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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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). -
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, -
Miombo Ecoregion Vision Report
MIOMBO ECOREGION VISION REPORT Jonathan Timberlake & Emmanuel Chidumayo December 2001 (published 2011) Occasional Publications in Biodiversity No. 20 WWF - SARPO MIOMBO ECOREGION VISION REPORT 2001 (revised August 2011) by Jonathan Timberlake & Emmanuel Chidumayo Occasional Publications in Biodiversity No. 20 Biodiversity Foundation for Africa P.O. Box FM730, Famona, Bulawayo, Zimbabwe PREFACE The Miombo Ecoregion Vision Report was commissioned in 2001 by the Southern Africa Regional Programme Office of the World Wide Fund for Nature (WWF SARPO). It represented the culmination of an ecoregion reconnaissance process led by Bruce Byers (see Byers 2001a, 2001b), followed by an ecoregion-scale mapping process of taxa and areas of interest or importance for various ecological and bio-physical parameters. The report was then used as a basis for more detailed discussions during a series of national workshops held across the region in the early part of 2002. The main purpose of the reconnaissance and visioning process was to initially outline the bio-physical extent and properties of the so-called Miombo Ecoregion (in practice, a collection of smaller previously described ecoregions), to identify the main areas of potential conservation interest and to identify appropriate activities and areas for conservation action. The outline and some features of the Miombo Ecoregion (later termed the Miombo– Mopane Ecoregion by Conservation International, or the Miombo–Mopane Woodlands and Grasslands) are often mentioned (e.g. Burgess et al. 2004). However, apart from two booklets (WWF SARPO 2001, 2003), few details or justifications are publically available, although a modified outline can be found in Frost, Timberlake & Chidumayo (2002). Over the years numerous requests have been made to use and refer to the original document and maps, which had only very restricted distribution. -
Chapter 15 the Mammals of Angola
Chapter 15 The Mammals of Angola Pedro Beja, Pedro Vaz Pinto, Luís Veríssimo, Elena Bersacola, Ezequiel Fabiano, Jorge M. Palmeirim, Ara Monadjem, Pedro Monterroso, Magdalena S. Svensson, and Peter John Taylor Abstract Scientific investigations on the mammals of Angola started over 150 years ago, but information remains scarce and scattered, with only one recent published account. Here we provide a synthesis of the mammals of Angola based on a thorough survey of primary and grey literature, as well as recent unpublished records. We present a short history of mammal research, and provide brief information on each species known to occur in the country. Particular attention is given to endemic and near endemic species. We also provide a zoogeographic outline and information on the conservation of Angolan mammals. We found confirmed records for 291 native species, most of which from the orders Rodentia (85), Chiroptera (73), Carnivora (39), and Cetartiodactyla (33). There is a large number of endemic and near endemic species, most of which are rodents or bats. The large diversity of species is favoured by the wide P. Beja (*) CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal CEABN-InBio, Centro de Ecologia Aplicada “Professor Baeta Neves”, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal e-mail: [email protected] P. Vaz Pinto Fundação Kissama, Luanda, Angola CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal e-mail: [email protected] L. Veríssimo Fundação Kissama, Luanda, Angola e-mail: [email protected] E. -
Zimbabwe Zambia Malawi Species Checklist Africa Vegetation Map
ZIMBABWE ZAMBIA MALAWI SPECIES CHECKLIST AFRICA VEGETATION MAP BIOMES DeserT (Namib; Sahara; Danakil) Semi-deserT (Karoo; Sahel; Chalbi) Arid SAvannah (Kalahari; Masai Steppe; Ogaden) Grassland (Highveld; Abyssinian) SEYCHELLES Mediterranean SCruB / Fynbos East AFrican Coastal FOrest & SCruB DrY Woodland (including Mopane) Moist woodland (including Miombo) Tropical Rainforest (Congo Basin; upper Guinea) AFrO-Montane FOrest & Grassland (Drakensberg; Nyika; Albertine rift; Abyssinian Highlands) Granitic Indian Ocean IslandS (Seychelles) INTRODUCTION The idea of this booklet is to enable you, as a Wilderness guest, to keep a detailed record of the mammals, birds, reptiles and amphibians that you observe during your travels. It also serves as a compact record of your African journey for future reference that hopefully sparks interest in other wildlife spheres when you return home or when travelling