Bonner Zoologische Beiträge
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An R Package for Visualizing Bayesian Phylogenetic Analyses from Revbayes
bioRxiv preprint doi: https://doi.org/10.1101/2021.05.10.443470; this version posted May 11, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes Carrie M. Tribble1, 2, 3, ∗, William A. Freyman4, Michael J. Landis5, Jun Ying Lim6, Joelle¨ Barido-Sottani7, Bjørn Tore Kopperud8, 9, Sebastian Hohna¨ 8, 9, and Michael R. May1, 2 1Department of Integrative Biology University of California, Berkeley, CA 94709, USA 2University Herbarium, University of California, Berkeley, CA 94709, USA 3Current address: School of Life Sciences, University of Hawai‘i at M¯anoa,Honolulu, HI, 96822, USA 423andMe, Inc., Sunnyvale, CA, 94086, USA 5Department of Biology, Washington University in St. Louis, MO 63130, USA 6School of Biological Sciences, Nanyang Technological University, Singapore 639798 7Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA 8GeoBio-Center, Ludwig-Maximilians-Universit¨atM¨unchen,80333 Munich, Germany 9Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universit¨atM¨unchen,80333 Munich, Germany ∗E-mail: [email protected] Summary 1. Statistical phylogenetic methods are the foundation for a wide range of evolutionary and epidemiological stud- ies. However, as these methods grow increasingly complex, users often encounter significant challenges with summarizing, visualizing, and communicating their key results. 2. We present RevGadgets, an R package for creating publication-quality figures from the results of a large variety of phylogenetic analyses performed in RevBayes (and other phylogenetic software packages). -
Wild Mammals of the Annapurna Conservation Area Cggk"0F{ ;+/If0f If]Qsf :Tgwf/L Jgohgt' Wild Mammals of the Annapurna Conservation Area - 2019
Wild Mammals of the Annapurna Conservation Area cGgk"0f{ ;+/If0f If]qsf :tgwf/L jGohGt' Wild Mammals of the Annapurna Conservation Area - 2019 ISBN 978-9937-8522-8-9978-9937-8522-8-9 9 789937 852289 National Trust for Nature Conservation Annapurna Conservation Area Project Khumaltar, Lalitpur, Nepal Hariyo Kharka, Pokhara, Kaski, Nepal National Trust for Nature Conservation P.O. Box: 3712, Kathmandu, Nepal P.O. Box: 183, Kaski, Nepal Tel: +977-1-5526571, 5526573, Fax: +977-1-5526570 Tel: +977-61-431102, 430802, Fax: +977-61-431203 Annapurna Conservation Area Project Email: [email protected] Email: [email protected] Website: www.ntnc.org.np Website: www.ntnc.org.np 2019 Wild Mammals of the Annapurna Conservation Area cGgk"0f{ ;+/If0f If]qsf :tgwf/L jGohGt' National Trust for Nature Conservation Annapurna Conservation Area Project 2019 Wild Mammals of the Annapurna Conservation Area cGgk"0f{ ;+/If0f If]qsf :tgwf/L jGohGt' Published by © NTNC-ACAP, 2019 All rights reserved Any reproduction in full or in part must mention the title and credit NTNC-ACAP. Reviewers Prof. Karan Bahadur Shah (Himalayan Nature), Dr. Naresh Subedi (NTNC, Khumaltar), Dr. Will Duckworth (IUCN) and Yadav Ghimirey (Friends of Nature, Nepal). Compilers Rishi Baral, Ashok Subedi and Shailendra Kumar Yadav Suggested Citation Baral R., Subedi A. & Yadav S.K. (Compilers), 2019. Wild Mammals of the Annapurna Conservation Area. National Trust for Nature Conservation, Annapurna Conservation Area Project, Pokhara, Nepal. First Edition : 700 Copies ISBN : 978-9937-8522-8-9 Front Cover : Yellow-bellied Weasel (Mustela kathiah), back cover: Orange- bellied Himalayan Squirrel (Dremomys lokriah). -
Solenodon Genome Reveals Convergent Evolution of Venom in Eulipotyphlan Mammals
Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals Nicholas R. Casewella,1, Daniel Petrasb,c, Daren C. Cardd,e,f, Vivek Suranseg, Alexis M. Mychajliwh,i,j, David Richardsk,l, Ivan Koludarovm, Laura-Oana Albulescua, Julien Slagboomn, Benjamin-Florian Hempelb, Neville M. Ngumk, Rosalind J. Kennerleyo, Jorge L. Broccap, Gareth Whiteleya, Robert A. Harrisona, Fiona M. S. Boltona, Jordan Debonoq, Freek J. Vonkr, Jessica Alföldis, Jeremy Johnsons, Elinor K. Karlssons,t, Kerstin Lindblad-Tohs,u, Ian R. Mellork, Roderich D. Süssmuthb, Bryan G. Fryq, Sanjaya Kuruppuv,w, Wayne C. Hodgsonv, Jeroen Kooln, Todd A. Castoed, Ian Barnesx, Kartik Sunagarg, Eivind A. B. Undheimy,z,aa, and