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Kundu S, Kamalakannan M, Mukherjee T, Banerjee D, Kim HW. Genetic Characterization and Insular Habitat Enveloping of Endangered Leaf-Nosed Bat, Hipposideros nicobarulae (Mammalia: Chiroptera) in India: Phylogenetic Inference and Conservation Implication. Genes (Basel) 2023; 14:genes14030765. [PMID: 36981035 PMCID: PMC10048616 DOI: 10.3390/genes14030765] [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: 02/28/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
The Nicobar leaf-nosed Bat (Hipposideros nicobarulae) was described in the early 20th century; however, its systematic classification has been debated for over 100 years. This endangered and endemic species has achieved species status through morphological data in the last 10 years. However, the genetic information and phylogenetic relationships of H. nicobarulae remain neglected. The generated mitochondrial cytochrome b gene (mtCytb) sequences (438 bp) of H. nicobarulae contains 53.42-53.65% AT composition and 1.82% variable sites. The studied species, H. nicobarulae maintains an 8.1% to 22.6% genetic distance from other Hipposideros species. The genetic divergence estimated in this study is congruent with the concept of gene speciation in bats. The Bayesian and Maximum-Likelihood phylogenies clearly discriminated all Hipposideros species and showed a sister relationship between H. nicobarulae and H. cf. antricola. Current mtCytb-based investigations of H. nicobarulae have confirmed the species status at the molecular level. Further, the MaxEnt-based species distribution modelling illustrates the most suitable habitat of H. nicobarulae (294 km2), of which the majority (171 km2) is located on Great Nicobar Island. The present study suggests rigorous sampling across the range, taxonomic coverage, the generation of multiple molecular markers (mitochondrial and nuclear), as well as more ecological information, which will help in understanding population genetic structure, habitat suitability, and the implementation of appropriate conservation action plans for H. nicobarulae and other Hipposideros species.
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Affiliation(s)
- Shantanu Kundu
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
| | | | - Tanoy Mukherjee
- Agricultural and Ecological Research Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Dhriti Banerjee
- Western Ghat Regional Centre, Zoological Survey of India, Kozhikode 673006, India
- Zoological Survey of India, M Block, New Alipore, Kolkata 700053, India
| | - Hyun-Woo Kim
- Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
- Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
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Public Health Awareness on Bat Rabies among Bat Handlers and Persons Residing near Bat Roosts in Makurdi, Nigeria. Pathogens 2022; 11:pathogens11090975. [PMID: 36145407 PMCID: PMC9505307 DOI: 10.3390/pathogens11090975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Rabies is a neglected disease endemic in Asia and Africa but is still a significant public and veterinary health threat. Whilst a key delicacy for the local diet, bats are a natural reservoir host for many viral zoonotic agents including lyssaviruses, the causative agent of rabies. Studies on knowledge and practices linked to the disease will help to identify gaps and define preventive strategies that may subsequently result in a reduction and the potential elimination of human rabies. In order to assess the public health awareness of bat rabies among specific population groups in Makurdi (Nigeria), structured questionnaires (n = 154) were administered by face-to-face interviews to bat handlers and persons residing near bat roost sites. A total of 59.7% of the respondents were persons residing near bat roost sites, 13% were bat hunters, 25.3% were bat meat consumers and 1.9% were university researchers. Only 6.5% of respondents reported using some form of personal protective equipment (PPE) ranging from hand gloves, face/nose masks and protective boots to lab coats/coveralls while handling bats, whilst the majority (93.5%) did not use any form of PPE. With a mean knowledge score of 8.34 out of a possible 12 points, 50.6% of respondents had good knowledge of bats and their disease-carrying potential, 39.6% had fair knowledge, while 9.7% had poor knowledge. Log linear models showed significant associations between knowledge score and level of education, as well as knowledge score and occupation. The latter highlights the requirement to enhance public education among bat handlers and persons residing near bat roosts on the need to protect themselves better, while handling bats particularly during processing of bats for food and on steps to take when exposed to bites from bats.
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Li YN, Yu WH, Thapa S, Wu Y. First representative complete mitochondrial genome of the Taphozous melanopogon Temminck, 1841 (Chiroptera: Emballonuridae) from China. Mitochondrial DNA B Resour 2022; 7:1291-1293. [PMID: 35866141 PMCID: PMC9295812 DOI: 10.1080/23802359.2022.2081940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
In this study, we present the first representative complete Taphozous melanopogon mitochondrial genome from China. Its mitochondrial genome was assembled and annotated using MitoZ. The genome is a circular molecule of 16,566 bp in length, including 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes, and a control region. Although maximum-likelihood and Bayesian inference phylogenetic trees indicate that the super family Emballonuridea forms a sister taxon with Noctilionidea instead of Vespertilionidea, mitochondrial genes provide only part of the phylogenetic information, and phylogenetic inferences utilizing nuclear genes are needed in future toward resolving phylogenetic relationship among Vespertilionidea, Noctilionidea, and Emballonuridea.
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Affiliation(s)
- Yan-nan Li
- Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou University, Guangzhou, PR China
| | - Wen-hua Yu
- Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou University, Guangzhou, PR China
| | - Sanjan Thapa
- Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou University, Guangzhou, PR China
| | - Yi Wu
- Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou University, Guangzhou, PR China
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4
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Tian J, Sun J, Li D, Wang N, Wang L, Zhang C, Meng X, Ji X, Suchard MA, Zhang X, Lai A, Su S, Veit M. Emerging viruses: Cross-species transmission of Coronaviruses, Filoviruses, Henipaviruses and Rotaviruses from bats. Cell Rep 2022; 39:110969. [PMID: 35679864 PMCID: PMC9148931 DOI: 10.1016/j.celrep.2022.110969] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/10/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022] Open
Abstract
Emerging infectious diseases, especially if caused by bat-borne viruses, significantly affect public health and the global economy. There is an urgent need to understand the mechanism of interspecies transmission, particularly to humans. Viral genetics; host factors, including polymorphisms in the receptors; and ecological, environmental, and population dynamics are major parameters to consider. Here, we describe the taxonomy, geographic distribution, and unique traits of bats associated with their importance as virus reservoirs. Then, we summarize the origin, intermediate hosts, and the current understanding of interspecies transmission of Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2, Nipah, Hendra, Ebola, Marburg virus, and rotaviruses. Finally, the molecular interactions of viral surface proteins with host cell receptors are examined, and a comparison of these interactions in humans, intermediate hosts, and bats is conducted. This uncovers adaptive mutations in virus spike protein that facilitate cross-species transmission and risk factors associated with the emergence of novel viruses from bats.
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5
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A bibliometric analysis of research trends in bat echolocation studies between 1970 and 2021. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2022.101654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Abstract
Upon infection, DNA viruses can be sensed by pattern recognition receptors (PRRs), leading to the activation of type I and III interferons to block infection. Therefore, viruses must inhibit these signaling pathways, avoid being detected, or both. Papillomavirus virions are trafficked from early endosomes to the Golgi apparatus and wait for the onset of mitosis to complete nuclear entry. This unique subcellular trafficking strategy avoids detection by cytoplasmic PRRs, a property that may contribute to the establishment of infection. However, as the capsid uncoats within acidic endosomal compartments, the viral DNA may be exposed to detection by Toll-like receptor 9 (TLR9). In this study, we characterized two new papillomaviruses from bats and used molecular archeology to demonstrate that their genomes altered their nucleotide compositions to avoid detection by TLR9, providing evidence that TLR9 acts as a PRR during papillomavirus infection. Furthermore, we showed that TLR9, like other components of the innate immune system, is under evolutionary selection in bats, providing the first direct evidence for coevolution between papillomaviruses and their hosts. Finally, we demonstrated that the cancer-associated human papillomaviruses show a reduction in CpG dinucleotides within a TLR9 recognition complex.