elsewhere on our fragile planet. Although always exciting to see, especially for the first-time Africa visitor, once you move beyond the cliché of the ‘Big Five’ you will soon realise that our wilderness areas offer much more than certain flagship animal species. Africa’s large mammals are certainly a big attraction that one never tires of, but it’s often the smaller mammals, diverse birdlife and incredible reptiles that draw one back again and again for another unparalleled visit. Seeing a breeding herd of elephant for instance will always be special but there is a certain thrill in seeing a Lichtenstein’s hartebeest, cheetah or a Lilian’s lovebird – to name but a few. As a globally discerning traveller, look beyond the obvious, and challenge yourself to learn as much about all wildlife aspects and the ecosystems through which you will travel on your safari. -
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. -
Bonner Zoologische Beiträge
ZOBODAT - www.zobodat.at Zoologisch-Botanische Datenbank/Zoological-Botanical Database Digitale Literatur/Digital Literature Zeitschrift/Journal: Bonn zoological Bulletin - früher Bonner Zoologische Beiträge. Jahr/Year: 1997/1998 Band/Volume: 47 Autor(en)/Author(s): Jenkins Paulina D., Ruedi Manuel, Catzeflis Francois M. Artikel/Article: A biochemical and morphological investigation of Suncus dayi (Dobson, 1888) and discussion of relationships in Suncus Hemprich & Ehrenberg, 1833, Crocidura Wagler, 1832, and Sylvisorex Thomas, 1904 (Insectivora: Soricidae) 257-276 © Biodiversity Heritage Library, http://www.biodiversitylibrary.org/; www.zoologicalbulletin.de; www.biologiezentrum.at Bonn. zool. Beitr. Bd. 47 H. 3-4 S. 257-276 Bonn, September 1998 A biochemical and morphological investigation of Suncus dayi (Dobson, 1888) and discussion of relationships in Suncus Hemprich & Ehrenberg, 1833, Crocidura Wagler, 1832, and Sylvisorex Thomas, 1904 (Insectívora: Soricidae) Paulina Jenkins, Manuel Ruedi, and Francois M. Catzeflis Abstract. A recent field expedition in South India yielded a series of seven specimens of Suncus dayi (Dobson, 1888), a poorly known crocidurine shrew collected in high- altitude wet evergreen forests in the Nilgiri Hills. The morphology (external, cranial, dental) of this species was investigated in a comparative study with a few taxa of the genera Suncus Hemprich & Ehrenberg, 1833 (e.g. S. stoliczkanus (Anderson, 1877), 5. fellowesgordoni Phillips, 1932), Sylvisorex Thomas, 1904 (e.g. S. morio (Gray, 1862); 5. granti Thomas, 1907 group) and Crocidura Wagler, 1832 (e.g. C attenuata Milne- Edwards, 1872). A biochemical survey of isozyme variation at 32 genetic loci allowed the estimation of the genetic differentiation between S. dayi and four other white-toothed shrews: Suncus murinus (Linnaeus, 1766), Crocidura olivieri (Lesson, 1827), C fuliginosa (Blyth, 1855) and C. -
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. -
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 -
Assessing Monkeypox Virus Prevalence in Small Mammals at the Human–Animal Interface in the Democratic Republic of the Congo
viruses Article Assessing Monkeypox Virus Prevalence in Small Mammals at the Human–Animal Interface in the Democratic Republic of the Congo Jeffrey B. Doty 1,*, Jean M. Malekani 2, Lem’s N. Kalemba 2, William T. Stanley 3, Benjamin P. Monroe 1, Yoshinori U. Nakazawa 1, Matthew R. Mauldin 1 ID , Trésor L. Bakambana 2, Tobit Liyandja Dja Liyandja 2, Zachary H. Braden 1, Ryan M. Wallace 1, Divin V. Malekani 2, Andrea M. McCollum 1, Nadia Gallardo-Romero 1, Ashley Kondas 1, A. Townsend Peterson 4 ID , Jorge E. Osorio 5, Tonie E. Rocke 6, Kevin L. Karem 1, Ginny L. Emerson 1 and Darin S. Carroll 1 1 U.S. Centers for Disease Control and Prevention, Poxvirus and Rabies Branch, 1600 Clifton Rd. NE, Atlanta, GA 30333, USA; [email protected] (B.P.M.); [email protected] (Y.U.N.); [email protected] (M.R.M.); [email protected] (Z.H.B.); [email protected] (R.M.W.); [email protected] (A.M.M.); [email protected] (N.G.-R.); [email protected] (A.K.); [email protected] (K.L.K.); [email protected] (G.L.E.); [email protected] (D.S.C.) 2 University of Kinshasa, Department of Biology, P.O. Box 218 Kinshasa XI, Democratic Republic of the Congo; [email protected] (J.M.M.); [email protected] (L.N.K.); [email protected] (T.L.B.); [email protected] (T.L.D.L.); [email protected] (D.V.M.) 3 Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL 60605, USA; wstanley@fieldmuseum.org 4 Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence, KS 66045, USA; [email protected] 5 University of Wisconsin, School of Veterinary Medicine, 2015 Linden Dr., Madison, WI 53706, USA; [email protected] 6 U.S.