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Willems F, Channing A. The status of Tomopterna pulchra Boulenger, 1896 (Anura: Pyxicephalidae). Zootaxa 2023; 5374:361-389. [PMID: 38220855 DOI: 10.11646/zootaxa.5374.3.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Indexed: 01/16/2024]
Abstract
Tomopterna pulchra (Boulenger, 1896) was described from Lake Tanganyika based on a single specimen. It was synonymised with Tomopterna tuberculosa (Boulenger, 1882) by Loveridge (1957) who noted that it did not fully agree with the description of T. tuberculosa, especially in the difference in dorsal colouration. Genetic differences show that two species are confused, although their advertisement calls and morphology are similar, except for the presence of a pale vertebral stripe mostly in eastern populations. We consider the advertisement calls, morphology, and genetic differences, and remove Tomopterna pulchra (Boulenger, 1896) from the synonymy of Tomopterna tuberculosa. Divergence dating shows that these two species separated in the mid-Miocene. Tomopterna pulchra breeds in rocky habitats, whereas T. tuberculosa breeds in sandy areas, typical of the genus. Based on genetically confirmed specimens, presently T. tuberculosa is known in the west (Angola and Namibia) while T. pulchra is only known from the east (Zambia and Tanzania). The examination of specimens for the presence or absence of a vertebral stripe infers that these species are widespread. Further work is required to determine if the two species are sympatric, and the extent of their ranges.
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Affiliation(s)
- Frank Willems
- Kigelia Solutions/Frank Willems Guiding and Ecology; Chisamba Park; PO Box 12; Fringilla; Zambia.
| | - Alan Channing
- Unit for Environmental Sciences and Management; North-West University; Potchefstroom 2520; South Africa.
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2
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Dufresnes C, Mahony S, Prasad VK, Kamei RG, Masroor R, Khan MA, Al-Johany AM, Gautam KB, Gupta SK, Borkin LJ, Melnikov DA, Rosanov JM, Skorinov DV, Borzée A, Jablonski D, Litvinchuk SN. Shedding light on taxonomic chaos: Diversity and distribution of South Asian skipper frogs (Anura, Dicroglossidae, Euphlyctis). SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2102686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Christophe Dufresnes
- LASER, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People’s Republic of China
| | - Stephen Mahony
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Vishal Kumar Prasad
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, People’s Republic of China
- Wildlife Institute of India, Chandrabani, Uttarakhand, India
| | - Rachunliu G. Kamei
- Department of Life Sciences, The Natural History Museum, London, UK
- 566 Kohima-Meriema Road (AH1), Meriema, Kohima, 797001, Nagaland, India
| | - Rafaqat Masroor
- Zoological Sciences Division, Pakistan Museum of Natural History, Garden Avenue, Shakarparian, 44000, Islamabad Pakistan
| | - Muazzam Ali Khan
- Department of Botany, Bacha Khan University Charsadda, Charsadda, KP, Pakistan
| | - Awadh M. Al-Johany
- Department of Zoology, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia
| | | | | | - Leo J. Borkin
- Laboratory of Herpetology, Zoological Institute, Russian Academy of Sciences, Saint Petersburg, 199034, Russia
| | - Daniel A. Melnikov
- Laboratory of Herpetology, Zoological Institute, Russian Academy of Sciences, Saint Petersburg, 199034, Russia
| | - Juriy M. Rosanov
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Dmitriy V. Skorinov
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Amaël Borzée
- Laboratory of Animal Behaviour and Conservation, College of Biology and the Environment, Nanjing Forestry University, People’s Republic of China
| | - Daniel Jablonski
- Department of Zoology, Comenius University, in Bratislava, Mlynská dolina, Ilkovičova 6, Bratislava, 842 15, Slovakia
| | - Spartak N. Litvinchuk
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, Russia
- Dagestan State University, Makhachkala, Russia
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3
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Bolotov IN, Pasupuleti R, Subba Rao NV, Unnikrishnan SK, Chan N, Lunn Z, Win T, Gofarov MY, Kondakov AV, Konopleva ES, Lyubas AA, Tomilova AA, Vikhrev IV, Pfenninger M, Düwel SS, Feldmeyer B, Nesemann HF, Nagel KO. Oriental freshwater mussels arose in East Gondwana and arrived to Asia on the Indian Plate and Burma Terrane. Sci Rep 2022; 12:1518. [PMID: 35087130 PMCID: PMC8795121 DOI: 10.1038/s41598-022-05257-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 01/10/2022] [Indexed: 12/21/2022] Open
Abstract
Freshwater mussels cannot spread through oceanic barriers and represent a suitable model to test the continental drift patterns. Here, we reconstruct the diversification of Oriental freshwater mussels (Unionidae) and revise their taxonomy. We show that the Indian Subcontinent harbors a rather taxonomically poor fauna, containing 25 freshwater mussel species from one subfamily (Parreysiinae). This subfamily most likely originated in East Gondwana in the Jurassic and its representatives arrived to Asia on two Gondwanan fragments (Indian Plate and Burma Terrane). We propose that the Burma Terrane was connected with the Indian Plate through the Greater India up to the terminal Cretaceous. Later on, during the entire Paleogene epoch, these blocks have served as isolated evolutionary hotspots for freshwater mussels. The Burma Terrane collided with mainland Asia in the Late Eocene, leading to the origin of the Mekong’s Indochinellini radiation. Our findings indicate that the Burma Terrane had played a major role as a Gondwanan “biotic ferry” alongside with the Indian Plate.
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Affiliation(s)
- Ivan N Bolotov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia. .,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia. .,SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, Cambridge, CB2 3QZ, UK.
| | - Rajeev Pasupuleti
- Institute of Molecular Biotechnology (IMBT), Technical University of Graz, Petersgasse 14, 8010, Graz, Austria
| | | | - Suresh Kumar Unnikrishnan
- Regional Facility for DNA Fingerprinting (RFDF), Rajiv Gandhi Centre for Biotechnology (RGCB), Trivandrum, 695014, Kerala, India
| | - Nyein Chan
- Fauna & Flora International - Myanmar Programme, 34 D/9 San Yae Twin Street, Kaba Aye Pagoda Road, Bahan Township, 11201, Yangon, Myanmar
| | - Zau Lunn
- Fauna & Flora International - Myanmar Programme, 34 D/9 San Yae Twin Street, Kaba Aye Pagoda Road, Bahan Township, 11201, Yangon, Myanmar.,Biology Department, University of New Brunswick, 100 Tucker Park Road, PO Box 5050, Saint John, NB, E2L 4L5, Canada
| | - Than Win
- Department of Zoology, Dawei University, 14043, Dawei, Tanintharyi Region, Myanmar
| | - Mikhail Y Gofarov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia
| | - Alexander V Kondakov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia.,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia
| | - Ekaterina S Konopleva
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia.,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia
| | - Artyom A Lyubas
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia
| | - Alena A Tomilova
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia.,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia
| | - Ilya V Vikhrev
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia.,Northern Arctic Federal University, Northern Dvina Emb. 17, 163002, Arkhangelsk, Russia.,SSC/IUCN - Mollusc Specialist Group, Species Survival Commission, International Union for Conservation of Nature, Cambridge, CB2 3QZ, UK
| | - Markus Pfenninger
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Sophie S Düwel
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Barbara Feldmeyer
- Molecular Ecology Group, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | | | - Karl-Otto Nagel
- Malacological Section, Senckenberg Research Institute and Natural History Museum Frankfurt/M., Senckenberganlage 25, 60325, Frankfurt am Main, Germany
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Box EK, Cleveland CA, Subramaniam K, Waltzek TB, Yabsley MJ. Molecular Confirmation of Ranavirus Infection in Amphibians From Chad, Africa. Front Vet Sci 2021; 8:733939. [PMID: 34604370 PMCID: PMC8481899 DOI: 10.3389/fvets.2021.733939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/16/2021] [Indexed: 11/22/2022] Open
Abstract
Ranaviruses are DNA viruses (Family Iridoviridae; Subfamily Alphairidovirinae) and ranaviral disease is considered an emerging infectious disease of ectothermic vertebrates. Ranavirus infection can have varying pathological effects on infected amphibians, reptiles, and fish, most notably causing significant mortality events and population declines. Despite having a broad global range with reports from six continents, only a single incidental finding in Xenopus longipes from mainland Africa (Cameroon) is known and lacks molecular confirmation. Thus, there is a considerable knowledge gap concerning ranaviruses in Africa. We opportunistically obtained tissue samples from 160 amphibians representing five genera (Hoplobatrachus, Hylarana, Ptychadena, Pyxicephalus, and Xenopus) and two turtles (Pelomedusa sp.) from Chad, Africa. Samples were tested for ranavirus infection using a conventional PCR assay targeting the major capsid protein (MCP). A total of 25/160 (16%) frogs tested positive including 15/87 (17%) Hoplobatrachus occipitalis, 10/58 (17%) Ptychadena spp., 0/3 Pyxicephalus spp., 0/9 Xenopus spp., and 0/3 Hylarana spp. One of two turtles tested positive. Partial MCP gene sequences indicated all samples were >98% similar to several frog virus 3 (FV3)-like sequences. Additional gene targets (DNA polymerase [DNApol], ribonucleotide reductase alpha [RNR- α], ribonucleotide reductase beta subunit [RNR- β]) were sequenced to provide further detailed classification of the virus. Sequences of individual gene targets indicate that the ranavirus detected in frogs in Chad is most similar to tiger frog virus (TFV), a FV3-like virus previously isolated from diseased amphibians cultured in China and Thailand. Full genome sequencing of one sample indicates that the Chad frog virus (CFV) is a well-supported sister group to the TFVs previously determined from Asia. This work represents the first molecular confirmation of ranaviruses from Africa and is a first step in comparing ranavirus phylogeography on a local and global scale.