Samuel T. Turveybb aCentre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom; bInstitut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany; cCollaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093; dDepartment of Biology, University of Texas at Arlington, Arlington, TX 76010; eDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; fMuseum of Comparative Zoology, Harvard University, Cambridge, MA 02138; gEvolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, 560012 Bangalore, India; hDepartment of Biology, Stanford University, Stanford, CA 94305; iDepartment of Rancho La Brea, Natural History Museum of Los Angeles County, Los Angeles, -
Molecular Phylogenetics of Shrews (Mammalia: Soricidae) Reveal Timing of Transcontinental Colonizations
Molecular Phylogenetics and Evolution 44 (2007) 126–137 www.elsevier.com/locate/ympev Molecular phylogenetics of shrews (Mammalia: Soricidae) reveal timing of transcontinental colonizations Sylvain Dubey a,*, Nicolas Salamin a, Satoshi D. Ohdachi b, Patrick Barrie`re c, Peter Vogel a a Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland b Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan c Laboratoire Ecobio UMR 6553, CNRS, Universite´ de Rennes 1, Station Biologique, F-35380, Paimpont, France Received 4 July 2006; revised 8 November 2006; accepted 7 December 2006 Available online 19 December 2006 Abstract We sequenced 2167 base pairs (bp) of mitochondrial DNA cytochrome b and 16S, and 1390 bp of nuclear genes BRCA1 and ApoB in shrews taxa (Eulipotyphla, family Soricidae). The aim was to study the relationships at higher taxonomic levels within this family, and in particular the position of difficult clades such as Anourosorex and Myosorex. The data confirmed two monophyletic subfamilies, Soric- inae and Crocidurinae. In the former, the tribes Anourosoricini, Blarinini, Nectogalini, Notiosoricini, and Soricini were supported. The latter was formed by the tribes Myosoricini and Crocidurini. The genus Suncus appeared to be paraphyletic and included Sylvisorex.We further suggest a biogeographical hypothesis, which shows that North America was colonized by three independent lineages of Soricinae during middle Miocene. Our hypothesis is congruent with the first fossil records for these taxa. Using molecular dating, the first exchang- es between Africa and Eurasia occurred during the middle Miocene. The last one took place in the Late Miocene, with the dispersion of the genus Crocidura through the old world. -
Terrestrial Small Mammals (Soricidae and Muridae) from the Gamba Complex of Protected Areas, Gabon: Species Composition and Comparison of Sampling Techniques
Terrestrial Small Mammals (Soricidae and Muridae) from the Gamba Complex of Protected Areas, Gabon: Species Composition and Comparison of Sampling Techniques Carrie 0'BRIEN\ William McSHEA^ Sylvain GUIMONDOU^ Patrick BARRIERE^ and Michael CARLETON^ 1 Introduction In this paper, we document species of terrestrial insectivores (Soricidae) and rodents (Muridae) The Guineo-Congolian region encompasses 2.8 mil- weighing less than 100 g that occur in the Gamba lion km"^ of lowland rainforest stretching from the Complex, compare faunal composition between coastal regions of West Africa to eastern Democratic coastal and inland sites, and test the success of dif- Republic of Congo (White 2001). The altitude is less ferent sampling protocols. In addition, we discuss than 1000 m except for a few higher peaks, and the our findings in the context of other mammal surveys rainfall averages 1600-2000 mm per year The region conducted in lowland rainforests of Central Africa. is renowned for both its plant and animal diversity, with an estimated 8000 species of plants (80% 2 Study Area endemic. White 1983) and 270 species of lowland mammals belonging to 120 genera (Grubb 2001, The Gamba Complex in southern Gabon comprises White 2001). Gabon, in the heart of the Guineo- the Ndogo and Ngové lagoons and their drainages and Congolian region, has some 80% of its original trop- encompasses over 11,000 km^ of coastal and inland ical moist forest remaining, which is the highest of rainforest. The major habitat types within the Complex all West, Central, and East African rainforest coun- include coastal scrub forest, mangrove forest, savan- tries (Naughton-Treves and Weber 2001). -
