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Nesi N, Tsagkogeorga G, Tsang SM, Nicolas V, Lalis A, Scanlon AT, Riesle-Sbarbaro SA, Wiantoro S, Hitch AT, Juste J, Pinzari CA, Bonaccorso FJ, Todd CM, Lim BK, Simmons NB, McGowen MR, Rossiter SJ. Interrogating Phylogenetic Discordance Resolves Deep Splits in the Rapid Radiation of Old World Fruit Bats (Chiroptera: Pteropodidae). Syst Biol 2021; 70:1077-1089. [PMID: 33693838 PMCID: PMC8513763 DOI: 10.1093/sysbio/syab013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/27/2021] [Accepted: 03/03/2021] [Indexed: 11/14/2022] Open
Abstract
The family Pteropodidae (Old World fruit bats) comprises $>$200 species distributed across the Old World tropics and subtropics. Most pteropodids feed on fruit, suggesting an early origin of frugivory, although several lineages have shifted to nectar-based diets. Pteropodids are of exceptional conservation concern with $>$50% of species considered threatened, yet the systematics of this group has long been debated, with uncertainty surrounding early splits attributed to an ancient rapid diversification. Resolving the relationships among the main pteropodid lineages is essential if we are to fully understand their evolutionary distinctiveness, and the extent to which these bats have transitioned to nectar-feeding. Here we generated orthologous sequences for $>$1400 nuclear protein-coding genes (2.8 million base pairs) across 114 species from 43 genera of Old World fruit bats (57% and 96% of extant species- and genus-level diversity, respectively), and combined phylogenomic inference with filtering by information content to resolve systematic relationships among the major lineages. Concatenation and coalescent-based methods recovered three distinct backbone topologies that were not able to be reconciled by filtering via phylogenetic information content. Concordance analysis and gene genealogy interrogation show that one topology is consistently the best supported, and that observed phylogenetic conflicts arise from both gene tree error and deep incomplete lineage sorting. In addition to resolving long-standing inconsistencies in the reported relationships among major lineages, we show that Old World fruit bats have likely undergone at least seven independent dietary transitions from frugivory to nectarivory. Finally, we use this phylogeny to identify and describe one new genus. [Chiroptera; coalescence; concordance; incomplete lineage sorting; nectar feeder; species tree; target enrichment.].
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Affiliation(s)
- Nicolas Nesi
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Susan M Tsang
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
- Zoology Section, National Museum of Natural History, Manila, Philippines
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Aude Lalis
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Annette T Scanlon
- School of Natural and Built Environments, University of South Australia, Mawson Lakes, SA, Australia
| | - Silke A Riesle-Sbarbaro
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Institute of Zoology, Zoological Society of London, London, UK
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Sigit Wiantoro
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Alan T Hitch
- Department of Wildlife, Fish, and Conservation Biology, University of California Davis, CA, USA
| | - Javier Juste
- Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio, Sevilla, Spain
| | | | | | - Christopher M Todd
- The Hawkesbury institute for the Environment, Western Sydney University, Australia
| | - Burton K Lim
- Royal Ontario Museum, Toronto, ON M5S 2C6, Canada
| | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, USA
| | - Michael R McGowen
- Department of Vertebrate Zoology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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2
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Isolation of a Novel Bat Rhabdovirus with Evidence of Human Exposure in China. mBio 2021; 13:e0287521. [PMID: 35164557 PMCID: PMC8844929 DOI: 10.1128/mbio.02875-21] [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: 11/24/2022] Open
Abstract
Bats are well-recognized reservoirs of zoonotic viruses. Several spillover events from bats to humans have been reported, causing severe epidemic or endemic diseases including severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), SARS-CoV, Middle East respiratory syndrome-CoV (MERS-CoV), henipaviruses, and filoviruses. In this study, a novel rhabdovirus species, provisionally named Rhinolophus rhabdovirus DPuer (DPRV), was identified from the horseshoe bat (Rhinolophus affinis) in Yunnan province, China, using next-generation sequencing. DPRV shedding in the spleen, liver, lung, and intestinal contents of wild bats with high viral loads was detected by real-time quantitative PCR, indicating that DPRV has tropism for multiple host tissues. Furthermore, DPRV can replicate in vitro in multiple mammalian cell lines, including BHK-21, A549, and MA104 cells, with the highest efficiency in hamster kidney cell line BHK-21, suggesting infectivity of DPRV in these cell line-derived hosts. Ultrastructure analysis revealed a characteristic bullet-shaped morphology and tightly clustered distribution of DPRV particles in the intracellular space. DPRV replicated efficiently in suckling mouse brains and caused death of suckling mice; death rates increased with passaging of DPRV in suckling mice. Moreover, 421 serum samples were collected from individuals who lived near the bat collection site and had fever symptoms within 1 year. DPRV-specific antibodies were detected in 20 (4.75%) human serum samples by indirect immunofluorescence assay. Furthermore, 10 (2.38%) serum samples were DPRV positive according to plaque reduction neutralization assay, which revealed potential transmission of DPRV from bats to humans and highlighted the potential public health risk. Potential vector association with DPRV was not found with negative viral RNA in bloodsucking arthropods. IMPORTANCE We identified a novel rhabdovirus from the horseshoe bat (Rhinolophus thomasi) in China with probable infectivity in humans. DPRV was isolated in vitro from several mammalian cell lines, indicating wide host tropism, excluding bats, of DPRV. DPRV replicated in the brains of suckling mice, and the death rate of suckling mice increased with passaging of DPRV in vivo. Serological tests indicated the possible infectivity of DPRV in humans and the potential transmission to humans. The present findings provide preliminary evidence for the potential risk of DPRV to public health. Additional studies with active surveillance are needed to address interspecies transmission and determine the pathogenicity of DPRV in humans.
