1
|
Bonnin N, Piel AK, Brown RP, Li Y, Connell JA, Avitto AN, Boubli JP, Chitayat A, Giles J, Gundlapally MS, Lipende I, Lonsdorf EV, Mjungu D, Mwacha D, Pintea L, Pusey AE, Raphael J, Wich SA, Wilson ML, Wroblewski EE, Hahn BH, Stewart FA. Barriers to chimpanzee gene flow at the south-east edge of their distribution. Mol Ecol 2023; 32:3842-3858. [PMID: 37277946 PMCID: PMC10421595 DOI: 10.1111/mec.16986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023]
Abstract
Populations on the edge of a species' distribution may represent an important source of adaptive diversity, yet these populations tend to be more fragmented and are more likely to be geographically isolated. Lack of genetic exchanges between such populations, due to barriers to animal movement, can not only compromise adaptive potential but also lead to the fixation of deleterious alleles. The south-eastern edge of chimpanzee distribution is particularly fragmented, and conflicting hypotheses have been proposed about population connectivity and viability. To address this uncertainty, we generated both mitochondrial and MiSeq-based microsatellite genotypes for 290 individuals ranging across western Tanzania. While shared mitochondrial haplotypes confirmed historical gene flow, our microsatellite analyses revealed two distinct clusters, suggesting two populations currently isolated from one another. However, we found evidence of high levels of gene flow maintained within each of these clusters, one of which covers an 18,000 km2 ecosystem. Landscape genetic analyses confirmed the presence of barriers to gene flow with rivers and bare habitats highly restricting chimpanzee movement. Our study demonstrates how advances in sequencing technologies, combined with the development of landscape genetics approaches, can resolve ambiguities in the genetic history of critical populations and better inform conservation efforts of endangered species.
Collapse
Affiliation(s)
- Noémie Bonnin
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
| | - Alex K. Piel
- Department of Anthropology, University College London, London, UK
| | - Richard P. Brown
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
| | - Yingying Li
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jesse A. Connell
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alexa N. Avitto
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jean P. Boubli
- School of Science, Engineering & Environment, University of Salford, Salford, UK
| | - Adrienne Chitayat
- Institute of Biodiversity and Ecological Dynamics, University of Amsterdam, The Netherlands
| | - Jasmin Giles
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Madhurima S. Gundlapally
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Iddi Lipende
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Elizabeth V. Lonsdorf
- Department of Psychology, Franklin and Marshall College, Lancaster, PA 17604, USA
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Deus Mjungu
- Gombe Stream Research Centre, The Jane Goodall Institute–Tanzania, P.O. Box 1182, Kigoma, Tanzania
| | - Dismas Mwacha
- Gombe Stream Research Centre, The Jane Goodall Institute–Tanzania, P.O. Box 1182, Kigoma, Tanzania
| | - Lilian Pintea
- Conservation Science Department, the Jane Goodall Institute, Washington, DC, 20036, USA
| | - Anne E. Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | | | - Serge A. Wich
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
- Institute of Biodiversity and Ecological Dynamics, University of Amsterdam, The Netherlands
| | - Michael L. Wilson
- Department of Anthropology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
- Institute on the Environment, University of Minnesota, St. Paul, MN 55108, USA
| | | | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Fiona A. Stewart
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK
- Department of Anthropology, University College London, London, UK
| |
Collapse
|
2
|
Zoonotic Abbreviata caucasica in Wild Chimpanzees ( Pan troglodytes verus) from Senegal. Pathogens 2020; 9:pathogens9070517. [PMID: 32605080 PMCID: PMC7400140 DOI: 10.3390/pathogens9070517] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/17/2022] Open
Abstract
Abbreviata caucasica (syn. Physaloptera mordens) has been reported in human and various non-human primates including great apes. The identification of this nematode is seldom performed and relies on egg characterization at the coproscopy, in the absence of any molecular tool. Following the recovery of two adult females of A. caucasica from the feces of wild Senegalese chimpanzees, morphometric characteristics were reported and new data on the width of the esophagus (0.268–0.287 mm) and on the cuticle structure (0.70–0.122 mm) were provided. The molecular characterization of a set of mitochondrial (cox1, 16S rRNA, 12S rRNA) and nuclear (18S rRNA and ITS2) partial genes was performed. Our phylogenetic analysis indicates for the first time that A. caucasica is monophyletic with Physaloptera species. A novel molecular tool was developed for the routine diagnosis of A. caucasica and the surveillance of Nematoda infestations. An A. caucasica-specific qPCR targeting the 12S gene was assessed. The assay was able to detect up to 1.13 × 10−3 eggs/g of fecal matter irrespective of its consistency, with an efficiency of 101.8% and a perfect adjustment (R2 = 0.99). The infection rate by A. caucasica in the chimpanzee fecal samples was 52.08%. Only 6.19% of the environmental samples were positive for nematode DNA and any for A. caucasica. Our findings indicate the need for further studies to clarify the epidemiology, circulation, life cycle, and possible pathological effects of this infestation using the molecular tool herein developed.
Collapse
|
3
|
The HLA A03 Supertype and Several Pan Species Major Histocompatibility Complex Class I A Allotypes Share a Preference for Binding Positively Charged Residues in the F Pocket: Implications for Controlling Retroviral Infections. J Virol 2020; 94:JVI.01960-19. [PMID: 32075930 DOI: 10.1128/jvi.01960-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/11/2020] [Indexed: 02/02/2023] Open
Abstract
The major histocompatibility complex (MHC) class I region of humans, chimpanzees (Pan troglodytes), and bonobos (Pan paniscus) is highly similar, and orthologues of HLA-A, -B, and -C are present in both Pan species. Based on functional characteristics, the different HLA-A allotypes are classified into different supertypes. One of them, the HLA A03 supertype, is widely distributed among different human populations. All contemporary known chimpanzee and bonobo MHC class I A allotypes cluster genetically into one of the six HLA-A families, the HLA-A1/A3/A11/A30 family. We report here that the peptide-binding motif of the Patr-A*05:01 allotype, which is commonly present in a cohort of western African chimpanzees, has a strong preference for binding peptides with basic amino acids at the carboxyl terminus. This phenomenon is shared with the family members of the HLA A03 supertype. Based on the chemical similarities in the peptide-binding pocket, we inferred that the preference for binding peptides with basic amino acids at the carboxyl terminus is widely present among the human, chimpanzee, and bonobo MHC-A allotypes. Subsequent in silico peptide-binding predictions illustrated that these allotypes have the capacity to target conserved parts of the proteome of human immunodeficiency virus type 1 (HIV-1) and the simian immunodeficiency virus SIVcpz.IMPORTANCE Most experimentally infected chimpanzees seem to control an HIV-1 infection and are therefore considered to be relatively resistant to developing AIDS. Contemporary free-ranging chimpanzees may carry SIVcpz, and there is evidence for AIDS-like symptoms in these free-ranging animals, whereas SIV infections in bonobos appear to be absent. In humans, the natural control of an HIV-1 infection is strongly associated with the presence of particular HLA class I allotypes. The ancestor of the contemporary living chimpanzees and bonobos survived a selective sweep targeting the MHC class I repertoire. We have put forward a hypothesis that this may have been caused by an ancestral retroviral infection similar to SIVcpz. Characterization of the relevant MHC allotypes may contribute to understanding the shaping of their immune repertoire. The abundant presence of MHC-A allotypes that prefer peptides with basic amino acids at the C termini suggests that these molecules may contribute to the control of retroviral infections in humans, chimpanzees, and bonobos.
Collapse
|
4
|
McLester E, Brown M, Stewart FA, Piel AK. Food abundance and weather influence habitat-specific ranging patterns in forest- and savanna mosaic-dwelling red-tailed monkeys (Cercopithecus ascanius). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 170:217-231. [PMID: 31423563 DOI: 10.1002/ajpa.23920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/16/2019] [Accepted: 08/01/2019] [Indexed: 12/30/2022]
Abstract
OBJECTIVES Primates that live in predominantly forested habitats and open, savanna mosaics should exhibit behavioral responses to differing food distributions and weather. We compared ecological constraints on red-tailed monkey ranging behavior in forest and savanna mosaic environments. Intraspecific variation in adaptations to these conditions may reflect similar pressures faced by hominins during the Plio-Pleistocene. METHODS We followed six groups in moist evergreen forest at Ngogo (Uganda) and one group in a savanna-woodland mosaic at the Issa Valley (Tanzania). We used spatial analyses to compare home range sizes and daily travel distances (DTD) between sites. We used measures of vegetation density and phenology to interpolate spatially explicit indices of food (fruit, flower, and leaves) abundance. We modeled DTD and range use against food abundance. We modeled DTD and at Issa hourly travel distances (HTD), against temperature and rainfall. RESULTS Compared to Issa, monkeys at Ngogo exhibited significantly smaller home ranges and less variation in DTD. DTD related negatively to fruit abundance, which had a stronger effect at Issa. DTD and HTD related negatively to temperature but not rainfall. This effect did not differ significantly between sites. Home range use did not relate to food abundance at either site. CONCLUSIONS Our results indicate food availability and thermoregulatory constraints influence red-tailed monkey ranging patterns. Intraspecific variation in home range sizes and DTD likely reflects different food distributions in closed and open habitats. We compare our results with hypotheses of evolved hominin behavior associated with the Plio-Pleistocene shift from similar closed to open environments.