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Affiliation(s)
- Erin K Box
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Christopher A Cleveland
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Kuttichantran Subramaniam
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Thomas B Waltzek
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Michael J Yabsley
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States
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5
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Akram A, Rais M, Lopez‐Hervas K, Tarvin RD, Saeed M, Bolnick DI, Cannatella DC. An insight into molecular taxonomy of bufonids, microhylids, and dicroglossid frogs: First genetic records from Pakistan. Ecol Evol 2021; 11:14175-14216. [PMID: 34707849 PMCID: PMC8525160 DOI: 10.1002/ece3.8134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 08/30/2021] [Accepted: 09/03/2021] [Indexed: 11/19/2022] Open
Abstract
The current study was focused on documentation of amphibian assemblage in North Punjab and Islamabad Capital Territory, Pakistan, by using mitochondrial gene sequences of 16S rRNA. Our study entailed 37% of the known amphibian species of the country. We provided a phylogenetic analysis based on 74 newly generated mitochondrial 16S rRNAs from nine species of genus Microlyla, Duttaphrynus, Allopaa, Nanorana, Sphaerotheca, Minervarya, Hoplobatrachus, and Euphlyctis. We employed the maximum-likelihood inference and Bayesian analysis to assess the taxonomic status of the samples obtained from Pakistan, with respect to other congeneric species from surrounding regions. Our findings confirmed the taxonomic status of South Asian anuran species Duttaphrynus stomaticus, Duttaphrynus melanostictus, Microhyla nilphamariensis, Allopaa hazarensis, Nanorana vicina, Sphaerotheca maskeyi (synonym: S. pashchima), Minervarya pierrei, Hoplobatrachus tigerinus, and Euphlyctis kalasgramensis in Pakistan. We have reported new country records of genus Minervarya ( M. pierrei). Minervarya pierrei was previously misidentified as Fejervarya limnocharis, due to dearth of genetic information. We provided the first genetic records of our endemic species N. vicina. The results revealed the taxonomic placement of N. vicina with respect to its congeners and validated the taxonomic status of N. vicina from its type locality (Murree) for the first time. The findings of the present study also indicated the paraphyletic relationship of A.- hazarensis with Nanorana species. So, based on our phylogenetic inferences, morphological characters, and habitat preferences, validity of generic status of A. hazarensis is undecided. As our data were not enough to resolve this issue, we suggest sequencing of additional mitochondrial and nuclear genes in the future studies to get a better resolution. We recommend carrying out extensive surveys throughout the country for proper scientific documentation of amphibians of Pakistan. Many new species, some of them might be endemic to Pakistan, are expected to be discovered, and taxonomic status of other species would be resolved.
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Affiliation(s)
- Ayesha Akram
- Herpetology LabDepartment of Wildlife ManagementPir Mehr Ali Shah Arid Agriculture University RawalpindiRawalpindiPakistan
| | - Muhammad Rais
- Herpetology LabDepartment of Wildlife ManagementPir Mehr Ali Shah Arid Agriculture University RawalpindiRawalpindiPakistan
| | - Karem Lopez‐Hervas
- Department of Wetland EcologyDoñana Biological StationConsejo Superior de Investigaciones CientíficasSevilleSpain
| | - Rebecca D. Tarvin
- Department of Integrative BiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
- Museum of Vertebrate Zoology and Department of Integrative BiologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Muhammad Saeed
- Herpetology LabDepartment of Wildlife ManagementPir Mehr Ali Shah Arid Agriculture University RawalpindiRawalpindiPakistan
| | - Daniel I. Bolnick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - David C. Cannatella
- Department of Integrative Biology and Biodiversity CenterUniversity of TexasAustinTexasUSA
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6
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Mohanty NP, Crottini A, Garcia RA, Measey J. Non-native populations and global invasion potential of the Indian bullfrog Hoplobatrachus tigerinus: a synthesis for risk-analysis. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02356-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Kusy D, Motyka M, Fusek L, Li Y, Bocek M, Bilkova R, Ruskova M, Bocak L. Sexually dimorphic characters and shared aposematic patterns mislead the morphology-based classification of the Lycini (Coleoptera: Lycidae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The Lycini (Elateroidea: Lycidae) contains > 400 species placed in four typologically based genera and numerous subgenera. We assembled a mito-ribosomal dataset representing ~100 species from the whole range and recovered a phylogeny rejecting Lycus and Lycostomus as polyphyletic assemblages. The male-specific wide elytra and elytral thorns are identified in unrelated Neolycus and Lycus. The morphological similarity based on sexual dimorphism and aposematic patterns defined terminal clades and misled the genus-rank classification. We delimit Neolycus, Rhyncheros reinst. name (= Thoracocalon syn. nov. = Lyconotus syn. nov.), LipernesLycostomus, Haplolycus and Lycus. Demosis and six subgenera of Lycus are synonymized with Lycus. Celiasis Laporte, 1840 is kept in the classification as a nomen dubium until any specimen is available. The deep lineages are known from the Americas and Asia. Africa was colonized by Lycus and Haplolycus. Each specific aposematic pattern occurs in a limited range, and the similar body shape and coloration evolved in unrelated sympatrically occurring lineages. High intraspecific polymorphism is putatively a result of the adaptation of various populations to local mimetic assemblages. Therefore, the delimitation of many phenotypically diverse species should be investigated.
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Affiliation(s)
- Dominik Kusy
- Laboratory of Diversity and Molecular Evolution, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Michal Motyka
- Laboratory of Diversity and Molecular Evolution, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Lukas Fusek
- Laboratory of Diversity and Molecular Evolution, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Yun Li
- Laboratory of Diversity and Molecular Evolution, Faculty of Science, Palacky University, Olomouc, Czech Republic
- Key Laboratory of Biodiversity Dynamics & Conservation, School of Life Sciences, Sun Yat Sen University, Guangzhou, Guangdong, People’s Republic of China
| | - Matej Bocek
- Laboratory of Diversity and Molecular Evolution, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Renata Bilkova
- Laboratory of Diversity and Molecular Evolution, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Michaela Ruskova
- Laboratory of Diversity and Molecular Evolution, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Ladislav Bocak
- Laboratory of Diversity and Molecular Evolution, Faculty of Science, Palacky University, Olomouc, Czech Republic
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8
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Crottini A, Rosa GM, Penny SG, Cocca W, Holderied MW, Rakotozafy LMS, Andreone F. A new stump-toed frog from the transitional forests of NW Madagascar (Anura, Microhylidae, Cophylinae, Stumpffia). Zookeys 2020; 933:139-164. [PMID: 32547290 PMCID: PMC7285848 DOI: 10.3897/zookeys.933.47619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 03/01/2020] [Indexed: 11/17/2022] Open
Abstract
A new species of the miniaturised microhylid frog genus Stumpffia, from north-western Madagascar, is described. Stumpffiafroschauerisp. nov. differs from all other described Stumpffia species in colouration and morphology and is genetically divergent (≥ 7% uncorrected p-distance to all other nominal species of the genus) in a fragment of the mitochondrial 16S rRNA gene and in a segment of the nuclear Rag-1 gene. The new species is reliably known only from a few specimens collected in the Sahamalaza (and surroundings) region. Its known distribution is limited to three forest patches severely threatened by fire, drought and high levels of forest clearance, thus suggesting a classification of “Critically Endangered” according to IUCN Red List criteria.
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Affiliation(s)
- Angelica Crottini
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO Associate Laboratory, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661, Vairão, Portugal Universidade do Porto Vairão Portugal
| | - Gonçalo M Rosa
- Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY London, UK Institute of Zoology, Zoological Society of London London United Kingdom.,Centro de Biologia Ambiental, Faculdade de Ciências da Universidade de Lisboa, Bloco C2, Campo Grande, 1749-016, Lisboa, Portugal Universidade de Lisboa Lisboa Portugal
| | - Samuel G Penny
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK University of Brighton Brighton United Kingdom
| | - Walter Cocca
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO Associate Laboratory, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas 7, 4485-661, Vairão, Portugal Universidade do Porto Vairão Portugal
| | - Marc W Holderied
- Life Sciences Building, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, UK University of Bristol Bristol United Kingdom
| | - Lovasoa M S Rakotozafy
- Mention Zoologie et Biodiversité Animale, Faculté des Sciences, Université d'Antananarivo, BP 906, Antananarivo (101), Madagascar Université d'Antananarivo Antananarivo Madagascar
| | - Franco Andreone
- Museo Regionale di Scienze Naturali, Sezione di Zoologia, Via G. Giolitti, 36, I-10123, Torino, Italy Museo Regionale di Scienze Naturali Torino Italy
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9
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The saprotrophic Pleurotus ostreatus species complex: late Eocene origin in East Asia, multiple dispersal, and complex speciation. IMA Fungus 2020; 11:10. [PMID: 32617259 PMCID: PMC7325090 DOI: 10.1186/s43008-020-00031-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/31/2020] [Indexed: 12/02/2022] Open
Abstract
The Pleurotus ostreatus species complex is saprotrophic and of significant economic and ecological importance. However, species delimitation has long been problematic because of phenotypic plasticity and morphological stasis. In addition, the evolutionary history is poorly understood due to limited sampling and insufficient gene fragments employed for phylogenetic analyses. Comprehensive sampling from Asia, Europe, North and South America and Africa was used to run phylogenetic analyses of the P. ostreatus species complex based on 40 nuclear single-copy orthologous genes using maximum likelihood and Bayesian inference analyses. Here, we present a robust phylogeny of the P. ostreatus species complex, fully resolved from the deepest nodes to species level. The P. ostreatus species complex was strongly supported as monophyletic, and 20 phylogenetic species were recognized, with seven putatively new species. Data from our molecular clock analyses suggested that divergence of the genus Pleurotus probably occurred in the late Jurassic, while the most recent common ancestor of the P. ostreatus species complex diversified about 39 Ma in East Asia. Species of the P. ostreatus complex might migrate from the East Asia into North America across the North Atlantic Land Bridge or the Bering Land Bridge at different times during the late Oligocene, late Miocene and late Pliocene, and then diversified in the Old and New Worlds simultaneously through multiple dispersal and vicariance events. The dispersal from East Asia to South America in the middle Oligocene was probably achieved by a long-distance dispersal event. Intensification of aridity and climate cooling events in the late Miocene and Quaternary glacial cycling probably had a significant influence on diversification patterns of the complex. The disjunctions among East Asia, Europe, North America and Africa within Clade IIc are hypothesized to be a result of allopatric speciation. Substrate transitions to Apiaceae probably occurred no earlier than 6 Ma. Biogeographic analyses suggested that the global cooling of the late Eocene, intensification of aridity caused by rapid uplift of the QTP and retreat of the Tethys Sea in the late Miocene, climate cooling events in Quaternary glacial cycling, and substrate transitions have contributed jointly to diversification of the species complex.