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Almeida FC, Simmons NB, Giannini NP. A Species-Level Phylogeny of Old World Fruit Bats with a New Higher-Level Classification of the Family Pteropodidae. AMERICAN MUSEUM NOVITATES 2020. [DOI: 10.1206/3950.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Francisca Cunha Almeida
- Instituto de Ecología, Genética y Evolución de Buenos Aires – CONICET, Buenos Aires, Argentina
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York
| | - Norberto P. Giannini
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York
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Hassanin A, Bonillo C, Tshikung D, Pongombo Shongo C, Pourrut X, Kadjo B, Nakouné E, Tu VT, Prié V, Goodman SM. Phylogeny of African fruit bats (Chiroptera, Pteropodidae) based on complete mitochondrial genomes. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12373] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Alexandre Hassanin
- Institut Systématique Evolution Biodiversité (ISYEB) Sorbonne Université MNHN CNRS EPHE Paris France
| | - Céline Bonillo
- Muséum National d'Histoire NaturelleUMS 2700 2AD Paris France
| | - Didier Tshikung
- Faculté de Médecine Vétérinaire Université de Lubumbashi Lubumbashi Democratic Republic of the Congo
| | - Célestin Pongombo Shongo
- Faculté de Médecine Vétérinaire Université de Lubumbashi Lubumbashi Democratic Republic of the Congo
| | - Xavier Pourrut
- Institut de Recherche pour le Développement UR 224 MIVEGEC Marseille France
| | - Blaise Kadjo
- UFR Biosciences Université Félix Houphouet‐Boigny Abidjan Côte d'Ivoire
| | | | - Vuong Tan Tu
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Vincent Prié
- Institut Systématique Evolution Biodiversité (ISYEB) Sorbonne Université MNHN CNRS EPHE Paris France
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Riesle‐Sbarbaro SA, Amponsah‐Mensah K, de Vries S, Nicolas V, Lalis A, Suu‐Ire R, Cunningham AA, Wood JLN, Sargan DR. The Gambian epauletted fruit bat shows increased genetic divergence in the Ethiopian highlands and in an area of rapid urbanization. Ecol Evol 2018; 8:12803-12820. [PMID: 30619584 PMCID: PMC6308866 DOI: 10.1002/ece3.4709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022] Open
Abstract
The Gambian epauletted fruit bat (Epomophorus gambianus) is an abundant species that roosts in both urban and rural settings. The possible role of E. gambianus as a reservoir host of zoonotic diseases underlines the need to better understand the species movement patterns. So far, neither observational nor phylogenetic studies have identified the dispersal range or behavior of this species. Comparative analyses of mitochondrial and nuclear markers from 20 localities across the known distribution of E. gambianus showed population panmixia, except for the populations in Ethiopia and southern Ghana (Accra and Ve-Golokwati). The Ethiopian population may be ancestral and is highly divergent to the species across the rest of its range, possibly reflecting isolation of an ancient colonization along an east-west axis. Mitochondrial haplotypes in the Accra population display a strong signature of a past bottleneck event; evidence of either an ancient or recent bottleneck using microsatellite data, however, was not detected. Demographic analyses identified population expansion in most of the colonies, except in the female line of descent in the Accra population. The molecular analyses of the colonies from Ethiopia and southern Ghana show gender dispersal bias, with the mitochondrial DNA fixation values over ten times those of the nuclear markers. These findings indicate free mixing of the species across great distances, which should inform future epidemiological studies.
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Affiliation(s)
- Silke A. Riesle‐Sbarbaro
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
- Institute of ZoologyZoological Society of London, Regents ParkLondonUK
| | | | - Stefan de Vries
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
- Present address:
Poultry Research and DevelopmentMSD Animal HealthBoxmeerThe Netherlands
| | - Violaine Nicolas
- Institut Systématique Evolution Biodiversité (ISYEB)Sorbonne Université, MNHN, CNRS, EPHEParisFrance
| | - Aude Lalis
- Institut Systématique Evolution Biodiversité (ISYEB)Sorbonne Université, MNHN, CNRS, EPHEParisFrance
| | - Richard Suu‐Ire
- Centre for African WetlandsUniversity of GhanaLegon, AccraGhana
- Wildlife Division of the Forestry CommissionAccraGhana
| | | | - James L. N. Wood
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
| | - David R. Sargan
- Department of Veterinary MedicineUniversity of CambridgeCambridgeUK
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6
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Centeno-Cuadros A, Hulva P, Romportl D, Santoro S, Stříbná T, Shohami D, Evin A, Tsoar A, Benda P, Horáček I, Nathan R. Habitat use, but not gene flow, is influenced by human activities in two ecotypes of Egyptian fruit bat (Rousettus aegyptiacus). Mol Ecol 2017; 26:6224-6237. [DOI: 10.1111/mec.14365] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/05/2017] [Indexed: 12/20/2022]
Affiliation(s)
- A. Centeno-Cuadros
- Movement Ecology Laboratory; Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences; Hebrew University of Jerusalem; Jerusalem Israel
- Department of Molecular Biology and Biochemical Engineering; University Pablo de Olavide; Sevilla Spain
| | - P. Hulva
- Department of Zoology; Charles University; Prague Czech Republic
- Department of Biology and Ecology; University of Ostrava; Ostrava Czech Republic
| | - D. Romportl
- Department of Physical Geography and Geoecology; Charles University in Prague; Prague Czech Republic
| | - S. Santoro
- Department of Molecular Biology and Biochemical Engineering; University Pablo de Olavide; Sevilla Spain
- Department of Ethology and Biodiversity Conservation; Estación Biológica de Doñana (CSIC); Seville Spain
| | - T. Stříbná
- Department of Zoology; Charles University; Prague Czech Republic
| | - D. Shohami
- Movement Ecology Laboratory; Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences; Hebrew University of Jerusalem; Jerusalem Israel
| | - A. Evin
- Institut des Sciences de l'Evolution; Université de Montpellier; Montpellier France
| | - A. Tsoar
- Movement Ecology Laboratory; Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences; Hebrew University of Jerusalem; Jerusalem Israel