Collapse
Affiliation(s)
- Edward McLester
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom
| | - Michelle Brown
- Department of Anthropology, University of California, Santa Barbara, California
| | - Fiona A Stewart
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom.,Greater Mahale Ecosystem Research and Conservation Project, Box 60118, Dar es Salaam, Tanzania
| | - Alex K Piel
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom.,Greater Mahale Ecosystem Research and Conservation Project, Box 60118, Dar es Salaam, Tanzania
| |
Collapse
|
5
|
Piel AK, Bonnin N, RamirezAmaya S, Wondra E, Stewart FA. Chimpanzees and their mammalian sympatriates in the Issa Valley, Tanzania. Afr J Ecol 2018. [DOI: 10.1111/aje.12570] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alex K. Piel
- Department of Biological Anthropology University of Cambridge Cambridge UK
- Greater Mahale Ecosystem Research and Conservation Project Dar es Salaam Tanzania
| | - Noemie Bonnin
- Greater Mahale Ecosystem Research and Conservation Project Dar es Salaam Tanzania
| | | | - Eden Wondra
- Greater Mahale Ecosystem Research and Conservation Project Dar es Salaam Tanzania
| | - Fiona A. Stewart
- Department of Biological Anthropology University of Cambridge Cambridge UK
- Greater Mahale Ecosystem Research and Conservation Project Dar es Salaam Tanzania
| |
Collapse
|
6
|
Brožová K, Modrý D, Dadáková E, Mapua MI, Piel AK, Stewart FA, Celer V, Hrazdilová K. PARV4 found in wild chimpanzee faeces: an alternate route of transmission? Arch Virol 2018; 164:573-578. [PMID: 30343383 DOI: 10.1007/s00705-018-4073-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/26/2018] [Indexed: 10/28/2022]
Abstract
Human parvovirus 4 (PARV4, family Parvoviridae, genus Tetraparvovirus) displays puzzling features, such as uncertain clinical importance/significance, unclear routes of transmission, and discontinuous geographical distribution. The origin, or the general reservoir, of human PARV4 infection is unknown. We aimed to detect and characterize PARV4 virus in faecal samples collected from two wild chimpanzee populations and 19 species of captive non-human primates. We aimed to investigate these species as a potential reservoir and alternate route of transmission on the African continent. From almost 500 samples screened, a single wild Pan troglodytes schweinfurthii sample tested positive. Full genome analysis, as well as single ORF phylogenies, confirmed species-specific PARV4 infection.
Collapse
Affiliation(s)
- Kristýna Brožová
- Department of Infectious Diseases and Microbiology, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic
| | - David Modrý
- Department of Pathological Morphology and Parasitology, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic.,Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic.,CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic
| | - Eva Dadáková
- Department of Infectious Diseases and Microbiology, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic
| | - Mwanahamisi I Mapua
- Department of Pathological Morphology and Parasitology, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic
| | - Alex K Piel
- School of Natural Sciences and Psychology, Liverpool John Moores University, Byrom Street, Liverpool, L33AF, UK.,Greater Mahale Ecosystem Research and Conservation Project (GMERC), Dar es Salaam, Tanzania
| | - Fiona A Stewart
- School of Natural Sciences and Psychology, Liverpool John Moores University, Byrom Street, Liverpool, L33AF, UK.,Greater Mahale Ecosystem Research and Conservation Project (GMERC), Dar es Salaam, Tanzania
| | - Vladimír Celer
- Department of Infectious Diseases and Microbiology, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic
| | - Kristýna Hrazdilová
- CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic. .,Department of Virology, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic.
| |
Collapse
|
7
|
Barbian HJ, Connell AJ, Avitto AN, Russell RM, Smith AG, Gundlapally MS, Shazad AL, Li Y, Bibollet‐Ruche F, Wroblewski EE, Mjungu D, Lonsdorf EV, Stewart FA, Piel AK, Pusey AE, Sharp PM, Hahn BH. CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees. Ecol Evol 2018; 8:7946-7963. [PMID: 30250675 PMCID: PMC6145012 DOI: 10.1002/ece3.4302] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/14/2018] [Accepted: 05/29/2018] [Indexed: 12/29/2022] Open
Abstract
Short tandem repeats (STRs), also known as microsatellites, are commonly used to noninvasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq-based approach for genotyping nonhabituated populations and performing comparative analyses across field sites. The new automated high-throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.
Collapse
Affiliation(s)
- Hannah J. Barbian
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Andrew Jesse Connell
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Alexa N. Avitto
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Ronnie M. Russell
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Andrew G. Smith
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Madhurima S. Gundlapally
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Alexander L. Shazad
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Yingying Li
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Frederic Bibollet‐Ruche
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| | - Emily E. Wroblewski
- Department of AnthropologyWashington University in St. LouisSt. LouisMissouri
| | | | | | - Fiona A. Stewart
- School of Natural Sciences and PsychologyLiverpool John Moores UniversityLiverpoolUK
| | - Alexander K. Piel
- School of Natural Sciences and PsychologyLiverpool John Moores UniversityLiverpoolUK
| | - Anne E. Pusey
- Department of Evolutionary AnthropologyDuke UniversityDurhamNorth Carolina
| | - Paul M. Sharp
- Institute of Evolutionary Biology and Centre for ImmunityInfection and EvolutionUniversity of EdinburghEdinburghUK
| | - Beatrice H. Hahn
- Departments of Microbiology and MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvania
| |
Collapse
|
8
|
Bowder D, Thompson J, Durst K, Hollingsead H, Hu D, Wei W, Xiang SH. Characterization of twin-cysteine motif in the V2-loop region of gp120 in primate lentiviruses. Virology 2018; 519:180-189. [DOI: 10.1016/j.virol.2018.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/15/2018] [Accepted: 04/17/2018] [Indexed: 10/17/2022]
|
9
|
Thoemmes MS, Stewart FA, Hernandez-Aguilar RA, Bertone MA, Baltzegar DA, Borski RJ, Cohen N, Coyle KP, Piel AK, Dunn RR. Ecology of sleeping: the microbial and arthropod associates of chimpanzee beds. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180382. [PMID: 29892462 PMCID: PMC5990838 DOI: 10.1098/rsos.180382] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/13/2018] [Indexed: 06/08/2023]
Abstract
The indoor environment created by the construction of homes and other buildings is often considered to be uniquely different from other environments. It is composed of organisms that are less diverse than those of the outdoors and strongly sourced by, or dependent upon, human bodies. Yet, no one has ever compared the composition of species found in contemporary human homes to that of other structures built by mammals, including those of non-human primates. Here we consider the microbes and arthropods found in chimpanzee beds, relative to the surrounding environment (n = 41 and 15 beds, respectively). Based on the study of human homes, we hypothesized that the microbes found in chimpanzee beds would be less diverse than those on nearby branches and leaves and that their beds would be primarily composed of body-associated organisms. However, we found that differences between wet and dry seasons and elevation above sea level explained nearly all of the observed variation in microbial diversity and community structure. While we can identify the presence of a chimpanzee based on the assemblage of bacteria, the dominant signal is that of environmental microbes. We found just four ectoparasitic arthropod specimens, none of which appears to be specialized on chimpanzees or their structures. These results suggest that the life to which chimpanzees are exposed while in their beds is predominately the same as that of the surrounding environment.
Collapse
Affiliation(s)
- Megan S. Thoemmes
- Department of Applied Ecology and Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, USA
| | - Fiona A. Stewart
- Ugalla Primate Project, Katavi Region, Tanzania
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, UK
| | - R. Adriana Hernandez-Aguilar
- Ugalla Primate Project, Katavi Region, Tanzania
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Matthew A. Bertone
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - David A. Baltzegar
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Genomic Sciences Laboratory, Office of Research, Innovation and Economic Development, North Carolina State University, Raleigh, NC, USA
| | - Russell J. Borski
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Naomi Cohen
- Ugalla Primate Project, Katavi Region, Tanzania
| | - Kaitlin P. Coyle
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Alexander K. Piel
- Ugalla Primate Project, Katavi Region, Tanzania
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Robert R. Dunn
- Department of Applied Ecology and Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, USA
- The Center for Macroecology, Ecology and Conservation, Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
10
|
Arandjelovic M, Vigilant L. Non-invasive genetic censusing and monitoring of primate populations. Am J Primatol 2018; 80:e22743. [PMID: 29457631 DOI: 10.1002/ajp.22743] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/16/2017] [Accepted: 01/14/2018] [Indexed: 02/06/2023]
Abstract
Knowing the density or abundance of primate populations is essential for their conservation management and contextualizing socio-demographic and behavioral observations. When direct counts of animals are not possible, genetic analysis of non-invasive samples collected from wildlife populations allows estimates of population size with higher accuracy and precision than is possible using indirect signs. Furthermore, in contrast to traditional indirect survey methods, prolonged or periodic genetic sampling across months or years enables inference of group membership, movement, dynamics, and some kin relationships. Data may also be used to estimate sex ratios, sex differences in dispersal distances, and detect gene flow among locations. Recent advances in capture-recapture models have further improved the precision of population estimates derived from non-invasive samples. Simulations using these methods have shown that the confidence interval of point estimates includes the true population size when assumptions of the models are met, and therefore this range of population size minima and maxima should be emphasized in population monitoring studies. Innovations such as the use of sniffer dogs or anti-poaching patrols for sample collection are important to ensure adequate sampling, and the expected development of efficient and cost-effective genotyping by sequencing methods for DNAs derived from non-invasive samples will automate and speed analyses.
