Characterization of New Simian Foamy Viruses from African Nonhuman Primates
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Arxiv:2101.10390V1 [Cs.LG] 25 Jan 2021 Terms of Quality, Increasing the Comparability and Reproducibil- Conservation and Education Initiatives
Introducing a Central African Primate Vocalisation Dataset for Automated Species Classification Joeri A. Zwerts1, Jelle Treep2, Casper S. Kaandorp2, Floor Meewis1, Amparo C. Koot1, Heysem Kaya3 1 Department of Biology, Utrecht University, Utrecht, The Netherlands 2 Information and Technology Services, Utrecht University, Utrecht, The Netherlands 3 Department of Information and Computing Sciences, Utrecht University, Utrecht, The Netherlands [email protected], [email protected] Abstract classifier capable of detecting species in the wild. This may also provide insights into whether this approach, of using sanctuary Automated classification of animal vocalisations is a poten- recordings, can be used to train classifiers for other species as tially powerful wildlife monitoring tool. Training robust clas- well, to aid in the development of cost-effective monitoring to sifiers requires sizable annotated datasets, which are not eas- meet modern conservation challenges. ily recorded in the wild. To circumvent this problem, we In this paper, we present the dataset, the semi-automatic an- recorded four primate species under semi-natural conditions in notation process that we used to speed up the manual annotation a wildlife sanctuary in Cameroon with the objective to train a process, and a benchmark species classification system. classifier capable of detecting species in the wild. Here, we introduce the collected dataset, describe our approach and ini- tial results of classifier development. To increase the efficiency 1.1. Related Work of the annotation process, we condensed the recordings with Multiple studies have applied automatic acoustic monitoring for an energy/change based automatic vocalisation detection. Seg- a variety of taxa including cetaceans [4], birds [5], bats [6], menting the annotated chunks into training, validation and test insects [7], amphibians [8], and forest elephants [9]. -
Analysis of 100 High-Coverage Genomes from a Pedigreed Captive Baboon Colony
Downloaded from genome.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press Resource Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony Jacqueline A. Robinson,1 Saurabh Belsare,1 Shifra Birnbaum,2 Deborah E. Newman,2 Jeannie Chan,2 Jeremy P. Glenn,2 Betsy Ferguson,3,4 Laura A. Cox,5,6 and Jeffrey D. Wall1 1Institute for Human Genetics, University of California, San Francisco, California 94143, USA; 2Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78245, USA; 3Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA; 4Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA; 5Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA; 6Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas 78245, USA Baboons (genus Papio) are broadly studied in the wild and in captivity. They are widely used as a nonhuman primate model for biomedical studies, and the Southwest National Primate Research Center (SNPRC) at Texas Biomedical Research Institute has maintained a large captive baboon colony for more than 50 yr. Unlike other model organisms, however, the genomic resources for baboons are severely lacking. This has hindered the progress of studies using baboons as a model for basic biology or human disease. Here, we describe a data set of 100 high-coverage whole-genome sequences obtained from the mixed colony of olive (P. anubis) and yellow (P. cynocephalus) baboons housed at the SNPRC. -
World's Most Endangered Primates
