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Din Dipita A, Missoup AD, Aguillon S, Lecompte E, Momboua BR, Chaber AL, Abernethy K, Njiokou F, Tindo M, Ntie S, Gaubert P. Genetic tracing of the illegal trade of the white-bellied pangolin (Phataginus tricuspis) in western Central Africa. Sci Rep 2024; 14:13131. [PMID: 38849460 PMCID: PMC11161582 DOI: 10.1038/s41598-024-63666-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/30/2024] [Indexed: 06/09/2024] Open
Abstract
The white-bellied pangolin is subject to intense trafficking, feeding both local and international trade networks. In order to assess its population genetics and trace its domestic trade, we genotyped 562 pangolins from local to large bushmeat markets in western central Africa. We show that the two lineages described from the study region (WCA and Gab) were overlapping in ranges, with limited introgression in southern Cameroon. There was a lack of genetic differentiation across WCA and a significant signature of isolation-by-distance possibly due to unsuspected dispersal capacities involving a Wahlund effect. We detected a c. 74.1-82.5% decline in the effective population size of WCA during the Middle Holocene. Private allele frequency tracing approach indicated up to 600 km sourcing distance by large urban markets from Cameroon, including Equatorial Guinea. The 20 species-specific microsatellite loci provided individual-level genotyping resolution and should be considered as valuable resources for future forensic applications. Because admixture was detected between lineages, we recommend a multi-locus approach for tracing the pangolin trade. The Yaoundé market was the main hub of the trade in the region, and thus should receive specific monitoring to mitigate pangolins' domestic trafficking. Our study also highlighted the weak implementation of CITES regulations at European borders.
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Affiliation(s)
- Alain Din Dipita
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, 24157, Douala, Cameroon.
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse Cedex 9, France.
| | - Alain Didier Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, 24157, Douala, Cameroon.
| | - Samantha Aguillon
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Emilie Lecompte
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Brice Roxan Momboua
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Anne-Lise Chaber
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide SA, Australia
| | - Katharine Abernethy
- African Forest Ecology Group, Biological and Environmental Sciences, University of Stirling, Stirling, UK
- Institut de Recherche en Ecologie Tropicale, Libreville, Gabon
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Faculté des Sciences, Universite de Yaoundé I, Yaoundé, 812, Cameroon
| | - Maurice Tindo
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, 24157, Douala, Cameroon
| | - Stephan Ntie
- Laboratoire de Biologie Moléculaire et Cellulaire (LABMC), Département de Biologie, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Philippe Gaubert
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse Cedex 9, France.
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal.
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Harper CM, Roach CS, Goldstein DM, Sylvester AD. Morphological variation of the Pan talus relative to that of Gorilla. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023. [PMID: 37300336 DOI: 10.1002/ajpa.24796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/27/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023]
Abstract
OBJECTIVES Differences in talar articular morphology relative to locomotion have recently been found within Pan and Gorilla. Whole-bone talar morphology within, and shared variation among, Pan and Gorilla (sub)species, however, has yet to be investigated. Here we separately analyze talar external shape within Pan (P. t. troglodytes, P. t. schweinfurthii, P. t. verus, P. paniscus) and Gorilla (G. g. gorilla, G. b. beringei, G. b. graueri) relative to degree of arboreality and body size. Pan and Gorilla are additionally analyzed together to determine if consistent shape differences exist within the genera. MATERIALS AND METHODS Talar external shape was quantified using a weighted spherical harmonic analysis. Shape variation both within and among Pan and Gorilla was described using principal component analyses. Root mean square distances were calculated between taxon averages, and resampling statistics conducted to test for pairwise differences. RESULTS P. t. verus (most arboreal Pan) talar shape significantly differs from other Pan taxa (p < 0.05 for pairwise comparisons) driven by more asymmetrical trochlear rims and a medially-set talar head. P. t. troglodytes, P. t. schweinfurthii, and P. paniscus do not significantly differ (p > 0.05 for pairwise comparisons). All gorilla taxa exhibit significantly different talar morphologies (p < 0.007 for pairwise comparisons). The more terrestrial subspecies of G. beringei and P. troglodytes exhibit a superoinferiorly taller talar head/neck complex. DISCUSSION P. t. verus exhibits talar morphologies that have been previously related to more frequent arboreality. The adaptations in the more terrestrial G. beringei and P. troglodytes subspecies may serve to facilitate load transmission.
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Affiliation(s)
- Christine M Harper
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey, USA
| | - Caleigh S Roach
- Krieger School of Arts and Sciences, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Deanna M Goldstein
- Department of Anatomical Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Adam D Sylvester
- Center for Functional Anatomy and Evolution, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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3
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Freedman AH, Harrigan RJ, Zhen Y, Hamilton AM, Smith TB. Evidence for ecotone speciation across an African rainforest-savanna gradient. Mol Ecol 2023; 32:2287-2300. [PMID: 36718952 DOI: 10.1111/mec.16867] [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: 06/03/2022] [Revised: 11/07/2022] [Accepted: 01/16/2023] [Indexed: 02/01/2023]
Abstract
Accelerating climate change and habitat loss make it imperative that plans to conserve biodiversity consider species' ability to adapt to changing environments. However, in biomes where biodiversity is highest, the evolutionary mechanisms responsible for generating adaptative variation and, ultimately, new species are frequently poorly understood. African rainforests represent one such biome, as decadal debates continue concerning the mechanisms generating African rainforest biodiversity. These debates hinge on the relative importance of geographic isolation versus divergent natural selection across environmental gradients. Hindering progress is a lack of robust tests of these competing hypotheses. Because African rainforests are severely at-risk due to climate change and other anthropogenic activities, addressing this long-standing debate is critical for making informed conservation decisions. We use demographic inference and allele frequency-environment relationships to investigate mechanisms of diversification in an African rainforest skink, Trachylepis affinis, a species inhabiting the gradient between rainforest and rainforest-savanna mosaic (ecotone). We provide compelling evidence of ecotone speciation, in which gene flow has all but ceased between rainforest and ecotone populations, at a level consistent with infrequent hybridization between sister species. Parallel patterns of genomic, morphological, and physiological divergence across this environmental gradient and pronounced allele frequency-environment correlation indicate speciation is mostly probably driven by ecological divergence, supporting a central role for divergent natural selection. Our results provide strong evidence for the importance of ecological gradients in African rainforest speciation and inform conservation strategies that preserve the processes that produce and maintain biodiversity.
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Affiliation(s)
- Adam H Freedman
- Faculty of Arts and Sciences Informatics Group, Harvard University, Cambridge, Massachusetts, USA
| | - Ryan J Harrigan
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
| | - Ying Zhen
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Alison M Hamilton
- Department of Biological Sciences, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Thomas B Smith
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
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4
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Hanegraef H, David R, Spoor F. Morphological variation of the maxilla in modern humans and African apes. J Hum Evol 2022; 168:103210. [PMID: 35617847 DOI: 10.1016/j.jhevol.2022.103210] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 04/11/2022] [Accepted: 04/15/2022] [Indexed: 11/25/2022]
Abstract
Differences in morphology among modern humans and African apes are frequently used when assessing whether hominin fossils should be attributed to a single species or represent evidence for taxic diversity. A good understanding of the degree and structure of the intergeneric, interspecific, and intraspecific variation, including aspects such as sexual dimorphism and age, are key in this context. Here we explore the variation and differences shown by the maxilla of extant hominines, as maxillary morphology is central in the diagnosis of several hominin taxa. Our sample includes adults of all currently recognized hominine species and subspecies, with a balanced species sex ratio. In addition, we compared the adults with a small sample of late juveniles. The morphology of the maxillae was captured using three-dimensional landmarks, and the size and shape were analyzed using geometric morphometric methods. Key observations are that 1) the maxillae of all extant hominine species and subspecies show statistically significant differences, but complete separation in shape is only seen at the genus level; 2) the degree of variation is not consistent between genera, with subspecies of Gorilla being more different from each other than are species of Pan; 3) the pattern of sexual shape dimorphism is different in Pan, Gorilla, and Homo, often showing opposite trends; and 4) differentiation between maxillary shapes is increased after adjustment for static intraspecific allometry. These results provide a taxonomically up-to-date comparative morphological framework to help interpret the hominin fossil record, and we discuss the practical implications in that context.