Collapse
Affiliation(s)
- Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| |
Collapse
|
11
|
DNA recovery from wild chimpanzee tools. PLoS One 2018; 13:e0189657. [PMID: 29298306 PMCID: PMC5751987 DOI: 10.1371/journal.pone.0189657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 11/29/2017] [Indexed: 11/19/2022] Open
Abstract
Most of our knowledge of wild chimpanzee behaviour stems from fewer than 10 long-term field sites. This bias limits studies to a potentially unrepresentative set of communities known to show great behavioural diversity on small geographic scales. Here, we introduce a new genetic approach to bridge the gap between behavioural material evidence in unhabituated chimpanzees and genetic advances in the field of primatology. The use of DNA analyses has revolutionised archaeological and primatological fields, whereby extraction of DNA from non-invasively collected samples allows researchers to reconstruct behaviour without ever directly observing individuals. We used commercially available forensic DNA kits to show that termite-fishing by wild chimpanzees (Pan troglodytes schweinfurthii) leaves behind detectable chimpanzee DNA evidence on tools. We then quantified the recovered DNA, compared the yield to that from faecal samples, and performed an initial assessment of mitochondrial and microsatellite markers to identify individuals. From 49 termite-fishing tools from the Issa Valley research site in western Tanzania, we recovered an average of 52 pg/μl chimpanzee DNA, compared to 376.2 pg/μl in faecal DNA extracts. Mitochondrial DNA haplotypes could be assigned to 41 of 49 tools (84%). Twenty-six tool DNA extracts yielded >25 pg/μl DNA and were selected for microsatellite analyses; genotypes were determined with confidence for 18 tools. These tools were used by a minimum of 11 individuals across the study period and termite mounds. These results demonstrate the utility of bio-molecular techniques and a primate archaeology approach in non-invasive monitoring and behavioural reconstruction of unhabituated primate populations.
Collapse
|
12
|
Dadáková E, Brožová K, Piel AK, Stewart FA, Modrý D, Celer V, Hrazdilová K. Adenovirus infection in savanna chimpanzees (Pan troglodytes schweinfurthii) in the Issa Valley, Tanzania. Arch Virol 2017; 163:191-196. [PMID: 28980083 DOI: 10.1007/s00705-017-3576-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/07/2017] [Indexed: 11/29/2022]
Abstract
Adenoviruses are a widespread cause of diverse human infections with recently confirmed zoonotic roots in African great apes. We focused on savanna-dwelling chimpanzees in the Issa Valley (Tanzania), which differ from those from forested sites in many aspects of behavior and ecology. PCR targeting the DNA polymerase gene detected AdV in 36.7% (69/188) of fecal samples. We detected five groups of strains belonging to the species Human mastadenovirus E and two distinct groups within the species Human mastadenovirus C based on partial hexon sequence. All detected AdVs from the Issa Valley are related to those from nearby Mahale and Gombe National Parks, suggesting chimpanzee movements and pathogen transmission.
Collapse
Affiliation(s)
- Eva Dadáková
- Department of Infectious Diseases and Microbiology, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic
| | - Kristýna Brožová
- Department of Infectious Diseases and Microbiology, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic
| | - Alex K Piel
- School of Natural Sciences and Psychology, Liverpool John Moores University, Byrum Street, Liverpool, L33AF, UK.,Ugalla Primate Project, Uvinza, Tanzania
| | - Fiona A Stewart
- School of Natural Sciences and Psychology, Liverpool John Moores University, Byrum Street, Liverpool, L33AF, UK.,Ugalla Primate Project, Uvinza, Tanzania
| | - David Modrý
- Department of Pathological Morphology and Parasitology, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic.,Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic.,CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic
| | - Vladimír Celer
- Department of Infectious Diseases and Microbiology, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic.,CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic
| | - Kristýna Hrazdilová
- CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences Brno, Palackého tř. 1946/1, 612 42, Brno, Czech Republic. .,Department of Virology, Veterinary Research Institute, Hudcova 296/70, 621 00, Brno, Czech Republic.
| |
Collapse
|
13
|
Piel AK, Strampelli P, Greathead E, Hernandez-Aguilar RA, Moore J, Stewart FA. The diet of open-habitat chimpanzees (Pan troglodytes schweinfurthii) in the Issa valley, western Tanzania. J Hum Evol 2017; 112:57-69. [PMID: 29037416 DOI: 10.1016/j.jhevol.2017.08.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 08/11/2017] [Accepted: 08/15/2017] [Indexed: 11/29/2022]
Abstract
Comparative data on the diets of extant primates inform hypotheses about hominin resource use. Historically, data describing chimpanzee diets stem primarily from forest-dwelling communities, and we lack comparative data from chimpanzees that live in mosaic habitats that more closely resemble those reconstructed for Plio-Pleistocene hominins. We present data on the diet of a partially-habituated community of open habitat chimpanzees (Pan troglodytes schweinfurthii) from the Issa valley, western Tanzania, collected over a four-year period. Based mostly on macroscopic faecal analysis, Issa chimpanzees consumed a minimum of 69 plant species. There was no relationship between plant consumption and either fruit availability or feeding tree density; the most frequently consumed plant species were found in riverine forests, with woodland species consumed more frequently during the late dry season. We conclude by contextualising these findings with those of other open-habitat chimpanzee sites, and also by discussing how our results contribute towards reconstructions of early hominin exploitation of mosaic landscapes.
Collapse
Affiliation(s)
- Alex K Piel
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom; Ugalla Primate Project, Box 108, Uvinza, Tanzania.
| | - Paolo Strampelli
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Emily Greathead
- Department of Archaeology and Anthropology, University of Cambridge, United Kingdom
| | - R Adriana Hernandez-Aguilar
- Ugalla Primate Project, Box 108, Uvinza, Tanzania; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Jim Moore
- Ugalla Primate Project, Box 108, Uvinza, Tanzania; Department of Anthropology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fiona A Stewart
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom; Ugalla Primate Project, Box 108, Uvinza, Tanzania; Department of Archaeology and Anthropology, University of Cambridge, United Kingdom
| |
Collapse
|
14
|
Moore J, Black J, Hernandez-Aguilar RA, Idani G, Piel A, Stewart F. Chimpanzee vertebrate consumption: Savanna and forest chimpanzees compared. J Hum Evol 2017; 112:30-40. [PMID: 29037414 DOI: 10.1016/j.jhevol.2017.09.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 08/30/2017] [Accepted: 09/01/2017] [Indexed: 11/29/2022]
Abstract
There is broad consensus among paleoanthropologists that meat-eating played a key role in the evolution of Homo, but the details of where, when, and why are hotly debated. It has been argued that increased faunivory was causally connected with hominin adaptation to open, savanna habitats. If savanna-dwelling chimpanzees eat meat more frequently than do forest chimpanzees, it would support the notion that open, dry, seasonal habitats promote hunting or scavenging by hominoids. Here we present observational and fecal analysis data on vertebrate consumption from several localities within the dry, open Ugalla region of Tanzania. Combining these with published fecal analyses, we summarize chimpanzee vertebrate consumption rates, showing quantitatively that savanna chimpanzee populations do not differ significantly from forest populations. Compared with forest populations, savanna chimpanzees consume smaller vertebrates that are less likely to be shared, and they do so more seasonally. Analyses of chimpanzee hunting that focus exclusively on capture of forest monkeys are thus difficult to apply to chimpanzee faunivory in open-country habitats and may be misleading when used to model early hominin behavior. These findings bear on discussions of why chimpanzees hunt and suggest that increases in hominin faunivory were related to differences between hominins and chimpanzees and/or differences between modern and Pliocene savanna woodland environments.