Alexis Museum Loan NM
STANFORD UNIVERSITY STANFORD, CALIFORNIA 94305-5020 DEPARTMENT OF BIOLOGY PH. 650.725.2655 371 Serrra Mall FAX 650.723.0589 http://www.stanford.edu/group/hadlylab/ [email protected] 4/26/13 Joseph A. Cook Division of Mammals The Museum of Southwestern Biology at the University of New Mexico Dear Joe: I am writing on behalf of my graduate student, Alexis Mychajliw and her collaborator, Nat Clarke, to request the sampling of museum specimens (tissue, skins, skeletons) for DNA extraction for use in our study on the evolution of venom genes within Eulipotyphlan mammals. Please find included in this request the catalogue numbers of the desired specimens, as well as a summary of the project in which they will be used. We have prioritized the use of frozen or ethanol preserved tissues to avoid the destruction of museum skins, and seek tissue samples from other museums if only skins are available for a species at MSB. The Hadly lab has extensive experience in the non-destructive sampling of specimens for genetic analyses. Thank you for your consideration and assistance with our research. Please contact Alexis ([email protected]) with any questions or concerns regarding our project or sampling protocols, or for any additional information necessary for your decision and the processing of this request. Alexis is a first-year student in my laboratory at Stanford and her project outline is attached. As we are located at Stanford University, we are unable to personally pick up loan materials from the MSB. We request that you ship materials to us in ethanol or buffer. -
Talpa Europaea), Captured in Central Poland in August 2013
www.nature.com/scientificreports OPEN Isolation and partial characterization of a highly divergent lineage of hantavirus Received: 25 October 2015 Accepted: 18 January 2016 from the European mole (Talpa Published: 19 February 2016 europaea) Se Hun Gu1, Mukesh Kumar1, Beata Sikorska2, Janusz Hejduk3, Janusz Markowski3, Marcin Markowski4, Paweł P. Liberski2 & Richard Yanagihara1 Genetically distinct hantaviruses have been identified in five species of fossorial moles (order Eulipotyphla, family Talpidae) from Eurasia and North America. Here, we report the isolation and partial characterization of a highly divergent hantavirus, named Nova virus (NVAV), from lung tissue of a European mole (Talpa europaea), captured in central Poland in August 2013. Typical hantavirus-like particles, measuring 80–120 nm in diameter, were found in NVAV-infected Vero E6 cells by transmission electron microscopy. Whole-genome sequences of the isolate, designated NVAV strain Te34, were identical to that amplified from the original lung tissue, and phylogenetic analysis of the full-length L, M and S segments, using maximum-likelihood and Bayesian methods, showed that NVAV was most closely related to hantaviruses harbored by insectivorous bats, consistent with an ancient evolutionary origin. Infant Swiss Webster mice, inoculated with NVAV by the intraperitoneal route, developed weight loss and hyperactivity, beginning at 16 days, followed by hind-limb paralysis and death. High NVAV RNA copies were detected in lung, liver, kidney, spleen and brain by quantitative real-time RT-PCR. Neuropathological examination showed astrocytic and microglial activation and neuronal loss. The first mole-borne hantavirus isolate will facilitate long-overdue studies on its infectivity and pathogenic potential in humans. -
BONNER ZOOLOGISCHE MONOGRAPHIEN, Nr
© Biodiversity Heritage Library, http://www.biodiversitylibrary.org/; www.zoologicalbulletin.de; www.zobodat.at THE SHREWS OF NIGERIA (MAMMALIA: SORICIDAE) by R. HUTTERER and D. C. D. HAPPOLD "luS. COMP. ZOOL L/PPARY MAY 26 1PR3 HAR VARD UNIVERSITY BONNER ZOOLOGISCHE MONOGRAPHIEN, Nr. 18 1983 Herausgeber: ZOOLOGISCHES FORSCHUNGSINSTITUT UND MUSEUM ALEXANDER KOENIG BONN © Biodiversity Heritage Library, http://www.biodiversitylibrary.org/; www.zoologicalbulletin.de; www.zobodat.at BONNER ZOOLOGISCHE MONOGRAPHIEN Die Serie wird vom Zoologischen Forschungsinstitut und Museum Alexander Koenig herausgegeben und bringt Originalarbeiten, die für eine Unterbringung in den ,, Bonner Zoologischen