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Marinotti O. What is in a name? Anopheles darlingi versus Nyssorhynchus darlingi. Trends Parasitol 2021; 37:856-858. [PMID: 34219031 DOI: 10.1016/j.pt.2021.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/07/2021] [Accepted: 06/07/2021] [Indexed: 11/24/2022]
Abstract
Taxonomic reassignments were suggested for Neotropical anopheline malaria vectors, elevating four monophyletic groups Kerteszia, Lophopodomyia, Nyssorhynchus, and Stethomyia to the genus level, upending their conventional status as subgenera of the genus Anopheles. Two questions are proposed. Do the advantages of reclassification outweigh its disadvantages? Is the reclassification generally accepted and/or scientifically imperative?
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2
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Affiliation(s)
- Alain Dubois
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle CNRS, Sorbonne Université, EPHE, Université des Antilles Reptiles & Amphibiens, CP 30, 25 rue Cuvier 75005 Paris (France)
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Dubois A. Nomenclatural consequences of the Oculudentavis khaungraae case, with comments on the practice of ‘retraction’ of scientific publications. ZOOSYSTEMA 2020. [DOI: 10.5252/zoosystema2020v42a23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Alain Dubois
- Institut de Systématique, Evolution, Biodiversité (ISYEB) Muséum national d′Histoire naturelle CNRS, Sorbonne Université, EPHE, Université des Antilles Reptiles & Amphibiens, CP 30 25 rue Cuvier 75005 Paris (France)
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4
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Shoemaker TR, Nyakarahuka L, Balinandi S, Ojwang J, Tumusiime A, Mulei S, Kyondo J, Lubwama B, Sekamatte M, Namutebi A, Tusiime P, Monje F, Mayanja M, Ssendagire S, Dahlke M, Kyazze S, Wetaka M, Makumbi I, Borchert J, Zufan S, Patel K, Whitmer S, Brown S, Davis WG, Klena JD, Nichol ST, Rollin PE, Lutwama J. First Laboratory-Confirmed Outbreak of Human and Animal Rift Valley Fever Virus in Uganda in 48 Years. Am J Trop Med Hyg 2020; 100:659-671. [PMID: 30675833 PMCID: PMC6402942 DOI: 10.4269/ajtmh.18-0732] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In March 2016, an outbreak of Rift Valley fever (RVF) was identified in Kabale district, southwestern Uganda. A comprehensive outbreak investigation was initiated, including human, livestock, and mosquito vector investigations. Overall, four cases of acute, nonfatal human disease were identified, three by RVF virus (RVFV) reverse transcriptase polymerase chain reaction (RT-PCR), and one by IgM and IgG serology. Investigations of cattle, sheep, and goat samples from homes and villages of confirmed and probable RVF cases and the Kabale central abattoir found that eight of 83 (10%) animals were positive for RVFV by IgG serology; one goat from the home of a confirmed case tested positive by RT-PCR. Whole genome sequencing from three clinical specimens was performed and phylogenetic analysis inferred the relatedness of 2016 RVFV with the 2006–2007 Kenya-2 clade, suggesting previous introduction of RVFV into southwestern Uganda. An entomological survey identified three of 298 pools (1%) of Aedes and Coquillettidia species that were RVFV positive by RT-PCR. This was the first identification of RVFV in Uganda in 48 years and the 10th independent viral hemorrhagic fever outbreak to be confirmed in Uganda since 2010.