Collapse
Affiliation(s)
- Jim Moore
- Anthropology Dept., University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Jessica Black
- Department of Psychology, University of Oklahoma, Dale Hall Tower, Room 705, 455 W. Lindsey, Norman, OK 73071, USA
| | - R Adriana Hernandez-Aguilar
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316 Oslo, Norway
| | - Gen'ichi Idani
- Wildlife Research Center, Kyoto University, 2-24 Sekiden-cho, Tanaka, Sakyo, 606-8203, Japan
| | - Alex Piel
- School of Natural Sciences and Psychology, Liverpool John Moores University, James Parsons Building, Rm653, Byrom Street, Liverpool, L3 3AF, UK
| | - Fiona Stewart
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, L3 3AF, UK
| |
Collapse
|
15
|
Almeida-Warren K, Sommer V, Piel AK, Pascual-Garrido A. Raw material procurement for termite fishing tools by wild chimpanzees in the Issa valley, Western Tanzania. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017. [PMID: 28621823 DOI: 10.1002/ajpa.23269] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OBJECTIVES Chimpanzee termite fishing has been studied for decades, yet the selective processes preceding the manufacture of fishing tools remain largely unexplored. We investigate raw material selection and potential evidence of forward planning in the chimpanzees of Issa valley, western Tanzania. MATERIALS AND METHODS Using traditional archaeological methods, we surveyed the location of plants from where chimpanzees sourced raw material to manufacture termite fishing tools, relative to targeted mounds. We measured raw material abundance to test for availability and selection. Statistics included Chi-Squared, two-tailed Wilcoxon, and Kruskall-Wallace tests. RESULTS Issa chimpanzees manufactured extraction tools only from bark, despite availability of other suitable materials (e.g., twigs), and selected particular plant species as raw material sources, which they often also exploit for food. Most plants were sourced 1-16 m away from the mound, with a maximum of 33 m. The line of sight from the targeted mound was obscured for a quarter of these plants. DISCUSSION The exclusive use of bark tools despite availability of other suitable materials indicates a possible cultural preference. The fact that Issa chimpanzees select specific plant species and travel some distance to source them suggests some degree of selectivity and, potentially, forward planning. Our results have implications for the reconstruction of early hominin behaviors, particularly with regard to the use of perishable tools, which remain archaeologically invisible.
Collapse
Affiliation(s)
- Katarina Almeida-Warren
- Department of Anthropology, University College London, London, WC1 E6BT, United Kingdom
- Institute of Cognitive and Evolutionary Anthropology, University of Oxford, Oxford, OX2 6PN, United Kingdom
| | - Volker Sommer
- Department of Anthropology, University College London, London, WC1 E6BT, United Kingdom
| | - Alex K Piel
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, L3 3AF, United Kingdom
- Ugalla Primate Project, PO Box 108, Uvinza, Tanzania
| | - Alejandra Pascual-Garrido
- RLAHA, School of Archaeology, Leverhulme Trust Early Career Fellow, University of Oxford, Oxford, OX1 3QY, United Kingdom
| |
Collapse
|
16
|
Locatelli S, Harrigan RJ, Sesink Clee PR, Mitchell MW, McKean KA, Smith TB, Gonder MK. Why Are Nigeria-Cameroon Chimpanzees (Pan troglodytes ellioti) Free of SIVcpz Infection? PLoS One 2016; 11:e0160788. [PMID: 27505066 PMCID: PMC4978404 DOI: 10.1371/journal.pone.0160788] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/24/2016] [Indexed: 12/26/2022] Open
Abstract
Simian immunodeficiency virus (SIV) naturally infects two subspecies of chimpanzee: Pan troglodytes troglodytes from Central Africa (SIVcpzPtt) and P. t. schweinfurtii from East Africa (SIVcpzPts), but is absent in P. t. verus from West Africa and appears to be absent in P. t. ellioti inhabiting Nigeria and western Cameroon. One explanation for this pattern is that P. t. troglodytes and P. t schweinfurthii may have acquired SIVcpz after their divergence from P. t. verus and P. t. ellioti. However, all of the subspecies, except P. t. verus, still occasionally exchange migrants making the absence of SIVcpz in P. t. ellioti puzzling. Sampling of P. t. ellioti has been minimal to date, particularly along the banks of the Sanaga River, where its range abuts that of P. t. troglodytes. This study had three objectives. First, we extended the sampling of SIVcpz across the range of chimpanzees north of the Sanaga River to address whether under-sampling might account for the absence of evidence for SIVcpz infection in P. t. ellioti. Second, we investigated how environmental variation is associated with the spread and prevalence of SIVcpz in the two chimpanzee subspecies inhabiting Cameroon since environmental variation has been shown to contribute to their divergence from one another. Finally, we compared the prevalence and distribution of SIVcpz with that of Simian Foamy Virus (SFV) to examine the role of ecology and behavior in shaping the distribution of diseases in wild host populations. The dataset includes previously published results on SIVcpz infection and SFVcpz as well as newly collected data, and represents over 1000 chimpanzee fecal samples from 41 locations across Cameroon. Results revealed that none of the 181 P. t. ellioti fecal samples collected across the range of P. t. ellioti tested positive for SIVcpz. In addition, species distribution models suggest that environmental variation contributes to differences in the distribution and prevalence of SIVcpz and SFVcpz. The ecological niches of these two viruses are largely non-overlapping, although stronger statistical support for this conclusion will require more sampling. Overall this study demonstrates that SIVcpz infection is absent or very rare in P. t. ellioti, despite multiple opportunities for transmission. The reasons for its absence remain unclear, but might be explained by one or more factors, including environmental variation, viral competition, and/or local adaptation—all of which should be explored in greater detail through continued surveillance of this region.
Collapse
Affiliation(s)
- Sabrina Locatelli
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement, INSERM U1175, and University of Montpellier, 34394 Montpellier, France
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- * E-mail:
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA, 90095, United States of America
| | - Paul R. Sesink Clee
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- Department of Biology, Drexel University, Philadelphia, PA, 19104, United States of America
| | - Matthew W Mitchell
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- Department of Biology, Drexel University, Philadelphia, PA, 19104, United States of America
| | - Kurt A. McKean
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
| | - Thomas B. Smith
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA, 90095, United States of America
| | - Mary Katherine Gonder
- Department of Biological Sciences, University at Albany – State University of New York, Albany, NY, 12222, United States of America
- Department of Biology, Drexel University, Philadelphia, PA, 19104, United States of America
| |
Collapse
|
17
|
Kalan AK, Piel AK, Mundry R, Wittig RM, Boesch C, Kühl HS. Passive acoustic monitoring reveals group ranging and territory use: a case study of wild chimpanzees (Pan troglodytes). Front Zool 2016; 13:34. [PMID: 27507999 PMCID: PMC4977853 DOI: 10.1186/s12983-016-0167-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 08/03/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Assessing the range and territories of wild mammals traditionally requires years of data collection and often involves directly following individuals or using tracking devices. Indirect and non-invasive methods of monitoring wildlife have therefore emerged as attractive alternatives due to their ability to collect data at large spatiotemporal scales using standardized remote sensing technologies. Here, we investigate the use of two novel passive acoustic monitoring (PAM) systems used to capture long-distance sounds produced by the same species, wild chimpanzees (Pan troglodytes), living in two different habitats: forest (Taï, Côte d'Ivoire) and savanna-woodland (Issa valley, Tanzania). RESULTS Using data collected independently at two field sites, we show that detections of chimpanzee sounds on autonomous recording devices were predicted by direct and indirect indices of chimpanzee presence. At Taï, the number of chimpanzee buttress drums detected on recording devices was positively influenced by the number of hours chimpanzees were seen ranging within a 1 km radius of a device. We observed a similar but weaker relationship within a 500 m radius. At Issa, the number of indirect chimpanzee observations positively predicted detections of chimpanzee loud calls on a recording device within a 500 m but not a 1 km radius. Moreover, using just seven months of PAM data, we could locate two known chimpanzee communities in Taï and observed monthly spatial variation in the center of activity for each group. CONCLUSIONS Our work shows PAM is a promising new tool for gathering information about the ranging behavior and habitat use of chimpanzees and can be easily adopted for other large territorial mammals, provided they produce long-distance acoustic signals that can be captured by autonomous recording devices (e.g., lions and wolves). With this study we hope to promote more interdisciplinary research in PAM to help overcome its challenges, particularly in data processing, to improve its wider application.
Collapse
Affiliation(s)
- Ammie K. Kalan
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Alex K. Piel
- School of Natural Sciences and Psychology, Liverpool John Moores University, James Parsons Building, Rm 653, Byrom Street, Liverpool, L3 3AF UK
- Ugalla Primate Project, Kigoma, Tanzania
| | - Roger Mundry
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Department of Developmental and Comparative Psychology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Roman M. Wittig
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, BP 1301, Abidjan 1, Côte d’Ivoire
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Wild Chimpanzee Foundation, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Hjalmar S. Kühl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| |
Collapse
|
18
|
The well-tempered SIV infection: Pathogenesis of SIV infection in natural hosts in the wild, with emphasis on virus transmission and early events post-infection that may contribute to protection from disease progression. INFECTION GENETICS AND EVOLUTION 2016; 46:308-323. [PMID: 27394696 DOI: 10.1016/j.meegid.2016.07.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 07/04/2016] [Accepted: 07/05/2016] [Indexed: 12/25/2022]
Abstract
African NHPs are infected by over 40 different simian immunodeficiency viruses. These viruses have coevolved with their hosts for long periods of time and, unlike HIV in humans, infection does not generally lead to disease progression. Chronic viral replication is maintained for the natural lifespan of the host, without loss of overall immune function. Lack of disease progression is not correlated with transmission, as SIV infection is highly prevalent in many African NHP species in the wild. The exact mechanisms by which these natural hosts of SIV avoid disease progression are still unclear, but a number of factors might play a role, including: (i) avoidance of microbial translocation from the gut lumen by preventing or repairing damage to the gut epithelium; (ii) control of immune activation and apoptosis following infection; (iii) establishment of an anti-inflammatory response that resolves chronic inflammation; (iv) maintenance of homeostasis of various immune cell populations, including NK cells, monocytes/macrophages, dendritic cells, Tregs, Th17 T-cells, and γδ T-cells; (v) restriction of CCR5 availability at mucosal sites; (vi) preservation of T-cell function associated with down-regulation of CD4 receptor. Some of these mechanisms might also be involved in protection of natural hosts from mother-to-infant SIV transmission during breastfeeding. The difficulty of performing invasive studies in the wild has prohibited investigation of the exact events surrounding transmission in natural hosts. Increased understanding of the mechanisms of SIV transmission in natural hosts, and of the early events post-transmission which may contribute to avoidance of disease progression, along with better comprehension of the factors involved in protection from SIV breastfeeding transmission in the natural hosts, could prove invaluable for the development of new prevention strategies for HIV.