| | - P. Benda
- Department of Zoology; Charles University; Prague Czech Republic
- Department of Zoology; National Museum (Natural History); Prague Czech Republic
| | - I. Horáček
- Department of Zoology; Charles University; Prague Czech Republic
| | - R. Nathan
- Movement Ecology Laboratory; Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences; Hebrew University of Jerusalem; Jerusalem Israel
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7
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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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8
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Bat Systematics in the Light of Unconstrained Analyses of a Comprehensive Molecular Supermatrix. J MAMM EVOL 2016. [DOI: 10.1007/s10914-016-9363-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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9
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Hassanin A, Nesi N, Marin J, Kadjo B, Pourrut X, Leroy É, Gembu GC, Musaba Akawa P, Ngoagouni C, Nakouné E, Ruedi M, Tshikung D, Pongombo Shongo C, Bonillo C. Comparative phylogeography of African fruit bats (Chiroptera, Pteropodidae) provide new insights into the outbreak of Ebola virus disease in West Africa, 2014–2016. C R Biol 2016; 339:517-528. [DOI: 10.1016/j.crvi.2016.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/08/2016] [Accepted: 09/13/2016] [Indexed: 11/30/2022]
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10
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McKee CD, Hayman DTS, Kosoy MY, Webb CT. Phylogenetic and geographic patterns of bartonella host shifts among bat species. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 44:382-394. [PMID: 27473781 PMCID: PMC5025394 DOI: 10.1016/j.meegid.2016.07.033] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/11/2016] [Accepted: 07/25/2016] [Indexed: 01/08/2023]
Abstract
The influence of factors contributing to parasite diversity in individual hosts and communities are increasingly studied, but there has been less focus on the dominant processes leading to parasite diversification. Using bartonella infections in bats as a model system, we explored the influence of three processes that can contribute to bartonella diversification and lineage formation: (1) spatial correlation in the invasion and transmission of bartonella among bats (phylogeography); (2) divergent adaptation of bartonellae to bat hosts and arthropod vectors; and (3) evolutionary codivergence between bats and bartonellae. Using a combination of global fit techniques and ancestral state reconstruction, we found that codivergence appears to be the dominant process leading to diversification of bartonella in bats, with lineages of bartonellae corresponding to separate bat suborders, superfamilies, and families. Furthermore, we estimated the rates at which bartonellae shift bat hosts across taxonomic scales (suborders, superfamilies, and families) and found that transition rates decrease with increasing taxonomic distance, providing support for a mechanism that can contribute to the observed evolutionary congruence between bats and their associated bartonellae. While bartonella diversification is associated with host sympatry, the influence of this factor is minor compared to the influence of codivergence and there is a clear indication that some bartonella lineages span multiple regions, particularly between Africa and Southeast Asia. Divergent adaptation of bartonellae to bat hosts and arthropod vectors is apparent and can dilute the overall pattern of codivergence, however its importance in the formation of Bartonella lineages in bats is small relative to codivergence. We argue that exploring all three of these processes yields a more complete understanding of bat-bartonella relationships and the evolution of the genus Bartonella, generally. Application of these methods to other infectious bacteria and viruses could uncover common processes that lead to parasite diversification and the formation of host-parasite relationships.
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Affiliation(s)
- Clifton D McKee
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA; Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA.
| | - David T S Hayman
- Molecular Epidemiology and Public Health Laboratory, Infectious Disease Research Centre, Massey University, Palmerston North 4442, New Zealand
| | - Michael Y Kosoy
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Colleen T Webb
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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11
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Peel AJ, Baker KS, Hayman DTS, Suu-Ire R, Breed AC, Gembu GC, Lembo T, Fernández-Loras A, Sargan DR, Fooks AR, Cunningham AA, Wood JLN. Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats, Eidolon helvum. Sci Data 2016; 3:160049. [PMID: 27479120 PMCID: PMC4968192 DOI: 10.1038/sdata.2016.49] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 05/19/2016] [Indexed: 11/24/2022] Open
Abstract
Bats, including African straw-coloured fruit bats (Eidolon helvum), have been highlighted as reservoirs of many recently emerged zoonotic viruses. This common, widespread and ecologically important species was the focus of longitudinal and continent-wide studies of the epidemiological and ecology of Lagos bat virus, henipaviruses and Achimota viruses. Here we present a spatial, morphological, demographic, genetic and serological dataset encompassing 2827 bats from nine countries over an 8-year period. Genetic data comprises cytochrome b mitochondrial sequences (n=608) and microsatellite genotypes from 18 loci (n=544). Tooth-cementum analyses (n=316) allowed derivation of rare age-specific serologic data for a lyssavirus, a henipavirus and two rubulaviruses. This dataset contributes a substantial volume of data on the ecology of E. helvum and its viruses and will be valuable for a wide range of studies, including viral transmission dynamic modelling in age-structured populations, investigation of seasonal reproductive asynchrony in wide-ranging species, ecological niche modelling, inference of island colonisation history, exploration of relationships between island and body size, and various spatial analyses of demographic, morphometric or serological data.