Primates in Peril The World’s 25 Most Endangered Primates 2016–2018 Edited by Christoph Schwitzer, Russell A. Mittermeier, Anthony B. Rylands, Federica Chiozza, Elizabeth A. Williamson, Elizabeth J. Macfie, Janette Wallis and Alison Cotton Illustrations by Stephen D. Nash IUCN SSC Primate Specialist Group (PSG) International Primatological Society (IPS) Conservation International (CI) Bristol Zoological Society (BZS) Published by: IUCN SSC Primate Specialist Group (PSG), International Primatological Society (IPS), Conservation International (CI), Bristol Zoological Society (BZS) Copyright: ©2017 Conservation International All rights reserved. No part of this report may be reproduced in any form or by any means without permission in writing from the publisher. Inquiries to the publisher should be directed to the following address: Russell A. Mittermeier, Chair, IUCN SSC Primate Specialist Group, Conservation International, 2011 Crystal Drive, Suite 500, Arlington, VA 22202, USA. Citation (report): Schwitzer, C., Mittermeier, R.A., Rylands, A.B., Chiozza, F., Williamson, E.A., Macfie, E.J., Wallis, J. and Cotton, A. (eds.). 2017. Primates in Peril: The World’s 25 Most Endangered Primates 2016–2018. IUCN SSC Primate Specialist Group (PSG), International Primatological Society (IPS), Conservation International (CI), and Bristol Zoological Society, Arlington, VA. 99 pp. Citation (species): Salmona, J., Patel, E.R., Chikhi, L. and Banks, M.A. 2017. Propithecus perrieri (Lavauden, 1931). In: C. Schwitzer, R.A. Mittermeier, A.B. Rylands, F. Chiozza, E.A. Williamson, E.J. Macfie, J. Wallis and A. Cotton (eds.), Primates in Peril: The World’s 25 Most Endangered Primates 2016–2018, pp. 40-43. IUCN SSC Primate Specialist Group (PSG), International Primatological Society (IPS), Conservation International (CI), and Bristol Zoological Society, Arlington, VA. -
Mandrillus Leucophaeus Poensis)
Ecology and Behavior of the Bioko Island Drill (Mandrillus leucophaeus poensis) A Thesis Submitted to the Faculty of Drexel University by Jacob Robert Owens in partial fulfillment of the requirements for the degree of Doctor of Philosophy December 2013 i © Copyright 2013 Jacob Robert Owens. All Rights Reserved ii Dedications To my wife, Jen. iii Acknowledgments The research presented herein was made possible by the financial support provided by Primate Conservation Inc., ExxonMobil Foundation, Mobil Equatorial Guinea, Inc., Margo Marsh Biodiversity Fund, and the Los Angeles Zoo. I would also like to express my gratitude to Dr. Teck-Kah Lim and the Drexel University Office of Graduate Studies for the Dissertation Fellowship and the invaluable time it provided me during the writing process. I thank the Government of Equatorial Guinea, the Ministry of Fisheries and the Environment, Ministry of Information, Press, and Radio, and the Ministry of Culture and Tourism for the opportunity to work and live in one of the most beautiful and unique places in the world. I am grateful to the faculty and staff of the National University of Equatorial Guinea who helped me navigate the geographic and bureaucratic landscape of Bioko Island. I would especially like to thank Jose Manuel Esara Echube, Claudio Posa Bohome, Maximilliano Fero Meñe, Eusebio Ondo Nguema, and Mariano Obama Bibang. The journey to my Ph.D. has been considerably more taxing than I expected, and I would not have been able to complete it without the assistance of an expansive list of people. I would like to thank all of you who have helped me through this process, many of whom I lack the space to do so specifically here. -
The Sex Lives of Female Olive Baboons (Papio Anubis)
Competition, coercion, and choice: The sex lives of female olive baboons (Papio anubis) DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Jessica Terese Walz Graduate Program in Anthropology The Ohio State University 2016 Dissertation Committee: Dawn M. Kitchen, Chair Douglas E. Crews W. Scott McGraw Copyrighted by Jessica Walz 2016 Abstract Since Darwin first described his theory of sexual selection, evolutionary biologists have used this framework to understand the potential for morphological, physiological, and behavioral traits to evolve within each sex. Recently, researchers have revealed important nuances in effects of sexual coercion, intersexual conflict, and sex role reversals. Among our closest relatives living in complex societies in which individuals interact outside of just the context of mating, the sexual and social lives of individuals are tightly intertwined. An important challenge to biological anthropologists is demonstrating whether female opportunities for mate choice are overridden by male- male competitive and male-female coercive strategies that dominate multi-male, multi- female societies. In this dissertation, I explore interactions between these various mechanisms of competition, coercion, and choice acting on the lives of female olive baboons to determine how they may influence expression of female behavioral and vocal signals, copulatory success with specific males, and the role of female competition in influencing mating patterns. I found females solicit specific males around the time of ovulation. Although what makes some males more preferred is less clear, there is evidence females choose males who might be better future protectors – males who will have long group tenures and are currently ascending the hierarchy. -