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Chiropteran (Chiroptera; Mammalia) taxonomy in light of modern methods and approaches. RUSSIAN JOURNAL OF THERIOLOGY 2021. [DOI: 10.15298/rusjtheriol.20.2.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Potter JHT, Davies KTJ, Yohe LR, Sanchez MKR, Rengifo EM, Struebig M, Warren K, Tsagkogeorga G, Lim BK, dos Reis M, Dávalos LM, Rossiter SJ. Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution. Mol Biol Evol 2021; 38:3864-3883. [PMID: 34426843 PMCID: PMC8382914 DOI: 10.1093/molbev/msab028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dietary adaptation is a major feature of phenotypic and ecological diversification, yet the genetic basis of dietary shifts is poorly understood. Among mammals, Neotropical leaf-nosed bats (family Phyllostomidae) show unmatched diversity in diet; from a putative insectivorous ancestor, phyllostomids have radiated to specialize on diverse food sources including blood, nectar, and fruit. To assess whether dietary diversification in this group was accompanied by molecular adaptations for changing metabolic demands, we sequenced 89 transcriptomes across 58 species and combined these with published data to compare ∼13,000 protein coding genes across 66 species. We tested for positive selection on focal lineages, including those inferred to have undergone dietary shifts. Unexpectedly, we found a broad signature of positive selection in the ancestral phyllostomid branch, spanning genes implicated in the metabolism of all major macronutrients, yet few positively selected genes at the inferred switch to plantivory. Branches corresponding to blood- and nectar-based diets showed selection in loci underpinning nitrogenous waste excretion and glycolysis, respectively. Intriguingly, patterns of selection in metabolism genes were mirrored by those in loci implicated in craniofacial remodeling, a trait previously linked to phyllostomid dietary specialization. Finally, we show that the null model of the widely-used branch-site test is likely to be misspecified, with the implication that the test is too conservative and probably under-reports true cases of positive selection. Our findings point to a complex picture of adaptive radiation, in which the evolution of new dietary specializations has been facilitated by early adaptations combined with the generation of new genetic variation.
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Affiliation(s)
- Joshua H T Potter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Kalina T J Davies
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Laurel R Yohe
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Department of Earth and Planetary Science, Yale University, 210 Whitney Ave, New Haven, CT, USA
| | - Miluska K R Sanchez
- Escuela Profesional de Ciencias Biológicas, Universidad Nacional de Piura, Piura, Peru
| | - Edgardo M Rengifo
- Escola Superior de Agricultura ‘Luiz de Queiroz,’ Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
- Centro de Investigación Biodiversidad Sostenible (BioS), Lima, Peru
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Kim Warren
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Mario dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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Franzen J, Soto S, Fasel NJ, Rüegg-van den Broek P, Veiga IB. Malignant Peripheral Nerve Sheath Tumour in a Seba's Short-Tailed Bat (Carollia perspicillata). J Comp Pathol 2021; 184:72-76. [PMID: 33894882 DOI: 10.1016/j.jcpa.2021.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 10/21/2022]
Abstract
There are few reports of tumours in bats, despite the fact that members of the Chiroptera order include 22.4% of all currently known mammal species. We now describe a case of malignant peripheral nerve sheath tumour (MPNST) in an adult female Seba's short-tailed bat (Carollia perspicillata) from a private zoo in Switzerland. The macroscopical and histological findings indicated that the MPNST originated from a dorsal spinal nerve root sheath in the lumbar region and metastasized to the spleen. Immunohistochemical labelling for glial fibrillary acid protein, S100 protein, neuron specific enolase and synaptophysin was negative. The cytoplasm of a few neoplastic cells labelled for smooth muscle actin and desmin. To our knowledge, this is the first report of a PNST in a member of the Chiroptera order.
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Affiliation(s)
- Jan Franzen
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
| | - Sara Soto
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nicolas J Fasel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Inês B Veiga
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Ito K, Tu VT, Eiting TP, Nojiri T, Koyabu D. On the Embryonic Development of the Nasal Turbinals and Their Homology in Bats. Front Cell Dev Biol 2021; 9:613545. [PMID: 33834019 PMCID: PMC8021794 DOI: 10.3389/fcell.2021.613545] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/08/2021] [Indexed: 01/27/2023] Open
Abstract
Multiple corrugated cartilaginous structures are formed within the mammalian nasal capsule, eventually developing into turbinals. Due to its complex and derived morphology, the homologies of the bat nasal turbinals have been highly disputed and uncertain. Tracing prenatal development has been proven to provide a means to resolve homological problems. To elucidate bat turbinate homology, we conducted the most comprehensive study to date on prenatal development of the nasal capsule. Using diffusible iodine-based contrast-enhanced computed tomography (diceCT), we studied in detail the 3D prenatal development of various bat species and non-bat laurasiatherians. We found that the structure previously identified as “maxilloturbinal” is not the true maxilloturbinal and is only part of the ethmoturbinal I pars anterior. Our results also allowed us to trace the evolutionary history of the nasal turbinals in bats. The turbinate structures are overall comparable between laurasiatherians and pteropodids, suggesting that pteropodids retain the ancestral laurasiatherian condition. The absence of the ethmoturbinal I pars posterior in yangochiropterans and rhinolophoids has possibly occurred independently by convergent evolution.
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Affiliation(s)
- Kai Ito
- Department of Anatomy, Tissue and Cell Biology, School of Dental Medicine, Tsurumi University, Yokohama, Japan
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thomas P Eiting
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, United States
| | - Taro Nojiri
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,The University Museum, The University of Tokyo, Tokyo, Japan
| | - Daisuke Koyabu
- Research and Development Center for Precision Medicine, University of Tsukuba, Tsukuba, Japan.,Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong.,Department of Molecular Craniofacial Embryology, Tokyo Medical and Dental University, Tokyo, Japan
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11
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Endocranial Cast Anatomy of the Extinct Hipposiderid Bats Palaeophyllophora and Hipposideros (Pseudorhinolophus) (Mammalia: Chiroptera). J MAMM EVOL 2021. [DOI: 10.1007/s10914-020-09522-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Sun DL, Gao YZ, Ge XY, Shi ZL, Zhou NY. Special Features of Bat Microbiota Differ From Those of Terrestrial Mammals. Front Microbiol 2020; 11:1040. [PMID: 32582057 PMCID: PMC7284282 DOI: 10.3389/fmicb.2020.01040] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 04/27/2020] [Indexed: 01/08/2023] Open
Abstract
Bats (order Chiroptera) are one of the most diverse and widely distributed group of mammals with a close relationship to humans. Over the past few decades, a number of studies have been performed on bat viruses; in contrast, bacterial pathogens carried by bats were largely neglected. As more bacterial pathogens are being identified from bats, the need to study their natural microbiota is becoming urgent. In the current study, fecal samples of four bat species from different locations of China were analyzed for their microbiota composition. Together with the results of others, we concluded that bat microbiota is most commonly dominated by Firmicutes and Proteobacteria; the strict anaerobic phylum Bacteroidetes, which is dominant in other terrestrial mammals, especially humans and mice, is relatively rare in bats. This phenomenon was interpreted as a result of a highly specified gastrointestinal tract in adaptation to the flying lifestyle of bats. Further comparative study implied that bat microbiota resemble those of the order Carnivora. To discover potential bacterial pathogens, a database was generated containing the 16S rRNA gene sequences of known bacterial pathogens. Potential bacterial pathogens belonging to 12 genera were detected such as Salmonella, Shigella, and Yersinia, among which some have been previously reported in bats. This study demonstrated high resolution and repeatability in detecting organisms of rare existence, and the results could be used as guidance for future bacterial pathogen isolation.