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Affiliation(s)
- Alison J Peel
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK.,Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK.,Environmental Futures Research Institute, Griffith University, Brisbane, Queensland 4111 Australia
| | - Kate S Baker
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK.,Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK.,Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Institute for Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - David T S Hayman
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK.,Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK.,Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Private Bag, 11 222, Palmerston North 4442, New Zealand
| | - Richard Suu-Ire
- Wildlife Division, Ghana Forestry Commission, Accra, Ghana.,University of Ghana, Faculty of Animal Biology and Conservation Science, Box LG 571, Legon, Accra, Ghana
| | - Andrew C Breed
- Animal and Plant Health Agency (APHA), Addlestone, Surrey KT15 3NB, UK
| | - Guy-Crispin Gembu
- Faculté des Sciences, Université de Kisangani, 4, Avenue Kithima, commune Makiso, BP 2012, Kisangani, République Démocratique du Congo
| | - Tiziana Lembo
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, Scotland
| | - Andrés Fernández-Loras
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK.,Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, Madrid 28006, Spain
| | - David R Sargan
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Anthony R Fooks
- Animal and Plant Health Agency (APHA), Addlestone, Surrey KT15 3NB, UK
| | - Andrew A Cunningham
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - James L N Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
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12
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Cunhaalmeida F, Giannini NP, Simmons NB. The Evolutionary History of the African Fruit Bats (Chiroptera: Pteropodidae). ACTA CHIROPTEROLOGICA 2016. [DOI: 10.3161/15081109acc2016.18.1.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Vidgen ME, de Jong C, Rose K, Hall J, Field HE, Smith CS. Novel paramyxoviruses in Australian flying-fox populations support host-virus co-evolution. J Gen Virol 2015; 96:1619-25. [PMID: 25701824 DOI: 10.1099/vir.0.000099] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Understanding the diversity of henipaviruses and related viruses is important in determining the viral ecology within flying-fox populations and assessing the potential threat posed by these agents. This study sought to identify the abundance and diversity of previously unknown paramyxoviruses (UPVs) in Australian flying-fox species (Pteropus alecto, Pteropus scapulatus, Pteropus poliocephalus and Pteropus conspicillatus) and in the Christmas Island species Pteropus melanotus natalis. Using a degenerative reverse transcription-PCR specific for the L gene of known species of the genus Henipavirus and two closely related paramyxovirus genera Respirovirus and Morbillivirus, we identified an abundance and diversity of previously UPVs, with a representative 31 UPVs clustering in eight distinct groups (100 UPVs/495 samples). No new henipaviruses were identified. The findings were consistent with a hypothesis of co-evolution of paramyxoviruses and their flying-fox hosts. Quantification of the degree of co-speciation between host and virus (beyond the scope of this study) would strengthen this hypothesis.
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Affiliation(s)
- Miranda E Vidgen
- 1Queensland Centre of Emerging Infectious Diseases, Biosecurity Queensland, Department of Agriculture, Fisheries and Forestry, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia 2School of Health and Sports Science, University of Sunshine Coast, 90 Sippy Down Drive, Sippy Downs, Queensland 4556, Australia
| | - Carol de Jong
- 1Queensland Centre of Emerging Infectious Diseases, Biosecurity Queensland, Department of Agriculture, Fisheries and Forestry, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia
| | - Karrie Rose
- 3Australian Registry of Wildlife Health, Taronga Conservation Society Australia, PO Box 20, Mosman, NSW 2088, Australia 4School of Public Health, Tropical Medicine and Rehabilitation Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Jane Hall
- 3Australian Registry of Wildlife Health, Taronga Conservation Society Australia, PO Box 20, Mosman, NSW 2088, Australia
| | - Hume E Field
- 1Queensland Centre of Emerging Infectious Diseases, Biosecurity Queensland, Department of Agriculture, Fisheries and Forestry, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia 5EcoHealth Alliance, 460 West 34th Street, New York, NY 10001, USA
| | - Craig S Smith
- 1Queensland Centre of Emerging Infectious Diseases, Biosecurity Queensland, Department of Agriculture, Fisheries and Forestry, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia
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14
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Shi JJ, Chan LM, Peel AJ, Lai R, Yoder AD, Goodman SM. A Deep Divergence Time between Sister Species ofEidolon(Pteropodidae) with Evidence for Widespread Panmixia. ACTA CHIROPTEROLOGICA 2014. [DOI: 10.3161/150811014x687242] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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15
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Peel AJ, Sargan DR, Baker KS, Hayman DTS, Barr JA, Crameri G, Suu-Ire R, Broder CC, Lembo T, Wang LF, Fooks AR, Rossiter SJ, Wood JLN, Cunningham AA. Continent-wide panmixia of an African fruit bat facilitates transmission of potentially zoonotic viruses. Nat Commun 2014; 4:2770. [PMID: 24253424 PMCID: PMC3836177 DOI: 10.1038/ncomms3770] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 10/15/2013] [Indexed: 12/23/2022] Open
Abstract
The straw-coloured fruit bat, Eidolon helvum, is Africa’s most widely distributed and commonly hunted fruit bat, often living in close proximity to human populations. This species has been identified as a reservoir of potentially zoonotic viruses, but uncertainties remain regarding viral transmission dynamics and mechanisms of persistence. Here we combine genetic and serological analyses of populations across Africa, to determine the extent of epidemiological connectivity among E. helvum populations. Multiple markers reveal panmixia across the continental range, at a greater geographical scale than previously recorded for any other mammal, whereas populations on remote islands were genetically distinct. Multiple serological assays reveal antibodies to henipaviruses and Lagos bat virus in all locations, including small isolated island populations, indicating that factors other than population size and connectivity may be responsible for viral persistence. Our findings have potentially important public health implications, and highlight a need to avoid disturbances which may precipitate viral spillover.