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10
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Riccieri A, Mancini E, Salvi D, Bologna MA. Phylogeny, biogeography and systematics of the hyper-diverse blister beetle genus Hycleus (Coleoptera: Meloidae). Mol Phylogenet Evol 2019; 144:106706. [PMID: 31830551 DOI: 10.1016/j.ympev.2019.106706] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 10/01/2019] [Accepted: 12/08/2019] [Indexed: 10/25/2022]
Abstract
Hycleus is a hyper-diverse genus of blister beetles including ~500 species widely distributed in the Old World, currently divided into three "sections" and into 45 "phenetic" species groups according to morphological characters. Recently the monophyly of Hycleus was questioned pointing out its paraphyly with respect to the genera Ceroctis and Paractenodia. In this study, we built a time-calibrated phylogenetic tree based on DNA sequence data from mitochondrial and nuclear genes obtained from 125 species, to understand the phylogenetic relationships among the species of this genus, to infer the biogeographic processes behind their diversification, and to assess their taxonomy and classification. Our results identified four main lineages one of which included the species belonging to Ceroctis and Paractenodia; therefore, both taxa are now referred to Hycleus as new synonyms. The three described sections of Hycleus resulted polyphyletic and are rejected, whereas several species groups represented well supported clades. Hycleus likely originated in Africa during the Early Miocene (~20 Mya), and subsequently spread in Europe and western Asia. Later, in the Late Miocene (~6 Mya) a Saharo-Sindian group branched off from the Palaearctic lineage, whereas the Oriental Region was colonized following a dispersal event through the Arabian Peninsula from the Afrotropical Region (~5 Mya).
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Affiliation(s)
- Alessandra Riccieri
- Department of Sciences, University "Roma Tre", Viale G. Marconi 446, 00146 Roma, Italy.
| | - Emiliano Mancini
- Department of Biology and Biotechnology "C. Darwin", "Sapienza" University of Rome, Viale dell'Università 32, 00186 Roma, Italy
| | - Daniele Salvi
- Department of Health, Life & Environmental Sciences, University of L'Aquila, Via Vetoio snc, 67100 L'Aquila-Coppito, Italy; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Marco A Bologna
- Department of Sciences, University "Roma Tre", Viale G. Marconi 446, 00146 Roma, Italy
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11
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Gonçalves DV, Brito JC. Second Sahelian amphibian endemism suggested by phylogeography of Groove crowned Bullfrog (
Hoplobatrachus occipitalis
) in western Sahel and hints of polyploid species formation. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Duarte Vasconcelos Gonçalves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
- Departamento de Biologia, Faculdade de Ciências Universidade do Porto Porto Portugal
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra) Barcelona Spain
| | - José Carlos Brito
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
- Departamento de Biologia, Faculdade de Ciências Universidade do Porto Porto Portugal
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Huang X, Deng T, Moore MJ, Wang H, Li Z, Lin N, Yusupov Z, Tojibaev KS, Wang Y, Sun H. Tropical Asian Origin, boreotropical migration and long-distance dispersal in Nettles (Urticeae, Urticaceae). Mol Phylogenet Evol 2019; 137:190-199. [DOI: 10.1016/j.ympev.2019.05.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 12/17/2022]
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Al-Qahtani AR, Amer SAM. First molecular identification of Euphlyctis ehrenbergii (Anura: Amphibia) inhabiting southwestern Saudi Arabia. THE EUROPEAN ZOOLOGICAL JOURNAL 2019. [DOI: 10.1080/24750263.2019.1609104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- A. R. Al-Qahtani
- Department of Biology, Faculty of Science, University of Bisha, Bisha, Saudi Arabia
| | - S. A. M. Amer
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
- Department of Forensic Biology, College of Forensic Sciences, Naif Arab University for Security Sciences, Riyadh, Saudi Arabia
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Phylogeography of Bellamya (Mollusca: Gastropoda: Viviparidae) snails on different continents: contrasting patterns of diversification in China and East Africa. BMC Evol Biol 2019; 19:82. [PMID: 30898091 PMCID: PMC6429760 DOI: 10.1186/s12862-019-1397-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 02/22/2019] [Indexed: 11/21/2022] Open
Abstract
Background Species diversity is determined by both local environmental conditions that control differentiation and extinction and the outcome of large-scale processes that affect migration. The latter primarily comprises climatic change and dynamic landscape alteration. In the past few million years, both Southeast Asia and Eastern Africa experienced drastic climatic and geological oscillations: in Southeast Asia, especially in China, the Tibetan Plateau significantly rose up, and the flow of the Yangtze River was reversed. In East Africa, lakes and rivers experienced frequent range expansions and regressions due to the African mega-droughts. To test how such climatic and geological histories of both regions relate to their respective regional species and genetic diversity, a large scale comparative phylogeographic study is essential. Bellamya, a species rich freshwater snail genus that is widely distributed across China and East Africa, represents a suitable model system to address this question. We sequenced mitochondrial and nuclear DNA for members of the genus from China and used published sequences from Africa and some other locations in Asia to investigate their phylogeny and distribution of genetic diversity. Results Our phylogenetic analysis revealed two monophyletic groups, one in China and one in East Africa. Within the Chinese group, Bellamya species show little genetic differentiation. In contrast, we observe fairly deep divergence among the East African lakes with almost every lake possessing its unique clade. Our results show that strong divergence does not necessarily depend on intrinsic characteristics of a species, but rather is related to the landscape dynamics of a region. Conclusion Our phylogenetic results suggest that the Bellamya in China and East Africa are independent phylogenetic clades with different evolutionary trajectories. The different climate and geological histories likely contributed to the diverging evolutionary patterns. Repeated range expansions and regressions of lakes likely contributed to the great divergence of Bellamya in East Africa, while reversal of the river courses and intermingling of different lineages had an opposite effect on Bellamya diversification in China. Electronic supplementary material The online version of this article (10.1186/s12862-019-1397-0) contains supplementary material, which is available to authorized users.
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Molecular Phylogeny, Diversity and Zoogeography of Net-Winged Beetles (Coleoptera: Lycidae). INSECTS 2018; 9:insects9040154. [PMID: 30388727 PMCID: PMC6315567 DOI: 10.3390/insects9040154] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/18/2018] [Accepted: 10/28/2018] [Indexed: 01/23/2023]
Abstract
We synthesize the evidence from molecular phylogenetics, extant distribution, and plate tectonics to present an insight in ancestral areas, dispersal routes and the effectiveness of geographic barriers for net-winged beetle tribes (Coleoptera: Lycidae). Samples from all zoogeographical realms were assembled and phylogenetic relationships for ~550 species and 25 tribes were inferred using nuclear rRNA and mtDNA markers. The analyses revealed well-supported clades at the rank of tribes as they have been defined using morphology, but a low support for relationships among them. Most tribes started their diversification in Southeast and East Asia or are endemic to this region. Slipinskiini and Dexorini are Afrotropical endemics and Calopterini, Eurrhacini, Thonalmini, and Leptolycini remained isolated in South America and the Caribbean after their separation from northern continents. Lycini, Calochromini, and Erotini support relationships between the Nearctic and eastern Palearctic faunas; Calochromini colonized the Afrotropical realm from East Asia and Metriorrhynchini Afrotropical and Oriental realms from the drifting Indian subcontinent. Most tribes occur in the Oriental and Sino-Japanese realms, the highest alpha-taxonomic diversity was identified in Malesian tropical rainforests. The turn-over at zoogeographical boundaries is discussed when only short distance over-sea colonization events were inferred. The lycid phylogeny shows that poor dispersers can be used for reconstruction of dispersal and vicariance history over a long time-span, but the current data are insufficient for reconstruction of the early phase of their diversification.