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Affiliation(s)
- Dong-Lei Sun
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yi-Zhou Gao
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xing-Yi Ge
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,College of Biology, Hunan University, Changsha, China
| | - Zheng-Li Shi
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ning-Yi Zhou
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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13
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Gaudioso PJ, Martínez JJ, Barquez RM, Díaz MM. Evolution of scapula shape in several families of bats (Chiroptera, Mammalia). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12383] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Pablo J. Gaudioso
- Programa de Investigaciones de Biodiversidad Argentina (PIDBA) Facultad de Ciencias Naturales e Instituto Miguel Lillo PCMA (Programa de Conservación de los Murciélagos de Argentina) Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Universidad Nacional de Tucumán Tucumán Argentina
- Instituto de Ambiente de Montaña y Regiones Áridas (IAMRA) Universidad Nacional de Chilecito Chilecito Argentina
| | - Juan J. Martínez
- Instituto de Ecorregiones Andinas (INECOA; CONICET‐UNJu) San Salvador de Jujuy Argentina
| | - Rubén M. Barquez
- Programa de Investigaciones de Biodiversidad Argentina (PIDBA) Facultad de Ciencias Naturales e Instituto Miguel Lillo PCMA (Programa de Conservación de los Murciélagos de Argentina) Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Universidad Nacional de Tucumán Tucumán Argentina
| | - M. Mónica Díaz
- Programa de Investigaciones de Biodiversidad Argentina (PIDBA) Facultad de Ciencias Naturales e Instituto Miguel Lillo PCMA (Programa de Conservación de los Murciélagos de Argentina) Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Universidad Nacional de Tucumán Tucumán Argentina
- Fundación Miguel Lillo Tucumán Argentina
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14
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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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15
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Volleth M, Müller S, Heller KG, Fahr J. Cytogenetic Investigations in Emballonuroidea. II. Chromosome Painting in Nycteridae Reveals Cytogenetic Signatures Pointing to Common Ancestry of Nycteris and Emballonura. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2019.21.2.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Marianne Volleth
- Department of Human Genetics, Otto-von-Guericke University, Leipziger Strasse 44, 39120 Magdeburg, Germany
| | - Stefan Müller
- Institute of Human Genetics, Munich University Hospital, Ludwig-Maximilian University, Goethestr. 29, 80336 Munich, Germany
| | | | - Jakob Fahr
- Institute of Experimental Ecology, Ulm University, Albert Einstein Allee 11, 89069 Ulm, Germany
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16
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Mahmoud NE, Fahmy MM, Abuowarda MM. Additional morphometric and phylogenetic studies on Mothocya melanosticta (Isopoda: Cymothoidae) parasitizing the Red Sea Nemipterus randalli fish in Egypt. J Parasit Dis 2020; 44:289-298. [PMID: 32508403 DOI: 10.1007/s12639-020-01194-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/07/2020] [Indexed: 11/27/2022] Open
Abstract
Cymothoidae, Leach, 1818 (Crustacea: Isopoda) are ectoparasites of marine, brackish and freshwater fishes that are reported to induce deleterious tissue impacts on the infested fish hosts. The present study aimed for the first-time screening of Mothocya melanosticta collected from the red sea fish Nemipterus randalli in Egypt. Surveillance study was conducted for isopod infestation among the Red Sea fish N. randalli revealing a total infestation rate of 40.96% with the species identified as M. melanosticta. The parasite species was isolated from the branchial cavity and gills. Morphometric description was estimated using dissecting stereo-microscope, and scanning electron microscope (SEM) provided new additional features for the isolated species including the microtrich sensillum in the body cuticle and the fine structure of the mouth parts and body appendages. Mitochondrial COI gene of M. melanosticta female isolated in the present study from N. randalli was detected for the first time in Egypt and recorded in the GenBank (MK168807). The study showed that the detected isopod species represents one monophyletic group closely affiliated to the genospecies of M. melanosticta, and can be distinguished clearly from other isopods genospecies. Based on the genetic distance values, lower level of genetic divergence was indicated within the genospecies of the present M. melanosticta isolated from Egypt and the same species isolated from India. The present investigation recorded N. randalli fish as a new host for the isopod M. melanosticta in Egypt and provided additional morphological features through SEM as well as molecular characterization of this isopod species for the first time.
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Affiliation(s)
- Nisreen E Mahmoud
- Department of Parasitolgy, Faculty of Veterinary Medicine, Cairo University, Giza, 12211 Egypt
| | - Magdy M Fahmy
- Department of Parasitolgy, Faculty of Veterinary Medicine, Cairo University, Giza, 12211 Egypt
| | - Mai M Abuowarda
- Department of Parasitolgy, Faculty of Veterinary Medicine, Cairo University, Giza, 12211 Egypt
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17
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Gamage AM, Zhu F, Ahn M, Foo RJH, Hey YY, Low DHW, Mendenhall IH, Dutertre CA, Wang LF. Immunophenotyping monocytes, macrophages and granulocytes in the Pteropodid bat Eonycteris spelaea. Sci Rep 2020; 10:309. [PMID: 31941952 PMCID: PMC6962400 DOI: 10.1038/s41598-019-57212-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 12/12/2019] [Indexed: 02/07/2023] Open
Abstract
Bats are asymptomatic reservoir hosts for several highly pathogenic viruses. Understanding this enigmatic relationship between bats and emerging zoonotic viruses requires tools and approaches which enable the comparative study of bat immune cell populations and their functions. We show that bat genomes have a conservation of immune marker genes which delineate phagocyte populations in humans, while lacking key mouse surface markers such as Ly6C and Ly6G. Cross-reactive antibodies against CD44, CD11b, CD14, MHC II, and CD206 were multiplexed to characterize circulating monocytes, granulocytes, bone-marrow derived macrophages (BMDMs) and lung alveolar macrophages (AMs) in the cave nectar bat Eonycteris spelaea. Transcriptional profiling of bat monocytes and BMDMs identified additional markers – including MARCO, CD68, CD163, CD172α, and CD88 – which can be used to further characterize bat myeloid populations. Bat cells often resembled their human counterparts when comparing immune parameters that are divergent between humans and mice, such as the expression patterns of certain immune cell markers. A genome-wide comparison of immune-related genes also revealed a much closer phylogenetic relationship between bats and humans compared to rodents. Taken together, this study provides a set of tools and a comparative framework which will be important for unravelling viral disease tolerance mechanisms in bats.
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Affiliation(s)
- Akshamal M Gamage
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Matae Ahn
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Randy Jee Hiang Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Ying Ying Hey
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Dolyce H W Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Charles-Antoine Dutertre
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.,Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
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18
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Peng X, He X, Sun Y, Liang J, Xie H, Wang J, Zhang L. Difference in glucose tolerance between phytophagous and insectivorous bats. J Comp Physiol B 2019; 189:751-756. [PMID: 31691155 DOI: 10.1007/s00360-019-01242-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/30/2019] [Accepted: 10/16/2019] [Indexed: 11/30/2022]
Abstract
Bats are mostly insectivorous or phytophagous. It is hypothesized that bats are evolved from small insectivorous mammals. Therefore, the digestive and metabolic systems of phytophagous and insectivorous bats must have evolved differently to adapt to their dietary habits. To investigate the difference in sugar tolerance in bats, we determined changes in blood glucose levels after intraperitoneal (i.p.) injection of glucose in three species of phytophagous and four species of insectivorous bats under resting conditions. Results showed that phytophagous bats eliminated blood glucose faster than insectivorous bats. All three species of fruit bats reduced blood glucose to fasting levels within 30-45 min, whereas all insectivorous bats failed to lower blood glucose to fasting levels even 120 min after i.p. glucose injection. Taken together, results of this study suggest that bats have undergone adaptations and become diversified in dietary habits.
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Affiliation(s)
- Xingwen Peng
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, China
| | - Xiangyang He
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, China
| | - Yunxiao Sun
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, China
| | - Jie Liang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, China
| | - Huanwang Xie
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, China
| | - Junhua Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, China.