Beiträgen" zu lang sind und eine Veröffentlichung als Monographie rechtfertigen. Anfragen bezüglich der Vorlage von Manuskripten und Bestellungen sind an die Schriftleitung zu richten. This series of monographs, published by the Zoological Research Institute and Museum Alexander Koenig, has been established for original contributions too long for inclusion in ,, Bonner Zoologische Beiträge". Correspondence concerning manuscripts for publication and purchase orders should be addressed to the editor. L' Institut de Recherches Zoologiques et Museum Alexander Koenig a etabli cette serie de monographies pour pouvoir publier des travaux zoologiques trop longs pour etre inclus dans les ,, Bonner Zoologische Beiträge". Toute correspondance concernant des manuscrits pour cette serie ou des commandes doivent etre adressees ä l'editeur. BONNER ZOOLOGISCHE MONOGRAPHIEN, Nr. 18, 1983 Preis 15,— DM Schriftleitung/Editor: G. Rheinwald Zoologisches Forschungsinstitut und Museum Alexander Koenig Adenauerallee 150—164, 5300 Bonn, Germany Druck: Rheinischer Landwirtschafts-Verlag G.m.b.H., Bonn ISSN 0302 — 67 IX © Biodiversity Heritage Library, http://www.biodiversitylibrary.org/; www.zoologicalbulletin.de; www.zobodat.at THE SHREWS OF NIGERIA (MAMMALIA: SORICIDAE) R. -
Bonner Zoologische Beiträge Band 56 Heft 3 Seiten 151-157 Bonn, September 2009
© Biodiversity Heritage Library, http://www.biodiversitylibrary.org/; www.zoologicalbulletin.de; www.biologiezentrum.at Bonner zoologische Beiträge Band 56 Heft 3 Seiten 151-157 Bonn, September 2009 A tiny new species of Sylvisorex (Mammalia: Soricidae) from the Bamenda Highlands, Cameroon Rainer Hutterer', Jan Riegert^ & Ondfej Sedlácek-^ ' Zoologisches Forschungsmuseum Alexander Koenig, Bonn, GeiTnany; - University of South Bohemia, Ceské Budéjovice, Czech Republic; Charles University, Praha, Czech Republic Abstract. A new species of shrew, Sylvisorex silvanonim n. sp., is described from specimens collected near Lake Bam- bili in the Bamenda Highlands of North West Cameroon. It is one of the smallest species of the genus occurrnig in the highlands of Cameroon and may be the sister taxon to 5. vitlcanontm from eastern Africa. Together with the rodents Colomys eisentrauti and Lophwomys eisentraiiti, the new species fonns a set of species currently known only from the Lake Bam- bili area. Keywords. Africa, Cameroon, Lake Bambili, forest, shrew, Sylvisorex, new species. 1. INTRODUCTION Shrews of the genus Sylvisorex Thomas, 1904 are restrict- Pellets of the African grass owl Tyto capensis were col- ed to lowland and montane forests of central Africa, from lected during November 200 1 in the lower of the two Cameroon/Nigeria in the northwest to Tanzania in the Bainbili volcano craters, about 8 kin SE from Bamenda southeast. Currently 12 extant species are recognized city, Bamenda Highlands, Cameroon (5° 55' N, 10° 14' (Hutterer 2005), but recent fieldwork has yielded fur- E, 2 400 m a.s.l.) (Riegert et al. 2008). Both volcano ther species that will be described in the near future. -
List of 28 Orders, 129 Families, 598 Genera and 1121 Species in Mammal Images Library 31 December 2013
What the American Society of Mammalogists has in the images library LIST OF 28 ORDERS, 129 FAMILIES, 598 GENERA AND 1121 SPECIES IN MAMMAL IMAGES LIBRARY 31 DECEMBER 2013 AFROSORICIDA (5 genera, 5 species) – golden moles and tenrecs CHRYSOCHLORIDAE - golden moles Chrysospalax villosus - Rough-haired Golden Mole TENRECIDAE - tenrecs 1. Echinops telfairi - Lesser Hedgehog Tenrec 2. Hemicentetes semispinosus – Lowland Streaked Tenrec 3. Microgale dobsoni - Dobson’s Shrew Tenrec 4. Tenrec ecaudatus – Tailless Tenrec ARTIODACTYLA (83 genera, 142 species) – paraxonic (mostly even-toed) ungulates ANTILOCAPRIDAE - pronghorns Antilocapra americana - Pronghorn BOVIDAE (46 genera) - cattle, sheep, goats, and antelopes 1. Addax nasomaculatus - Addax 2. Aepyceros melampus - Impala 3. Alcelaphus buselaphus - Hartebeest 4. Alcelaphus caama – Red Hartebeest 5. Ammotragus lervia - Barbary Sheep 6. Antidorcas marsupialis - Springbok 7. Antilope cervicapra – Blackbuck 8. Beatragus hunter – Hunter’s Hartebeest 9. Bison bison - American Bison 10. Bison bonasus - European Bison 11. Bos frontalis - Gaur 12. Bos javanicus - Banteng 