The Consequences of Habitat Loss and Fragmentation on the Distribution, Population Size, Habitat Preferences, Feeding and Rangin
The consequences of habitat loss and fragmentation on the distribution, population size, habitat preferences, feeding and ranging Ecology of grivet monkey (Cercopithecus aethiopes aethiops) on the human dominated habitats of north Shoa, Amhara, Ethiopia: A Study of human-grivet monkey conflict 1 Table of contents Page 1. Introduction 1 1.1. Background And Justifications 3 1.2. Statement Of The Problem 6 1.3. Objectives 7 1.3.1. General Objective 7 1.3.2. Specific Objectives 8 1.4. Research Hypotheses Under Investigation 8 2. Description Of The Study Area 8 3. Methodology 11 3.1. Habitat Stratification, Vegetation Mapping And Land Use Cover 11 Change 3.2. Distribution Pattern And Population Estimate Of Grivet Monkey 11 3.3. Behavioral Data 12 3.4. Human Grivet Monkey Conflict 15 3.5. Habitat Loss And Fragmentation 15 4. Expected Output 16 5. Challenges Of The Project 16 6. References 17 i 1. Introduction World mammals status analysis on global scale shows that primates are the most threatened mammals (Schipper et al., 2008) making them indicators for investigating vulnerability to threats. Habitat loss and destruction are often considered to be the most serious threat to many tropical primate populations because of agricultural expansion, livestock grazing, logging, and human settlement (Cowlishaw and Dunbar, 2000). Deforestation and forest fragmentation have marched together with the expansion of agricultural frontiers, resulting in both habitat loss and subdivision of the remaining habitat (Michalski and Peres, 2005). This forest degradation results in reduction in size or fragmentation of the original forest habitat (Fahrig, 2003). Habitat fragmentation is often defined as a process during which “a large expanse of habitat is transformed into a number of smaller patches of smaller total area, isolated from each other by a matrix of habitats unlike the original”. -
Emergence of Unique Primate T-Lymphotropic Viruses Among Central African Bushmeat Hunters
Emergence of unique primate T-lymphotropic viruses among central African bushmeat hunters Nathan D. Wolfe*†‡, Walid Heneine§, Jean K. Carr¶, Albert D. Garcia§, Vedapuri Shanmugam§, Ubald Tamoufe*ʈ, Judith N. Torimiroʈ, A. Tassy Prosser†, Matthew LeBretonʈ, Eitel Mpoudi-Ngoleʈ, Francine E. McCutchan*¶, Deborah L. Birx**, Thomas M. Folks§, Donald S. Burke*†, and William M. Switzer§†† Departments of *Epidemiology, †International Health, and ‡Molecular Microbiology and Immunology, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD 21205; §Laboratory Branch, Division of HIV͞AIDS Prevention, National Center for HIV, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30333; ¶Henry M. Jackson Foundation, Rockville, MD 20850; ʈArmy Health Research Center, Yaounde, Cameroon; and **Walter Reed Army Institute of Research, Rockville, MD 20850 Edited by John M. Coffin, Tufts University School of Medicine, Boston, and approved April 11, 2005 (received for review March 2, 2005) The human T-lymphotropic viruses (HTLVs) types 1 and 2 origi- There has been no evidence that STLVs cross into people nated independently and are related to distinct lineages of simian occupationally exposed to NHPs in laboratories and primate T-lymphotropic viruses (STLV-1 and STLV-2, respectively). These centers, as has been documented for other primate retroviruses, facts, along with the finding that HTLV-1 diversity appears to have including simian immunodeficiency virus, simian foamy virus resulted from multiple cross-species transmissions of STLV-1, sug- (SFV), and simian type D retrovirus (12–15). Nevertheless, gest that contact between humans and infected nonhuman pri- zoonotic transmission of STLV to human populations naturally mates (NHPs) may result in HTLV emergence. -