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Jongsma GF, Barej MF, Barratt CD, Burger M, Conradie W, Ernst R, Greenbaum E, Hirschfeld M, Leaché AD, Penner J, Portik DM, Zassi-Boulou AG, Rödel MO, Blackburn DC. Diversity and biogeography of frogs in the genus Amnirana (Anura: Ranidae) across sub-Saharan Africa. Mol Phylogenet Evol 2018; 120:274-285. [DOI: 10.1016/j.ympev.2017.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 10/18/2022]
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17
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Suwannapoom C, Yuan ZY, A Poyarkov N, Yan F, Kamtaeja S, W Murphy R, Che J. A new species of genus Fejervarya (Anura: Dicroglossidae) from northern Thailand. Zool Res 2018; 37:327-337. [PMID: 28105797 PMCID: PMC5359320 DOI: 10.13918/j.issn.2095-8137.2016.6.327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
We describe a new species of frog in the dicroglossid genus Fejervarya from Ban Monjong, Omkoi District, Chiang Mai Province, northern Thailand. Analysis of DNA sequence data from the mitochondrial gene 16S, advertisement calls, and morphological distinctiveness support recognition of the new species. Matrilineal genealogy suggests that the new population from Chiang Mai is a sister taxon to the South Asian clade that includes F. syhadrensis, F. granosa, and F. pierrei. The new species, Fejervarya chiangmaiensissp. nov., differs morphologically from its congeners by its relatively small body size and proportions and the presence of dorsal warts and dermal ridges. Discovery of this new species indicates that the biodiversity of amphibians in this region remains underestimated.
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Affiliation(s)
- Chatmongkon Suwannapoom
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; Division of Fishery, School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla Yunnan 666303, China
| | - Zhi-Yong Yuan
- College of Forestry, Southwest Forestry University, Kunming Yunnan 650224, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla Yunnan 666303, China
| | - Nikolay A Poyarkov
- Department of Vertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Leninskiye Gory Moscow 119991, Russia; Joint Russian-Vietnamese Tropical Research and Technological Center Under the A. N. Severtsov Institute of Ecology and Evolution RAS, South Branch, Ho Chi Minh City, Vietnam
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla Yunnan 666303, China
| | - Somboon Kamtaeja
- Faculty of Education, Chiang Rai Rajabhat University, Chiang Rai 57100, Thailand
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto M5S 2C6, Canada
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla Yunnan 666303, China.
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Sultana N, Igawa T, Islam MM, Hasan M, Alam MS, Komaki S, Kawamura K, Khan MMR, Sumida M. Inter- and intra-specific genetic divergence of Asian tiger frogs (genus Hoplobatrachus), with special reference to the population structure of H. tigerinus in Bangladesh. Genes Genet Syst 2017; 91:217-227. [PMID: 27452042 DOI: 10.1266/ggs.16-00006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The five frog species of the genus Hoplobatrachus are widely distributed in Asia and Africa, with Asia being considered the genus' origin. However, the evolutionary relationships of Asian Hoplobatrachus species remain ambiguous. Additionally, genetic diversity and fundamental differentiation processes within species have not been studied. We conducted molecular phylogenetic analysis on Asian Hoplobatrachus frogs and population genetic analysis on H. tigerinus in Bangladesh using the mitochondrial CYTB gene and 21 microsatellite markers. The resultant phylogenetic tree revealed monophyly in each species, notwithstanding the involvement of cryptic species in H. chinensis and H. tigerinus, which are evident from the higher genetic divergence between populations. Bayesian inference of population structure revealed genetic divergence between western and eastern H. tigerinus populations in Bangladesh, suggesting restricted gene flow caused by barriers posed by major rivers. However, genetic distances among populations were generally low. A discrete population is located in the low riverine delta region, which likely reflects long-distance dispersal. These results strongly suggest that the environment specific to this river system has maintained the population structure of H. tigerinus in this region.
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Affiliation(s)
- Nasrin Sultana
- Institute for amphibian Biology, Graduate School of Science, Hiroshima University
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McLaughlin CM, Lampis S, Mechkarska M, Coquet L, Jouenne T, King JD, Mangoni ML, Lukic ML, Scorciapino MA, Conlon JM. Purification, Conformational Analysis, and Properties of a Family of Tigerinin Peptides from Skin Secretions of the Crowned Bullfrog Hoplobatrachus occipitalis. JOURNAL OF NATURAL PRODUCTS 2016; 79:2350-2356. [PMID: 27560386 DOI: 10.1021/acs.jnatprod.6b00494] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Four host-defense peptides belonging to the tigerinin family (tigerinin-1O: RICTPIPFPMCY; tigerinin-2O: RTCIPIPLVMC; tigerinin-3O: RICTAIPLPMCL; and tigerinin-4O: RTCIPIPPVCF) were isolated from skin secretions of the African crowned bullfrog Hoplobatrachus occipitalis. In aqueous solution at pH 4.8, the cyclic domain of tigerinin-2O adopts a rigid amphipathic conformation that incorporates a flexible N-terminal tail. The tigerinins lacked antimicrobial (MIC > 100 μM) and hemolytic (LC50 > 500 μM) activities but, at a concentration of 20 μg/mL, significantly (P < 0.05) inhibited production of interferon-γ (IFN-γ) by peritoneal cells from C57BL/6 mice without affecting production of IL-10 and IL-17. Tigerinin-2O and -4O inhibited IFN-γ production at concentrations as low as 1 μg/mL. The tigerinins significantly (P ≤ 0.05) stimulated the rate of insulin release from BRIN-BD11 clonal β-cells without compromising the integrity of the plasma membrane. Tigerinin-1O was the most potent (threshold concentration 1 nM) and the most effective (395% increase over basal rate at a concentration of 1 μM). Tigerinin-4O was the most potent and effective peptide in stimulating the rate of glucagon-like peptide-1 release from GLUTag enteroendocrine cells (threshold concentration 10 nM; 289% increase over basal rate at 1 μM). Tigerinin peptides have potential for development into agents for the treatment of patients with type 2 diabetes.
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Affiliation(s)
- Christopher M McLaughlin
- SAAD Centre for Pharmacy and Diabetes, School of Biomedical Sciences, University of Ulster , Coleraine, U.K
| | - Sandrina Lampis
- Department of Chemical and Geological Sciences and Department of Biomedical Sciences, Biochemistry Unit, University of Cagliari , Cagliari, Italy
| | - Milena Mechkarska
- SAAD Centre for Pharmacy and Diabetes, School of Biomedical Sciences, University of Ulster , Coleraine, U.K
| | - Laurent Coquet
- CNRS UMR 6270, PISSARO, University of Rouen, Institute for Research and Innovation in Biomedicine (IRIB) , Mont-Saint-Aignan, France
| | - Thierry Jouenne
- CNRS UMR 6270, PISSARO, University of Rouen, Institute for Research and Innovation in Biomedicine (IRIB) , Mont-Saint-Aignan, France
| | - Jay D King
- Rare Species Conservatory Foundation , St. Louis, Missouri, United States
| | - Maria Luisa Mangoni
- Instituto Pasteur-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome , Rome, Italy
| | - Miodrag L Lukic
- Center for Molecular Medicine, Faculty of Medicine, University of Kragujevac , Kragujevac, Serbia
| | - Mariano A Scorciapino
- Department of Chemical and Geological Sciences and Department of Biomedical Sciences, Biochemistry Unit, University of Cagliari , Cagliari, Italy
| | - J Michael Conlon
- SAAD Centre for Pharmacy and Diabetes, School of Biomedical Sciences, University of Ulster , Coleraine, U.K
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Huang JF, Li L, van der Werff H, Li HW, Rohwer JG, Crayn DM, Meng HH, van der Merwe M, Conran JG, Li J. Origins and evolution of cinnamon and camphor: A phylogenetic and historical biogeographical analysis of the Cinnamomum group (Lauraceae). Mol Phylogenet Evol 2016; 96:33-44. [DOI: 10.1016/j.ympev.2015.12.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 12/04/2015] [Accepted: 12/11/2015] [Indexed: 10/22/2022]
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Phylogenetic relationships, character evolution and biogeographic diversification of Pogostemon s.l. (Lamiaceae). Mol Phylogenet Evol 2016; 98:184-200. [PMID: 26923493 DOI: 10.1016/j.ympev.2016.01.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 01/19/2016] [Accepted: 01/29/2016] [Indexed: 11/22/2022]
Abstract
Pogostemon (Lamiaceae; Lamioideae) sensu lato is a large genus consisting of about 80 species with a disjunct African/Asian distribution. The infrageneric taxonomy of the genus has historically been troublesome due to morphological variability and putative convergent evolution within the genus. Notably, some species of Pogostemon are obligately aquatic, perhaps the only Lamiaceae taxa which exhibit this trait. Phylogenetic analyses using the nuclear ribosomal internal transcribed spacer (ITS) and five plastid regions (matK, rbcL, rps16, trnH-psbA, trnL-F), confirmed the monophyly of Pogostemon and its sister relationship with the genus Anisomeles. Pogostemon was resolved into two major clades, and none of the three morphologically defined subgenera of Pogostemon were supported as monophyletic. Inflorescence type (spikes with more than two lateral branches vs. a single terminal spike, or rarely with two lateral branches) is phylogenetically informative and consistent with the two main clades we recovered. Accordingly, a new infrageneric classification of Pogostemon consisting of two subgenera is proposed. Molecular dating and biogeographic diversification analyses suggest that Pogostemon split from its sister genus in southern and southeast Asia in the early Miocene. The early strengthening of the Asia monsoon system that was triggered by the uplifting of the Qinghai-Tibetan Plateau may have played an important role in the subsequent diversification of the genus. In addition, our results suggest that transoceanic long-distance dispersal of Pogostemon from Asia to Africa occurred at least twice, once in the late Miocene and again during the late-Miocene/early-Pliocene.