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19
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Solari S, Sotero-Caio CG, Baker RJ. Advances in systematics of bats: towards a consensus on species delimitation and classifications through integrative taxonomy. J Mammal 2019. [DOI: 10.1093/jmammal/gyy168] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Sergio Solari
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Cibele G Sotero-Caio
- Departamento de Genética, Universidade Federal de Pernambuco, Cidade Universitária, Recife, PE, Brazil
| | - Robert J Baker
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
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20
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Springer MS, Emerling CA, Gatesy J, Randall J, Collin MA, Hecker N, Hiller M, Delsuc F. Odontogenic ameloblast-associated (ODAM) is inactivated in toothless/enamelless placental mammals and toothed whales. BMC Evol Biol 2019; 19:31. [PMID: 30674270 PMCID: PMC6343362 DOI: 10.1186/s12862-019-1359-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 01/11/2019] [Indexed: 11/10/2022] Open
Abstract
Background The gene for odontogenic ameloblast-associated (ODAM) is a member of the secretory calcium-binding phosphoprotein gene family. ODAM is primarily expressed in dental tissues including the enamel organ and the junctional epithelium, and may also have pleiotropic functions that are unrelated to teeth. Here, we leverage the power of natural selection to test competing hypotheses that ODAM is tooth-specific versus pleiotropic. Specifically, we compiled and screened complete protein-coding sequences, plus sequences for flanking intronic regions, for ODAM in 165 placental mammals to determine if this gene contains inactivating mutations in lineages that either lack teeth (baleen whales, pangolins, anteaters) or lack enamel on their teeth (aardvarks, sloths, armadillos), as would be expected if the only essential functions of ODAM are related to tooth development and the adhesion of the gingival junctional epithelium to the enamel tooth surface. Results We discovered inactivating mutations in all species of placental mammals that either lack teeth or lack enamel on their teeth. A surprising result is that ODAM is also inactivated in a few additional lineages including all toothed whales that were examined. We hypothesize that ODAM inactivation is related to the simplified outer enamel surface of toothed whales. An alternate hypothesis is that ODAM inactivation in toothed whales may be related to altered antimicrobial functions of the junctional epithelium in aquatic habitats. Selection analyses on ODAM sequences revealed that the composite dN/dS value for pseudogenic branches is close to 1.0 as expected for a neutrally evolving pseudogene. DN/dS values on transitional branches were used to estimate ODAM inactivation times. In the case of pangolins, ODAM was inactivated ~ 65 million years ago, which is older than the oldest pangolin fossil (Eomanis, 47 Ma) and suggests an even more ancient loss or simplification of teeth in this lineage. Conclusion Our results validate the hypothesis that the only essential functions of ODAM that are maintained by natural selection are related to tooth development and/or the maintenance of a healthy junctional epithelium that attaches to the enamel surface of teeth. Electronic supplementary material The online version of this article (10.1186/s12862-019-1359-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA.
| | - Christopher A Emerling
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.,Department of Biology, Whittier College, Whittier, CA, 90602, USA
| | - John Gatesy
- Division of Vertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
| | - Jason Randall
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Matthew A Collin
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Nikolai Hecker
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Frédéric Delsuc
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
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21
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Simões BF, Foley NM, Hughes GM, Zhao H, Zhang S, Rossiter SJ, Teeling EC. As Blind as a Bat? Opsin Phylogenetics Illuminates the Evolution of Color Vision in Bats. Mol Biol Evol 2019; 36:54-68. [PMID: 30476197 PMCID: PMC6340466 DOI: 10.1093/molbev/msy192] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Through their unique use of sophisticated laryngeal echolocation bats are considered sensory specialists amongst mammals and represent an excellent model in which to explore sensory perception. Although several studies have shown that the evolution of vision is linked to ecological niche adaptation in other mammalian lineages, this has not yet been fully explored in bats. Recent molecular analysis of the opsin genes, which encode the photosensitive pigments underpinning color vision, have implicated high-duty cycle (HDC) echolocation and the adoption of cave roosting habits in the degeneration of color vision in bats. However, insufficient sampling of relevant taxa has hindered definitive testing of these hypotheses. To address this, novel sequence data was generated for the SWS1 and MWS/LWS opsin genes and combined with existing data to comprehensively sample species representing diverse echolocation types and niches (SWS1 n = 115; MWS/LWS n = 45). A combination of phylogenetic analysis, ancestral state reconstruction, and selective pressure analyses were used to reconstruct the evolution of these visual pigments in bats and revealed that although both genes are evolving under purifying selection in bats, MWS/LWS is highly conserved but SWS1 is highly variable. Spectral tuning analyses revealed that MWS/LWS opsin is tuned to a long wavelength, 555-560 nm in the bat ancestor and the majority of extant taxa. The presence of UV vision in bats is supported by our spectral tuning analysis, but phylogenetic analyses demonstrated that the SWS1 opsin gene has undergone pseudogenization in several lineages. We do not find support for a link between the evolution of HDC echolocation and the pseudogenization of the SWS1 gene in bats, instead we show the SWS1 opsin is functional in the HDC echolocator, Pteronotus parnellii. Pseudogenization of the SWS1 is correlated with cave roosting habits in the majority of pteropodid species. Together these results demonstrate that the loss of UV vision in bats is more widespread than was previously considered and further elucidate the role of ecological niche specialization in the evolution of vision in bats.
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Affiliation(s)
- Bruno F Simões
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
- School of Earth Science, University of Bristol, Bristol, United Kingdom
- School of Biological Science, The University of Adelaide, South Australia, Australia
| | - Nicole M Foley
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Graham M Hughes
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - Huabin Zhao
- Department of Ecology and Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Emma C Teeling
- UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
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22
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Jebb D, Foley NM, Whelan CV, Touzalin F, Puechmaille SJ, Teeling EC. Population level mitogenomics of long-lived bats reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing. Sci Rep 2018; 8:13634. [PMID: 30206380 PMCID: PMC6134106 DOI: 10.1038/s41598-018-31093-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/26/2018] [Indexed: 12/30/2022] Open
Abstract
Bats are the only mammals capable of true, powered flight, which drives an extremely high metabolic rate. The "Free Radical Theory of Ageing" (FTRA) posits that a high metabolic rate causes mitochondrial heteroplasmy and the progressive ageing phenotype. Contrary to this, bats are the longest-lived order of mammals given their small size and high metabolic rate. To investigate if bats exhibit increased mitochondrial heteroplasmy with age, we performed targeted, deep sequencing of mitogenomes and measured point heteroplasmy in wild, long lived Myotis myotis. Blood was sampled from 195 individuals, aged between <1 and at 6+ years old, and whole mitochondria deep-sequenced, with a subset sampled over multiple years. The majority of heteroplasmies were at a low frequency and were transitions. Oxidative mutations were present in only a small number of individuals, suggesting local oxidative stress events. Cohort data showed no significant increase in heteroplasmy with age, while longitudinal data from recaptured individuals showed heteroplasmy is dynamic, and does not increase uniformly over time. We show that bats do not suffer from the predicted, inevitable increase in heteroplasmy as posited by the FRTA, instead heteroplasmy was found to be dynamic, questioning its presumed role as a primary driver of ageing.
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Affiliation(s)
- David Jebb
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nicole M Foley
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor V Whelan
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Frédéric Touzalin
- Laboratoire Evolution et Diversité Biologique, Université Toulouse 3, Paul Sabatier, 31062, Toulouse Cedex 09, France
| | - Sebastien J Puechmaille
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Applied Zoology and Conservation, Zoological Institute, Greifswald University, Greifswald, Germany
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland.
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23
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Kries K, Barros MAS, Duytschaever G, Orkin JD, Janiak MC, Pessoa DMA, Melin AD. Colour vision variation in leaf-nosed bats (Phyllostomidae): Links to cave roosting and dietary specialization. Mol Ecol 2018; 27:3627-3640. [PMID: 30059176 DOI: 10.1111/mec.14818] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 06/15/2018] [Accepted: 06/21/2018] [Indexed: 11/30/2022]
Abstract
Bats are a diverse radiation of mammals of enduring interest for understanding the evolution of sensory specialization. Colour vision variation among species has previously been linked to roosting preferences and echolocation form in the suborder Yinpterochiroptera, yet questions remain about the roles of diet and habitat in shaping bat visual ecology. We sequenced OPN1SW and OPN1LW opsin genes for 20 species of leaf-nosed bats (family Phyllostomidae; suborder Yangochiroptera) with diverse roosting and dietary ecologies, along with one vespertilionid species (Myotis lavali). OPN1LW genes appear intact for all species, and predicted spectral tuning of long-wavelength opsins varied among lineages. OPN1SW genes appear intact and under purifying selection for Myotis lavali and most phyllostomid bats, with two exceptions: (a) We found evidence of ancient OPN1SW pseudogenization in the vampire bat lineage, and loss-of-function mutations in all three species of extant vampire bats; (b) we additionally found a recent, independently derived OPN1SW pseudogene in Lonchophylla mordax, a cave-roosting species. These mutations in leaf-nosed bats are independent of the OPN1SW pseudogenization events previously reported in Yinpterochiropterans. Therefore, the evolution of monochromacy (complete colour blindness) has occurred in both suborders of bats and under various evolutionary drivers; we find independent support for the hypothesis that obligate cave roosting drives colour vision loss. We additionally suggest that haematophagous dietary specialization and corresponding selection on nonvisual senses led to loss of colour vision through evolutionary sensory trade-off. Our results underscore the evolutionary plasticity of opsins among nocturnal mammals.