13. Bos taurus -Auroch 14. Boselaphus tragocamelus - Nilgai 15. Bubalus bubalis - Water Buffalo 16. Bubalus depressicornis - Anoa 17. Bubalus quarlesi - Mountain Anoa 18. Budorcas taxicolor - Takin 19. Capra caucasica - Tur 20. Capra falconeri - Markhor 21. Capra hircus - Goat 22. Capra nubiana – Nubian Ibex 23. Capra pyrenaica – Spanish Ibex 24. Capricornis crispus – Japanese Serow 25. Cephalophus jentinki - Jentink's Duiker 26. Cephalophus natalensis – Red Duiker 1 What the American Society of Mammalogists has in the images library 27. Cephalophus niger – Black Duiker 28. Cephalophus rufilatus – Red-flanked Duiker 29. Cephalophus silvicultor - Yellow-backed Duiker 30. Cephalophus zebra - Zebra Duiker 31. Connochaetes gnou - Black Wildebeest 32. Connochaetes taurinus - Blue Wildebeest 33. Damaliscus korrigum – Topi 34. -
2014 Annual Reports of the Trustees, Standing Committees, Affiliates, and Ombudspersons
American Society of Mammalogists Annual Reports of the Trustees, Standing Committees, Affiliates, and Ombudspersons 94th Annual Meeting Renaissance Convention Center Hotel Oklahoma City, Oklahoma 6-10 June 2014 1 Table of Contents I. Secretary-Treasurers Report ....................................................................................................... 3 II. ASM Board of Trustees ............................................................................................................ 10 III. Standing Committees .............................................................................................................. 12 Animal Care and Use Committee .......................................................................... 12 Archives Committee ............................................................................................... 14 Checklist Committee .............................................................................................. 15 Conservation Committee ....................................................................................... 17 Conservation Awards Committee .......................................................................... 18 Coordination Committee ....................................................................................... 19 Development Committee ........................................................................................ 20 Education and Graduate Students Committee ....................................................... 22 Grants-in-Aid Committee -
Urotrichus Talpoides)
Molecular phylogeny of a newfound hantavirus in the Japanese shrew mole (Urotrichus talpoides) Satoru Arai*, Satoshi D. Ohdachi†, Mitsuhiko Asakawa‡, Hae Ji Kang§, Gabor Mocz¶, Jiro Arikawaʈ, Nobuhiko Okabe*, and Richard Yanagihara§** *Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan; †Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan; ‡School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan; §John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813; ¶Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96822; and ʈInstitute for Animal Experimentation, Hokkaido University, Sapporo 060-8638, Japan Communicated by Ralph M. Garruto, Binghamton University, Binghamton, NY, September 10, 2008 (received for review August 8, 2008) Recent molecular evidence of genetically distinct hantaviruses in primers based on the TPMV genome, we have targeted the shrews, captured in widely separated geographical regions, cor- discovery of hantaviruses in shrew species from widely separated roborates decades-old reports of hantavirus antigens in shrew geographical regions, including the Chinese mole shrew (Anouro- tissues. Apart from challenging the conventional view that rodents sorex squamipes) from Vietnam (21), Eurasian common shrew are the principal reservoir hosts, the recently identified soricid- (Sorex araneus) from Switzerland (22), northern short-tailed shrew borne hantaviruses raise the possibility that other soricomorphs, (Blarina brevicauda), masked shrew (Sorex cinereus), and dusky notably talpids, similarly harbor hantaviruses. In analyzing RNA shrew (Sorex monticolus) from the United States (23, 24) and Ussuri extracts from lung tissues of the Japanese shrew mole (Urotrichus white-toothed shrew (Crocidura lasiura) from Korea (J.-W.