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Portik DM, Papenfuss TJ. Historical biogeography resolves the origins of endemic Arabian toad lineages (Anura: Bufonidae): Evidence for ancient vicariance and dispersal events with the Horn of Africa and South Asia. BMC Evol Biol 2015; 15:152. [PMID: 26245197 PMCID: PMC4527211 DOI: 10.1186/s12862-015-0417-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 06/10/2015] [Indexed: 11/21/2022] Open
Abstract
Background The Arabian Peninsula is home to a unique fauna that has assembled and evolved throughout the course of major geophysical events, including the separation of the Arabian Plate from Africa and subsequent collision with Eurasia. Opportunities for faunal exchanges with particular continents occurred in temporally distinct periods, and the presence of African, Western Eurasian, and South Asian derived taxa on the Arabian Peninsula signifies the complexity of these historical biogeographic events. The six true toad species (family Bufonidae) endemic to the Arabian Peninsula present a considerable taxonomic and biogeographic challenge because they are part of a global bufonid radiation, including several genera surrounding the Arabian Peninsula, and difficult to discriminate morphologically. As they could be derived from African, Western Eurasian, or South Asian toad groups, elucidating their evolutionary relationships has important implications for historical biogeography. Here, we analyze a global molecular data set of 243 bufonid lineages, with an emphasis on new sampling from the Horn of Africa, Western Eurasia, South Asia, and the Arabian Peninsula, to reconstruct the evolutionary relationships of the Arabian species. We produce a robust time-calibrated phylogeny to infer the biogeographic history of this group on and around the Arabian Peninsula. Results Our phylogenetic analyses indicate two of the endemic Arabian toad species, “Bufo” tihamicus and “Bufo” arabicus, evolved independently within the African genus Amietophrynus. We confirm the Arabian species Duttaphrynus dhufarensis is of South Asian origin, but do not find evidence for the Asian genus Duttaphrynus being present in the Horn of Africa, discrediting a previously proposed Asian bufonid dispersal event to Africa. We also do not find evidence of the African genus Amietophrynus occurring in South Asia, suggesting that unlike many other vertebrate taxa, toads have not used the Arabian Peninsula as a stepping-stone for trans-continental dispersal. Our divergence dating estimates strongly suggest the formation of the Red Sea drove simultaneous divergences between two of the Arabian species (A. tihamicus comb. nov. and A. arabicus comb. nov.) and their closest mainland African relatives in the Early Miocene. We estimate the divergence of D. dhufarensis with its closest South Asian relatives occurred in the mid to Late Miocene, suggesting the temporary or permanent land connections between the Arabian plate and Eurasia facilitated dispersal of this lineage to the Arabian Peninsula. Conclusions The Arabian bufonid assemblage, despite being comparatively depauperate with respect to surrounding continents, exemplifies the faunal pattern of the Arabian Peninsula, namely being a complex admixture of African, Western Eurasian, and South Asian elements. The historical biogeographic patterns exhibited by Arabian toads and their allies are concordant with studies of other vertebrate taxa, building support for the role of major geological events in driving simultaneous vicariance and dispersal events around the Arabian Peninsula. Although many taxa or groups exhibiting disjunct Afro-Arabian distributions appear to have dispersed more recently from the Horn of Africa via a southern land bridge or overwater dispersal, both Amietophrynus tihamicus and A. arabicus likely represent true African relicts resulting from vicariance associated with the Red Sea formation, a pattern that so far is rare among the vertebrate species investigated. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0417-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel M Portik
- Museum of Vertebrate Zoology and Department of Integrative Biology, 3101 Valley Life Sciences Building, University of California, Berkeley, CA, 94720-3160, USA.
| | - Theodore J Papenfuss
- Museum of Vertebrate Zoology and Department of Integrative Biology, 3101 Valley Life Sciences Building, University of California, Berkeley, CA, 94720-3160, USA.
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Yu D, Zhang J, Li P, Zheng R, Shao C. Do cryptic species exist in Hoplobatrachus rugulosus? An examination using four nuclear genes, the cyt b gene and the complete MT genome. PLoS One 2015; 10:e0124825. [PMID: 25875761 PMCID: PMC4395372 DOI: 10.1371/journal.pone.0124825] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 03/18/2015] [Indexed: 11/18/2022] Open
Abstract
he Chinese tiger frog Hoplobatrachus rugulosus is widely distributed in southern China, Malaysia, Myanmar, Thailand, and Vietnam. It is listed in Appendix II of CITES as the only Class II nationally-protected frog in China. The bred tiger frog known as the Thailand tiger frog, is also identified as H. rugulosus. Our analysis of the Cyt b gene showed high genetic divergence (13.8%) between wild and bred samples of tiger frog. Unexpected genetic divergence of the complete mt genome (14.0%) was also observed between wild and bred samples of tiger frog. Yet, the nuclear genes (NCX1, Rag1, Rhod, Tyr) showed little divergence between them. Despite this and their very similar morphology, the features of the mitochondrial genome including genetic divergence of other genes, different three-dimensional structures of ND5 proteins, and gene rearrangements indicate that H. rugulosus may be a cryptic species complex. Using Bayesian inference, maximum likelihood, and maximum parsimony analyses, Hoplobatrachus was resolved as a sister clade to Euphlyctis, and H. rugulosus (BT) as a sister clade to H. rugulosus (WT). We suggest that we should prevent Thailand tiger frogs (bred type) from escaping into wild environments lest they produce hybrids with Chinese tiger frogs (wild type).
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Affiliation(s)
- Danna Yu
- Institute of Ecology, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China
| | - Jiayong Zhang
- Institute of Ecology, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu Province, China
| | - Rongquan Zheng
- Institute of Ecology, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
- Institute of Special Aquaculture Source, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
| | - Chen Shao
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang Province, China
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Phylogeny and historical biogeography of Isodon (Lamiaceae): rapid radiation in south-west China and Miocene overland dispersal into Africa. Mol Phylogenet Evol 2014; 77:183-94. [PMID: 24792085 DOI: 10.1016/j.ympev.2014.04.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 04/10/2014] [Accepted: 04/16/2014] [Indexed: 11/22/2022]
Abstract
Rapid organismal radiations occurring on the Qinghai-Tibetan Plateau (QTP) and the mechanisms underlying Asia-Africa intercontinental disjunctions have both attracted much attention from evolutionary biologists. Here we use the genus Isodon (Lamiaceae), a primarily East Asian lineage with disjunct species in central and southern Africa, as a case study to shed light upon these processes. The molecular phylogeny and biogeographic history of Isodon were reconstructed using sequences of three plastid markers, the nuclear ribosomal internal transcribed spacer (nrITS), and a low-copy nuclear gene (LEAFY intron II). The evolution of chromosome numbers in this genus was also investigated using probabilistic models. Our results support a monophyletic Isodon that includes the two disjunct African species, both of which likely formed through allopolyploidy. An overland migration from Asia to Africa through Arabia during the early Miocene is proposed as the most likely explanation for the present disjunct distribution of Isodon. The opening of the Red Sea in the middle Miocene may appear to have had a major role in disrupting floristic exchange between Asia and Africa. In addition, a rapid radiation of Isodon was suggested to occur in the late Miocene. It corresponds with one of the major uplifts of the QTP and subsequent aridification events. Our results support the hypothesis that geological and climatic events play important roles in driving biological diversification of organisms distributed in the QTP area.
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Evans SE, Groenke JR, Jones MEH, Turner AH, Krause DW. New material of Beelzebufo, a hyperossified frog (Amphibia: Anura) from the late cretaceous of Madagascar. PLoS One 2014; 9:e87236. [PMID: 24489877 PMCID: PMC3905036 DOI: 10.1371/journal.pone.0087236] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/18/2013] [Indexed: 01/12/2023] Open
Abstract
The extant anuran fauna of Madagascar is exceptionally rich and almost completely endemic. In recent years, many new species have been described and understanding of the history and relationships of this fauna has been greatly advanced by molecular studies, but very little is known of the fossil history of frogs on the island. Beelzebufo ampinga, the first named pre-Holocene frog from Madagascar, was described in 2008 on the basis of numerous disarticulated cranial and postcranial elements from the Upper Cretaceous (Maastrichtian) Maevarano Formation of Madagascar. These specimens documented the presence of a hyperossified taxon that differed strikingly from extant Malagasy frogs in its large size and heavy coarse cranial exostosis. Here we describe and analyse new, articulated, and more complete material of the skull, vertebral column, and hind limb, as well as additional isolated elements discovered since 2008. μCT scans allow a detailed understanding of both internal and external morphology and permit a more accurate reconstruction. The new material shows Beelzebufo to have been even more bizarre than originally interpreted, with large posterolateral skull flanges and sculptured vertebral spine tables. The apparent absence of a tympanic membrane, the strong cranial exostosis, and vertebral morphology suggest it may have burrowed during seasonally arid conditions, which have been interpreted for the Maevarano Formation from independent sedimentological and taphonomic evidence. New phylogenetic analyses, incorporating both morphological and molecular data, continue to place Beelzebufo with hyloid rather than ranoid frogs. Within Hyloidea, Beelzebufo still groups with the South American Ceratophryidae thus continuing to pose difficulties with both biogeographic interpretations and prior molecular divergence dates.