Collapse
|
19
|
Molecular identification of Entamoeba species in savanna woodland chimpanzees (Pan troglodytes schweinfurthii). Parasitology 2016; 143:741-8. [PMID: 26935395 DOI: 10.1017/s0031182016000263] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
To address the molecular diversity and occurrence of pathogenic species of the genus Entamoeba spp. in wild non-human primates (NHP) we conducted molecular-phylogenetic analyses on Entamoeba from wild chimpanzees living in the Issa Valley, Tanzania. We compared the sensitivity of molecular [using a genus-specific polymerase chain reaction (PCR)] and coproscopic detection (merthiolate-iodine-formaldehyde concentration) of Entamoeba spp. We identified Entamoeba spp. in 72 chimpanzee fecal samples (79%) subjected to species-specific PCRs for six Entamoeba species/groups (Entamoeba histolytica, Entamoeba nuttalli, Entamoeba dispar, Entamoeba moshkovskii, Entamoeba coli and Entamoeba polecki ST2). We recorded three Entamoeba species: E. coli (47%), E. dispar (16%), Entamoeba hartmanni (51%). Coproscopically, we could only distinguish the cysts of complex E. histolytica/dispar/moshkovskii/nuttalli and E. coli. Molecular prevalence of entamoebas was higher than the prevalence based on the coproscopic examination. Our molecular phylogenies showed that sequences of E. dispar and E. coli from Issa chimpanzees are closely related to sequences from humans and other NHP from GenBank. The results showed that wild chimpanzees harbour Entamoeba species similar to those occurring in humans; however, no pathogenic species were detected. Molecular-phylogenetic methods are critical to improve diagnostics of entamoebas in wild NHP and for determining an accurate prevalence of Entamoeba species.
Collapse
|
20
|
Barbian HJ, Li Y, Ramirez M, Klase Z, Lipende I, Mjungu D, Moeller AH, Wilson ML, Pusey AE, Lonsdorf EV, Bushman FD, Hahn BH. Destabilization of the gut microbiome marks the end-stage of simian immunodeficiency virus infection in wild chimpanzees. Am J Primatol 2015; 80. [PMID: 26676710 DOI: 10.1002/ajp.22515] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/20/2015] [Accepted: 12/01/2015] [Indexed: 12/17/2022]
Abstract
Enteric dysbiosis is a characteristic feature of progressive human immunodeficiency virus type 1 (HIV-1) infection but has not been observed in simian immunodeficiency virus (SIVmac)-infected macaques, including in animals with end-stage disease. This has raised questions concerning the mechanisms underlying the HIV-1 associated enteropathy, with factors other than virus infection, such as lifestyle and antibiotic use, implicated as playing possible causal roles. Simian immunodeficiency virus of chimpanzees (SIVcpz) is also associated with increased mortality in wild-living communities, and like HIV-1 and SIVmac, can cause CD4+ T cell depletion and immunodeficiency in infected individuals. Given the central role of the intestinal microbiome in mammalian health, we asked whether gut microbial constituents could be identified that are indicative of SIVcpz status and/or disease progression. Here, we characterized the gut microbiome of SIVcpz-infected and -uninfected chimpanzees in Gombe National Park, Tanzania. Subjecting a small number of fecal samples (N = 9) to metagenomic (shotgun) sequencing, we found bacteria of the family Prevotellaceae to be enriched in SIVcpz-infected chimpanzees. However, 16S rRNA gene sequencing of a larger number of samples (N = 123) failed to show significant differences in both the composition and diversity (alpha and beta) of gut bacterial communities between infected (N = 24) and uninfected (N = 26) chimpanzees. Similarly, chimpanzee stool-associated circular virus (Chi-SCV) and chimpanzee adenovirus (ChAdV) identified by metagenomic sequencing were neither more prevalent nor more abundant in SIVcpz-infected individuals. However, fecal samples collected from SIVcpz-infected chimpanzees within 5 months before their AIDS-related death exhibited significant compositional changes in their gut bacteriome. These data indicate that SIVcpz-infected chimpanzees retain a stable gut microbiome throughout much of their natural infection course, with a significant destabilization of bacterial (but not viral) communities observed only in individuals with known immunodeficiency within the last several months before their death. Am. J. Primatol. 80:e22515, 2018. © 2015 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Hannah J Barbian
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Miguel Ramirez
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zachary Klase
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania
| | | | - Deus Mjungu
- Gombe Stream Research Center, Kigoma, Tanzania
| | - Andrew H Moeller
- Department of Integrative Biology, University of California, Berkeley, California.,Miller Institute for Basic Research, University of California, Berkeley, California
| | - Michael L Wilson
- Department of Anthropology, University of Minnesota, Minneapolis, Minnesota.,Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota
| | - Anne E Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina
| | - Elizabeth V Lonsdorf
- Department of Psychology, Franklin and Marshall College, Lancaster, Pennsylvania
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania
| |
Collapse
|
21
|
African origin of the malaria parasite Plasmodium vivax. Nat Commun 2015; 5:3346. [PMID: 24557500 PMCID: PMC4089193 DOI: 10.1038/ncomms4346] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/29/2014] [Indexed: 01/12/2023] Open
Abstract
Plasmodium vivax is the leading cause of human malaria in Asia and Latin America but is absent from most of central Africa due to the near fixation of a mutation that inhibits the expression of its receptor, the Duffy antigen, on human erythrocytes. The emergence of this protective allele is not understood because P. vivax is believed to have originated in Asia. Here we show, using a non-invasive approach, that wild chimpanzees and gorillas throughout central Africa are endemically infected with parasites that are closely related to human P. vivax. Sequence analyses reveal that ape parasites lack host specificity and are much more diverse than human parasites, which form a monophyletic lineage within the ape parasite radiation. These findings indicate that human P. vivax is of African origin and likely selected for the Duffy-negative mutation. All extant human P. vivax parasites are derived from a single ancestor that escaped out of Africa.
Collapse
|
22
|
Boué V, Locatelli S, Boucher F, Ayouba A, Butel C, Esteban A, Okouga AP, Ndoungouet A, Motsch P, Le Flohic G, Ngari P, Prugnolle F, Ollomo B, Rouet F, Liégeois F. High Rate of Simian Immunodeficiency Virus (SIV) Infections in Wild Chimpanzees in Northeastern Gabon. Viruses 2015; 7:4997-5015. [PMID: 26389939 PMCID: PMC4584299 DOI: 10.3390/v7092855] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/22/2015] [Accepted: 08/25/2015] [Indexed: 11/17/2022] Open
Abstract
The emergence of HIV-1 groups M, N, O, and P is the result of four independent cross-species transmissions between chimpanzees (cpz) and gorillas (gor) from central/south Cameroon and humans respectively. Although the first two SIVcpz were identified in wild-born captive chimpanzees in Gabon in 1989, no study has been conducted so far in wild chimpanzees in Gabon. To document the SIVcpz infection rate, genetic diversity, and routes of virus transmission, we analyzed 1458 faecal samples collected in 16 different locations across the country, and we conducted follow-up missions in two of them. We found 380 SIV antibody positive samples in 6 different locations in the north and northeast. We determined the number of individuals collected by microsatellite analysis and obtained an adjusted SIV prevalence of 39.45%. We performed parental analysis to investigate viral spread between and within communities and found that SIVs were epidemiologically linked and were transmitted by both horizontal and vertical routes. We amplified pol and gp41 fragments and obtained 57 new SIVcpzPtt strains from three sites. All strains, but one, clustered together within a specific phylogeographic clade. Given that these SIV positive samples have been collected nearby villages and that humans continue to encroach in ape's territories, the emergence of a new HIV in this area needs to be considered.
Collapse
Affiliation(s)
- Vanina Boué
- UMI 233 "TransVIHMI", IRD / UM-INSERM U1175/ UM1, 34394 Montpellier, France.
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
| | - Sabrina Locatelli
- UMI 233 "TransVIHMI", IRD / UM-INSERM U1175/ UM1, 34394 Montpellier, France.
| | - Floriane Boucher
- UMI 233 "TransVIHMI", IRD / UM-INSERM U1175/ UM1, 34394 Montpellier, France.