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Affiliation(s)
- Hester Hanegraef
- Centre for Human Evolution Research, Natural History Museum, London, United Kingdom; Department of Anthropology, University College London, London, United Kingdom.
| | - Romain David
- Centre for Human Evolution Research, Natural History Museum, London, United Kingdom; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fred Spoor
- Centre for Human Evolution Research, Natural History Museum, London, United Kingdom; Department of Anthropology, University College London, London, United Kingdom; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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5
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Stover DA, Housman G, Stone AC, Rosenberg MS, Verrelli BC. Evolutionary Genetic Signatures of Selection on Bone-Related Variation within Human and Chimpanzee Populations. Genes (Basel) 2022; 13:183. [PMID: 35205228 PMCID: PMC8871609 DOI: 10.3390/genes13020183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 02/06/2023] Open
Abstract
Bone strength and the incidence and severity of skeletal disorders vary significantly among human populations, due in part to underlying genetic differentiation. While clinical models predict that this variation is largely deleterious, natural population variation unrelated to disease can go unnoticed, altering our perception of how natural selection has shaped bone morphologies over deep and recent time periods. Here, we conduct the first comparative population-based genetic analysis of the main bone structural protein gene, collagen type I α 1 (COL1A1), in clinical and 1000 Genomes Project datasets in humans, and in natural populations of chimpanzees. Contrary to predictions from clinical studies, we reveal abundant COL1A1 amino acid variation, predicted to have little association with disease in the natural population. We also find signatures of positive selection associated with intron haplotype structure, linkage disequilibrium, and population differentiation in regions of known gene expression regulation in humans and chimpanzees. These results recall how recent and deep evolutionary regimes can be linked, in that bone morphology differences that developed among vertebrates over 450 million years of evolution are the result of positive selection on subtle type I collagen functional variation segregating within populations over time.
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Affiliation(s)
- Daryn A. Stover
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
- Arizona State University at Lake Havasu, Lake Havasu, AZ 86403, USA
| | - Genevieve Housman
- Section of Genetic Medicine, University of Chicago, Chicago, IL 60637, USA;
| | - Anne C. Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA;
| | - Michael S. Rosenberg
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Brian C. Verrelli
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA;
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA 23284, USA;
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6
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Barratt CD, Lester JD, Gratton P, Onstein RE, Kalan AK, McCarthy MS, Bocksberger G, White LC, Vigilant L, Dieguez P, Abdulai B, Aebischer T, Agbor A, Assumang AK, Bailey E, Bessone M, Buys B, Carvalho JS, Chancellor R, Cohen H, Danquah E, Deschner T, Dongmo ZN, Doumbé OA, Dupain J, Duvall CS, Eno-Nku M, Etoga G, Galat-Luong A, Garriga R, Gatti S, Ghiurghi A, Goedmakers A, Granjon AC, Hakizimana D, Head J, Hedwig D, Herbinger I, Hermans V, Jones S, Junker J, Kadam P, Kambi M, Kienast I, Kouakou CY, N Goran KP, Langergraber KE, Lapuente J, Laudisoit A, Lee KC, Maisels F, Mirghani N, Moore D, Morgan B, Morgan D, Neil E, Nicholl S, Nkembi L, Ntongho A, Orbell C, Ormsby LJ, Pacheco L, Piel AK, Pintea L, Plumptre AJ, Rundus A, Sanz C, Sommer V, Sop T, Stewart FA, Sunderland-Groves J, Tagg N, Todd A, Ton E, van Schijndel J, VanLeeuwe H, Vendras E, Welsh A, Wenceslau JFC, Wessling EG, Willie J, Wittig RM, Yoshihiro N, Yuh YG, Yurkiw K, Boesch C, Arandjelovic M, Kühl H. Quantitative estimates of glacial refugia for chimpanzees (Pan troglodytes) since the Last Interglacial (120,000 BP). Am J Primatol 2021; 83:e23320. [PMID: 34402081 DOI: 10.1002/ajp.23320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 07/06/2021] [Accepted: 07/28/2021] [Indexed: 11/12/2022]
Abstract
Paleoclimate reconstructions have enhanced our understanding of how past climates have shaped present-day biodiversity. We hypothesize that the geographic extent of Pleistocene forest refugia and suitable habitat fluctuated significantly in time during the late Quaternary for chimpanzees (Pan troglodytes). Using bioclimatic variables representing monthly temperature and precipitation estimates, past human population density data, and an extensive database of georeferenced presence points, we built a model of changing habitat suitability for chimpanzees at fine spatio-temporal scales dating back to the Last Interglacial (120,000 BP). Our models cover a spatial resolution of 0.0467° (approximately 5.19 km2 grid cells) and a temporal resolution of between 1000 and 4000 years. Using our model, we mapped habitat stability over time using three approaches, comparing our modeled stability estimates to existing knowledge of Afrotropical refugia, as well as contemporary patterns of major keystone tropical food resources used by chimpanzees, figs (Moraceae), and palms (Arecacae). Results show habitat stability congruent with known glacial refugia across Africa, suggesting their extents may have been underestimated for chimpanzees, with potentially up to approximately 60,000 km2 of previously unrecognized glacial refugia. The refugia we highlight coincide with higher species richness for figs and palms. Our results provide spatio-temporally explicit insights into the role of refugia across the chimpanzee range, forming the empirical foundation for developing and testing hypotheses about behavioral, ecological, and genetic diversity with additional data. This methodology can be applied to other species and geographic areas when sufficient data are available.
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Affiliation(s)
- Christopher D Barratt
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany.,Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jack D Lester
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Paolo Gratton
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Biology, University of Rome "Tor Vergata", Roma, Italy
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Ammie K Kalan
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Maureen S McCarthy
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Gaëlle Bocksberger
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lauren C White
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Paula Dieguez
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Barrie Abdulai
- Research for Evidence-based and Achievable Decisions Sierra Leone (READ-SL), Sierra Leone
| | - Thierry Aebischer
- Conservation et Plan d'aménagement de l'Aire de Conservation de Chinko, African Parks Network, Chinko Project, Kocho, RCA and active collaborator of the University of Fribourg, WegmannLab, Fribourg, Switzerland
| | - Anthony Agbor
- African Parks Centurion Building, Lonehill, South Africa
| | - Alfred K Assumang
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Emma Bailey
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mattia Bessone
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Joana S Carvalho
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Rebecca Chancellor
- Departments of Anthropology & Sociology and Psychology, West Chester University, West Chester, Pennsylvania, USA
| | - Heather Cohen
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Tobias Deschner
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | - Jef Dupain
- Antwerp Zoo Foundation, Antwerp Zoo Society, Antwerpen, Belgium
| | - Chris S Duvall
- Department of Geography and Environmental Studies, University of New Mexico, Albuquerque, New Mexico, USA
| | - Manasseh Eno-Nku
- World Wide Fund for Nature, Panda House Bastos, Yaounde, Cameroon
| | - Gilles Etoga
- World Wide Fund for Nature, Panda House Bastos, Yaounde, Cameroon
| | - Anh Galat-Luong
- IRD (The French National Research Institute for Development), France
| | - Rosa Garriga
- Tacugama Chimpanzee Sanctuary, Freetown, Sierra Leone
| | - Sylvain Gatti
- West African Primate Conservation Action (WAPCA), Accra, Ghana
| | | | | | - Anne-Céline Granjon
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Josephine Head
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Daniela Hedwig
- Elephant Listening Project, Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
| | | | - Veerle Hermans
- Taï Chimpanzee Project, CSRS, Abidjan, Ivory Coast.,Centre for Research and Conservation, Antwerp Zoo Society, Antwerpen, Belgium
| | - Sorrel Jones
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jessica Junker
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Parag Kadam
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, UK
| | - Mohamed Kambi
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ivonne Kienast
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Kouamé P N Goran
- World Wide Fund for Nature, Panda House Bastos, Yaounde, Cameroon
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Institute of Human Origins, Arizona State University, Tempe, Arizona, USA
| | - Juan Lapuente
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Comoé Chimpanzee Conservation Project, Comoé National Park, Kakpin, Ivory Coast
| | - Anne Laudisoit
- Ecohealth Alliance, New York City, New York, USA.,Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerpen, Belgium
| | - Kevin C Lee
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Fiona Maisels
- Wildlife Conservation Society (WCS), Bronx, New York, USA.,Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK
| | - Nadia Mirghani
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
| | - Deborah Moore
- Department of Anthropology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Bethan Morgan
- Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK.,San Diego Zoo Global, Escondido, California, USA.,Ebo Forest Research Project, Yaounde, Cameroon
| | - David Morgan
- Lester E Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, Illinois, USA