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Affiliation(s)
- Susan E. Evans
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Joseph R. Groenke
- Department of Anatomical Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Marc E. H. Jones
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- School of Earth and Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Alan H. Turner
- Department of Anatomical Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - David W. Krause
- Department of Anatomical Sciences, Stony Brook University, Stony Brook, New York, United States of America
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26
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Samonds KE, Godfrey LR, Ali JR, Goodman SM, Vences M, Sutherland MR, Irwin MT, Krause DW. Imperfect isolation: factors and filters shaping Madagascar's extant vertebrate fauna. PLoS One 2013; 8:e62086. [PMID: 23626770 PMCID: PMC3633922 DOI: 10.1371/journal.pone.0062086] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 03/17/2013] [Indexed: 01/15/2023] Open
Abstract
Analyses of phylogenetic topology and estimates of divergence timing have facilitated a reconstruction of Madagascar's colonization events by vertebrate animals, but that information alone does not reveal the major factors shaping the island's biogeographic history. Here, we examine profiles of Malagasy vertebrate clades through time within the context of the island's paleogeographical evolution to determine how particular events influenced the arrival of the island's extant groups. First we compare vertebrate profiles on Madagascar before and after selected events; then we compare tetrapod profiles on Madagascar to contemporary tetrapod compositions globally. We show that changes from the Mesozoic to the Cenozoic in the proportions of Madagascar's tetrapod clades (particularly its increase in the representation of birds and mammals) are tied to changes in their relative proportions elsewhere on the globe. Differences in the representation of vertebrate classes from the Mesozoic to the Cenozoic reflect the effects of extinction (i.e., the non-random susceptibility of the different vertebrate clades to purported catastrophic global events 65 million years ago), and new evolutionary opportunities for a subset of vertebrates with the relatively high potential for transoceanic dispersal potential. In comparison, changes in vertebrate class representation during the Cenozoic are minor. Despite the fact that the island's isolation has resulted in high vertebrate endemism and a unique and taxonomically imbalanced extant vertebrate assemblage (both hailed as testimony to its long isolation), that isolation was never complete. Indeed, Madagascar's extant tetrapod fauna owes more to colonization during the Cenozoic than to earlier arrivals. Madagascar's unusual vertebrate assemblage needs to be understood with reference to the basal character of clades originating prior to the K-T extinction, as well as to the differential transoceanic dispersal advantage of other, more recently arriving clades. Thus, the composition of Madagascar's endemic vertebrate assemblage itself provides evidence of the island's paleogeographic history.
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Affiliation(s)
- Karen E Samonds
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America.
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27
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Poulakakis N, Kapli P, Kardamaki A, Skourtanioti E, Göcmen B, Ilgaz Ç, Kumlutaş Y, Avci A, Lymberakis P. Comparative phylogeography of six herpetofauna species in Cyprus: late Miocene to Pleistocene colonization routes. Biol J Linn Soc Lond 2013. [DOI: 10.1111/j.1095-8312.2012.02039.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Nikos Poulakakis
- Molecular Systematics Lab; Natural History Museum of Crete; University of Crete; Iraklion Crete Greece
- Biology Department; University of Crete; Iraklion Crete Greece
| | - Paschalia Kapli
- Molecular Systematics Lab; Natural History Museum of Crete; University of Crete; Iraklion Crete Greece
- Biology Department; University of Crete; Iraklion Crete Greece
| | - Afroditi Kardamaki
- Molecular Systematics Lab; Natural History Museum of Crete; University of Crete; Iraklion Crete Greece
- Biology Department; University of Crete; Iraklion Crete Greece
| | - Eirini Skourtanioti
- Molecular Systematics Lab; Natural History Museum of Crete; University of Crete; Iraklion Crete Greece
- Biology Department; University of Crete; Iraklion Crete Greece
| | - Bayram Göcmen
- Faculty of Science; Department of Biology; Ege University; 35100 Bornova/İzmir Turkey
| | - Çetin Ilgaz
- Faculty of Science; Department of Biology; Dokuz Eylül University; 35160 Buca/İzmir Turkey
| | - Yusuf Kumlutaş
- Faculty of Science; Department of Biology; Dokuz Eylül University; 35160 Buca/İzmir Turkey
| | - Aziz Avci
- Faculty of Science and Arts; Department of Biology; Adnan Menderes University; 09010 Aydın Turkey
| | - Petros Lymberakis
- Molecular Systematics Lab; Natural History Museum of Crete; University of Crete; Iraklion Crete Greece
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28
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Nair A, Gopalan SV, George S, Kumar KS, Teacher AGF, Merilä J. EndemicIndiranaFrogs of the Western Ghats Biodiversity Hotspot. ANN ZOOL FENN 2012. [DOI: 10.5735/086.049.0501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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29
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Krosch MN, Schutze MK, Armstrong KF, Graham GC, Yeates DK, Clarke AR. A molecular phylogeny for the Tribe Dacini (Diptera: Tephritidae): Systematic and biogeographic implications. Mol Phylogenet Evol 2012; 64:513-23. [DOI: 10.1016/j.ympev.2012.05.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 05/01/2012] [Accepted: 05/10/2012] [Indexed: 11/16/2022]
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30
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Hasan M, Islam MM, Khan MR, Alam MS, Kurabayashi A, Igawa T, Kuramoto M, Sumida M. Cryptic anuran biodiversity in Bangladesh revealed by mitochondrial 16S rRNA gene sequences. Zoolog Sci 2012; 29:162-72. [PMID: 22379983 DOI: 10.2108/zsj.29.162] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To survey the diversity of anuran species in Bangladesh, we compared mitochondrial 16S rRNA gene sequences (approximately 1.4 kbp) from 107 Bangladesh frog specimens. The results of genetic divergence and phylogenetic analyses incorporating data from related species revealed the occurrence of at least eight cryptic species. Hoplobatrachus tigerinus from two districts diverged considerably, indicating the involvement of a cryptic species. Two Fejervarya sp. (large and medium types) and Hylarana cf. taipehensis formed lineages distinct from related species and are probably new species. Microhyla cf. ornata differed from M. ornata with respect to type locality area and involved two distinct species. In addition, we found that Hylarana sp. and Microhyla sp. did not match congeners examined to date in either morphology or 16S rRNA sequence. The occurrence of M. fissipes was tentatively suggested. Consequently, at least, 19 species were found from Bangladesh in this study. These findings revealed a rich anuran biodiversity in Bangladesh, which is unexpected considering the rather simple topographic features of the country.
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Affiliation(s)
- Mahmudul Hasan
- Institute for Amphibian Biology, Hiroshima University, Higashihiroshima, Japan
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31
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Nair A, Gopalan SV, George S, Kumar KS, Teacher AGF, Merilä J. High cryptic diversity of endemicIndiranafrogs in the Western Ghats biodiversity hotspot. Anim Conserv 2012. [DOI: 10.1111/j.1469-1795.2012.00539.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- A. Nair
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; Helsinki; Finland
| | - S. V. Gopalan
- Chemical Biology; Rajiv Gandhi Centre for Biotechnology; Thiruvananthapuram; Kerala; India
| | - S. George
- Chemical Biology; Rajiv Gandhi Centre for Biotechnology; Thiruvananthapuram; Kerala; India
| | - K. S. Kumar
- Chemical Biology; Rajiv Gandhi Centre for Biotechnology; Thiruvananthapuram; Kerala; India
| | | | - J. Merilä
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; Helsinki; Finland
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32
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Pansook A, Khonsue W, Piyapattanakorn S, Pariyanonth P. Phylogenetic relationships among Hoplobatrachus rugulosus in Thailand as inferred from mitochondrial DNA sequences of the cytochrome-b gene (Amphibia, Anura, Dicroglossidae). Zoolog Sci 2012; 29:54-9. [PMID: 22233497 DOI: 10.2108/zsj.29.54] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A fragment (564 bp) of the mitochondrial cytochrome-b (Cyt-b) gene was studied for 73 individual rice field frogs (Hoplobatrachus rugulosus) from 18 geographical locations (populations) within Thailand. Sequence analysis revealed the presence of 12 haplotypes, with five haplotypes being represented in two or more populations, and the other seven being population-distinct haplotypes. Phylogenetic analysis by maximum parsimony, maximum likelihood, and neighbor joining analyses all placed the 12 haplotypes into two distinct and well-separated clades with high bootstrap support, reflecting the high sequence divergences between the clades (25.3-32.3%). The mountain ranges and the Isthmus of Kra are likely to have played important roles in hindering gene flow among H. rugulosus populations in Thailand. From the sequence divergence values, the two clades of H. rugulosus can be classified into two distinct species, and therefore, the strains of H. rugulosus bred in farm stocks should be restricted to a population of one clade so as to avoid cross breeding between the two clades.
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Affiliation(s)
- Anusorn Pansook
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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33
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Bain RH, Hurley MM. A Biogeographic Synthesis of the Amphibians and Reptiles of Indochina. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2011. [DOI: 10.1206/360.1] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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34
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Oaks JR. A TIME-CALIBRATED SPECIES TREE OF CROCODYLIA REVEALS A RECENT RADIATION OF THE TRUE CROCODILES. Evolution 2011; 65:3285-97. [PMID: 22023592 DOI: 10.1111/j.1558-5646.2011.01373.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jamie R Oaks
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.
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35
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Alam MS, Kurabayashi A, Hayashi Y, Sano N, Khan MR, Fujii T, Sumida M. Complete mitochondrial genomes and novel gene rearrangements in two dicroglossid frogs, Hoplobatrachus tigerinus and Euphlyctis hexadactylus, from Bangladesh. Genes Genet Syst 2011; 85:219-32. [PMID: 21041980 DOI: 10.1266/ggs.85.219] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We determined the complete nucleotide sequences of mitochondrial (mt) genomes from two dicroglossid frogs, Hoplobatrachus tigerinus (Indian Bullfrog) and Euphlyctis hexadactylus (Indian Green frog). The genome sizes are 20462 bp in H. tigerinus and 20280 bp in E. hexadactylus. Although both genomes encode the typical 37 mt genes, the following unique features are observed: 1) the ND5 genes are duplicated in H. tigerinus that have completely identical sequences, whereas duplicated ND5 genes in E. hexadactylus possessed dissimilar substitutions; 2) duplicated control region (CR) in H. tigerinus has almost identical sequences whereas single control region (CR) was found in E. hexadactylus; 3) the tRNA-Leu (CUN) gene is translocated from the LTPF tRNA cluster to downstream of ND5-1 in H. tigerinus, and the tRNA-Pro gene is translocated from the LTPF tRNA cluster to downstream of CR in E. hexadactylus; 4) pseudo tRNA-Leu (CUN) and tRNA-Pro genes are observed in E. hexadactylus; and 5) two tRNA-Met genes are encoded in both species, as observed in the previously reported dicroglossid mt genomes. Almost all observed gene rearrangements in H. tigerinus and E. hexadactylus can be explained by the tandem duplication and random loss model, except translocation of tRNA-Pro in E. hexadactylus. The novel mt genomic features found in this study may be useful for future phylogenetic studies in the dicroglossid taxa. However, the mt genome with interesting features found in the present study reveal a high level of variation of gene order and gene content, inspiring more research to understand the mechanisms behind gene and genome evolution in the dicroglossid and as well as in the amphibian taxa in future studies.