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
| | - Ahidjo Ayouba
- UMI 233 "TransVIHMI", IRD / UM-INSERM U1175/ UM1, 34394 Montpellier, France.
| | - Christelle Butel
- UMI 233 "TransVIHMI", IRD / UM-INSERM U1175/ UM1, 34394 Montpellier, France.
| | - Amandine Esteban
- UMI 233 "TransVIHMI", IRD / UM-INSERM U1175/ UM1, 34394 Montpellier, France.
| | | | | | - Peggy Motsch
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
| | | | - Paul Ngari
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
| | - Franck Prugnolle
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
- Laboratoire Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution, Contrôle, UMR 224IRD/CNRS/UM1, 34394 Montpellier, France4 Institut Pasteur du Cambodge, Phnom-Penh BP 983, Royaume du Cambodge.
| | - Benjamin Ollomo
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
| | - François Rouet
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
- Institut Pasteur du Cambodge, Phnom-Penh BP 983, Royaume du Cambodge.
| | - Florian Liégeois
- UMI 233 "TransVIHMI", IRD / UM-INSERM U1175/ UM1, 34394 Montpellier, France.
- Centre International de Recherches Médicales, BP 769 Franceville, Gabon.
| |
Collapse
|
23
|
Uchtmann N, Herrmann JA, Hahn EC, Beasley VR. Barriers to, Efforts in, and Optimization of Integrated One Health Surveillance: A Review and Synthesis. ECOHEALTH 2015; 12:368-384. [PMID: 25894955 DOI: 10.1007/s10393-015-1022-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 02/16/2015] [Accepted: 03/05/2015] [Indexed: 06/04/2023]
Abstract
Insufficient data from existing surveillance systems underlie societal tolerance of acute and slow-onset health disasters that threaten, harm, and kill vast numbers of humans, animals, and plants. Here we describe barriers to integrated "One Health" surveillance, including those related to a lack of medical services, professional divisions, incompatible vocabularies, isolated data sets, and territorial borders. We draw from publications of experts who justify broader and more integrated surveillance, education, and stewardship focused on preventing and mitigating disease emergence and re-emergence. In addition, we highlight efforts from Illinois, the United States and the broader world, pointing to examples of relevant education; ways to acquire, compile, and analyze diagnostic and syndromic data; mapping of diseases of humans and animals; and rapid communication of findings and recommendations. For the future, we propose using needed outcomes for health and sustainability to set priorities for One Health programs of education, surveillance, and stewardship. Professionals and paraprofessionals should gather, interpret, and widely communicate the implications of data, not only on infectious diseases, but also on toxic agents, malnutrition, ecological damage, the grave impacts of warfare, societal drivers underlying these problems, and the effectiveness of specific countermeasures.
Collapse
Affiliation(s)
- Nathaniel Uchtmann
- College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - John Arthur Herrmann
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, 1008 W. Hazelwood Dr., Urbana, IL, 61802, USA.
| | - Edwin C Hahn
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, 2001 S. Lincoln Avenue, Urbana, IL, 61802, USA.
| | - Val Richard Beasley
- Department of Veterinary and Biomedical Sciences, College of Agricultural Sciences, The Pennsylvania State University, 115 Henning Building, University Park, PA, 16802, USA.
| |
Collapse
|
24
|
De Nys HM, Madinda NF, Merkel K, Robbins M, Boesch C, Leendertz FH, Calvignac-Spencer S. A cautionary note on fecal sampling and molecular epidemiology in predatory wild great apes. Am J Primatol 2015; 77:833-40. [PMID: 26031302 DOI: 10.1002/ajp.22418] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/18/2015] [Accepted: 03/22/2015] [Indexed: 11/06/2022]
Abstract
Fecal samples are an important source of information on parasites (viruses, prokaryotes, or eukaryotes) infecting wild great apes. Molecular analysis of fecal samples has already been used for deciphering the origins of major human pathogens such as HIV-1 or Plasmodium falciparum. However, for apes that hunt (chimpanzees and bonobos), detection of parasite nucleic acids may reflect either true infection of the host of interest or ingestion of an infected prey, for example, another non-human primate. To determine the potential magnitude of this issue, we estimated the prevalence of prey DNA in fecal samples obtained from two wild chimpanzee communities. We observed values >15%, which are higher than or close to the fecal detection rates of many great ape parasites. Contamination of fecal samples with parasite DNA from dietary origin may therefore occasionally impact non-invasive epidemiological studies. This problem can be addressed (at least partially) by monitoring the presence of prey DNA.
Collapse
Affiliation(s)
- Hélène Marie De Nys
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Nordufer, Berlin, Germany.,Department of Primatology, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany.,Laboratory of Parasitology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan, Merelbeke, Belgium
| | - Nadège Freda Madinda
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Nordufer, Berlin, Germany.,Department of Primatology, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany.,Institut de Recherches en Ecologie Tropicale, Libreville, Gabon
| | - Kevin Merkel
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Nordufer, Berlin, Germany
| | - Martha Robbins
- Department of Primatology, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
| | - Christophe Boesch
- Department of Primatology, Max-Planck-Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
| | | | | |
Collapse
|
25
|
Barbian HJ, Decker JM, Bibollet-Ruche F, Galimidi RP, West AP, Learn GH, Parrish NF, Iyer SS, Li Y, Pace CS, Song R, Huang Y, Denny TN, Mouquet H, Martin L, Acharya P, Zhang B, Kwong PD, Mascola JR, Verrips CT, Strokappe NM, Rutten L, McCoy LE, Weiss RA, Brown CS, Jackson R, Silvestri G, Connors M, Burton DR, Shaw GM, Nussenzweig MC, Bjorkman PJ, Ho DD, Farzan M, Hahn BH. Neutralization properties of simian immunodeficiency viruses infecting chimpanzees and gorillas. mBio 2015; 6:e00296-15. [PMID: 25900654 PMCID: PMC4453581 DOI: 10.1128/mbio.00296-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 03/19/2015] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED Broadly cross-reactive neutralizing antibodies (bNabs) represent powerful tools to combat human immunodeficiency virus type 1 (HIV-1) infection. Here, we examined whether HIV-1-specific bNabs are capable of cross-neutralizing distantly related simian immunodeficiency viruses (SIVs) infecting central (Pan troglodytes troglodytes) (SIVcpzPtt) and eastern (Pan troglodytes schweinfurthii) (SIVcpzPts) chimpanzees (n = 11) as well as western gorillas (Gorilla gorilla gorilla) (SIVgor) (n = 1). We found that bNabs directed against the CD4 binding site (n = 10), peptidoglycans at the base of variable loop 3 (V3) (n = 5), and epitopes at the interface of surface (gp120) and membrane-bound (gp41) envelope glycoproteins (n = 5) failed to neutralize SIVcpz and SIVgor strains. In addition, apex V2-directed bNabs (n = 3) as well as llama-derived (heavy chain only) antibodies (n = 6) recognizing both the CD4 binding site and gp41 epitopes were either completely inactive or neutralized only a fraction of SIVcpzPtt strains. In contrast, one antibody targeting the membrane-proximal external region (MPER) of gp41 (10E8), functional CD4 and CCR5 receptor mimetics (eCD4-Ig, eCD4-Ig(mim2), CD4-218.3-E51, and CD4-218.3-E51-mim2), as well as mono- and bispecific anti-human CD4 (iMab and LM52) and CCR5 (PRO140, PRO140-10E8) receptor antibodies neutralized >90% of SIVcpz and SIVgor strains with low-nanomolar (0.13 to 8.4 nM) potency. Importantly, the latter antibodies blocked virus entry not only in TZM-bl cells but also in Cf2Th cells expressing chimpanzee CD4 and CCR5 and neutralized SIVcpz in chimpanzee CD4(+) T cells, with 50% inhibitory concentrations (IC50s) ranging from 3.6 to 40.5 nM. These findings provide new insight into the protective capacity of anti-HIV-1 bNabs and identify candidates for further development to combat SIVcpz infection. IMPORTANCE SIVcpz is widespread in wild-living chimpanzees and can cause AIDS-like immunopathology and clinical disease. HIV-1 infection of humans can be controlled by antiretroviral therapy; however, treatment of wild-living African apes with current drug regimens is not feasible. Nonetheless, it may be possible to curb the spread of SIVcpz in select ape communities using vectored immunoprophylaxis and/or therapy. Here, we show that antibodies and antibody-like inhibitors developed to combat HIV-1 infection in humans are capable of neutralizing genetically diverse SIVcpz and SIVgor strains with considerable breadth and potency, including in primary chimpanzee CD4(+) T cells. These reagents provide an important first step toward translating intervention strategies currently developed to treat and prevent AIDS in humans to SIV-infected apes.