New Range Record for the Lesser Spot-Nosed Guenon (Cercopithecus Petaurista) in Southeastern Senegal Jill D
Anthropology Publications Anthropology 2010 New Range Record for the Lesser Spot-nosed Guenon (Cercopithecus petaurista) in Southeastern Senegal Jill D. Pruetz Iowa State University, [email protected] A. Socha Iowa State University D. Kante Fongoli Savanna Chimpanzee Project Follow this and additional works at: http://lib.dr.iastate.edu/anthr_pubs Part of the Biological and Physical Anthropology Commons, and the Other Anthropology Commons The ompc lete bibliographic information for this item can be found at http://lib.dr.iastate.edu/ anthr_pubs/12. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Anthropology at Iowa State University Digital Repository. It has been accepted for inclusion in Anthropology Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. African Primates 7 (1): 64-66 (2010) New Range Record for the Lesser Spot-nosed Guenon (Cercopithecus petaurista) in Southeastern Senegal J. D. Pruetz1, A. Socha1 & D. Kante2 1 Department of Anthropology, Iowa State University, Ames, IA USA 2 Fongoli Savanna Chimpanzee Project, Kedougou, Senegal INTRODUCTION tree height in gallery forest is 12.5 m (Pruetz et al., 2008). The lesser spot-nosed guenon (Cercopithecus petaurista The site has two ravines, referred to as Sakoto and Kerouani, Schreber 1774) was known to range, historically, in the which are separated by woodland and wooded grassland. southwestern or Casamance region of Senegal (Dupuy The various non-human primates present at Fongoli are 1971); its status in that country has been questionable in sympatric with humans living in the area. -
Intellectualism and Interesting Facts on Baboons (Papio Anubis Les.; Family: Cercopithecidae) (The Olive Baboons) in Yankari Game Reserve, Bauchi, Nigeria
International Journal of Research Studies in Zoology (IJRSZ) Volume 3, Issue 2, 2017, PP 51-55 ISSN 2454-941X http://dx.doi.org/10.20431/2454-941X.0302004 www.arcjournals.org Intellectualism and Interesting Facts on Baboons (Papio anubis Les.; Family: Cercopithecidae) (the olive baboons) in Yankari Game Reserve, Bauchi, Nigeria Ukwubile Cletus Anes Department of Science Laboratory Technology, Biology Unit, School of Science and Technology, Federal Polytechnic Bali, Nigeria. Abstract: Baboons are the type of monkey that are found in African forests and the Arabians. There are five species of baboons worldwide which are distributed in different habitats such as tropical rainforests, savannas, open woodlands and semi-arid areas. A close observation made on baboons at the Yankari Game Reserve(YGR), showed that they feed on various foods which are the reason they are known as pests as well as they are scavengers on elephant's dung. Apart from poaching activity by humans, baboons at YGR are also threatened by loss of habitat due to regular predatory activity by a lion (Pathera leo) in the reserve on the baboons. Out of the five species, only one species (Papio anubis) are found in the large population at the Yankari Game Reserve. This increase in the population of the olive baboons at the YGR has become a source of concern to tourists and researchers who visit the reserve. Due to frequent visits by people to the reserve, the baboons has developed a high level of intellectualism as well as tricks to overcome the dominance by humans encroaching their habitat. Some of these behaviours are groupings, pretence, and acrobatics. -
Colobus Guereza
Lauck et al. Retrovirology 2013, 10:107 http://www.retrovirology.com/content/10/1/107 RESEARCH Open Access Discovery and full genome characterization of two highly divergent simian immunodeficiency viruses infecting black-and-white colobus monkeys (Colobus guereza) in Kibale National Park, Uganda Michael Lauck1, William M Switzer2, Samuel D Sibley3, David Hyeroba4, Alex Tumukunde4, Geoffrey Weny4, Bill Taylor5, Anupama Shankar2, Nelson Ting6, Colin A Chapman4,7,8, Thomas C Friedrich1,3, Tony L Goldberg1,3,4 and David H O'Connor1,9* Abstract Background: African non-human primates (NHPs) are natural hosts for simian immunodeficiency viruses (SIV), the zoonotic transmission of which led to the emergence of HIV-1 and HIV-2. However, our understanding of SIV diversity and evolution is limited by incomplete taxonomic and geographic sampling of