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Affiliation(s)
- Mohammad Shafiqul Alam
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Japan
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36
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Estimated evolutionary tempo of East Asian gobionid fishes (Teleostei: Cyprinidae) from mitochondrial DNA sequence data. CHINESE SCIENCE BULLETIN-CHINESE 2010. [DOI: 10.1007/s11434-010-3159-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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37
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Ren Z, Zhu B, Ma E, Wen J, Tu T, Cao Y, Hasegawa M, Zhong Y. Complete nucleotide sequence and gene arrangement of the mitochondrial genome of the crab-eating frog Fejervarya cancrivora and evolutionary implications. Gene 2009; 441:148-55. [DOI: 10.1016/j.gene.2008.09.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2008] [Revised: 09/08/2008] [Accepted: 09/10/2008] [Indexed: 10/21/2022]
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38
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Re-examination of the phylogeny of Rhacophoridae (Anura) based on mitochondrial and nuclear DNA. Mol Phylogenet Evol 2009; 50:571-9. [DOI: 10.1016/j.ympev.2008.11.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Revised: 11/26/2008] [Accepted: 11/26/2008] [Indexed: 11/19/2022]
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39
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Verneau O, Du Preez LH, Laurent V, Raharivololoniaina L, Glaw F, Vences M. The double odyssey of Madagascan polystome flatworms leads to new insights on the origins of their amphibian hosts. Proc Biol Sci 2009; 276:1575-83. [PMID: 19203917 DOI: 10.1098/rspb.2008.1530] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Polystomatid flatworms are parasites of high host specificity, which mainly infect amphibian hosts. Only one polystome species has so far been recorded from Madagascar despite the high species richness and endemicity of amphibians on this island. Out of the 86 screened Malagasy frog species, we recovered polystomes from 25 in the families Ptychadenidae and Mantellidae. Molecular phylogenetic analysis uncovered an unexpected diversity of polystome species belonging to two separate clades: one forming a lineage within the genus Metapolystoma, with one species in Ptychadena and several species in the mantellid host genera Aglyptodactylus and Boophis; and the second corresponding to an undescribed genus that was found in the species of the subfamily Mantellinae in the family Mantellidae. The phylogenetic position of the undescribed genus along with molecular dating suggests that it may have colonized Madagascar in the Late Mesozoic or Early Cainozoic. By contrast, the more recent origin of Metapolystoma in Madagascar at ca 14-2 Myr ago strongly suggests that the ancestors of Ptychadena mascareniensis colonized Madagascar naturally by overseas dispersal, carrying their Metapolystoma parasites. Our findings provide a striking example of how parasite data can supply novel insights into the biogeographic history of their hosts.
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Affiliation(s)
- Olivier Verneau
- Parasitologie Fonctionnelle et Evolutive, Université de Perpignan Via Domitia, 66860 Perpignan Cedex, France.
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40
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Kwok HF, Chen T, Ivanyi C, Shaw C. DNA in Amphibian and Reptile Venom Permits Access to Genomes without Specimen Sacrifice. GENOMICS INSIGHTS 2008. [DOI: 10.4137/gei.s1039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Amphibian defensive skin secretions and reptile venoms are rich sources of bioactive peptides with potential pharmacological/pharmaceutical applications. As amphibian and reptile populations are in rapid global decline, our research group has been developing analytical methods that permit generation of robust molecular data from non-invasive skin secretion samples and venom samples. While previously we have demonstrated that parallel proteome and venom gland transcriptome analyses can be performed on such samples, here we report the presence of DNA that facilitates the more widely-used applications of gene sequencing, such as molecular phylogenetics, in a non-invasive manner that circumvents specimen sacrifice. From this “surrogate” tissue, we acquired partial 12S and 16S rRNA gene sequences that are presented for illustration purposes. Thus from a single sample of amphibian skin secretion and reptile venom, robust and complementary proteome, transcriptome and genome data can be generated for applications in diverse scientific disciplines.
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Affiliation(s)
- Hang Fai Kwok
- Molecular Therapeutics Research, School of Pharmacy, Medical Biology Centre, Queen's University Belfast, BT9 7BL Northern Ireland, U.K
- School of Biomedical Sciences, University of Ulster, Coleraine BT52 1SA, Northern Ireland, U.K
| | - Tianbao Chen
- Molecular Therapeutics Research, School of Pharmacy, Medical Biology Centre, Queen's University Belfast, BT9 7BL Northern Ireland, U.K
| | - Craig Ivanyi
- The Arizona-Sonora Desert Museum, Kinney Road, Tucson, Arizona 85743-8918, U.S.A
| | - Chris Shaw
- Molecular Therapeutics Research, School of Pharmacy, Medical Biology Centre, Queen's University Belfast, BT9 7BL Northern Ireland, U.K
- School of Biomedical Sciences, University of Ulster, Coleraine BT52 1SA, Northern Ireland, U.K
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41
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YU GUOHUA, RAO DINGQI, YANG JUNXING, ZHANG MINGWANG. Phylogenetic relationships among Rhacophorinae (Rhacophoridae, Anura, Amphibia), with an emphasis on the Chinese species. Zool J Linn Soc 2008. [DOI: 10.1111/j.1096-3642.2008.00404.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Alam MS, Igawa T, Khan MMR, Islam MM, Kuramoto M, Matsui M, Kurabayashi A, Sumida M. Genetic divergence and evolutionary relationships in six species of genera Hoplobatrachus and Euphlyctis (Amphibia: Anura) from Bangladesh and other Asian countries revealed by mitochondrial gene sequences. Mol Phylogenet Evol 2008; 48:515-27. [PMID: 18513995 DOI: 10.1016/j.ympev.2008.04.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 04/08/2008] [Accepted: 04/13/2008] [Indexed: 10/22/2022]
Abstract
To elucidate the species composition, genetic divergence, evolutionary relationships, and divergence time of Hoplobatrachus and Euphlyctis frogs (subfamily Dicroglossinae, family Ranidae) in Bangladesh and other Asian countries, we analyzed the mitochondrial Cyt b, 12S, and 16S rRNA genes of 252 specimens. Our phylogenetic analyses showed 13 major clades corresponding to several cryptic species as well as to nominal species in the two genera. The results suggested monophyly of Asian Hoplobatrachus species, but the position of African Hoplobatrachus occipitalis was not clarified. Nucleotide divergence and phylogenetic data suggested the presence of allopatric cryptic species allied to Euphlyctis hexadactylus in Sundarban, Bangladesh and several parapatric cryptic species in the Western Ghats, India. The presence of at least two allopatric cryptic species among diverged Euphlyctis cyanophlyctis in Bangladesh, India, and Sri Lanka was also suggested. In some cases, our estimated divergence times matched the paleogeological events of South and Southeast Asian regions that may have led to the divergence of Hoplobatrachus and Euphlyctis taxa. Especially, land formation at Bangladesh (15-10Ma) may have allowed the spread of these frog taxa to Southeast Asian areas, and the aridification of central India (5.1-1.6Ma) might have affected the gene flow of widely distributed species. The present study revealed prior underestimation of the richness of the amphibian fauna in this region, indicating the possible occurrence of many cryptic species among these groups.
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Affiliation(s)
- Mohammad Shafiqul Alam
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima 739-8526, Japan
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43
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KÖHLER FRANK, GLAUBRECHT MATTHIAS. Out of Asia and into India: on the molecular phylogeny and biogeography of the endemic freshwater gastropod Paracrostoma Cossmann, 1900 (Caenogastropoda: Pachychilidae). Biol J Linn Soc Lond 2007. [DOI: 10.1111/j.1095-8312.2007.00866.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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44
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Lymberakis P, Poulakakis N, Manthalou G, Tsigenopoulos CS, Magoulas A, Mylonas M. Mitochondrial phylogeography of Rana (Pelophylax) populations in the Eastern Mediterranean region. Mol Phylogenet Evol 2007; 44:115-25. [PMID: 17467301 DOI: 10.1016/j.ympev.2007.03.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Revised: 01/12/2007] [Accepted: 03/08/2007] [Indexed: 10/23/2022]
Abstract
Phylogenetic relationships in the western fraction of Rana (Pelophylax) have not been resolved till now, even though several works have been devoted to the subject. Here, we infer phylogenetic relationships among the species distributed in the area of the Eastern Mediterranean, comparing partial mitochondrial DNA sequences for the cytochrome b and 16S rRNA genes. The obtained molecular data clearly indicate that Western Palearctic water frogs underwent a basal radiation into at least 3 major lineages (the perezi, the lessonae, and the rindibunda/bedriagae lineages) advocating an upper Miocene speciation. Moreover, we consider that within the rindibunda/bedriagae lineage, R. (P.) ridibunda, R. (P.) epeirotica, R. (P.) cretensis, R. (P.) bedriagae, R. (P.) cerigensis and R. (P.) kurtmuelleri were differentiated from a common ancestor through a series of vicariant and dispersal events, during the last approximately 5Mya, even though the specific rank of some taxa may be questionable, such as R. cerigensis in respect with R. bedriagae and R. kurtmuelleri in respect with R. ridibunda.