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Affiliation(s)
- Alison J Peel
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.,Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - David R Sargan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Kate S Baker
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.,Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.,Wellcome Trust Sanger Institute, A1301, Hinxton, Cambridgeshire, CB101SA, UK
| | - David T S Hayman
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.,Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.,Wildlife Zoonoses and Vector-Borne Diseases Research Group, Department of Virology, Animal Health and Veterinary Laboratories Agency, Weybridge, New Haw, Addlestone, Surrey, KT15 3NB, UK.,Department of Biology, Colorado State University, Fort Collins, Colorado, CO 80523, USA.,Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Jennifer A Barr
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, 3220, Australia
| | - Gary Crameri
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, 3220, Australia
| | - Richard Suu-Ire
- Wildlife Division, Ghana Forestry Commission, Accra, Ghana.,University of Ghana, Faculty of Animal Biology and Conservation Science, Box LG 571, Legon, Accra, Ghana
| | - Christopher C Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, 20814-4799, USA
| | - Tiziana Lembo
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, U.K
| | - Lin-Fa Wang
- CSIRO Australian Animal Health Laboratory, Geelong, Victoria, 3220, Australia.,Duke-NUS Graduate Medical School, Singapore 169857
| | - Anthony R Fooks
- Department of Biology, Colorado State University, Fort Collins, Colorado, CO 80523, USA.,University of Clinical Infection, Microbiology and Immunology, Liverpool, L3 5TQ, UK
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - James L N Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Andrew A Cunningham
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
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16
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Nesi N, Kadjo B, Pourrut X, Leroy E, Pongombo Shongo C, Cruaud C, Hassanin A. Molecular systematics and phylogeography of the tribe Myonycterini (Mammalia, Pteropodidae) inferred from mitochondrial and nuclear markers. Mol Phylogenet Evol 2013; 66:126-37. [DOI: 10.1016/j.ympev.2012.09.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 09/14/2012] [Accepted: 09/15/2012] [Indexed: 10/27/2022]
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17
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Hulva P, Marešová T, Dundarova H, Bilgin R, Benda P, Bartonička T, Horáček I. Environmental margin and island evolution in Middle Eastern populations of the Egyptian fruit bat. Mol Ecol 2012; 21:6104-16. [PMID: 23094994 DOI: 10.1111/mec.12078] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 09/07/2012] [Accepted: 09/10/2012] [Indexed: 11/29/2022]
Abstract
Here, we present a study of the population genetic architecture and microevolution of the Egyptian fruit bat (Rousettus aegyptiacus) at the environmental margins in the Middle East using mitochondrial sequences and nuclear microsatellites. In contrast to the rather homogenous population structure typical of cave-dwelling bats in climax tropical ecosystems, a relatively pronounced isolation by distance and population diversification was observed. The evolution of this pattern could be ascribed to the complicated demographic history at higher latitudes related to the range margin fragmentation and complex geomorphology of the studied area. Lineages from East Africa and Arabia show divergent positions. Within the northwestern unit, the most marked pattern of the microsatellite data set is connected with insularity, as demonstrated by the separate status of populations from Saharan oases and Cyprus. These demes also exhibit a reduction in genetic variability, which is presumably connected with founder effects, drift and other potential factors related to island evolution as site-specific selection. Genetic clustering indicates a semipermeability of the desert barriers in the Sahara and Arabian Peninsula and a corridor role of the Nile Valley. The results emphasize the role of the island environment in restricting the gene flow in megabats, which is also corroborated by biogeographic patterns within the family, and suggests the possibility of nascent island speciation on Cyprus. Demographic analyses suggest that the colonization of the region was connected to the spread of agricultural plants; therefore, the peripatric processes described above might be because of or strengthened by anthropogenic changes in the environment.
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Affiliation(s)
- P Hulva
- Department of Zoology, Charles University, Viničná 7, 128 44, Prague 2, Czech Republic.
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18
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Almeida FC, Giannini NP, DeSalle R, Simmons NB. Evolutionary relationships of the old world fruit bats (Chiroptera, Pteropodidae): another star phylogeny? BMC Evol Biol 2011; 11:281. [PMID: 21961908 PMCID: PMC3199269 DOI: 10.1186/1471-2148-11-281] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 09/30/2011] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The family Pteropodidae comprises bats commonly known as megabats or Old World fruit bats. Molecular phylogenetic studies of pteropodids have provided considerable insight into intrafamilial relationships, but these studies have included only a fraction of the extant diversity (a maximum of 26 out of the 46 currently recognized genera) and have failed to resolve deep relationships among internal clades. Here we readdress the systematics of pteropodids by applying a strategy to try to resolve ancient relationships within Pteropodidae, while providing further insight into subgroup membership, by 1) increasing the taxonomic sample to 42 genera; 2) increasing the number of characters (to >8,000 bp) and nuclear genomic representation; 3) minimizing missing data; 4) controlling for sequence bias; and 5) using appropriate data partitioning and models of sequence evolution. RESULTS Our analyses recovered six principal clades and one additional independent lineage (consisting of a single genus) within Pteropodidae. Reciprocal monophyly of these groups was highly supported and generally congruent among the different methods and datasets used. Likewise, most relationships within these principal clades were well resolved and statistically supported. Relationships among the 7 principal groups, however, were poorly supported in all analyses. This result could not be explained by any detectable systematic bias in the data or incongruence among loci. The SOWH test confirmed that basal branches' lengths were not different from zero, which points to closely-spaced cladogenesis as the most likely explanation for the poor resolution of the deep pteropodid relationships. Simulations suggest that an increase in the amount of sequence data is likely to solve this problem. CONCLUSIONS The phylogenetic hypothesis generated here provides a robust framework for a revised cladistic classification of Pteropodidae into subfamilies and tribes and will greatly contribute to the understanding of character evolution and biogeography of pteropodids. The inability of our data to resolve the deepest relationships of the major pteropodid lineages suggests an explosive diversification soon after origin of the crown pteropodids. Several characteristics of pteropodids are consistent with this conclusion, including high species diversity, great morphological diversity, and presence of key innovations in relation to their sister group.