| | - Emily Neil
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sonia Nicholl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Louis Nkembi
- Environment and Rural Development Foundation, Buea, Cameroon
| | - Anne Ntongho
- World Wide Fund for Nature, Panda House Bastos, Yaounde, Cameroon
| | | | - Lucy Jayne Ormsby
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Alex K Piel
- Department of Anthropology, University College London, London, UK
| | | | - Andrew J Plumptre
- Key Biodiversity Area Secretariat, c/o BirdLife International, Cambridge, UK
| | - Aaron Rundus
- Department of Psychology, West Chester University, West Chester, Pennsylvania, USA
| | - Crickette Sanz
- Department of Anthropology, Washington University in St. Louis, Saint Louis, Missouri, USA.,Wildlife Conservation Society, Congo Program, Brazzaville, Republic of Congo
| | - Volker Sommer
- Department of Anthropology, University College London, London, UK.,Gashaka Primate Project, Serti, Taraba State, Nigeria
| | - Tenekwetche Sop
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany.,Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fiona A Stewart
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK.,Wildlife Conservation Society, Congo Program, Brazzaville, Republic of Congo
| | | | - Nikki Tagg
- Centre for Research and Conservation, Antwerp Zoo Society, Antwerpen, Belgium
| | | | - Els Ton
- Chimbo Foundation, Oudemirdum, Netherlands
| | | | | | - Elleni Vendras
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Adam Welsh
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Erin G Wessling
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jacob Willie
- Centre for Research and Conservation, Antwerp Zoo Society, Antwerpen, Belgium
| | - Roman M Wittig
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Taï Chimpanzee Project, CSRS, Abidjan, Ivory Coast
| | | | - Yisa Ginath Yuh
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Geography, Planning and Environmental Studies, University of Concordia, Montréal, Quebec, Canada
| | - Kyle Yurkiw
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Pan Verus Project, Outamba-Kilimi National Park, Sierra Leone
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hjalmar Kühl
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany.,Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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7
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Abstract
Understanding variation in host-associated microbial communities is important given the relevance of microbiomes to host physiology and health. Using 560 fecal samples collected from wild chimpanzees (Pan troglodytes) across their range, we assessed how geography, genetics, climate, vegetation, and diet relate to gut microbial community structure (prokaryotes, eukaryotic parasites) at multiple spatial scales. We observed a high degree of regional specificity in the microbiome composition, which was associated with host genetics, available plant foods, and potentially with cultural differences in tool use, which affect diet. Genetic differences drove community composition at large scales, while vegetation and potentially tool use drove within-region differences, likely due to their influence on diet. Unlike industrialized human populations in the United States, where regional differences in the gut microbiome are undetectable, chimpanzee gut microbiomes are far more variable across space, suggesting that technological developments have decoupled humans from their local environments, obscuring regional differences that could have been important during human evolution. IMPORTANCE Gut microbial communities are drivers of primate physiology and health, but the factors that influence the gut microbiome in wild primate populations remain largely undetermined. We report data from a continent-wide survey of wild chimpanzee gut microbiota and highlight the effects of genetics, vegetation, and potentially even tool use at different spatial scales on the chimpanzee gut microbiome, including bacteria, archaea, and eukaryotic parasites. Microbial community dissimilarity was strongly correlated with chimpanzee population genetic dissimilarity, and vegetation composition and consumption of algae, honey, nuts, and termites were potentially associated with additional divergence in microbial communities between sampling sites. Our results suggest that host genetics, geography, and climate play a far stronger role in structuring the gut microbiome in chimpanzees than in humans.
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8
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Allen KE, Greenbaum E, Hime PM, Tapondjou N. WP, Sterkhova VV, Kusamba C, Rödel M, Penner J, Peterson AT, Brown RM. Rivers, not refugia, drove diversification in arboreal, sub-Saharan African snakes. Ecol Evol 2021; 11:6133-6152. [PMID: 34141208 PMCID: PMC8207163 DOI: 10.1002/ece3.7429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 12/26/2022] Open
Abstract
The relative roles of rivers versus refugia in shaping the high levels of species diversity in tropical rainforests have been widely debated for decades. Only recently has it become possible to take an integrative approach to test predictions derived from these hypotheses using genomic sequencing and paleo-species distribution modeling. Herein, we tested the predictions of the classic river, refuge, and river-refuge hypotheses on diversification in the arboreal sub-Saharan African snake genus Toxicodryas. We used dated phylogeographic inferences, population clustering analyses, demographic model selection, and paleo-distribution modeling to conduct a phylogenomic and historical demographic analysis of this genus. Our results revealed significant population genetic structure within both Toxicodryas species, corresponding geographically to river barriers and divergence times from the mid-Miocene to Pliocene. Our demographic analyses supported the interpretation that rivers are indications of strong barriers to gene flow among populations since their divergence. Additionally, we found no support for a major contraction of suitable habitat during the last glacial maximum, allowing us to reject both the refuge and river-refuge hypotheses in favor of the river-barrier hypothesis. Based on conservative interpretations of our species delimitation analyses with the Sanger and ddRAD data sets, two new cryptic species are identified from east-central Africa. This study highlights the complexity of diversification dynamics in the African tropics and the advantages of integrative approaches to studying speciation in tropical regions.
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Affiliation(s)
- Kaitlin E. Allen
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Eli Greenbaum
- Department of Biological SciencesUniversity of Texas at El PasoEl PasoTXUSA
| | - Paul M. Hime
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Walter P. Tapondjou N.
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Viktoria V. Sterkhova
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Chifundera Kusamba
- Laboratoire d’Hérpétologie, Département de BiologieCentre de Recherche en Sciences NaturellesLwiroDemocratic Republic of Congo
| | - Mark‐Oliver Rödel
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Johannes Penner
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
- Chair of Wildlife Ecology and ManagementUniversity of FreiburgFreiburgGermany
| | - A. Townsend Peterson
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Rafe M. Brown
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
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9
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Palmer A, Sommer V, Msindai JN. Hybrid apes in the Anthropocene: Burden or asset for conservation? PEOPLE AND NATURE 2021; 3:573-586. [PMID: 34805779 PMCID: PMC8581989 DOI: 10.1002/pan3.10214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/01/2021] [Indexed: 11/08/2022] Open
Abstract
Conservationists often view hybrid animals as problematic, at least if anthropogenic influence caused the intermixing to occur. However, critics propose that humans should respect non-human autonomy, reject and accept the creatures they have helped to create.Based on two case studies of our own ethological, genetic and ethnographic research about chimpanzee and orangutan subspecies hybrids, we assess what, if anything, should be done about such animals. We consider problems posed by cross-bred apes relating to: (a) Breeding-Do hybrids really experience reduced reproductive success? How are population-level concerns and welfare of individual animals balanced in conservation breeding? (b) Essentialism-Are anti-hybrid arguments based on essentialist or purist thinking? Does essentialism vary by conservation context? (c) Pragmatism-How do socio-economic circumstances influence whether hybrids are embraced or ignored? Does the erosion of 'untouched nature' render hybrids more important?We show that answers to these questions are complex and context-specific, and that therefore decisions should be made on a case-by-case basis. For example, we find that anti-hybrid arguments are essentialist in some cases (e.g. ape management in zoos) but not in others (e.g. ape reintroduction). Thus, rather than present recommendations, we conclude by posing nine questions that conservationists should ask themselves when making decisions about taxonomic hybrids. A free Plain Language Summary can be found within the Supporting Information of this article.
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Affiliation(s)
- Alexandra Palmer
- School of Geography and the EnvironmentUniversity of OxfordOxfordUK
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10
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Couvreur TL, Dauby G, Blach‐Overgaard A, Deblauwe V, Dessein S, Droissart V, Hardy OJ, Harris DJ, Janssens SB, Ley AC, Mackinder BA, Sonké B, Sosef MS, Stévart T, Svenning J, Wieringa JJ, Faye A, Missoup AD, Tolley KA, Nicolas V, Ntie S, Fluteau F, Robin C, Guillocheau F, Barboni D, Sepulchre P. Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna. Biol Rev Camb Philos Soc 2021; 96:16-51. [PMID: 32924323 PMCID: PMC7821006 DOI: 10.1111/brv.12644] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/30/2022]
Abstract
Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.