NHPs, particularly in East Africa. In this study, we screened blood specimens from nine black-and-white colobus monkeys (Colobus guereza occidentalis) from Kibale National Park, Uganda, for novel SIVs using a combination of serology and “unbiased” deep-sequencing, a method that does not rely on genetic similarity to previously characterized viruses. Results: We identified two novel and divergent SIVs, tentatively named SIVkcol-1 and SIVkcol-2, and assembled genomes covering the entire coding region for each virus. SIVkcol-1 and SIVkcol-2 were detected in three and four animals, respectively, but with no animals co-infected. Phylogenetic analyses showed that SIVkcol-1 and SIVkcol-2 form a lineage with SIVcol, previously discovered in black-and-white colobus from Cameroon. Although SIVkcol-1 and SIVkcol-2 were isolated from the same host population in Uganda, SIVkcol-1 is more closely related to SIVcol than to SIVkcol-2. -
Rapid Evolution of Animal Mitochondrial DNA (Primates/Restriction Endonuclease Cleavage Maps/Gel Electrophoresis/DNA Melting) WESLEY M
Proc. Natl. Acad. Sci. USA Vol. 76, No. 4, pp. 1967-1971, April 1979 Genetics Rapid evolution of animal mitochondrial DNA (primates/restriction endonuclease cleavage maps/gel electrophoresis/DNA melting) WESLEY M. BROWN, MATTHEW GEORGE, JR., AND ALLAN C. WILSON Department of Biochemistry, University of California, Berkeley, California 94720 Communicated by Bruce N. Ames, February 8,1979 ABSTRACT Mitochondrial DNA was purified from four lines of human (Homo sapiens) and guenon (green monkey, species of higher primates (Guinea baboon, rhesus macaque, Cercopithecus aethiops) cells used were, respectively, HeLa guenon, and human) and digested with 11 restriction endonu- (strain S3) and BSC-1. cleases. A cleavage map was constructed for the mitochondrial DNA of each species. Comparison of the maps, aligned with Preparation of mtDNA. The preparation of mtDNA from respect to the origin and direction of DNA replication, revealed cultured cells was as described (9). For preparation from liver, that the species differ from one another at most of the cleavage the samples (either fresh or frozen) were first minced, then sites. The degree of divergence in nucleotide sequence at these homogenized at high speed in a Waring blender in 5 vol of cold sites was calculated from the fraction of cleavage sites shared 10 mM NaCl/10 mM Tris/I mM EDTA buffer (pH 7.8) and by each pair of species. By plotting the degree of divergence in then treated in the same manner as the cultured cell homoge- mitochondrial DNA against time of divergence, the rate of base substitution could be calculated from the initial slope of the nates. -
AFRICAN PRIMATES the Journal of the Africa Section of the IUCN SSC Primate Specialist Group
Volume 9 2014 ISSN 1093-8966 AFRICAN PRIMATES The Journal of the Africa Section of the IUCN SSC Primate Specialist Group Editor-in-Chief: Janette Wallis PSG Chairman: Russell A. Mittermeier PSG Deputy Chair: Anthony B. Rylands Red List Authorities: Sanjay Molur, Christoph Schwitzer, and Liz Williamson African Primates The Journal of the Africa Section of the IUCN SSC Primate Specialist Group ISSN 1093-8966 African Primates Editorial Board IUCN/SSC Primate Specialist Group Janette Wallis – Editor-in-Chief Chairman: Russell A. Mittermeier Deputy Chair: Anthony B. Rylands University of Oklahoma, Norman, OK USA Simon Bearder Vice Chair, Section on Great Apes:Liz Williamson Oxford Brookes University, Oxford, UK Vice-Chair, Section on Small Apes: Benjamin M. Rawson R. Patrick Boundja Regional Vice-Chairs – Neotropics Wildlife Conservation Society, Congo; Univ of Mass, USA Mesoamerica: Liliana Cortés-Ortiz Thomas M. Butynski Andean Countries: Erwin Palacios and Eckhard W. Heymann Sustainability Centre Eastern Africa, Nanyuki, Kenya Brazil and the Guianas: M. Cecília M. Kierulff, Fabiano Rodrigues Phillip Cronje de Melo, and Maurício Talebi Jane Goodall Institute, Mpumalanga, South Africa Regional Vice Chairs – Africa Edem A. Eniang W. Scott McGraw, David N. M. Mbora, and Janette Wallis Biodiversity Preservation Center, Calabar, Nigeria Colin Groves Regional Vice Chairs – Madagascar Christoph Schwitzer and Jonah Ratsimbazafy Australian National University, Canberra, Australia Michael A. Huffman Regional Vice Chairs – Asia Kyoto University, Inuyama,