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Affiliation(s)
- Francisca C Almeida
- American Museum of Natural History, Division of Vertebrate Zoology, Department of Mammalogy, Central Park West at 79th Street, New York, NY 10024, USA
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park West at 79th Street, New York, NY 10024, USA
- Universitat de Barcelona, Departament de Genètica, Diagonal 645, Barcelona, 08028, Spain
| | - Norberto P Giannini
- American Museum of Natural History, Division of Vertebrate Zoology, Department of Mammalogy, Central Park West at 79th Street, New York, NY 10024, USA
- CONICET, Programa de Investigaciones de Biodiversidad Argentina, Universidad Nacional de Tucumán, Facultad de Ciencias Naturales e Instituto Miguel Lillo, Miguel Lillo 205, Tucumán, CP 4000, Argentina
| | - Rob DeSalle
- American Museum of Natural History, Sackler Institute for Comparative Genomics, Central Park West at 79th Street, New York, NY 10024, USA
| | - Nancy B Simmons
- American Museum of Natural History, Division of Vertebrate Zoology, Department of Mammalogy, Central Park West at 79th Street, New York, NY 10024, USA
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19
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Nesi N, Nakouné E, Cruaud C, Hassanin A. DNA barcoding of African fruit bats (Mammalia, Pteropodidae). The mitochondrial genome does not provide a reliable discrimination between Epomophorus gambianus and Micropteropus pusillus. C R Biol 2011; 334:544-54. [DOI: 10.1016/j.crvi.2011.05.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 05/18/2011] [Accepted: 05/18/2011] [Indexed: 10/18/2022]
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20
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Goodman SM, Chan LM, Nowak MD, Yoder AD. Phylogeny and biogeography of western Indian Ocean Rousettus (Chiroptera: Pteropodidae). J Mammal 2010; 91:593-606. [PMID: 32287379 PMCID: PMC7108659 DOI: 10.1644/09-mamm-a-283.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 12/29/2009] [Indexed: 11/17/2022] Open
Abstract
We examined patterns of genetic variation in Rousettus madagascariensis from Madagascar and R. obliviosus from the Comoros (Grande Comore, Anjouan, and Mohéli). Genetic distances among individuals on the basis of 1,130 base pairs of the mitochondrial cytochrome b (Cytb) locus were estimated from specimens collected from 17 sites on Madagascar, 3 sites on Grande Comore, 3 sites on Anjouan, and 2 sites on Mohéli. We observed little variation in Madagascar and nearshore island samples (maximum 1.1%) and interisland Comoros samples (maximum 1.8%). In contrast, pairwise distances between different sampled sites on Madagascar and the Comoros varied from 8.5% to 13.2%. For 131 Malagasy animals, 69 unique haplotypes were recovered with 86 variable sites, and for 44 Comorian individuals, 17 unique haplotypes were found with 30 variable sites. No haplotype was shared between Madagascar and the Comoros, adding to previous morphological evidence that these 2 populations should be considered separate species. Cytb data showed that Rousettus populations of Madagascar (including nearshore islands) and the Comoros are respectively monophyletic and display no geographic structure in haplotype diversity, and that R. madagascariensis and R. obliviosus are strongly supported as sister to each other relative to other Rousettus species. Genotypic data from 6 microsatellite loci confirm lack of geographic structure in either of the 2 species. In pairwise tests of population differentiation, the only significant values were between samples from the Comoro Islands and Madagascar (including nearshore islands). Estimates of current and historical demographic parameters support population expansion in both the Comoros and Madagascar. These data suggest a more recent and rapid demographic expansion in Madagascar in comparison with greater population stability on the Comoros. On the basis of available evidence, open-water crossings approaching 300 km seem rarely traversed by Rousettus, and, if successful, can result in genetic isolation and subsequent differentiation.
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Affiliation(s)
- Steven M. Goodman
- Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605, USA, and Vahatra, BP 3972, Antananarivo 101, Madagascar
| | - Lauren M. Chan
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
| | - Michael D. Nowak
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
| | - Anne D. Yoder
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
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21
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Almeida FC, Giannini NP, DeSalle R, Simmons NB. The phylogenetic relationships of cynopterine fruit bats (Chiroptera: Pteropodidae: Cynopterinae). Mol Phylogenet Evol 2009; 53:772-83. [PMID: 19660560 DOI: 10.1016/j.ympev.2009.07.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Revised: 07/25/2009] [Accepted: 07/29/2009] [Indexed: 10/20/2022]
Abstract
The subfamily Cynopterinae comprises ca. 24 species of pteropodid bats (Family Pteropodidae) distributed exclusively in South and Southeast Asia. Although some studies have supported monophyly of the subfamily, molecular analyses have produced contradictory results and there has been little agreement on relationships of cynopterines to other megabat groups. However, no previous studies have included a complete sampling of cynopterine genera. Here we describe a phylogenetic analysis of Cynopterinae based on more than 6000 bp from six different genes sampled in representatives of all 14 recognized genera. Our results support the monophyly of Cynopterinae but refute a close relationship of cynopterines with Nyctimeninae. Within Cynopterinae, our analyses consistently recovered two monophyletic clades, which we recommend be recognized formally as tribes: Cynopterini and Balionycterini. Biogeographic analyses indicate a Sundaland origin of the Cynopterinae and divergence date estimates suggest different timing of diversification of the two major cynopterine clades.
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Affiliation(s)
- Francisca C Almeida
- American Museum of Natural History, Division of Vertebrate Zoology, Department of Mammalogy, Central Park West at 79th Street, New York, NY 10024, USA.
