera) in the South Pacific. ACTA CHIROPTEROLOGICA 2016. [DOI: 10.3161/15081109acc2016.18.2.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Amy L. Russell
- Department of Biology, Grand Valley State University, Allendale, Michigan 49401, USA
| | - Veronica A. Brown
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Ruth C. B. Utzurrum
- Department of Marine and Wildlife Resources, Pago Pago, American Samoa 96899, USA
| | - Anne P. Brooke
- Department of Marine and Wildlife Resources, Pago Pago, American Samoa 96899, USA
| | - Lisa A. Wolf
- Department of Biology, University of Oregon, Eugene, Oregon 97403, USA
| | - Gary F. Mccracken
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
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Larsen PA, Hayes CE, Wilkins MA, Gomard Y, Sookhareea R, Yoder AD, Goodman SM. Population Genetics of the Mauritian Flying Fox,Pteropus niger. ACTA CHIROPTEROLOGICA 2014. [DOI: 10.3161/150811014x687251] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Each flying fox on its own branch: A phylogenetic tree for Pteropus and related genera (Chiroptera: Pteropodidae). Mol Phylogenet Evol 2014; 77:83-95. [DOI: 10.1016/j.ympev.2014.03.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/09/2014] [Accepted: 03/11/2014] [Indexed: 11/20/2022]
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20
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Okada A, Suzuki H, Inaba M, Horikoshi K, Shindo J. Genetic Structure and Cryptic Genealogy of the Bonin Flying FoxPteropus pselaphonRevealed by Mitochondrial DNA and Microsatellite Markers. ACTA CHIROPTEROLOGICA 2014. [DOI: 10.3161/150811014x683237] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Buden DW, Helgen KM, Wiles GJ. Taxonomy, distribution, and natural history of flying foxes (Chiroptera, Pteropodidae) in the Mortlock Islands and Chuuk State, Caroline Islands. Zookeys 2013:97-135. [PMID: 24194666 PMCID: PMC3817444 DOI: 10.3897/zookeys.345.5840] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/17/2013] [Indexed: 11/12/2022] Open
Abstract
The taxonomy, biology, and population status of flying foxes (Pteropus spp.) remain little investigated in the Caroline Islands, Micronesia, where multiple endemic taxa occur. Our study evaluated the taxonomic relationships between the flying foxes of the Mortlock Islands (a subgroup of the Carolines) and two closely related taxa from elsewhere in the region, and involved the first ever field study of the Mortlock population. Through a review of historical literature, the name Pteropus pelagicus Kittlitz, 1836 is resurrected to replace the prevailing but younger name Pteropus phaeocephalus Thomas, 1882 for the flying fox of the Mortlocks. On the basis of cranial and external morphological comparisons, Pteropus pelagicus is united taxonomically with Pteropus insularis "Hombron and Jacquinot, 1842" (with authority herein emended to Jacquinot and Pucheran 1853), and the two formerly monotypic species are now treated as subspecies - Pteropus pelagicus pelagicus in the Mortlocks, and Pteropus phaeocephalus insularis on the islands of Chuuk Lagoon and Namonuito Atoll. The closest relative of Pteropus pelagicus is Pteropus tokudae Tate, 1934, of Guam, which is best regarded as a distinct species. Pteropus pelagicus pelagicus is the only known resident bat in the Mortlock Islands, a chain of more than 100 atoll islands with a total land area of <12 km(2). Based on field observations in 2004, we estimated a population size of 925-1,200 bats, most of which occurred on Satawan and Lukunor Atolls, the two largest and southernmost atolls in the chain. Bats were absent on Nama Island and possibly extirpated from Losap Atoll in the northern Mortlocks. Resident Mortlockese indicated bats were more common in the past, but that the population generally has remained stable in recent years. Most Pteropus phaeocephalus pelagicus roosted alone or in groups of 5-10 bats; a roost of 27 was the largest noted. Diet is comprised of at least eight plant species, with breadfruit (Artocarpus spp.) being a preferred food. Records of females with young (April, July) and pregnant females (July) suggest an extended breeding season. Pteropus pelagicus pelagicus appears most threatened by the prospect of sea level rise associated with global climate change, which has the potential to submerge or reduce the size of atolls in the Mortlocks. Occasional severe typhoons probably temporarily reduce populations on heavily damaged atolls, but hunting and ongoing habitat loss are not current problems for the subspecies.
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Affiliation(s)
- Donald W Buden
- Division of Natural Sciences and Mathematics, College of Micronesia-FSM, P.O. Box 159, Kolonia, Pohnpei 96941, Federated States of Micronesia
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Oyler-McCance SJ, Valdez EW, O'Shea TJ, Fike JA. Genetic characterization of the Pacific sheath-tailed bat (Emballonura semicaudata rotensis) using mitochondrial DNA sequence data. J Mammal 2013. [DOI: 10.1644/13-mamm-a-006.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Ma H, Ma C, Li X, Xu Z, Feng N, Ma L. The complete mitochondrial genome sequence and gene organization of the mud crab (Scylla paramamosain) with phylogenetic consideration. Gene 2013; 519:120-7. [PMID: 23384716 DOI: 10.1016/j.gene.2013.01.028] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/14/2013] [Accepted: 01/17/2013] [Indexed: 11/24/2022]
Abstract
The complete mitochondrial genome is of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In the present study, we determined the complete mitochondrial genome DNA sequence of the mud crab (Scylla paramamosain) by 454 deep sequencing and Sanger sequencing approaches. The complete genome DNA was 15,824 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). Of 37 genes, twenty-three were encoded by the heavy strand (H-strand), while the other ones were encoded by light strand (L-strand). The gene order in the mitochondrial genome was largely identical to those obtained in most arthropods, although the relative position of gene tRNA(His) differed from other arthropods. Among 13 protein-coding genes, three (ATPase subunit 6 (ATP6), NADH dehydrogenase subunits 1 (ND1) and ND3) started with a rare start codon ATT, whereas, one gene cytochrome c oxidase subunit I (COI) ended with the incomplete stop codon TA. All 22 tRNAs could fold into a typical clover-leaf secondary structure, with the gene sizes ranging from 63 to 73 bp. The phylogenetic analysis based on 12 concatenated protein-coding genes showed that the molecular genetic relationship of 19 species of 11 genera was identical to the traditional taxonomy.
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Affiliation(s)
- Hongyu Ma
- Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China
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