Collapse
Affiliation(s)
- Hannah J Barbian
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Julie M Decker
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Frederic Bibollet-Ruche
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rachel P Galimidi
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, USA
| | - Anthony P West
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, USA
| | - Gerald H Learn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nicholas F Parrish
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shilpa S Iyer
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yingying Li
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Ruijiang Song
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, USA
| | - Thomas N Denny
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Loic Martin
- CEA, iBiTecS, Service d'Ingénierie Moléculaire des Protéines, Gif-sur-Yvette, France
| | - Priyamvada Acharya
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Nika M Strokappe
- Biomolecular Imaging (BMI), Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Lucy Rutten
- Biomolecular Imaging (BMI), Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Robin A Weiss
- Division of Infection and Immunity, University College London, London, United Kingdom
| | | | | | - Guido Silvestri
- Yerkes Regional Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology and Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, USA
| | - Michael Farzan
- Department of Immunology and Microbial Science, The Scripps Research Institute, Jupiter, Florida, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
26
|
Genetic Analyses Suggest Male Philopatry and Territoriality in Savanna-Woodland Chimpanzees (Pan troglodytes schweinfurthii) of Ugalla, Tanzania. INT J PRIMATOL 2015. [DOI: 10.1007/s10764-015-9830-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
27
|
Russak SM. Using Patch Focals to Study Unhabituated Dry-Habitat Chimpanzees (Pan troglodytes schweinfurthii) and Sympatric Fauna at Issa, Ugalla, Tanzania. INT J PRIMATOL 2014. [DOI: 10.1007/s10764-014-9803-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
28
|
|
29
|
Gastrointestinal Parasites of Savanna Chimpanzees (Pan troglodytes schweinfurthii) in Ugalla, Tanzania. INT J PRIMATOL 2014. [DOI: 10.1007/s10764-014-9753-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
30
|
Genetic diversity at the edge: comparative assessment of Y-chromosome and autosomal diversity in eastern chimpanzees (Pan troglodytes schweinfurthii) of Ugalla, Tanzania. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0556-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
31
|
Moore DL, Vigilant L. A population estimate of chimpanzees (Pan troglodytes schweinfurthii) in the Ugalla region using standard and spatially explicit genetic capture-recapture methods. Am J Primatol 2013; 76:335-46. [PMID: 24357255 DOI: 10.1002/ajp.22237] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 10/07/2013] [Accepted: 10/22/2013] [Indexed: 11/09/2022]
Abstract
Population parameters such as size, density, and distribution of a species across a landscape are important metrics that inform conservation science and are key to management strategies. In this study, we used genetic capture-recapture methods to estimate the population size and density of the little-studied chimpanzees in the Ugalla region of western Tanzania. From 237 fecal samples collected non-invasively over a 10-month period, we identified a minimum of 113 individuals. Based on the two-innate rate method (TIRM) modeled in the software capwire, we obtained a maximum-likelihood estimate of 322 (CI 227-373) individuals over the 624 km(2) area surveyed. Using a spatially explicit capture-recapture (SECR) method, we estimated a population density of 0.25 (CI 0.16-0.38) individuals/km(2) . Observations of nests and search effort data revealed areas of more intense usage. The findings of this study are an important step in the characterization of the Ugalla chimpanzees, and substantially improve our understanding of the number of chimpanzees that occupy this savanna-woodland region at the easternmost extent of the geographic range of this endangered subspecies.
Collapse
Affiliation(s)
- Deborah L Moore
- Department of Anthropology, University of Texas at San Antonio, San Antonio, Texas; Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | |
Collapse
|
32
|
Sleeping site selection by savanna chimpanzees in Ugalla, Tanzania. Primates 2013; 55:269-82. [PMID: 24293003 DOI: 10.1007/s10329-013-0400-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 11/14/2013] [Indexed: 10/26/2022]
Abstract
We examined sleeping site selection by chimpanzees (Pan troglodytes) in the Ugalla savanna woodland area, western Tanzania, from 1994 to 2012. We established 488 km of line transects and recorded 379 chimpanzee beds within 30 m perpendicular to the transects. Comparisons between 60 × 60 m(2) quadrats containing new and recent beds and the remaining quadrats without beds along the transects indicated that evergreen forests accounted for disproportionately more area in quadrats with beds than in those without beds during both the dry and rainy seasons. In Ugalla, chimpanzees coexist with lions (Panthera leo) and leopards (Panthera pardus). They may sleep in forests to reduce predation risk by these carnivores, as trees are dense and the canopy is high and closed. The angle of slope was steeper in quadrats containing beds than in those without beds during the dry season, whereas the angle was less steep in quadrats with beds than in those without beds during the rainy season. Additionally, fewer beds were found further from forests. The distance between beds and forests during the dry season was shorter than that during the rainy season. Chimpanzees may sleep in or near forests and on slopes because of water pools in the valley forests along the slopes during the dry season. Quadrats with beds were at slightly higher altitude than those without beds during the rainy season; however, the difference was not significant during the dry season. The number of beds found in or close to feeding trees was not related to the fruiting period. Sleeping site selection by chimpanzees may be affected by predation pressure and water availability in the savanna woodland area.
Collapse
|
33
|
Stewart FA, Piel AK. Termite fishing by wild chimpanzees: new data from Ugalla, western Tanzania. Primates 2013; 55:35-40. [PMID: 23720026 DOI: 10.1007/s10329-013-0362-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/13/2013] [Indexed: 11/24/2022]
Abstract
Chimpanzees manufacture flexible fishing probes to fish for termites in Issa, Ugalla, western Tanzania. These termite-fishing tools are similar in size and material to those used by long-studied communities of chimpanzees in western Tanzania (Pan troglodytes schweinfurthii) and in West Africa (P. t. verus), but not central African populations (P. t. troglodytes). This report adds to the patchwork of evidence of termite-fishing tool use behaviour by chimpanzees across Africa.
Collapse
Affiliation(s)
- Fiona A Stewart
- Division of Biological Anthropology, University of Cambridge, Pembroke Street, Cambridge, CB2 3QG, UK,
| | | |
Collapse
|
34
|
Piel AK, Stewart FA, Pintea L, Li Y, Ramirez MA, Loy DE, Crystal PA, Learn GH, Knapp LA, Sharp PM, Hahn BH. The malagarasi river does not form an absolute barrier to chimpanzee movement in Western Tanzania. PLoS One 2013; 8:e58965. [PMID: 23536841 PMCID: PMC3594223 DOI: 10.1371/journal.pone.0058965] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/08/2013] [Indexed: 11/19/2022] Open
Abstract
The Malagarasi River has long been thought to be a barrier to chimpanzee movements in western Tanzania. This potential geographic boundary could affect chimpanzee ranging behavior, population connectivity and pathogen transmission, and thus has implications for conservation strategies and government policy. Indeed, based on mitochondrial DNA sequence comparisons it was recently argued that chimpanzees from communities to the north and to the south of the Malagarasi are surprisingly distantly related, suggesting that the river prevents gene flow. To investigate this, we conducted a survey along the Malagarasi River. We found a ford comprised of rocks that researchers could cross on foot. On a trail leading to this ford, we collected 13 fresh fecal samples containing chimpanzee DNA, two of which tested positive for SIVcpz. We also found chimpanzee feces within the riverbed. Taken together, this evidence suggests that the Malagarasi River is not an absolute barrier to chimpanzee movements and communities from the areas to the north and south should be considered a single population. These results have important consequences for our understanding of gene flow, disease dynamics and conservation management.
Collapse
Affiliation(s)
- Alex K Piel
- Department of Anthropology, University of California San Diego, San Diego, California, United States of America.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Stewart FA, Pruetz JD. Do chimpanzee nests serve an anti-predatory function? Am J Primatol 2013; 75:593-604. [PMID: 23471670 DOI: 10.1002/ajp.22138] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 12/16/2012] [Accepted: 01/11/2013] [Indexed: 11/12/2022]
Abstract
Sleep is a vulnerable state for animals as it compromises the ability to detect predators. The evolution of shelter construction in the great apes may have been a solution to the trade-off between restorative sleep and predation-risk, which allowed a large bodied ape to sleep recumbent in a safe, comfortable spot. In this article we review the evidence of predator pressure on great apes and specifically investigate the potential influence of predation-risk on chimpanzee nesting behavior by comparing nests between chimpanzees living in a habitat of several potential predators (Issa, Ugalla, Tanzania) and a habitat relatively devoid of predators (Fongoli, Senegal). Chimpanzees in Issa did not nest more frequently in forest vegetation than chimpanzees in Fongoli although forest vegetation is expected to provide greater opportunity for escape from terrestrial predators. Nor do chimpanzees in Issa nest in larger groups or aggregate together more than Fongoli chimpanzees, as would be expected if larger groups provide protection from or greater detection of predators. Nests in Issa also did not appear to provide greater opportunities for escape than nests in Fongoli. Chimpanzees in Issa nested more frequently within the same tree as other community members, which may indicate that these chimpanzees nest in greater proximity than chimpanzees in Fongoli. Finally, Issa chimpanzees built their nests proportionately higher and more peripherally within trees. The selection of high and peripheral nesting locations within trees may make Issa chimpanzees inaccessible to potential predators. Many factors influence nest site selection in chimpanzees, of which danger from terrestrial predators is likely to be one.