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Affiliation(s)
| | - Gilles Dauby
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - Anne Blach‐Overgaard
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Vincent Deblauwe
- Center for Tropical Research (CTR), Institute of the Environment and SustainabilityUniversity of California, Los Angeles (UCLA)Los AngelesCA90095U.S.A.
- International Institute of Tropical Agriculture (IITA)YaoundéCameroon
| | | | - Vincent Droissart
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Oliver J. Hardy
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - David J. Harris
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghU.K.
| | | | - Alexandra C. Ley
- Institut für Geobotanik und Botanischer GartenUniversity Halle‐WittenbergNeuwerk 21Halle06108Germany
| | | | - Bonaventure Sonké
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
| | | | - Tariq Stévart
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Jens‐Christian Svenning
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Jan J. Wieringa
- Naturalis Biodiversity CenterDarwinweg 2Leiden2333 CRThe Netherlands
| | - Adama Faye
- Laboratoire National de Recherches sur les Productions Végétales (LNRPV)Institut Sénégalais de Recherches Agricoles (ISRA)Route des Hydrocarbures, Bel Air BP 1386‐ CP18524DakarSenegal
| | - Alain D. Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of ScienceUniversity of DoualaPO Box 24157DoualaCameroon
| | - Krystal A. Tolley
- South African National Biodiversity InstituteKirstenbosch Research CentrePrivate Bag X7, ClaremontCape Town7735South Africa
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandPrivate Bag 3Wits2050South Africa
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHEUniversité des AntillesCP51, 57 rue CuvierParis75005France
| | - Stéphan Ntie
- Département de Biologie, Faculté des SciencesUniversité des Sciences et Techniques de MasukuFrancevilleBP 941Gabon
| | - Frédiéric Fluteau
- Institut de Physique du Globe de Paris, CNRSUniversité de ParisParisF‐75005France
| | - Cécile Robin
- CNRS, Géosciences Rennes, UMR6118University of RennesRennes35042France
| | | | - Doris Barboni
- CEREGE, Aix‐Marseille University, CNRS, IRD, Collège de France, INRA, Technopole Arbois MéditerranéeBP80Aix‐en‐Provence cedex413545France
| | - Pierre Sepulchre
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA‐CNRS‐UVSQUniversité Paris‐SaclayGif‐sur‐YvetteF‐91191France
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11
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Vangenot C, Nunes JM, Doxiadis GM, Poloni ES, Bontrop RE, de Groot NG, Sanchez-Mazas A. Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans indicate highly conserved mechanisms of MHC molecular evolution. BMC Evol Biol 2020; 20:119. [PMID: 32933484 PMCID: PMC7491122 DOI: 10.1186/s12862-020-01669-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 08/06/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Many species are threatened with extinction as their population sizes decrease with changing environments or face novel pathogenic threats. A reduction of genetic diversity at major histocompatibility complex (MHC) genes may have dramatic effects on populations' survival, as these genes play a key role in adaptive immunity. This might be the case for chimpanzees, the MHC genes of which reveal signatures of an ancient selective sweep likely due to a viral epidemic that reduced their population size a few million years ago. To better assess how this past event affected MHC variation in chimpanzees compared to humans, we analysed several indexes of genetic diversity and linkage disequilibrium across seven MHC genes on four cohorts of chimpanzees and we compared them to those estimated at orthologous HLA genes in a large set of human populations. RESULTS Interestingly, the analyses uncovered similar patterns of both molecular diversity and linkage disequilibrium across the seven MHC genes in chimpanzees and humans. Indeed, in both species the greatest allelic richness and heterozygosity were found at loci A, B, C and DRB1, the greatest nucleotide diversity at loci DRB1, DQA1 and DQB1, and both significant global linkage disequilibrium and the greatest proportions of haplotypes in linkage disequilibrium were observed at pairs DQA1 ~ DQB1, DQA1 ~ DRB1, DQB1 ~ DRB1 and B ~ C. Our results also showed that, despite some differences among loci, the levels of genetic diversity and linkage disequilibrium observed in contemporary chimpanzees were globally similar to those estimated in small isolated human populations, in contrast to significant differences compared to large populations. CONCLUSIONS We conclude, first, that highly conserved mechanisms shaped the diversity of orthologous MHC genes in chimpanzees and humans. Furthermore, our findings support the hypothesis that an ancient demographic decline affecting the chimpanzee populations - like that ascribed to a viral epidemic - exerted a substantial effect on the molecular diversity of their MHC genes, albeit not more pronounced than that experienced by HLA genes in human populations that underwent rapid genetic drift during humans' peopling history. We thus propose a model where chimpanzees' MHC genes regenerated molecular variation through recombination/gene conversion and/or balancing selection after the selective sweep.
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Affiliation(s)
- Christelle Vangenot
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - José Manuel Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Gaby M Doxiadis
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288, GJ, Rijswijk, The Netherlands
| | - Estella S Poloni
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288, GJ, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288, GJ, Rijswijk, The Netherlands
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland. .,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.
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12
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Environmental variability supports chimpanzee behavioural diversity. Nat Commun 2020; 11:4451. [PMID: 32934202 PMCID: PMC7493986 DOI: 10.1038/s41467-020-18176-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 08/07/2020] [Indexed: 11/18/2022] Open
Abstract
Large brains and behavioural innovation are positively correlated, species-specific traits, associated with the behavioural flexibility animals need for adapting to seasonal and unpredictable habitats. Similar ecological challenges would have been important drivers throughout human evolution. However, studies examining the influence of environmental variability on within-species behavioural diversity are lacking despite the critical assumption that population diversification precedes genetic divergence and speciation. Here, using a dataset of 144 wild chimpanzee (Pan troglodytes) communities, we show that chimpanzees exhibit greater behavioural diversity in environments with more variability — in both recent and historical timescales. Notably, distance from Pleistocene forest refugia is associated with the presence of a larger number of behavioural traits, including both tool and non-tool use behaviours. Since more than half of the behaviours investigated are also likely to be cultural, we suggest that environmental variability was a critical evolutionary force promoting the behavioural, as well as cultural diversification of great apes. Environmental variability is one potential driver of behavioural and cultural diversity in humans and other animals. Here, the authors show that chimpanzee behavioural diversity is higher in habitats that are more seasonal and historically unstable, and in savannah woodland relative to forested sites.
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13
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Abstract
While non-human primate studies have long been conducted in laboratories, and more recently at zoological parks, sanctuaries are increasingly considered a viable setting for research. Accredited sanctuaries in non-range countries house thousands of primates formerly used as subjects of medical research, trained performers or personal pets. In range countries, however, sanctuaries typically house orphaned primates confiscated from illegal poaching and the bushmeat and pet trafficking trades. Although the primary mission of these sanctuaries is to rescue and rehabilitate residents, many of these organizations are increasingly willing to participate in non-invasive research. Notably, from a scientific standpoint, most sanctuaries provide potential advantages over traditional settings, such as large, naturalistic physical and social environments which may result in more relevant models of primates' free-ranging wild counterparts than other captive settings. As a result, an impressive scope of research in the fields of primate behaviour, cognition, veterinary science, genetics and physiology have been studied in sanctuaries. In this review, we examine the range and form of research that has been conducted at accredited sanctuaries around the world. We also describe the potential challenges of sanctuary-based work and the considerations that external researchers may face when deciding to collaborate with primate sanctuaries on their research projects.