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22
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Multiple colonisations of the western Indian Ocean by Pteropus fruit bats (Megachiroptera: Pteropodidae): The furthest islands were colonised first. Mol Phylogenet Evol 2009; 51:294-303. [DOI: 10.1016/j.ympev.2009.02.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 02/08/2009] [Accepted: 02/16/2009] [Indexed: 11/20/2022]
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23
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Characterization of 22 microsatellite marker loci in the Madagascar rousette (Rousettus madagascariensis). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9679-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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24
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Esselstyn JA, Garcia HJD, Saulog MG, Heaney LR. A New Species ofDesmalopex(Pteropodidae) from the Philippines, with a Phylogenetic Analysis of the Pteropodini. J Mammal 2008. [DOI: 10.1644/07-mamm-a-285.1] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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25
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JUSTE JAVIER, IBÁÑEZ CARLOS, MACHORDOM ANNIE. Morphological and allozyme variation of Eidolon helvum (Mammalia: Megachiroptera) in the islands of the Gulf of Guinea. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2000.tb01262.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Peterson AT, Papeş M, Carroll DS, Leirs H, Johnson KM. Mammal Taxa Constituting Potential Coevolved Reservoirs of Filoviruses. J Mammal 2007. [DOI: 10.1644/06-mamm-a-280r1.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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27
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Dubey S, Salamin N, Ohdachi SD, Barrière P, Vogel P. Molecular phylogenetics of shrews (Mammalia: Soricidae) reveal timing of transcontinental colonizations. Mol Phylogenet Evol 2007; 44:126-37. [DOI: 10.1016/j.ympev.2006.12.002] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Revised: 11/08/2006] [Accepted: 12/07/2006] [Indexed: 10/23/2022]
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28
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Leader N, Mokady O, Yom-Tov Y. Indirect flight of an African bat to Israel: an example of the potential for zoonotic pathogens to move between continents. Vector Borne Zoonotic Dis 2006; 6:347-50. [PMID: 17187568 DOI: 10.1089/vbz.2006.6.347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The transmission of harmful pathogens during commercial air flights is an increasing health concern. A potential, yet relatively overlooked source of zoonotic infectious diseases involves collisions of birds and bats with aircraft and long distance transport of their carcasses. We report a case of aerial transportation of the remains of an African fruit bat over three continents, following a collision with an aircraft, and demonstrate the relative ease with which zoonotic pathogens, such as rabies virus or other viruses associated with bats, may cross national boundaries and continents even. Improper handling and disposal of animal remains by airport personnel, may lead to exposure of both humans and local fauna to exotic pathogens. This in turn may trigger an epidemic with potentially devastating results.
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Affiliation(s)
- Noam Leader
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.
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29
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Gaubert P, Cordeiro-Estrela P. Phylogenetic systematics and tempo of evolution of the Viverrinae (Mammalia, Carnivora, Viverridae) within feliformians: Implications for faunal exchanges between Asia and Africa. Mol Phylogenet Evol 2006; 41:266-78. [PMID: 16837215 DOI: 10.1016/j.ympev.2006.05.034] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Revised: 04/03/2006] [Accepted: 05/19/2006] [Indexed: 11/24/2022]
Abstract
We reconstructed the phylogeny of the subfamily Viverrinae (Mammalia, Carnivora, Viverridae) using a approximately 3kb data set in order to reassess timing and patterns of faunal exchanges between Asia and Africa. Maximum parsimony, maximum likelihood, and Bayesian analyses of separated and combined matrices (cytochrome b, transthyretin intron I and IRBP exon 1 [IRBP1]) recovered all the well-supported relationships within feliformian lineages. In addition, IRBP1 supported paraphyly of genus Herpestes and contributed to the resolution of equivocal hypotheses within Viverridae, including (1) the monophyly of Viverrinae, and (2) Viverricula sister-group of the other terrestrial civets (Civettictis and Viverra). The combined analysis yielded a robust phylogeny, recovering monophyly of Prionodontidae and yielding high posterior probabilities for nodes (1) (Prionodontidae, Felidae) and (2) ((Felidae, Prionodontidae), ((Hyaenidae, (Herpestidae, Eupleridae)), Viverridae)). Using a fossil cross-validation method, we estimated the emergence of Viverridae at 34.29Myr, with a separation between the three traditional subfamilies Hemigalinae, Paradoxurinae, and Viverrinae during the Late Oligocene-Early Miocene. The terrestrial civets and the splits between (1) Civettictis and Viverra and (2) Poiana and Genetta were estimated to appear during the Middle Miocene. Parsimony- and maximum likelihood-based methods yielded unambiguous ancestral area reconstructions, including the Asian origin of the family Viverridae, the subfamily Viverrinae, the terrestrial civets and the clade (Civettictis, Viverra). On the grounds of genetic distances, morphological divergence, and divergence time estimates, we propose the erection of the subfamily Genettinae (including Genetta and Poiana). Our analyses suggested two independent migration events from Asia to Africa, during the Middle Miocene (Civettictis) and between the Late Oligocene and Middle Miocene (Genettinae). These results are in agreement with the hypothesis of Miocene routes from Asia to Africa-via the Arabian microplate-that would have involved several independent events of migrations. Couched in the context of the viverrid fossil record, our study calls for a revision of the paleontological data in order to fully appreciate the complexity of Afro-Asian faunal exchanges.
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Affiliation(s)
- Philippe Gaubert
- Estación Biológica de Doñana (CSIC), Departamento de Biología Aplicada, Avenida María Luisa s/n Pabellón del Perú, 41013 Sevilla, Spain.
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30
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Roberts TE. History, ocean channels, and distance determine phylogeographic patterns in three widespread Philippine fruit bats (Pteropodidae). Mol Ecol 2006; 15:2183-99. [PMID: 16780434 DOI: 10.1111/j.1365-294x.2006.02928.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The comparative phylogeography of widespread, codistributed species provides unique insights into regional biodiversity and diversification patterns. I used partial DNA sequences of the mitochondrial genes ND2 and cyt b to investigate phylogeographic structure in three widespread Philippine fruit bats. Ptenochirus jagori is endemic to the oceanic region of the Philippines and is most abundant in lowland primary forest. Macroglossus minimus and Cynopterus brachyotis are most common in disturbed and open habitats and are not endemic. In all three, genetic differentiation is present at multiple spatial scales and is associated to some degree with Pleistocene landbridge island groups. In P. jagori and C. brachyotis, genetic distance is correlated with geographic distance; in C. brachyotis and M. minimus, it is correlated with the sea-crossing distance between islands. P. jagori has the least overall genetic structure of these three species, whereas C. brachyotis and M. minimus have more geographic association among haplotypes, suggesting that phylogeographic patterns are linked to ecology and habitat preference. However, contrary to expectation, the two widespread, disturbed habitat species have more structure than the endemic species. Mismatch distributions suggest rapid changes in effective population size in C. brachyotis and P. jagori, whereas M. minimus appears to be demographically more stable. Geologic and geographic history are important in structuring variation, and phylogeographic patterns are the result of dynamic long-term processes rather than simply reflecting current conditions.