Collapse
Affiliation(s)
- Fiona A Stewart
- Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom.
| | | |
Collapse
|
36
|
Prevalence and climatic associated factors of Cryptosporidium sp. infections in savanna chimpanzees from Ugalla, Western Tanzania. Parasitol Res 2012; 112:393-9. [DOI: 10.1007/s00436-012-3147-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Accepted: 09/23/2012] [Indexed: 10/27/2022]
|
37
|
Souquière S, Makuwa M, Sallé B, Kazanji M. New strain of simian immunodeficiency virus identified in wild-born chimpanzees from central Africa. PLoS One 2012; 7:e44298. [PMID: 22984489 PMCID: PMC3440395 DOI: 10.1371/journal.pone.0044298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 08/01/2012] [Indexed: 12/27/2022] Open
Abstract
Studies of primate lentiviruses continue to provide information about the evolution of simian immunodeficiency viruses (SIVs) and the origin and emergence of HIV since chimpanzees in west–central Africa (Pan troglodytes troglodytes) were recognized as the reservoir of SIVcpzPtt viruses, which have been related phylogenetically to HIV-1. Using in-house peptide ELISAs to study SIV prevalence, we tested 104 wild-born captive chimpanzees from Gabon and Congo. We identified two new cases of SIVcpz infection in Gabon and characterized a new SIVcpz strain, SIVcpzPtt-Gab4. The complete sequence (9093 bp) was obtained by a PCR-based ‘genome walking’ approach to generate 17 overlapping fragments. Phylogenetic analyses of separated genes (gag, pol-vif and env-nef) showed that SIVcpzPtt-Gab4 is closely related to SIVcpzPtt-Gab1 and SIVcpzPtt-Gab2. No significant variation in viral load was observed during 3 years of follow-up, but a significantly lower CD4+ T cells count was found in infected than in uninfected chimpanzees (p<0.05). No clinical symptoms of SIV infection were observed in the SIV-positive chimpanzees. Further field studies with non-invasive methods are needed to determine the prevalence, geographic distribution, species association, and natural history of SIVcpz strains in the chimpanzee habitat in Gabon.
Collapse
Affiliation(s)
- Sandrine Souquière
- Unité de Rétrovirologie, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Maria Makuwa
- Unité de Rétrovirologie, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Bettina Sallé
- Centre de Primatologie, Centre International de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon
| | - Mirdad Kazanji
- Unité de Rétrovirologie, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
- Institut Pasteur de Bangui, Réseau International des Instituts Pasteur, Bangui, Central African Republic
- * E-mail:
| |
Collapse
|
38
|
Eastern chimpanzees, but not bonobos, represent a simian immunodeficiency virus reservoir. J Virol 2012; 86:10776-91. [PMID: 22837215 DOI: 10.1128/jvi.01498-12] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Chimpanzees in west central Africa (Pan troglodytes troglodytes) are endemically infected with simian immunodeficiency viruses (SIVcpzPtt) that have crossed the species barrier to humans and gorillas on at least five occasions, generating pandemic and nonpandemic forms of human immunodeficiency virus type 1 (HIV-1) as well as gorilla SIV (SIVgor). Chimpanzees in east Africa (Pan troglodytes schweinfurthii) are also infected with SIVcpz; however, their viruses (SIVcpzPts) have never been found in humans. To examine whether this is due to a paucity of natural infections, we used noninvasive methods to screen wild-living eastern chimpanzees in the Democratic Republic of the Congo (DRC), Uganda, and Rwanda. We also screened bonobos (Pan paniscus) in the DRC, a species not previously tested for SIV in the wild. Fecal samples (n = 3,108) were collected at 50 field sites, tested for species and subspecies origin, and screened for SIVcpz antibodies and nucleic acids. Of 2,565 samples from eastern chimpanzees, 323 were antibody positive and 92 contained viral RNA. The antibody-positive samples represented 76 individuals from 19 field sites, all sampled north of the Congo River in an area spanning 250,000 km(2). In this region, SIVcpzPts was common and widespread, with seven field sites exhibiting infection rates of 30% or greater. The overall prevalence of SIVcpzPts infection was 13.4% (95% confidence interval, 10.7% to 16.5%). In contrast, none of the 543 bonobo samples from six sites was antibody positive. All newly identified SIVcpzPts strains clustered in strict accordance to their subspecies origin; however, they exhibited considerable genetic diversity, especially in protein domains known to be under strong host selection pressure. Thus, the absence of SIVcpzPts zoonoses cannot be explained by an insufficient primate reservoir. Instead, greater adaptive hurdles may have prevented the successful colonization of humans by P. t. schweinfurthii viruses.
Collapse
|
39
|
Noninvasive follow-up of simian immunodeficiency virus infection in wild-living nonhabituated western lowland gorillas in Cameroon. J Virol 2012; 86:9760-72. [PMID: 22740419 DOI: 10.1128/jvi.01186-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Simian immunodeficiency viruses infecting western lowland gorillas (SIVgor) are closely related to HIV-1 and are most likely the ancestors of HIV-1 groups O and P. At present, limited data are available on genetic diversity, transmission, viral evolution, and pathogenicity of SIVgor in its natural host. Between 2004 and 2011, 961 putative gorilla fecal samples were collected at the Campo Ma'an National Park, Cameroon. Among them, 16% cross-reacted with HIV-1 antibodies, corresponding to at least 34 infected gorillas. Combining host genotyping and field data, we identified four social groups composed of 7 to 15 individuals each, with SIV rates ranging from 13% to 29%. Eleven SIVgor-infected gorillas were sampled multiple times; two most likely seroconverted during the study period, showing that SIVgor continues to spread. Phylogenetic analysis of partial env and pol sequences revealed cocirculation of closely related and divergent strains among gorillas from the same social group, indicating SIVgor transmissions within and between groups. Parental links could be inferred for some gorillas infected with closely related strains, suggesting vertical transmission, but horizontal transmission by sexual or aggressive behavior was also suspected. Intrahost molecular evolution in one gorilla over a 5-year period showed viral adaptations characteristic of escape mutants, i.e., V1V2 loop elongation and an increased number of glycosylation sites. Here we show for the first time the feasibility of noninvasive monitoring of nonhabituated gorillas to study SIVgor infection over time at both the individual and population levels. This approach can also be applied more generally to study other pathogens in wildlife.
Collapse
|
40
|
Bibollet-Ruche F, Heigele A, Keele BF, Easlick JL, Decker JM, Takehisa J, Learn G, Sharp PM, Hahn BH, Kirchhoff F. Efficient SIVcpz replication in human lymphoid tissue requires viral matrix protein adaptation. J Clin Invest 2012; 122:1644-52. [PMID: 22505456 DOI: 10.1172/jci61429] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 03/05/2012] [Indexed: 12/20/2022] Open
Abstract
SIVs infecting wild-living apes in west central Africa have crossed the species barrier to humans on at least four different occasions, one of which spawned the AIDS pandemic. Although the chimpanzee precursor of pandemic HIV-1 strains must have been able to infect humans, the capacity of SIVcpz strains to replicate in human lymphoid tissues (HLTs) is not known. Here, we show that SIVcpz strains from two chimpanzee subspecies are capable of replicating in human tonsillary explant cultures, albeit only at low titers. However, SIVcpz replication in HLT was significantly improved after introduction of a previously identified human-specific adaptation at position 30 in the viral Gag matrix protein. An Arg or Lys at this position significantly increased SIVcpz replication in HLT, while the same mutation reduced viral replication in chimpanzee-derived CD4(+) T cells. Thus, naturally occurring SIVcpz strains are capable of infecting HLTs, the major site of HIV-1 replication in vivo. However, efficient replication requires the acquisition of a host-specific adaptation in the viral matrix protein. These results identify Gag matrix as a major determinant of SIVcpz replication fitness in humans and suggest a critical role in the emergence of HIV/AIDS.
Collapse
Affiliation(s)
- Frederic Bibollet-Ruche
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6060, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Cross-species transmission of simian retroviruses: how and why they could lead to the emergence of new diseases in the human population. AIDS 2012; 26:659-73. [PMID: 22441170 DOI: 10.1097/qad.0b013e328350fb68] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The HIV-1 group M epidemic illustrates the extraordinary impact and consequences resulting from a single zoonotic transmission. Exposure to blood or other secretions of infected animals, through hunting and butchering of bushmeat, or through bites and scratches inflicted by pet nonhuman primates (NHPs), represent the most plausible source for human infection with simian immunodeficiency virus (SIV), simian T-cell lymphotropic virus (STLV) and simian foamy virus. The chance for cross-species transmissions could increase when frequency of exposure and retrovirus prevalence is high. According to the most recent data, human exposure to SIV or STLV appears heterogeneous across the African countries surveyed. Exposure is not sufficient to trigger disease: viral and host molecular characteristics and compatibility are fundamental factors to establish infection. A successful species jump is achieved when the pathogen becomes transmissible between individuals within the new host population. To spread efficiently, HIV likely required changes in human behavior. Given the increasing exposure to NHP pathogens through hunting and butchering, it is likely that SIV and other simian viruses are still transmitted to the human population. The behavioral and socio-economic context of the twenty-first century provides favorable conditions for the emergence and spread of new epidemics. Therefore, it is important to evaluate which retroviruses the human population is exposed to and to better understand how these viruses enter, infect, adapt and spread to its new host.
Collapse
|