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Affiliation(s)
- Trevor R Shoemaker
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia.,Viral Special Pathogens Branch, Centers for Disease Control and Prevention-Uganda, Entebbe, Uganda
| | - Luke Nyakarahuka
- Department of Biosecurity, Ecosystems and Veterinary Public Health, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Stephen Balinandi
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention-Uganda, Entebbe, Uganda
| | - Joseph Ojwang
- Global Health Security Unit, Centers for Disease Control and Prevention-Uganda, Kampala, Uganda
| | - Alex Tumusiime
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention-Uganda, Entebbe, Uganda
| | - Sophia Mulei
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jackson Kyondo
- Department of Biosecurity, Ecosystems and Veterinary Public Health, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | | | | | | | - Fred Monje
- Ministry of Agriculture, Animal Industry and Fisheries, Kampala, Uganda
| | - Martin Mayanja
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Melissa Dahlke
- Public Health Emergency Operations Centre, Ministry of Health, Kampala, Uganda
| | - Simon Kyazze
- Public Health Emergency Operations Centre, Ministry of Health, Kampala, Uganda
| | - Milton Wetaka
- Public Health Emergency Operations Centre, Ministry of Health, Kampala, Uganda
| | - Issa Makumbi
- Public Health Emergency Operations Centre, Ministry of Health, Kampala, Uganda
| | - Jeff Borchert
- Global Health Security Unit, Centers for Disease Control and Prevention-Uganda, Kampala, Uganda
| | - Sara Zufan
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Ketan Patel
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Shannon Whitmer
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Shelley Brown
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - William G Davis
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John D Klena
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Stuart T Nichol
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Pierre E Rollin
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Julius Lutwama
- Department of Arbovirology, Emerging and Reemerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
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Abstract
BACKGROUND In order to designate the various concepts of taxa in biology, evolution and paleontology, scientists have developed various rules on how to create unique names for taxa. Different Codes of Nomenclature have been developed for animals, plants, fungi, bacteria etc., with standard sets of Rules that govern the formation, publication and application of the nomina of extant and extinct species. These Codes are the result of decades of discussions, workshops, publications and revisions. The structure and complexity of these Codes have been criticized many times by zoologists. This project aims, using the International Code of Zoological Nomenclature as a case study, to show that the structure of these Codes is better reflected and understood as networks. METHODS The majority of the text of the Code has been divided into hundreds of Nodes of different types, connected to each other with different types of Edges to form a network. The various mathematical descriptors of the entire system, as well as for the elements of the network, have been conceptually framed to help describing and understanding the Code as a network. RESULTS The network of the Code comprises 1,379 Nodes, which are connected with 11,276 Edges. The structure of the Code can be accurately described as a network, a mathematical structure that is better suited than any kind of linear text publication to reflect its structure. DISCUSSION Thinking of the Code as a network allows a better, in-depth understanding of the Code itself, as the user can navigate in a more efficient way, as well as to depict and analyze all the implied connections between the various parts of the Code that are not visible immediately. The network of the Code is an open access tool that could also help teaching, using and disseminating the Code. More importantly, this network is a powerful tool that allows identifying a priori the parts of the Code that could be potentially affected by upcoming amendment and revisions. This kind of analysis is not limited to nomenclature, as it could be applied to other fields that use complex textbooks with long editing history, such as Law, Medicine and Linguistics.
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Affiliation(s)
- Evangelos Vlachos
- CONICET - Museo Paleontológico Egidio Feruglio, Trelew, Chubut, Argentina
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6
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Viana STFL, Carvalho MRD. Squalus rancureli Fourmanoir, 1979, a new junior synonym of the blacktailed spurdog S. melanurus Fourmanoir, 1979, and updated diagnosis of S. bucephalus Last, Séret & Pogonoski, 2007 from New Caledonia (Squaliformes, Squalidae). ZOOSYSTEMA 2018. [DOI: 10.5252/zoosystema2018v40a9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Sarah T. F. L. Viana
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travess
| | - Marcelo R. De Carvalho
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travess
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Nicolas V, Mataame A, Crochet PA, Geniez P, Fahd S, Ohler A. Phylogeography and ecological niche modeling unravel the evolutionary history of the African green toad,Bufotes boulengeri boulengeri(Amphibia: Bufonidae), through the Quaternary. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
| | | | - Pierre-André Crochet
- CEFE UMR 5175, CNRS; EPHE; Université de Montpellier; Université Paul-Valéry Montpellier EPHE; Montpellier France
| | - Philippe Geniez
- PSL Research University; CEFE UMR 5175; CNRS, Université de Montpellier, Université Paul-Valéry Montpellier; EPHE; Biogéographie et Ecologie des Vertébrés; Montpellier France
| | - Soumia Fahd
- Laboratoire “Ecologie, Biodiversité et Environnement”; Département de Biologie; Faculté des Sciences de Tétouan; Université Abdelmalek Essaâdi; Tétouan Morocco
| | - Annemarie Ohler
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
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8
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Warren A, Patterson DJ, Dunthorn M, Clamp JC, Achilles‐Day UE, Aescht E, Al‐Farraj SA, Al‐Quraishy S, Al‐Rasheid K, Carr M, Day JG, Dellinger M, El‐Serehy HA, Fan Y, Gao F, Gao S, Gong J, Gupta R, Hu X, Kamra K, Langlois G, Lin X, Lipscomb D, Lobban CS, Luporini P, Lynn DH, Ma H, Macek M, Mackenzie‐Dodds J, Makhija S, Mansergh RI, Martín‐Cereceda M, McMiller N, Montagnes DJ, Nikolaeva S, Ong'ondo GO, Pérez‐Uz B, Purushothaman J, Quintela‐Alonso P, Rotterová J, Santoferrara L, Shao C, Shen Z, Shi X, Song W, Stoeck T, La Terza A, Vallesi A, Wang M, Weisse T, Wiackowski K, Wu L, Xu K, Yi Z, Zufall R, Agatha S. Beyond the "Code": A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora). J Eukaryot Microbiol 2017; 64:539-554. [PMID: 28061024 PMCID: PMC5697677 DOI: 10.1111/jeu.12391] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 10/27/2016] [Accepted: 12/21/2016] [Indexed: 11/30/2022]
Abstract
Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigations of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN-BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN-BC proposes to populate The Ciliate Guide, an online database, with biodiversity-related data and metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data.