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Affiliation(s)
- Stephen R Ross
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, 2001 North Clark St., Chicago, IL 60614, USA
| | - Jesse G Leinwand
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, 2001 North Clark St., Chicago, IL 60614, USA
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14
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Abwe EE, Morgan BJ, Doudja R, Kentatchime F, Mba F, Dadjo A, Venditti DM, Mitchell MW, Fosso B, Mounga A, Fotso RC, Gonder MK. Dietary Ecology of the Nigeria–Cameroon Chimpanzee (Pan troglodytes ellioti). INT J PRIMATOL 2020. [DOI: 10.1007/s10764-020-00138-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Hashimoto-Gotoh A, Yoshikawa R, Nakagawa S, Okamoto M, Miyazawa T. Phylogenetic analyses reveal that simian foamy virus isolated from Japanese Yakushima macaques (Macaca fuscata yakui) is distinct from most of Japanese Hondo macaques (Macaca fuscata fuscata). Gene 2020; 734:144382. [PMID: 31978513 DOI: 10.1016/j.gene.2020.144382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 11/25/2022]
Abstract
Japanese macaque (Macaca fuscata) is an indigenous Old World monkey (OWM) species that inhabits the Japanese archipelago. There are two subspecies of Japanese macaque: Yakushima macaque (M. f. yakui) which inhabits Yakushima Island exclusively, and Hondo macaque (M. f. fuscata) which inhabits the mainland of Japan. Yakushima macaque is considered to be branched off from a certain parental macaque group that had inhabited the mainland of Japan. However, the process of sub-speciation of the Yakushima macaque is still unclear at present. In this study, to gain new insight into the process of sub-speciation of Japanese macaque, we utilized the simian foamy virus (SFV) as a marker. SFVs are found in virtually all primates except humans and undergo species-specific cospeciation with the hosts. The phylogenetic analysis of conserved regions of the env gene in SFVs remarkably resembled that of the OWMs with high statistical confidence. The phylogenetic analyses also indicated that there are four (1-4) genotypes among Asian OWMs investigated. SFVs derived from Asian OWMs except Yakushima macaque were classified as genotypes 1-3, whereas SFVs isolated from all Yakushima macaques and one Hondo macaque were classified as genotype 4. Interestingly, genotype 4 was firstly branched off from the rest of the genotypes, which might indicate that the macaques infected with genotype 4 SFV were derived from the "older" population of Japanese macaques. The high prevalence of genotype 4 SFVs among Yakushima macaque might reflect the possibility that they are a descendant of the population settled earlier, which has been geographically isolated in Yakushima Island.
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Affiliation(s)
- Akira Hashimoto-Gotoh
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Rokusuke Yoshikawa
- National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan; Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 259-1193, Japan
| | - Munehiro Okamoto
- Center for Human Evolution Modeling Research, Primate Research Institute, Kyoto University, Aichi 484-8506, Japan
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan; International Research Unit of Advanced Future Studies, Kyoto University, Kyoto 606-8502, Japan.
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16
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Caspers LM, Ferrie GM, Wolfe K, Hoffman EA. Subspecific identity and a comparison of genetic diversity between wild and ex situ wildebeest. Zoo Biol 2020; 39:129-140. [PMID: 31904139 DOI: 10.1002/zoo.21530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 08/01/2019] [Accepted: 12/18/2019] [Indexed: 11/11/2022]
Abstract
The original North American ex situ wildebeest population was believed to originate from the white-bearded wildebeest (Connochaetes taurinus albojubatus), which is both morphologically distinct and geographically separated from the brindled wildebeest (C. t. taurinus). However, after an import of wildebeest into North America in 2001, managers have suspected that white-bearded and brindled wildebeest were mixed in herds at multiple institutions. We sequenced the mitochondrial control region (d-loop) from a portion of the managed North American population and compared our sequences with previously published sequences from wild individuals to determine the subspecific identity and genetic diversity of our ex situ population. We were able to confidently identify C. t. albojubatus as the subspecies identity of the sampled portion of our population. Within our population, haplotype and nucleotide diversity were low (0.169 and 0.001, respectively) with a single common haplotype (H1) containing 41 of the 45 individuals sequenced, while two rare haplotypes (H2 and H3) were derived from three individuals and a single individual, respectively. Nucleotide and haplotype diversity were greater overall in the wild populations compared with our managed population. However, C. t. albojubatus was found to exhibit lower nucleotide diversity in both wild and ex situ populations when compared to other wild subspecies. Though the overall goal of the North American wildebeest population is for public education and not reintroduction, maintaining genetic diversity is vital for the long-term viability of this managed population, which may benefit from periodic supplementation of wild animals.
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Affiliation(s)
- Lauren M Caspers
- Department of Biology, University of Central Florida, Orlando, Florida
| | - Gina M Ferrie
- Disney's Animals, Science, and Environment, Disney's Animal Kingdom, Lake Buena Vista, Florida
| | - Kristen Wolfe
- Disney's Animals, Science, and Environment, Disney's Animal Kingdom, Lake Buena Vista, Florida
| | - Eric A Hoffman
- Department of Biology, University of Central Florida, Orlando, Florida
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17
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Chaves PB, Magnus T, Jerusalinsky L, Talebi M, Strier KB, Breves P, Tabacow F, Teixeira RHF, Moreira L, Hack ROE, Milagres A, Pissinatti A, de Melo FR, Pessutti C, Mendes SL, Margarido TC, Fagundes V, Di Fiore A, Bonatto SL. Phylogeographic evidence for two species of muriqui (genus Brachyteles). Am J Primatol 2019; 81:e23066. [PMID: 31736121 DOI: 10.1002/ajp.23066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/14/2019] [Accepted: 10/25/2019] [Indexed: 11/06/2022]
Abstract
The taxonomy of muriquis, the largest extant primates in the New World, is controversial. While some specialists argue for a monotypic genus (Brachyteles arachnoides), others favor a two-species classification, splitting northern muriquis (Brachyteles hypoxanthus) from southern muriquis (B. arachnoides). This uncertainty affects how we study the differences between these highly endangered and charismatic primates, as well as the design of more effective conservation programs. To address this issue, between 2003 and 2017 we collected over 230 muriqui fecal samples across the genus' distribution in the Brazilian Atlantic Forest, extracted DNA from these samples, and sequenced 423 base pairs of the mitochondrial DNA (mtDNA) control region. Phylogenetic and species delimitation analyses of our sequence dataset robustly support two reciprocally monophyletic groups corresponding to northern and southern muriquis separated by an average 12.7% genetic distance. The phylogeographic break between these lineages seems to be associated with the Paraíba do Sul River and coincides with the transition between the north and south Atlantic Forest biogeographic zones. Published divergence estimates from whole mitochondrial genomes and nuclear loci date the split between northern and southern muriquis to the Early Pleistocene (ca. 2.0 mya), and our new mtDNA dataset places the coalescence time for each of these two clades near the last interglacial (ca. 120-80 kya). Our results, together with both phenotypic and ecological differences, support recognizing northern and southern muriquis as sister species that should be managed as distinct evolutionarily significant units. Given that only a few thousand muriquis remain in nature, it is imperative that conservation strategies are tailored to protect both species from extinction.
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Affiliation(s)
- Paulo B Chaves
- Department of Anthropology, New York University, New York, New York.,New York Consortium in Evolutionary Primatology (NYCEP), New York, New York
| | - Tielli Magnus
- Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Leandro Jerusalinsky
- Centro Nacional de Pesquisa e Conservação de Primatas Brasileiros, Instituto Chico Mendes de Conservação da Biodiversidade, João Pessoa, Paraíba, Brazil
| | - Maurício Talebi
- Laboratório de Ecologia Aplicada e Conservação (LECON), Departamento de Ciências Ambientais, Universidade Federal de São Paulo, Diadema, São Paulo, Brazil.,Instituto Pró-Muriqui, São Paulo, São Paulo, Brazil
| | - Karen B Strier
- Department of Anthropology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Paula Breves
- Diretoria de Biodiversidade, Sociedade Ecoatlântica, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda Tabacow
- Muriqui Instituto de Biodiversidade, Caratinga, Minas Gerais, Brazil
| | - Rodrigo H F Teixeira
- Programa de Pós-graduação em Animais Selvagens, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo, Brazil
| | - Leandro Moreira
- Muriqui Instituto de Biodiversidade, Caratinga, Minas Gerais, Brazil
| | - Robson O E Hack
- Divisão de Meio Ambiente, Departamento de Recursos Ambientais, Instituto de Tecnologia para o Desenvolvimento (Lactec), Curitiba, Paraná, Brazil.,Programa de Pós-Graduação em Desenvolvimento de Tecnologia, Instituto de Tecnologia para o Desenvolvimento e Instituto de Engenharia do Paraná, Curitiba, Paraná, Brazil
| | - Adriana Milagres
- Programa de Pós-graduação em Ecologia Aplicada, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Alcides Pissinatti
- Centro de Primatologia do Rio de Janeiro, Instituto Estadual do Ambiente, Guapimirim, Rio de Janeiro, Brazil
| | - Fabiano R de Melo
- Unidade Acadêmica Especial de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.,Departamento de Engenharia Florestal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Cecília Pessutti
- Parque Zoológico Municipal Quinzinho de Barros, Sorocaba, São Paulo, Brazil
| | - Sérgio L Mendes
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Tereza C Margarido
- Departamento de Pesquisa e Conservação da Fauna, Prefeitura Municipal de Curitiba, Curitiba, Paraná, Brazil
| | - Valéria Fagundes
- Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Anthony Di Fiore
- Department of Anthropology, Primate Molecular Ecology and Evolution Laboratory, The University of Texas at Austin, Austin, Texas
| | - Sandro L Bonatto
- Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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18
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Yaxley KJ, Foley RA. Reconstructing the ancestral phenotypes of great apes and humans (Homininae) using subspecies-level phylogenies. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Owing to their close affinity, the African great apes are of interest in the study of human evolution. Although numerous researchers have described the ancestors we share with these species with reference to extant great apes, few have done so with phylogenetic comparative methods. One obstacle to the application of these techniques is the within-species phenotypic variation found in this group. Here, we leverage this variation, modelling common ancestors using ancestral state reconstructions (ASRs) with reference to subspecies-level trait data. A subspecies-level phylogeny of the African great apes and humans was estimated from full-genome mitochondrial DNA sequences and used to implement ASRs for 14 continuous traits known to vary between great ape subspecies. Although the inclusion of within-species phenotypic variation increased the phylogenetic signal for our traits and improved the performance of our ASRs, whether this was done through the inclusion of subspecies phylogeny or through the use of existing methods made little difference. Our ASRs corroborate previous findings that the last common ancestor of humans, chimpanzees and bonobos was a chimp-like animal, but also suggest that the last common ancestor of humans, chimpanzees, bonobos and gorillas was an animal unlike any extant African great ape.