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Affiliation(s)
- P Lymberakis
- Natural History Museum of Crete, University of Crete, Irakleio, Crete, Greece
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45
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Sumida M, Kotaki M, Islam MM, Djong TH, Igawa T, Kondo Y, Matsui M, Anslem DS, Khonsue W, Nishioka M. Evolutionary Relationships and Reproductive Isolating Mechanisms in the Rice Frog (Fejervarya limnocharis) Species Complex from Sri Lanka, Thailand, Taiwan and Japan, Inferred from mtDNA Gene Sequences, Allozymes, and Crossing Experiments. Zoolog Sci 2007; 24:547-62. [PMID: 17867856 DOI: 10.2108/zsj.24.547] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Accepted: 01/07/2007] [Indexed: 11/17/2022]
Abstract
The rice frog (Fejervarya limnocharis) species complex is widely distributed, from India to Japan, and most prevalently in Southeast Asia. Conspicuous morphological variation has been reported for this species complex throughout its distribution range. In the present study, we used mtDNA gene sequence and allozyme analyses to infer evolutionary affinities within this species complex using eight populations (Sri Lanka; Bangkok and Ranong in Thailand; Taiwan; and Hiroshima, Okinawa, Ishigaki and Iriomote in Japan). We also conducted crossing experiments among four populations from Japan, Thailand, and Sri Lanka in order to find out more about the reproductive isolating mechanisms that might exist among the East, Southeast, and South Asian populations of this species complex. The crossing experiments revealed that the Sri Lanka population is reproductively isolated from the Hiroshima, Bangkok, and Ranong populations by complete hybrid inviability, and that the Bangkok population may be reproductively isolated from the Hiroshima population by partial hybrid inviability. Thus, it is not unreasonable to regard the Sri Lanka population as a species separated from F. limnocharis. The mtDNA and allozyme data showed that the Ranong population is most closely related to the Bangkok population in nuclear genome, but more similar to the Okinawa and Taiwan populations in mtDNA genome. The present, preliminary survey may raise questions about the species status of these particular populations and also about the nature of the biological species concept.
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Affiliation(s)
- Masayuki Sumida
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan.
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46
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Che J, Pang J, Zhao H, Wu GF, Zhao EM, Zhang YP. Molecular phylogeny of the Chinese ranids inferred from nuclear and mitochondrial DNA sequences. BIOCHEM SYST ECOL 2007. [DOI: 10.1016/j.bse.2006.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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47
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Gaubert P, Cordeiro-Estrela P. Phylogenetic systematics and tempo of evolution of the Viverrinae (Mammalia, Carnivora, Viverridae) within feliformians: Implications for faunal exchanges between Asia and Africa. Mol Phylogenet Evol 2006; 41:266-78. [PMID: 16837215 DOI: 10.1016/j.ympev.2006.05.034] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Revised: 04/03/2006] [Accepted: 05/19/2006] [Indexed: 11/24/2022]
Abstract
We reconstructed the phylogeny of the subfamily Viverrinae (Mammalia, Carnivora, Viverridae) using a approximately 3kb data set in order to reassess timing and patterns of faunal exchanges between Asia and Africa. Maximum parsimony, maximum likelihood, and Bayesian analyses of separated and combined matrices (cytochrome b, transthyretin intron I and IRBP exon 1 [IRBP1]) recovered all the well-supported relationships within feliformian lineages. In addition, IRBP1 supported paraphyly of genus Herpestes and contributed to the resolution of equivocal hypotheses within Viverridae, including (1) the monophyly of Viverrinae, and (2) Viverricula sister-group of the other terrestrial civets (Civettictis and Viverra). The combined analysis yielded a robust phylogeny, recovering monophyly of Prionodontidae and yielding high posterior probabilities for nodes (1) (Prionodontidae, Felidae) and (2) ((Felidae, Prionodontidae), ((Hyaenidae, (Herpestidae, Eupleridae)), Viverridae)). Using a fossil cross-validation method, we estimated the emergence of Viverridae at 34.29Myr, with a separation between the three traditional subfamilies Hemigalinae, Paradoxurinae, and Viverrinae during the Late Oligocene-Early Miocene. The terrestrial civets and the splits between (1) Civettictis and Viverra and (2) Poiana and Genetta were estimated to appear during the Middle Miocene. Parsimony- and maximum likelihood-based methods yielded unambiguous ancestral area reconstructions, including the Asian origin of the family Viverridae, the subfamily Viverrinae, the terrestrial civets and the clade (Civettictis, Viverra). On the grounds of genetic distances, morphological divergence, and divergence time estimates, we propose the erection of the subfamily Genettinae (including Genetta and Poiana). Our analyses suggested two independent migration events from Asia to Africa, during the Middle Miocene (Civettictis) and between the Late Oligocene and Middle Miocene (Genettinae). These results are in agreement with the hypothesis of Miocene routes from Asia to Africa-via the Arabian microplate-that would have involved several independent events of migrations. Couched in the context of the viverrid fossil record, our study calls for a revision of the paleontological data in order to fully appreciate the complexity of Afro-Asian faunal exchanges.
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Affiliation(s)
- Philippe Gaubert
- Estación Biológica de Doñana (CSIC), Departamento de Biología Aplicada, Avenida María Luisa s/n Pabellón del Perú, 41013 Sevilla, Spain.
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Bossuyt F, Brown RM, Hillis DM, Cannatella DC, Milinkovitch MC. Phylogeny and Biogeography of a Cosmopolitan Frog Radiation: Late Cretaceous Diversification Resulted in Continent-Scale Endemism in the Family Ranidae. Syst Biol 2006; 55:579-94. [PMID: 16857652 DOI: 10.1080/10635150600812551] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Ranidae is a large anuran group with a nearly cosmopolitan distribution. We investigated the phylogenetic relationships and early biogeographic history of ranid frogs, using 104 representatives of all subfamilies and families, sampled from throughout their distribution. Analyses of approximately 1570 bp of nuclear gene fragments (Rag-1, rhod, Tyr) and approximately 2100 bp of the mitochondrial genome (12S rRNA, tRNAVAL, 16S rRNA) indicate that the monophyly of several taxa can be rejected with high confidence. Our tree is characterized by a clear historical association of each major clade with one Gondwanan plate. This prevalence of continent-scale endemism suggests that plate tectonics has played a major role in the distribution of ranid frogs. We performed dispersal-vicariance analyses, as well as analyses constrained by paleogeographic data, to estimate ancestral distributions during early ranid diversification. Additionally, we used molecular clock analyses to evaluate whether these scenarios fit the temporal framework of continental breakup. Our analyses suggest that a scenario in which the ancestors of several clades (Rhacophorinae, Dicroglossinae, Raninae) reached Eurasia via the Indian subcontinent, and the ancestor of Ceratobatrachinae entered via the Australia-New Guinea plate, best fits the paleogeographic models and requires the fewest number of dispersal/vicariance events. However, several alternatives, in which part of the ranid fauna colonized Laurasia from Africa, are not significantly worse. Most importantly, all hypotheses make clear predictions as to where to expect key fossils and where to sample other living ranids, and thus constitute a strong basis for further research.
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Affiliation(s)
- Franky Bossuyt
- Biology Department, Unit of Ecology & Systematics, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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FROST DARRELR, GRANT TARAN, FAIVOVICH JULIÁN, BAIN RAOULH, HAAS ALEXANDER, HADDAD CÉLIOF, DE SÁ RAFAELO, CHANNING ALAN, WILKINSON MARK, DONNELLAN STEPHENC, RAXWORTHY CHRISTOPHERJ, CAMPBELL JONATHANA, BLOTTO BORISL, MOLER PAUL, DREWES ROBERTC, NUSSBAUM RONALDA, LYNCH JOHND, GREEN DAVIDM, WHEELER WARDC. THE AMPHIBIAN TREE OF LIFE. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2006. [DOI: 10.1206/0003-0090(2006)297[0001:tatol]2.0.co;2] [Citation(s) in RCA: 1225] [Impact Index Per Article: 68.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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van der Meijden A, Vences M, Hoegg S, Meyer A. A previously unrecognized radiation of ranid frogs in Southern Africa revealed by nuclear and mitochondrial DNA sequences. Mol Phylogenet Evol 2005; 37:674-85. [PMID: 15975829 DOI: 10.1016/j.ympev.2005.05.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Revised: 05/01/2005] [Accepted: 05/03/2005] [Indexed: 11/20/2022]
Abstract
In sub-Saharan Africa, amphibians are represented by a large number of endemic frog genera and species of incompletely clarified phylogenetic relationships. This applies especially to African frogs of the family Ranidae. We provide a molecular phylogenetic hypothesis for ranids, including 11 of the 12 African endemic genera. Analysis of nuclear (rag-1, rag-2, and rhodopsin genes) and mitochondrial markers (12S and 16S ribosomal RNA genes) provide evidence for an endemic clade of African genera of high morphological and ecological diversity thus far assigned to up to five different subfamilies: Afrana, Cacosternum, Natalobatrachus, Pyxicephalus, Strongylopus, and Tomopterna. This clade has its highest species diversity in southern Africa, suggesting a possible biogeographic connection with the Cape Floral Region. Bayesian estimates of divergence times place the initial diversification of the southern African ranid clade at approximately 62-85 million years ago, concurrent with the onset of the radiation of Afrotherian mammals. These and other African ranids (Conraua, Petropedetes, Phrynobatrachus, and Ptychadena) are placed basally within the Ranoidae with respect to the Eurasian groups, which suggests an African origin for this whole epifamily.
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Affiliation(s)
- Arie van der Meijden
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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