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Affiliation(s)
- Alan Warren
- Department of Life SciencesNatural History MuseumLondonSW7 5BDUnited Kingdom
| | | | - Micah Dunthorn
- Department of EcologyUniversity of KaiserslauternKaiserslautern67663Germany
| | - John C. Clamp
- Department of Biological and Biomedical SciencesNorth Carolina Central UniversityDurhamNorth Carolina27707USA
| | - Undine E.M. Achilles‐Day
- Department of Life and Environmental SciencesBournemouth UniversityBournemouthBH12 5BBUnited Kingdom
| | - Erna Aescht
- Biology Center of the Upper Austrian MuseumLinzA‐4040Austria
| | | | | | | | - Martin Carr
- Department of Biological SciencesUniversity of HuddersfieldHuddersfieldHD1 3DHUnited Kingdom
| | - John G. Day
- Scottish Association for Marine ScienceObanPA37 1QAUnited Kingdom
| | | | | | - Yangbo Fan
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity OceanUniversity of ChinaQingdao266003China
| | - Feng Gao
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity OceanUniversity of ChinaQingdao266003China
| | - Shan Gao
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity OceanUniversity of ChinaQingdao266003China
| | - Jun Gong
- Yantai Institute of Coastal Zone ResearchChinese Academy of SciencesYantai264003China
| | - Renu Gupta
- Maitreyi CollegeUniversity of DelhiNew Delhi110021India
| | - Xiaozhong Hu
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity OceanUniversity of ChinaQingdao266003China
| | - Komal Kamra
- SGTB Khalsa CollegeUniversity of DelhiDelhi110007India
| | - Gaytha Langlois
- Department of Science & TechnologyBryant UniversitySmithfieldRhode Island02917USA
| | - Xiaofeng Lin
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life ScienceSouth China Normal UniversityGuangzhou510631China
| | - Diana Lipscomb
- Department of Biological SciencesGeorge Washington UniversityWashingtonDistrict of Columbia20052USA
| | | | - Pierangelo Luporini
- School of Biosciences and Veterinary MedicineUniversity of CamerinoCamerino (MC)62032Italy
| | - Denis H. Lynn
- Department of Integrative BiologyUniversity of GuelphGuelphONN1G 2W1Canada
| | - Honggang Ma
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity OceanUniversity of ChinaQingdao266003China
| | - Miroslav Macek
- Tropical Limnology Research Project, FES IztacalaUniversidad National Autonoma de MéxicoEdo. México 540 90Mexico
| | | | - Seema Makhija
- Acharya Narendra Dev CollegeUniversity of DelhiNew Delhi110019India
| | - Robert I. Mansergh
- Institute of Marine SciencesUniversity of PortsmouthPortsmouthPO4 9LYUnited Kingdom
| | - Mercedes Martín‐Cereceda
- Departamento de Microbiología III, Facultad de BiologíaUniversidad Complutense de MadridMadrid28040Spain
| | - Nettie McMiller
- Department of Biological and Biomedical SciencesNorth Carolina Central UniversityDurhamNorth Carolina27707USA
| | - David J.S. Montagnes
- Institute of Integrative BiologyUniversity of LiverpoolLiverpoolL69 7ZBUnited Kingdom
| | - Svetlana Nikolaeva
- Department of Earth SciencesNatural History MuseumLondonSW7 5BDUnited Kingdom
- Kazan Federal University, Kremlyovskaya ul. 18Kazan 420000Russia
| | | | - Blanca Pérez‐Uz
- Departamento de Microbiología III, Facultad de BiologíaUniversidad Complutense de MadridMadrid28040Spain
| | | | - Pablo Quintela‐Alonso
- Departamento de Microbiología III, Facultad de BiologíaUniversidad Complutense de MadridMadrid28040Spain
| | - Johana Rotterová
- Department of ZoologyCharles University in PraguePrague12744Czech Republic
| | | | - Chen Shao
- Key Laboratory of Biomedical Information EngineeringXi'an Jiaotong UniversityXi'an710049China
| | - Zhuo Shen
- Research Center of Hydrobiology, College of Life Science and TechnologyJinan UniversityGuangzhou510632China
| | - Xinlu Shi
- College of Life and Environmental SciencesHangzhou Normal UniversityHangzhou310036China
| | - Weibo Song
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity OceanUniversity of ChinaQingdao266003China
| | - Thorsten Stoeck
- Department of EcologyUniversity of KaiserslauternKaiserslautern67663Germany
| | - Antonietta La Terza
- School of Biosciences and Veterinary MedicineUniversity of CamerinoCamerino (MC)62032Italy