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Affiliation(s)
- Kelly Kries
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri
| | - Marília A S Barros
- Department of Physiology, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Gwen Duytschaever
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Joseph D Orkin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Mareike C Janiak
- Department of Anthropology, Rutgers University, New Brunswick, New Jersey
| | - Daniel M A Pessoa
- Department of Physiology, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada.,Department of Medical Genetics, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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24
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Donath A, Stadler PF. Split-inducing indels in phylogenomic analysis. Algorithms Mol Biol 2018; 13:12. [PMID: 30026791 PMCID: PMC6047143 DOI: 10.1186/s13015-018-0130-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 06/16/2018] [Indexed: 11/13/2022] Open
Abstract
Background Most phylogenetic studies using molecular data treat gaps in multiple sequence alignments as missing data or even completely exclude alignment columns that contain gaps. Results Here we show that gap patterns in large-scale, genome-wide alignments are themselves phylogenetically informative and can be used to infer reliable phylogenies provided the gap data are properly filtered to reduce noise introduced by the alignment method. We introduce here the notion of split-inducing indels (splids) that define an approximate bipartition of the taxon set. We show both in simulated data and in case studies on real-life data that splids can be efficiently extracted from phylogenomic data sets. Conclusions Suitably processed gap patterns extracted from genome-wide alignment provide a surprisingly clear phylogenetic signal and an allow the inference of accurate phylogenetic trees. Electronic supplementary material The online version of this article (10.1186/s13015-018-0130-7) contains supplementary material, which is available to authorized users.
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25
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Chromosomal Evolution in Chiroptera. Genes (Basel) 2017; 8:genes8100272. [PMID: 29027987 PMCID: PMC5664122 DOI: 10.3390/genes8100272] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 01/05/2023] Open
Abstract
Chiroptera is the second largest order among mammals, with over 1300 species in 21 extant families. The group is extremely diverse in several aspects of its natural history, including dietary strategies, ecology, behavior and morphology. Bat genomes show ample chromosome diversity (from 2n = 14 to 62). As with other mammalian orders, Chiroptera is characterized by clades with low, moderate and extreme chromosomal change. In this article, we will discuss trends of karyotypic evolution within distinct bat lineages (especially Phyllostomidae, Hipposideridae and Rhinolophidae), focusing on two perspectives: evolution of genome architecture, modes of chromosomal evolution, and the use of chromosome data to resolve taxonomic problems.
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26
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Gaudry MJ, Jastroch M, Treberg JR, Hofreiter M, Paijmans JLA, Starrett J, Wales N, Signore AV, Springer MS, Campbell KL. Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades. SCIENCE ADVANCES 2017; 3:e1602878. [PMID: 28706989 PMCID: PMC5507634 DOI: 10.1126/sciadv.1602878] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 06/21/2017] [Indexed: 05/08/2023]
Abstract
Mitochondrial uncoupling protein 1 (UCP1) is essential for nonshivering thermogenesis in brown adipose tissue and is widely accepted to have played a key thermoregulatory role in small-bodied and neonatal placental mammals that enabled the exploitation of cold environments. We map ucp1 sequences from 133 mammals onto a species tree constructed from a ~51-kb sequence alignment and show that inactivating mutations have occurred in at least 8 of the 18 traditional placental orders, thereby challenging the physiological importance of UCP1 across Placentalia. Selection and timetree analyses further reveal that ucp1 inactivations temporally correspond with strong secondary reductions in metabolic intensity in xenarthrans and pangolins, or in six other lineages coincided with a ~30 million-year episode of global cooling in the Paleogene that promoted sharp increases in body mass and cladogenesis evident in the fossil record. Our findings also demonstrate that members of various lineages (for example, cetaceans, horses, woolly mammoths, Steller's sea cows) evolved extreme cold hardiness in the absence of UCP1-mediated thermogenesis. Finally, we identify ucp1 inactivation as a historical contingency that is linked to the current low species diversity of clades lacking functional UCP1, thus providing the first evidence for species selection related to the presence or absence of a single gene product.
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Affiliation(s)
- Michael J. Gaudry
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Martin Jastroch
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Parkring 13, 85748 Garching, Germany
- Department of Animal Physiology, Faculty of Biology, Philipps University of Marburg, D-35032 Marburg, Germany
| | - Jason R. Treberg
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Michael Hofreiter
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | | | - James Starrett
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Anthony V. Signore
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Mark S. Springer
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Kevin L. Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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27
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Stern A, Yeh MT, Zinger T, Smith M, Wright C, Ling G, Nielsen R, Macadam A, Andino R. The Evolutionary Pathway to Virulence of an RNA Virus. Cell 2017; 169:35-46.e19. [PMID: 28340348 DOI: 10.1016/j.cell.2017.03.013] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 01/03/2017] [Accepted: 03/06/2017] [Indexed: 12/31/2022]
Abstract
Paralytic polio once afflicted almost half a million children each year. The attenuated oral polio vaccine (OPV) has enabled world-wide vaccination efforts, which resulted in nearly complete control of the disease. However, poliovirus eradication is hampered globally by epidemics of vaccine-derived polio. Here, we describe a combined theoretical and experimental strategy that describes the molecular events leading from OPV to virulent strains. We discover that similar evolutionary events occur in most epidemics. The mutations and the evolutionary trajectories driving these epidemics are replicated using a simple cell-based experimental setup where the rate of evolution is intentionally accelerated. Furthermore, mutations accumulating during epidemics increase the replication fitness of the virus in cell culture and increase virulence in an animal model. Our study uncovers the evolutionary strategies by which vaccine strains become pathogenic and provides a powerful framework for rational design of safer vaccine strains and for forecasting virulence of viruses. VIDEO ABSTRACT.
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Affiliation(s)
- Adi Stern
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv 6997801, Israel.
| | - Ming Te Yeh
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tal Zinger
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Matt Smith
- Division of Virology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - Caroline Wright
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Guy Ling
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Rasmus Nielsen
- Department of Integrative Biology; Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew Macadam
- Division of Virology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
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28
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Clozato CL, Miranda FR, Lara-Ruiz P, Collevatti RG, Santos FR. Population structure and genetic diversity of the giant anteater (Myrmecophaga tridactyla: Myrmecophagidae, Pilosa) in Brazil. Genet Mol Biol 2017; 40:50-60. [PMID: 28199447 PMCID: PMC5409771 DOI: 10.1590/1678-4685-gmb-2016-0104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/30/2016] [Indexed: 11/30/2022] Open
Abstract
The giant anteater (Myrmecophaga tridactyla, Pilosa, Linnaeus 1758)
belongs to the mammalian order Pilosa and presents a large distribution along South
America, occupying a great variety of habitats. It is listed in the IUCN Red List of
threatened species as Vulnerable. Despite threatened, there is a lack of studies
regarding its genetic variability. The aim of this study was to examine the genetic
diversity and patterns of genetic structure within remaining populations. We analyzed
77 individuals from seven different populations distributed in four biomes across
Brazil: Cerrado, Pantanal, Atlantic Forest and Amazon Forest. We sequenced two
mitochondrial markers (control region and Cyt-b) and two nuclear markers (AMELY and
RAG2). We found high genetic diversity within subpopulations from
National Parks of Serra da Canastra and Emas, both within the Cerrado biome, with
signs of population expansion. Besides, we found a notable population structure
between populations from the Cerrado/Pantanal and Amazon Forest biomes. This data is
a major contribution to the knowledge of the evolutionary history of the species and
to future management actions concerning its conservation.