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Affiliation(s)
| | - Robert A Foley
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, UK
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19
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Admixture in Mammals and How to Understand Its Functional Implications. Bioessays 2019; 41:e1900123. [DOI: 10.1002/bies.201900123] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/03/2019] [Indexed: 12/13/2022]
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20
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Dykes SJ, Pilbrow VC. A mathematical landmark-based method for measuring worn molars in hominoid systematics. PeerJ 2019; 7:e6990. [PMID: 31198638 PMCID: PMC6535218 DOI: 10.7717/peerj.6990] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/20/2019] [Indexed: 11/30/2022] Open
Abstract
Worn teeth pose a major limitation to researchers in the fields of extinct and extant hominoid systematics because they lack clearly identifiable anatomical landmarks needed to take measurements on the crown enamel surface and are typically discarded from a study. This is particularly detrimental when sample sizes for some groups are already characteristically low, if there is an imbalance between samples representing populations, sexes or dietary strategies, or if the worn teeth in question are type specimens of fossil species or other key specimens. This study proposes a methodology based predominantly on mathematically-derived landmarks for measuring size and shape features of molars, irrespective of wear. With 110 specimens of lower second molars from five species of extant hominoids (Pan troglodytes, P. paniscus, Gorilla gorilla, G. beringei, Homo sapiens), n ≥ 20 per species, n ≥ 10 per subspecies, good species separation in morphospace is achieved in a principal components analysis. Classification accuracy in a discriminant function analysis is 96.4% at the species level and 88.2% at the subspecies level (92.7% and 79.1%, respectively, on cross-validation). The classification accuracy compares favorably to that achieved by anatomically-derived measurements based on published research (94% and 84% at the species and subspecies level respectively; 91% and 76% on cross-validation). The mathematical landmarking methodology is rapid and uncomplicated. The results support the use of mathematical landmarks to enable the inclusion of worn molar teeth in dental studies so as to maximize sample sizes and restore balance between populations and/or sexes in hominoid systematic studies.
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Affiliation(s)
- Susan J. Dykes
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
- School of Geosciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Varsha C. Pilbrow
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Australia
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21
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Bibollet-Ruche F, Russell RM, Liu W, Stewart-Jones GBE, Sherrill-Mix S, Li Y, Learn GH, Smith AG, Gondim MVP, Plenderleith LJ, Decker JM, Easlick JL, Wetzel KS, Collman RG, Ding S, Finzi A, Ayouba A, Peeters M, Leendertz FH, van Schijndel J, Goedmakers A, Ton E, Boesch C, Kuehl H, Arandjelovic M, Dieguez P, Murai M, Colin C, Koops K, Speede S, Gonder MK, Muller MN, Sanz CM, Morgan DB, Atencia R, Cox D, Piel AK, Stewart FA, Ndjango JBN, Mjungu D, Lonsdorf EV, Pusey AE, Kwong PD, Sharp PM, Shaw GM, Hahn BH. CD4 receptor diversity in chimpanzees protects against SIV infection. Proc Natl Acad Sci U S A 2019; 116:3229-3238. [PMID: 30718403 PMCID: PMC6386711 DOI: 10.1073/pnas.1821197116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Human and simian immunodeficiency viruses (HIV/SIVs) use CD4 as the primary receptor to enter target cells. Here, we show that the chimpanzee CD4 is highly polymorphic, with nine coding variants present in wild populations, and that this diversity interferes with SIV envelope (Env)-CD4 interactions. Testing the replication fitness of SIVcpz strains in CD4+ T cells from captive chimpanzees, we found that certain viruses were unable to infect cells from certain hosts. These differences were recapitulated in CD4 transfection assays, which revealed a strong association between CD4 genotypes and SIVcpz infection phenotypes. The most striking differences were observed for three substitutions (Q25R, Q40R, and P68T), with P68T generating a second N-linked glycosylation site (N66) in addition to an invariant N32 encoded by all chimpanzee CD4 alleles. In silico modeling and site-directed mutagenesis identified charged residues at the CD4-Env interface and clashes between CD4- and Env-encoded glycans as mechanisms of inhibition. CD4 polymorphisms also reduced Env-mediated cell entry of monkey SIVs, which was dependent on at least one D1 domain glycan. CD4 allele frequencies varied among wild chimpanzees, with high diversity in all but the western subspecies, which appeared to have undergone a selective sweep. One allele was associated with lower SIVcpz prevalence rates in the wild. These results indicate that substitutions in the D1 domain of the chimpanzee CD4 can prevent SIV cell entry. Although some SIVcpz strains have adapted to utilize these variants, CD4 diversity is maintained, protecting chimpanzees against infection with SIVcpz and other SIVs to which they are exposed.