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Affiliation(s)
- Trina E Roberts
- University of Chicago, Committee on Evolutionary Biology, 1025 E. 57th St., Culver Hall 402, Chicago, IL 60637, USA.
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31
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Giannini NP, Simmons NB. Conflict and congruence in a combined DNA-morphology analysis of megachiropteran bat relationships (Mammalia: Chiroptera: Pteropodidae). Cladistics 2005; 21:411-437. [DOI: 10.1111/j.1096-0031.2005.00083.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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32
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Giannini NP, Simmons NB. A phylogeny of megachiropteran bats (Mammalia: Chiroptera: Pteropodidae) based on direct optimization analysis of one nuclear and four mitochondrial genes. Cladistics 2005; 19:496-511. [DOI: 10.1111/j.1096-0031.2003.tb00385.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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33
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Stadelmann B, Herrera LG, Arroyo-Cabrales J, Flores-Martínez JJ, May BP, Ruedi M. Molecular Systematics of the Fishing Bat Myotis (Pizonyx) vivesi. J Mammal 2004. [DOI: 10.1644/1545-1542(2004)085<0133:msotfb>2.0.co;2] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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34
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Hulva P, Horáček I. Craseonycteris thonglongyai(Chiroptera: Craseonycteridae) is a Rhinolophoid: Molecular Evidence from Cytochromeb. ACTA CHIROPTEROLOGICA 2002. [DOI: 10.3161/001.004.0201] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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35
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Jones KE, Purvis A, MacLarnon A, Bininda-Emonds ORP, Simmons NB. A phylogenetic supertree of the bats (Mammalia: Chiroptera). Biol Rev Camb Philos Soc 2002; 77:223-59. [PMID: 12056748 DOI: 10.1017/s1464793101005899] [Citation(s) in RCA: 227] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We present the first estimate of the phylogenetic relationships among all 916 extant and nine recently extinct species of bats Mammalia: Chiroptera), a group that accounts for almost one-quarter of extant mammalian diversity. This phylogeny was derived by combining 105 estimates of bat phylogenetic relationships published since 1970 using the supertree construction technique of Matrix Representation with Parsimony (MRP). Despite the explosive growth in the number of phylogenetic studies of bats since 1990, phylogenetic relationships in the order have been studied non-randomly. For example, over one-third of all bat systematic studies to date have locused on relationships within Phyllostomidae, whereas relationships within clades such as Kerivoulinae and Murinae have never been studied using cladistic methods. Resolution in the supertree similarly differs among clades: overall resolution is poor (46.4%, of a fully bifurcating solution) but reaches 100% in some groups (e.g. relationships within Mormoopidae). The supertree analysis does not support a recent proposal that Microchiroptera is paraphyletic with respect to Megachiroptera, as the majority of source topologies support microbat monophyly. Although it is not a substitute for comprehensive phylogenetic analyses of primary molecular and morphological data, the bat supertree provides a useful tool for future phylogenetic comparative and macroevolutionary studies. Additionally, it identifies clades that have been little studied, highlights groups within which relationships are controversial, and like all phylogenetic studies, provides preliminary hypotheses that can form starting points for future phylogenetic studies of bats.
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Affiliation(s)
- Kate E Jones
- Department of Biology, Imperial College at Silwood Park, Ascot, Berkshire, UK.
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36
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Juste J, López-González C, Strauss RE. Analysis of asymmetries in the African fruit bats Eidolon helvum and Rousettus egyptiacus (Mammalia: Megachiroptera) from the islands of the Gulf of Guinea. II. Integration and levels of multivariate fluctuating asymmetry across a geographical range. J Evol Biol 2001. [DOI: 10.1046/j.1420-9101.2001.00299.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Quérouil S, Hutterer R, Barrière P, Colyn M, Kerbis Peterhans JC, Verheyen E. Phylogeny and evolution of African shrews (Mammalia: Soricidae) inferred from 16s rRNA sequences. Mol Phylogenet Evol 2001; 20:185-95. [PMID: 11476628 DOI: 10.1006/mpev.2001.0974] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Current phylogenetic hypotheses on the African Crocidurinae (Soricidae) are based upon morpho-anatomical, karyological, and allozyme studies. The present study attempts to resolve the interrelationships among African Crocidurinae and their relationships to Eurasian Crocidurinae and to the subfamily Soricinae, on the basis of partial mitochondrial 16s rRNA sequences (549 bp). This is the first molecular study to include all but one of the nine currently recognized African shrew genera. In agreement with current views, two major lineages emerge. The first lineage includes Myosorex and Congosorex and supports the existence of a myosoricine taxon. The second lineage includes the six remaining genera. The genus Sylvisorex appears to be polyphyletic, whereas species of the controversial genus Crocidura are monophyletic. The genus Suncus presumably originated in Africa. The monospecific genera Ruwenzorisorex and Scutisorex and the two representatives of Paracrocidura cluster with species of other genera. Grouping patterns of species from different continents suggest that there have been multiple exchanges between Africa and Eurasia. The time estimates of these exchanges, inferred from two independent fossil-based calibrations of a molecular clock, coincide with the time estimates for migration events in other mammalian taxa.
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Affiliation(s)
- S Quérouil
- Laboratoire Ethologie, Evolution, et Ecologie, Station Biologique, CNRS-U.M.R. 6552, Université de Rennes I, F-35380 Paimpont, France
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