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Affiliation(s)
- Camila L Clozato
- Laboratório de Biodiversidade e Evolução Molecular, Departamento de Biologia Geral, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.,Projeto Tamanduá, São Paulo, SP, Brazil
| | - Flávia R Miranda
- Laboratório de Biodiversidade e Evolução Molecular, Departamento de Biologia Geral, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.,Projeto Tamanduá, São Paulo, SP, Brazil
| | - Paula Lara-Ruiz
- Laboratório de Biodiversidade e Evolução Molecular, Departamento de Biologia Geral, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Rosane G Collevatti
- Laboratorio de Genética e Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás (UFG), Goiânia, GO, Brazil
| | - Fabrício R Santos
- Laboratório de Biodiversidade e Evolução Molecular, Departamento de Biologia Geral, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
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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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Chawana R, Patzke N, Alagaili AN, Bennett NC, Mohammed OB, Kaswera-Kyamakya C, Gilissen E, Ihunwo AO, Pettigrew JD, Manger PR. The Distribution of Ki-67 and Doublecortin Immunopositive Cells in the Brains of Three Microchiropteran Species, Hipposideros fuliginosus, Triaenops persicus, and Asellia tridens. Anat Rec (Hoboken) 2016; 299:1548-1560. [PMID: 27532288 DOI: 10.1002/ar.23460] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/24/2016] [Accepted: 06/09/2016] [Indexed: 01/26/2023]
Abstract
This study uses Ki-67 and doublecortin (DCX) immunohistochemistry to delineate potential neurogenic zones, migratory pathways, and terminal fields associated with adult neurogenesis in the brains of three microchiropterans. As with most mammals studied to date, the canonical subgranular and subventricular neurogenic zones were observed. Distinct labeling of newly born cells and immature neurons within the dentate gyrus of the hippocampus was observed in all species. A distinct rostral migratory stream (RMS) that appears to split around the medial aspect of the caudate nucleus was observed. These two rostral stream divisions appear to merge at the rostroventral corner of the caudate nucleus to turn and enter the olfactory bulb, where a large terminal field of immature neurons was observed. DCX immunolabeled neurons were observed mostly in the rostral neocortex, but a potential migratory stream to the neocortex was not identified. A broad swathe of newly born cells and immature neurons was found between the caudoventral division of the RMS and the piriform cortex. In addition, occasional immature neurons were observed in the amygdala and DCX-immunopositive axons were observed in the anterior commissure. While the majority of these features have been found in several mammal species, the large number of DCX immunolabeled cells found between the RMS and the piriform cortex and the presence of DCX immunostained axons in the anterior commissure are features only observed in microchiropterans and insectivores to date. In the diphyletic scenario of chiropteran evolution, these observations align the microchiropterans with the insectivores. Anat Rec, 299:1548-1560, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Richard Chawana
- School of Anatomical Sciences Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, 2193, Johannesburg, Republic of South Africa
| | - Nina Patzke
- School of Anatomical Sciences Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, 2193, Johannesburg, Republic of South Africa
| | - Abdulaziz N Alagaili
- KSU Mammals Research Chair, Department, of Zoology, College of Science, King Saud University, Box, 2455, Riyadh, 11451, Saudi Arabia.,Saudi Wildlife Authority, Riyadh, 11575, Saudi Arabia
| | - Nigel C Bennett
- KSU Mammals Research Chair, Department, of Zoology, College of Science, King Saud University, Box, 2455, Riyadh, 11451, Saudi Arabia.,Department of Zoology and Entomology, University of Pretoria, Pretoria, 0002, South Africa
| | - Osama B Mohammed
- KSU Mammals Research Chair, Department, of Zoology, College of Science, King Saud University, Box, 2455, Riyadh, 11451, Saudi Arabia
| | | | - Emmanuel Gilissen
- Department of African Zoology, Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080, Tervuren, Belgium.,Laboratory of Histology and Neuropathology, Université Libre de Bruxelles, Brussels, 1070, Belgium.,Department of Anthropology, University of Arkansas, Fayetteville, Arkansas
| | - Amadi O Ihunwo
- School of Anatomical Sciences Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, 2193, Johannesburg, Republic of South Africa
| | - John D Pettigrew
- Queensland Brain Institute, University of Queensland, 4072, St. Lucia, Australia
| | - Paul R Manger
- School of Anatomical Sciences Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, 2193, Johannesburg, Republic of South Africa.
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31
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Lei M, Dong D. Phylogenomic analyses of bat subordinal relationships based on transcriptome data. Sci Rep 2016; 6:27726. [PMID: 27291671 PMCID: PMC4904216 DOI: 10.1038/srep27726] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/24/2016] [Indexed: 11/28/2022] Open
Abstract
Bats, order Chiroptera, are one of the largest monophyletic clades in mammals. Based on morphology and behaviour bats were once differentiated into two suborders Megachiroptera and Microchiroptera Recently, researchers proposed alternative views of chiropteran classification (suborders Yinpterochiroptera and Yangochiroptera) based on morphological, molecular and fossil evidence. Since genome-scale data can significantly increase the number of informative characters for analysis, transcriptome RNA-seq data for 12 bat taxa were generated in an attempt to resolve bat subordinal relationships at the genome level. Phylogenetic reconstructions were conducted using up to 1470 orthologous genes and 634,288 aligned sites. We found strong support for the Yinpterochiroptera-Yangochiroptera classification. Next, we built expression distance matrices for each species and reconstructed gene expression trees. The tree is highly consistent with sequence-based phylogeny. We also examined the influence of taxa sampling on the performance of phylogenetic methods, and found that the topology is robust to sampling. Relaxed molecular clock estimates the divergence between Yinpterochiroptera and Yangochiroptera around 63 million years ago. The most recent common ancestor of Yinpterochiroptera, corresponding to the split between Rhinolophoidea and Pteropodidae (Old World Fruit bats), is estimated to have occurred 60 million years ago. Our work provided a valuable resource to further explore the evolutionary relationship within bats.
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Affiliation(s)
- Ming Lei
- Laboratory of Molecular Ecology and Evolution, Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Dong Dong
- Laboratory of Molecular Ecology and Evolution, Institute of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
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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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33
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Gregorin R, Moras LM, Acosta LH, Vasconcellos KL, Poma JL, dos Santos FR, Paca RC. A new species of Eumops (Chiroptera: Molossidae) from southeastern Brazil and Bolivia. Mamm Biol 2016. [DOI: 10.1016/j.mambio.2016.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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34
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Nuclear organisation of some immunohistochemically identifiable neural systems in five species of insectivore —Crocidura cyanea, Crocidura olivieri, Sylvisorex ollula, Paraechinus aethiopicus and Atelerix frontalis. J Chem Neuroanat 2016; 72:34-52. [DOI: 10.1016/j.jchemneu.2015.12.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/22/2015] [Accepted: 12/22/2015] [Indexed: 11/23/2022]
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35
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Integrating Ontogeny of Echolocation and Locomotion Gives Unique Insights into the Origin of Bats. J MAMM EVOL 2016. [DOI: 10.1007/s10914-016-9324-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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36
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Abstract
Recent studies have clearly shown that bats are the reservoir hosts of a wide diversity of novel viruses with representatives from most of the known animal virus families. In many respects bats make ideal reservoir hosts for viruses: they are the only mammals that fly, thus assisting in virus dispersal; they roost in large numbers, thus aiding transmission cycles; some bats hibernate over winter, thus providing a mechanism for viruses to persist between seasons; and genetic factors may play a role in the ability of bats to host viruses without resulting in clinical disease. Within the broad diversity of viruses found in bats are some important neurological pathogens, including rabies and other lyssaviruses, and Hendra and Nipah viruses, two recently described viruses that have been placed in a new genus, Henipaviruses in the family Paramyxoviridae. In addition, bats can also act as alternative hosts for the flaviviruses Japanese encephalitis and St Louis encephalitis viruses, two important mosquito-borne encephalitogenic viruses, and bats can assist in the dispersal and over-wintering of these viruses. Bats are also the reservoir hosts of progenitors of SARS and MERS coronaviruses, although other animals act as spillover hosts. This chapter presents the physiological and ecological factors affecting the ability of bats to act as reservoirs of neurotropic viruses, and describes the major transmission cycles leading to human infection.