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Affiliation(s)
| | - Ronnie M Russell
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Weimin Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Guillaume B E Stewart-Jones
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Yingying Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gerald H Learn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Andrew G Smith
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Marcos V P Gondim
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
| | - Julie M Decker
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Juliet L Easlick
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Katherine S Wetzel
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ronald G Collman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Shilei Ding
- Département de Microbiologie, Infectiologie et Immunologie, Centre de Recherche du Centre Hospitalier de L'Université de Montréal, Montréal, QC H2X0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H2X0A9, Canada
| | - Andrés Finzi
- Département de Microbiologie, Infectiologie et Immunologie, Centre de Recherche du Centre Hospitalier de L'Université de Montréal, Montréal, QC H2X0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H2X0A9, Canada
| | - Ahidjo Ayouba
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - Martine Peeters
- Recherche Translationnelle Appliquée au VIH et aux Maladies Infectieuses, Institut de Recherche pour le Développement, University of Montpellier, INSERM, 34090 Montpellier, France
| | - Fabian H Leendertz
- Research Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, 13353 Berlin, Germany
| | - Joost van Schijndel
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Chimbo Foundation, 1011 PW Amsterdam, The Netherlands
| | | | - Els Ton
- Chimbo Foundation, 1011 PW Amsterdam, The Netherlands
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Hjalmar Kuehl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Paula Dieguez
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mizuki Murai
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christelle Colin
- Projet Primates France, Centre de Conservation pour Chimpanzés, BP 36 Faranah, Republic of Guinea
| | - Kathelijne Koops
- Department of Anthropology, University of Zurich, CH-8006 Zurich, Switzerland
| | - Sheri Speede
- Sanaga-Yong Chimpanzee Rescue Center, In Defense of Animals-Africa, Portland, OR 97204
| | - Mary K Gonder
- Department of Biology, Drexel University, Philadelphia, PA 19104
| | - Martin N Muller
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131
| | - Crickette M Sanz
- Department of Anthropology, Washington University in St. Louis, St Louis, MO 63130
- Congo Program, Wildlife Conservation Society, BP 14537 Brazzaville, Republic of the Congo
| | - David B Morgan
- Congo Program, Wildlife Conservation Society, BP 14537 Brazzaville, Republic of the Congo
- Lester E. Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, IL 60614
| | - Rebecca Atencia
- Tchimpounga Chimpanzee Rehabilitation Center, The Jane Goodall Institute-Congo, BP 1206 Pointe Noire, Republic of Congo
| | - Debby Cox
- Tchimpounga Chimpanzee Rehabilitation Center, The Jane Goodall Institute-Congo, BP 1206 Pointe Noire, Republic of Congo
- Africa Programs, The Jane Goodall Institute, Vienna, VA 22182
| | - Alex K Piel
- School of Natural Sciences and Psychology, Liverpool John Moores University, L3 3AF Liverpool, United Kingdom
| | - Fiona A Stewart
- School of Natural Sciences and Psychology, Liverpool John Moores University, L3 3AF Liverpool, United Kingdom
| | - Jean-Bosco N Ndjango
- Department of Ecology and Management of Plant and Animal Resources, Faculty of Sciences, University of Kisangani, BP 2012 Kisangani, Democratic Republic of the Congo
| | - Deus Mjungu
- Gombe Stream Research Centre, The Jane Goodall Institute, Kigoma, Tanzania
| | | | - Anne E Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Paul M Sharp
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL Edinburgh, United Kingdom
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104
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22
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Abwe EE, Morgan BJ, Tchiengue B, Kentatchime F, Doudja R, Ketchen ME, Teguia E, Ambahe R, Venditti DM, Mitchell MW, Fosso B, Mounga A, Fotso RC, Gonder MK. Habitat differentiation among three Nigeria-Cameroon chimpanzee ( Pan troglodytes ellioti) populations. Ecol Evol 2019; 9:1489-1500. [PMID: 30805176 PMCID: PMC6374666 DOI: 10.1002/ece3.4871] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/29/2018] [Accepted: 12/04/2018] [Indexed: 11/18/2022] Open
Abstract
Ecological niche models (ENMs) are often used to predict species distribution patterns from datasets that describe abiotic and biotic factors at coarse spatial scales. Ground-truthing ENMs provide important information about how these factors relate to species-specific requirements at a scale that is biologically relevant for the species. Chimpanzees are territorial and have a predominantly frugivorous diet. The spatial and temporal variation in fruit availability for different chimpanzee populations is thus crucial, but rarely depicted in ENMs. The genetic and geographic distinction within Nigeria-Cameroon chimpanzee (Pan troglodytes ellioti) populations represents a unique opportunity to understand fine scale species-relevant ecological variation in relation to ENMs. In Cameroon, P. t. ellioti is composed of two genetically distinct populations that occupy different niches: rainforests in western Cameroon and forest-woodland-savanna mosaic (ecotone) in central Cameroon. We investigated habitat variation at three representative sites using chimpanzee-relevant environmental variables, including fruit availability, to assess how these variables distinguish these niches from one another. Contrary to the assumption of most ENM studies that intact forest is essential for the survival of chimpanzees, we hypothesized that the ecotone and human-modified habitats in Cameroon have sufficient resources to sustain large chimpanzee populations. Rainfall, and the diversity, density, and size of trees were higher at the rainforest. The ecotone had a higher density of terrestrial herbs and lianas. Fruit availability was higher at Ganga (ecotone) than at Bekob and Njuma. Seasonal variation in fruit availability was highest at Ganga, and periods of fruit scarcity were longer than at the rainforest sites. Introduced and secondary forest species linked with anthropogenic modification were common at Bekob, which reduced seasonality in fruit availability. Our findings highlight the value of incorporating fine scale species-relevant ecological data to create more realistic models, which have implications for local conservation planning efforts.
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Affiliation(s)
- Ekwoge E. Abwe
- Department of BiologyDrexel UniversityPhiladelphiaPennsylvania
- Ebo Forest Research ProjectYaoundéCameroon
- San Diego Zoo GlobalSan DiegoCalifornia
| | - Bethan J. Morgan
- Ebo Forest Research ProjectYaoundéCameroon
- San Diego Zoo GlobalSan DiegoCalifornia
| | | | | | - Roger Doudja
- Ministry of Forestry and WildlifeYaoundéCameroon
| | | | - Eric Teguia
- Wildlife Conservation SocietyYaoundéCameroon
| | | | | | - Matthew W. Mitchell
- Department of BiologyDrexel UniversityPhiladelphiaPennsylvania
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania
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23
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Rediscovery of Red Wolf Ghost Alleles in a Canid Population Along the American Gulf Coast. Genes (Basel) 2018; 9:genes9120618. [PMID: 30544757 PMCID: PMC6315914 DOI: 10.3390/genes9120618] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 11/17/2022] Open
Abstract
Rediscovering species once thought to be extinct or on the edge of extinction is rare. Red wolves have been extinct along the American Gulf Coast since 1980, with their last populations found in coastal Louisiana and Texas. We report the rediscovery of red wolf ghost alleles in a canid population on Galveston Island, Texas. We analyzed over 7000 single nucleotide polymorphisms (SNPs) in 60 canid representatives from all legally recognized North American Canis species and two phenotypically ambiguous canids from Galveston Island. We found notably high Bayesian cluster assignments of the Galveston canids to captive red wolves with extensive sharing of red wolf private alleles. Today, the only known extant wild red wolves persist in a reintroduced population in North Carolina, which is dwindling amongst political and taxonomic controversy. Our rediscovery of red wolf ancestry after almost 40 years introduces both positive opportunities for additional conservation action and difficult policy challenges.
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24
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Hey J, Chung Y, Sethuraman A, Lachance J, Tishkoff S, Sousa VC, Wang Y. Phylogeny Estimation by Integration over Isolation with Migration Models. Mol Biol Evol 2018; 35:2805-2818. [PMID: 30137463 PMCID: PMC6231491 DOI: 10.1093/molbev/msy162] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Phylogeny estimation is difficult for closely related populations and species, especially if they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain Monte Carlo method with a state space that includes all possible phylogenies in a full Isolation-with-Migration model framework. The method is based on a new type of genealogy augmentation called a "hidden genealogy" that enables efficient updating of the phylogeny. This is the first likelihood-based method to fully incorporate directional gene flow and genetic drift for estimation of a species or population phylogeny. Application to human hunter-gatherer populations from Africa revealed a clear phylogenetic history, with strong support for gene exchange with an unsampled ghost population, and relatively ancient divergence between a ghost population and modern human populations, consistent with human/archaic divergence. In contrast, a study of five chimpanzee populations reveals a clear phylogeny with several pairs of populations having exchanged DNA, but does not support a history with an unsampled ghost population.