| | - Adriana Vallesi
- School of Biosciences and Veterinary MedicineUniversity of CamerinoCamerino (MC)62032Italy
| | - Mei Wang
- Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity OceanUniversity of ChinaQingdao266003China
| | - Thomas Weisse
- Research Institute for LimnologyUniversity of InnsbruckMondsee5310Austria
| | | | - Lei Wu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life ScienceSouth China Normal UniversityGuangzhou510631China
| | - Kuidong Xu
- Institute of OceanologyChinese Academy of SciencesQingdao266071China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life ScienceSouth China Normal UniversityGuangzhou510631China
| | - Rebecca Zufall
- Department of Biology and BiochemistryUniversity of HoustonHoustonTexas77006‐5001USA
| | - Sabine Agatha
- Department of Ecology and EvolutionUniversity of SalzburgSalzburgA‐5020Austria
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Nicolson N, Challis K, Tucker A, Knapp S. Impact of e-publication changes in the International Code of Nomenclature for algae, fungi and plants (Melbourne Code, 2012) - did we need to "run for our lives"? BMC Evol Biol 2017; 17:116. [PMID: 28545387 PMCID: PMC5445455 DOI: 10.1186/s12862-017-0961-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/09/2017] [Indexed: 11/20/2022] Open
Abstract
Background At the Nomenclature Section of the XVIII International Botanical Congress in Melbourne, Australia (IBC), the botanical community voted to allow electronic publication of nomenclatural acts for algae, fungi and plants, and to abolish the rule requiring Latin descriptions or diagnoses for new taxa. Since the 1st January 2012, botanists have been able to publish new names in electronic journals and may use Latin or English as the language of description or diagnosis. Results Using data on vascular plants from the International Plant Names Index (IPNI) spanning the time period in which these changes occurred, we analysed trajectories in publication trends and assessed the impact of these new rules for descriptions of new species and nomenclatural acts. The data show that the ability to publish electronically has not “opened the floodgates” to an avalanche of sloppy nomenclature, but concomitantly neither has there been a massive expansion in the number of names published, nor of new authors and titles participating in publication of botanical nomenclature. Conclusions The e-publication changes introduced in the Melbourne Code have gained acceptance, and botanists are using these new techniques to describe and publish their work. They have not, however, accelerated the rate of plant species description or participation in biodiversity discovery as was hoped. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0961-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicky Nicolson
- Biodiversity Informatics & Spatial Analysis, Royal Botanic Gardens, Kew, Richmond Surrey, TW9 3AA, UK.,Department of Computer Science, Brunel University London, Uxbridge, UB8 3PH, UK
| | | | - Allan Tucker
- Department of Computer Science, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Sandra Knapp
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
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Weigmann S. Reply to Borsa (2017): Comment on 'Annotated checklist of the living sharks, batoids and chimaeras (Chondrichthyes) of the world, with a focus on biogeographical diversity by Weigmann (2016)'. J Fish Biol 2017; 90:1176-1181. [PMID: 28026873 DOI: 10.1111/jfb.13234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/01/2016] [Indexed: 06/06/2023]
Affiliation(s)
- S Weigmann
- Elasmo-Lab, Elasmobranch Research Laboratory, Schlägertwiete 5b, 21335, Lüneburg, Germany
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11
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Kirejtshuk AG, Nel A, Kirejtshuk PA. Taxonomy of the reticulate beetles of the subfamily Cupedinae (Coleoptera, Archostemata), with a review of the historical development. ACTA ACUST UNITED AC 2016; 13:61-190. [DOI: 10.15298/invertzool.13.2.01] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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