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Affiliation(s)
- Carol Shoshkes Reiss
- Departments of Biology and Neural Science, New York University, New York, New York USA
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37
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Khwanmunee J, Leelawatwattana L, Prapunpoj P. Gene structure and evolution of transthyretin in the order Chiroptera. Genetica 2015; 144:71-83. [PMID: 26681450 DOI: 10.1007/s10709-015-9879-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 12/13/2015] [Indexed: 11/26/2022]
Abstract
Bats are mammals in the order Chiroptera. Although many extensive morphologic and molecular genetics analyses have been attempted, phylogenetic relationships of bats has not been completely resolved. The paraphyly of microbats is of particular controversy that needs to be confirmed. In this study, we attempted to use the nucleotide sequence of transthyretin (TTR) intron 1 to resolve the relationship among bats. To explore its utility, the complete sequences of TTR gene and intron 1 region of bats in Vespertilionidae: genus Eptesicus (Eptesicus fuscus) and genus Myotis (Myotis brandtii, Myotis davidii, and Myotis lucifugus), and Pteropodidae (Pteropus alecto and Pteropus vampyrus) were extracted from the retrieved sequences, whereas those of Rhinoluphus affinis and Scotophilus kuhlii were amplified and sequenced. The derived overall amino sequences of bat TTRs were found to be very similar to those in other eutherians but differed from those in other classes of vertebrates. However, missing of amino acids from N-terminal or C-terminal region was observed. The phylogenetic analysis of amino acid sequences suggested bat and other eutherian TTRs lineal descent from a single most recent common ancestor which differed from those of non-placental mammals and the other classes of vertebrates. The splicing of bat TTR precursor mRNAs was similar to those of other eutherian but different from those of marsupial, bird, reptile and amphibian. Based on TTR intron 1 sequence, the inferred evolutionary relationship within Chiroptera revealed more closely relatedness of R. affinis to megabats than to microbats. Accordingly, the paraphyly of microbats was suggested.
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Affiliation(s)
- Jiraporn Khwanmunee
- Department of Biochemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Ladda Leelawatwattana
- Department of Biochemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Porntip Prapunpoj
- Department of Biochemistry, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand.
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38
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Hahn MW, Nakhleh L. Irrational exuberance for resolved species trees. Evolution 2015; 70:7-17. [DOI: 10.1111/evo.12832] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 11/25/2015] [Accepted: 11/30/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Matthew W. Hahn
- Department of Biology; Indiana University; Bloomington Indiana 47405
- School of Informatics and Computing; Indiana University; Bloomington Indiana 47405
| | - Luay Nakhleh
- Department of Computer Science; Rice University; Houston Texas 77005
- BioSciences; Rice University; Houston Texas 77005
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39
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Lee AK, Kulcsar KA, Elliott O, Khiabanian H, Nagle ER, Jones MEB, Amman BR, Sanchez-Lockhart M, Towner JS, Palacios G, Rabadan R. De novo transcriptome reconstruction and annotation of the Egyptian rousette bat. BMC Genomics 2015; 16:1033. [PMID: 26643810 PMCID: PMC4672546 DOI: 10.1186/s12864-015-2124-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/22/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The Egyptian Rousette bat (Rousettus aegyptiacus), a common fruit bat species found throughout Africa and the Middle East, was recently identified as a natural reservoir host of Marburg virus. With Ebola virus, Marburg virus is a member of the family Filoviridae that causes severe hemorrhagic fever disease in humans and nonhuman primates, but results in little to no pathological consequences in bats. Understanding host-pathogen interactions within reservoir host species and how it differs from hosts that experience severe disease is an important aspect of evaluating viral pathogenesis and developing novel therapeutics and methods of prevention. RESULTS Progress in studying bat reservoir host responses to virus infection is hampered by the lack of host-specific reagents required for immunological studies. In order to establish a basis for the design of reagents, we sequenced, assembled, and annotated the R. aegyptiacus transcriptome. We performed de novo transcriptome assembly using deep RNA sequencing data from 11 distinct tissues from one male and one female bat. We observed high similarity between this transcriptome and those available from other bat species. Gene expression analysis demonstrated clustering of expression profiles by tissue, where we also identified enrichment of tissue-specific gene ontology terms. In addition, we identified and experimentally validated the expression of novel coding transcripts that may be specific to this species. CONCLUSION We comprehensively characterized the R. aegyptiacus transcriptome de novo. This transcriptome will be an important resource for understanding bat immunology, physiology, disease pathogenesis, and virus transmission.
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Affiliation(s)
- Albert K Lee
- Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Ave, New York, USA.
- Department of Systems Biology, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Ave, New York, USA.
| | - Kirsten A Kulcsar
- United States Army Medical Research Institute for Infectious Disease, Center for Genome Sciences, 1425 Porter St, Ft Detrick, 21702, USA.
| | - Oliver Elliott
- Department of Systems Biology, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Ave, New York, USA.
| | - Hossein Khiabanian
- Department of Systems Biology, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Ave, New York, USA.
| | - Elyse R Nagle
- United States Army Medical Research Institute for Infectious Disease, Center for Genome Sciences, 1425 Porter St, Ft Detrick, 21702, USA.
| | - Megan E B Jones
- Centers for Disease Control and Prevention, Viral Special Pathogens Branch, 1600 Clifton Rd. NE, Atlanta, 30333, USA.
| | - Brian R Amman
- Centers for Disease Control and Prevention, Viral Special Pathogens Branch, 1600 Clifton Rd. NE, Atlanta, 30333, USA.
| | - Mariano Sanchez-Lockhart
- United States Army Medical Research Institute for Infectious Disease, Center for Genome Sciences, 1425 Porter St, Ft Detrick, 21702, USA.
| | - Jonathan S Towner
- Centers for Disease Control and Prevention, Viral Special Pathogens Branch, 1600 Clifton Rd. NE, Atlanta, 30333, USA.
| | - Gustavo Palacios
- United States Army Medical Research Institute for Infectious Disease, Center for Genome Sciences, 1425 Porter St, Ft Detrick, 21702, USA.
- National Center for Biodefense and Infectious Disease, George Mason University, Manassas, 20110, USA.
| | - Raul Rabadan
- Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Ave, New York, USA.
- Department of Systems Biology, Columbia University College of Physicians and Surgeons, 1130 St. Nicholas Ave, New York, USA.
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40
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Calvey T, Alagaili AN, Bertelsen MF, Bhagwandin A, Pettigrew JD, Manger PR. Nuclear organization of some immunohistochemically identifiable neural systems in two species of the Euarchontoglires: A Lagomorph, Lepus capensis , and a Scandentia, Tupaia belangeri. J Chem Neuroanat 2015; 70:1-19. [DOI: 10.1016/j.jchemneu.2015.10.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 10/29/2015] [Accepted: 10/29/2015] [Indexed: 11/16/2022]
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41
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Shi JJ, Rabosky DL. Speciation dynamics during the global radiation of extant bats. Evolution 2015; 69:1528-1545. [DOI: 10.1111/evo.12681] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 05/04/2015] [Indexed: 02/03/2023]
Affiliation(s)
- Jeff J. Shi
- Department of Ecology and Evolutionary Biology and Museum of Zoology; University of Michigan; Ann Arbor Michigan 48109
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology; University of Michigan; Ann Arbor Michigan 48109
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42
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Nonecholocating Fruit Bats Produce Biosonar Clicks with Their Wings. Curr Biol 2014; 24:2962-7. [DOI: 10.1016/j.cub.2014.10.077] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/20/2014] [Accepted: 10/29/2014] [Indexed: 11/23/2022]
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43
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Foley NM, Thong VD, Soisook P, Goodman SM, Armstrong KN, Jacobs DS, Puechmaille SJ, Teeling EC. How and why overcome the impediments to resolution: lessons from rhinolophid and hipposiderid bats. Mol Biol Evol 2014; 32:313-33. [PMID: 25433366 PMCID: PMC4769323 DOI: 10.1093/molbev/msu329] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The phylogenetic and taxonomic relationships among the Old World leaf-nosed bats (Hipposideridae) and the closely related horseshoe bats (Rhinolophidae) remain unresolved. In this study, we generated a novel approximately 10-kb molecular data set of 19 nuclear exon and intron gene fragments for 40 bat species to elucidate the phylogenetic relationships within the families Rhinolophidae and Hipposideridae. We estimated divergence times and explored potential reasons for any incongruent phylogenetic signal. We demonstrated the effects of outlier taxa and genes on phylogenetic reconstructions and compared the relative performance of intron and exon data to resolve phylogenetic relationships. Phylogenetic analyses produced a well-resolved phylogeny, supporting the familial status of Hipposideridae and demonstrated the paraphyly of the largest genus, Hipposideros. A fossil-calibrated timetree and biogeographical analyses estimated that Rhinolophidae and Hipposideridae diverged in Africa during the Eocene approximately 42 Ma. The phylogram, the timetree, and a unique retrotransposon insertion supported the elevation of the subtribe Rhinonycterina to family level and which is diagnosed herein. Comparative analysis of diversification rates showed that the speciose genera Rhinolophus and Hipposideros underwent diversification during the Mid-Miocene Climatic Optimum. The intron versus exon analyses demonstrated the improved nodal support provided by introns for our optimal tree, an important finding for large-scale phylogenomic studies, which typically rely on exon data alone. With the recent outbreak of Middle East respiratory syndrome, caused by a novel coronavirus, the study of these species is urgent as they are considered the natural reservoir for emergent severe acute respiratory syndrome (SARS)-like coronaviruses. It has been shown that host phylogeny is the primary factor that determines a virus’s persistence, replicative ability, and can act as a predictor of new emerging disease. Therefore, this newly resolved phylogeny can be used to direct future assessments of viral diversity and to elucidate the origin and development of SARS-like coronaviruses in mammals.
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Affiliation(s)
- Nicole M Foley
- School of Biology & Environmental Science, University College Dublin, Belfield, Dublin, Ireland
| | - Vu Dinh Thong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Steven M Goodman
- Field Museum of Natural History, Chicago, IL, USA Association Vahatra, Antananarivo, Madagascar
| | - Kyle N Armstrong
- Australian Centre for Evolutionary Biology & Biodiversity, The University of Adelaide, Adelaide, South Australia, Australia South Australian Museum, Adelaide, South Australia, Australia
| | - David S Jacobs
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Sébastien J Puechmaille
- School of Biology & Environmental Science, University College Dublin, Belfield, Dublin, Ireland Zoological Institute and Museum, Greifswald University, Greifswald, Germany
| | - Emma C Teeling
- School of Biology & Environmental Science, University College Dublin, Belfield, Dublin, Ireland
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Establishment of Myotis myotis cell lines--model for investigation of host-pathogen interaction in a natural host for emerging viruses. PLoS One 2014; 9:e109795. [PMID: 25295526 PMCID: PMC4190323 DOI: 10.1371/journal.pone.0109795] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 09/13/2014] [Indexed: 11/17/2022] Open
Abstract
Bats are found to be the natural reservoirs for many emerging viruses. In most cases, severe clinical signs caused by such virus infections are normally not seen in bats. This indicates differences in the virus-host interactions and underlines the necessity to develop natural host related models to study these phenomena. Due to the strict protection of European bat species, immortalized cell lines are the only alternative to investigate the innate anti-virus immune mechanisms. Here, we report about the establishment and functional characterization of Myotis myotis derived cell lines from different tissues: brain (MmBr), tonsil (MmTo), peritoneal cavity (MmPca), nasal epithelium (MmNep) and nervus olfactorius (MmNol) after immortalization by SV 40 large T antigen. The usefulness of these cell lines to study antiviral responses has been confirmed by analysis of their susceptibility to lyssavirus infection and the mRNA patterns of immune-relevant genes after poly I:C stimulation. Performed experiments indicated varying susceptibility to lyssavirus infection with MmBr being considerably less susceptible than the other cell lines. Further investigation demonstrated a strong activation of interferon mediated antiviral response in MmBr contributing to its resistance. The pattern recognition receptors: RIG-I and MDA5 were highly up-regulated during rabies virus infection in MmBr, suggesting their involvement in promotion of antiviral responses. The presence of CD14 and CD68 in MmBr suggested MmBr cells are microglia-like cells which play a key role in host defense against infections in the central nervous system (CNS). Thus the expression pattern of MmBr combined with the observed limitation of lyssavirus replication underpin a protective mechanism of the CNS controlling the lyssavirus infection. Overall, the established cell lines are important tools to analyze antiviral innate immunity in M. myotis against neurotropic virus infections and present a valuable tool for a broad spectrum of future investigations in cellular biology of M. myotis.
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45
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Shinohara A, Kawada SI, Son NT, Koshimoto C, Endo H, Can DN, Suzuki H. Molecular phylogeny of East and Southeast Asian fossorial moles (Lipotyphla, Talpidae). J Mammal 2014. [DOI: 10.1644/13-mamm-a-135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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46
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Som A. Causes, consequences and solutions of phylogenetic incongruence. Brief Bioinform 2014; 16:536-48. [PMID: 24872401 DOI: 10.1093/bib/bbu015] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/05/2014] [Indexed: 11/14/2022] Open
Abstract
Phylogenetic analysis is used to recover the evolutionary history of species, genes or proteins. Understanding phylogenetic relationships between organisms is a prerequisite of almost any evolutionary study, as contemporary species all share a common history through their ancestry. Moreover, it is important because of its wide applications that include understanding genome organization, epidemiological investigations, predicting protein functions, and deciding the genes to be analyzed in comparative studies. Despite immense progress in recent years, phylogenetic reconstruction involves many challenges that create uncertainty with respect to the true evolutionary relationships of the species or genes analyzed. One of the most notable difficulties is the widespread occurrence of incongruence among methods and also among individual genes or different genomic regions. Presence of widespread incongruence inhibits successful revealing of evolutionary relationships and applications of phylogenetic analysis. In this article, I concisely review the effect of various factors that cause incongruence in molecular phylogenies, the advances in the field that resolved some factors, and explore unresolved factors that cause incongruence along with possible ways for tackling them.
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Ammerman LK, Brashear WA, Bartlett SN. Further Evidence for the Basal Divergence ofCheiromeles(Chiroptera: Molossidae). ACTA CHIROPTEROLOGICA 2013. [DOI: 10.3161/150811013x678946] [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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48
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Ramasindrazana B, Goodman SM, Rakotondramanana CF, Schoeman MC. Morphological and Echolocation Call Variation in Malagasy Trident Bats,TriaenopsDobson, 1871 (Chiroptera: Hipposideridae). ACTA CHIROPTEROLOGICA 2013. [DOI: 10.3161/150811013x679053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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49
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Tsagkogeorga G, Parker J, Stupka E, Cotton J, Rossiter S. Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats. Curr Biol 2013; 23:2262-2267. [DOI: 10.1016/j.cub.2013.09.014] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/22/2013] [Accepted: 09/05/2013] [Indexed: 10/26/2022]
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50
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Cellular location and major terminal networks of the orexinergic system in the brain of two megachiropterans. J Chem Neuroanat 2013; 53:64-71. [DOI: 10.1016/j.jchemneu.2013.09.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/05/2013] [Accepted: 09/05/2013] [Indexed: 11/19/2022]
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