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Affiliation(s)
- Jody Hey
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
| | - Yujin Chung
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
- The Department of Applied Statistics, Kyonggi University, Suwon, South Korea
| | - Arun Sethuraman
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA
| | - Joseph Lachance
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Georgia Institute of Technology, Atlanta, GA
| | - Sarah Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Vitor C Sousa
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ
- University of Lisbon, Lisboa, Portugal
| | - Yong Wang
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ
- Ancestry, San Francisco, CA
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25
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Mitchell MW, Locatelli S, Abwe EE, Ghobrial L, Gonder MK. Male-Driven Differences in Chimpanzee (Pan troglodytes) Population Genetic Structure Across Three Habitats in Cameroon and Nigeria. INT J PRIMATOL 2018. [DOI: 10.1007/s10764-018-0053-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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26
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Jongsma GF, Barej MF, Barratt CD, Burger M, Conradie W, Ernst R, Greenbaum E, Hirschfeld M, Leaché AD, Penner J, Portik DM, Zassi-Boulou AG, Rödel MO, Blackburn DC. Diversity and biogeography of frogs in the genus Amnirana (Anura: Ranidae) across sub-Saharan Africa. Mol Phylogenet Evol 2018; 120:274-285. [DOI: 10.1016/j.ympev.2017.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 11/30/2017] [Accepted: 12/05/2017] [Indexed: 10/18/2022]
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27
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Fuchs J, De Swardt DH, Oatley G, Fjeldså J, Bowie RCK. Habitat‐driven diversification, hybridization and cryptic diversity in the Fork‐tailed Drongo (Passeriformes: Dicruridae:
Dicrurus adsimilis
). ZOOL SCR 2018. [DOI: 10.1111/zsc.12274] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité UMR7205 CNRS MNHN UPMC EPHE Sorbonne Universités, Muséum National d'Histoire Naturelle Paris France
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California Berkeley CA USA
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute University of Cape Town Rondebosch South Africa
| | | | - Graeme Oatley
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute University of Cape Town Rondebosch South Africa
- Department of Zoology and Lab of Ornithology Faculty of Science Palacky University Olomouc Czech Republic
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California Berkeley CA USA
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute University of Cape Town Rondebosch South Africa
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28
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Huntley JW, Harvey JA, Pavia M, Boano G, Voelker G. The systematics and biogeography of the Bearded Greenbuls (Aves: Criniger) reveals the impact of Plio-Pleistocene forest fragmentation on Afro-tropical avian diversity. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jerry W Huntley
- Department of Wildlife and Fisheries Sciences, Texas A&M University, TX, USA
| | - Johanna A Harvey
- Department of Wildlife and Fisheries Sciences, Texas A&M University, TX, USA
| | - Marco Pavia
- University of Torino, DST, via Valperga Caluso Torino, Italy
| | - Giovanni Boano
- Museo Civico di Storia Naturale, Cascina Vigna, Carmagnola, Italy
| | - Gary Voelker
- Department of Wildlife and Fisheries Sciences, Texas A&M University, TX, USA
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29
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Hernandez-Rodriguez J, Arandjelovic M, Lester J, de Filippo C, Weihmann A, Meyer M, Angedakin S, Casals F, Navarro A, Vigilant L, Kühl HS, Langergraber K, Boesch C, Hughes D, Marques-Bonet T. The impact of endogenous content, replicates and pooling on genome capture from faecal samples. Mol Ecol Resour 2017; 18:319-333. [PMID: 29058768 PMCID: PMC5900898 DOI: 10.1111/1755-0998.12728] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/06/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022]
Abstract
Target-capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of noninvasive samples such as faeces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries. Second, we assessed the influence of using more than one faecal sample, extract and/or library from the same individual, to evaluate its effect on the molecular complexity of the experiment. We validated our experiments with 18 chimpanzee faecal samples collected from two field sites as a part of the Pan African Programme: The Cultured Chimpanzee. Those two field sites are in Kibale National Park, Uganda (N = 9) and Loango National Park, Gabon (N = 9). We demonstrate that at least 16 libraries can be pooled, target enriched through hybridization, and sequenced allowing for the genotyping of 951,949 exome markers for population genetic analyses. Further, we observe that molecule richness, and thus, data acquisition, increase when using multiple libraries from the same extract or multiple extracts from the same sample. Finally, repeated captures significantly decrease the proportion of off-target reads from 34.15% after one capture round to 7.83% after two capture rounds, supporting our conclusion that two rounds of target enrichment are advisable when using complex faecal samples.
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Affiliation(s)
- Jessica Hernandez-Rodriguez
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jack Lester
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Antje Weihmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Samuel Angedakin
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Arcadi Navarro
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hjalmar S Kühl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Leipzig, Germany
| | - Kevin Langergraber
- School of Human Evolution & Social Change, Arizona State University, Tempe, AZ, USA
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - David Hughes
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tomas Marques-Bonet
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Schroeder L, von Cramon-Taubadel N. The evolution of hominoid cranial diversity: A quantitative genetic approach. Evolution 2017; 71:2634-2649. [DOI: 10.1111/evo.13361] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/03/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Lauren Schroeder
- Department of Anthropology; University of Toronto Mississauga; Mississauga ON L5L 1C6 Canada
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology; University at Buffalo; SUNY, Buffalo New York 14261
- Human Evolution Research Institute; University of Cape Town; Rondebosch 7701 South Africa
| | - Noreen von Cramon-Taubadel
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology; University at Buffalo; SUNY, Buffalo New York 14261
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31
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Portik DM, Leaché AD, Rivera D, Barej MF, Burger M, Hirschfeld M, Rödel M, Blackburn DC, Fujita MK. Evaluating mechanisms of diversification in a Guineo‐Congolian tropical forest frog using demographic model selection. Mol Ecol 2017; 26:5245-5263. [DOI: 10.1111/mec.14266] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/17/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Daniel M. Portik
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Adam D. Leaché
- Department of Biology University of Washington Seattle WA USA
- Burke Museum of Natural History and Culture University of Washington Seattle WA USA
| | - Danielle Rivera
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Michael F. Barej
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - Marius Burger
- African Amphibian Conservation Research Group Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
- Flora Fauna & Man Ecological Services Ltd. Tortola British Virgin Island
| | - Mareike Hirschfeld
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - Mark‐Oliver Rödel
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - David C. Blackburn
- Florida Museum of Natural History University of Florida Gainesville FL USA
| | - Matthew K. Fujita
- Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington TX USA
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Huntley JW, Voelker G. A tale of the nearly tail-less: the effects of Plio-Pleistocene climate change on the diversification of the African avian genusSylvietta. ZOOL SCR 2017. [DOI: 10.1111/zsc.12240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jerry W. Huntley
- Department of Wildlife and Fisheries Sciences; Texas A&M University; 210 Nagle Hall College Station TX 77843 USA
| | - Gary Voelker
- Department of Wildlife and Fisheries Sciences; Texas A&M University; 210 Nagle Hall College Station TX 77843 USA
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33
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Aronsen GP, Kirkham M. Inventory and Assessment of thePan troglodytes(Blumenbach, 1799) Skeletal Collection Housed at the Yale Peabody Museum. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2017. [DOI: 10.3374/014.058.0107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Gary P. Aronsen
- Department of Anthropology, Biological Anthropology Laboratories, Yale University, P.O. Box 208277, New Haven CT 06520-8277 USA
| | - Megan Kirkham
- Division of Anthropology, Peabody Museum of Natural History, Yale University, New Haven CT USA
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34
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Pruetz JD, Ontl KB, Cleaveland E, Lindshield S, Marshack J, Wessling EG. Intragroup Lethal Aggression in West African Chimpanzees (Pan troglodytes verus): Inferred Killing of a Former Alpha Male at Fongoli, Senegal. INT J PRIMATOL 2017. [DOI: 10.1007/s10764-016-9942-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Gryseels S, Baird SJE, Borremans B, Makundi R, Leirs H, Goüy de Bellocq J. When Viruses Don't Go Viral: The Importance of Host Phylogeographic Structure in the Spatial Spread of Arenaviruses. PLoS Pathog 2017; 13:e1006073. [PMID: 28076397 PMCID: PMC5226678 DOI: 10.1371/journal.ppat.1006073] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/17/2016] [Indexed: 01/07/2023] Open
Abstract
Many emerging infections are RNA virus spillovers from animal reservoirs. Reservoir identification is necessary for predicting the geographic extent of infection risk, but rarely are taxonomic levels below the animal species considered as reservoir, and only key circumstances in nature and methodology allow intrinsic virus-host associations to be distinguished from simple geographic (co-)isolation. We sampled and genetically characterized in detail a contact zone of two subtaxa of the rodent Mastomys natalensis in Tanzania. We find two distinct arenaviruses, Gairo and Morogoro virus, each spatially confined to a single M. natalensis subtaxon, only co-occurring at the contact zone’s centre. Inter-subtaxon hybridization at this centre and a continuum of quality habitat for M. natalensis show that both viruses have the ecological opportunity to spread into the other substaxon’s range, but do not, strongly suggesting host-intrinsic barriers. Such barriers could explain why human cases of another M. natalensis-borne arenavirus, Lassa virus, are limited to West Africa. Reservoirs of zoonotic viruses are usually equated with a particular wildlife species. It is rarely assessed whether genetic groups below the species level may instead represent the actual reservoir, though this would have major implications on estimations of the zoonosis’ spatial distribution. Here we investigate whether geographically and genetically distinct subtaxa of the widespread African rodent Mastomys natalensis carry distinct arenaviruses, by sampling in detail across a contact zone of two of these subtaxa. Ongoing hybridization shows that individuals of the subtaxa are in direct physical contact, in principle allowing viral exchange, yet neither of the two arenaviruses -Gairo and Morogoro virus- were found to have crossed the zone. Such intraspecific genetic barriers to arenavirus spatial spread have important implications for our understanding of the related Lassa arenavirus, a pathogen potentially lethal to humans of which Mastomys natalensis is also the main reservoir. Although Lassa virus appears to infect several secondary hosts, its distribution is restricted to West Africa and matches that of another M. natalensis subtaxon. Our data thus indicates that it is because of M. natalensis intraspecific distinctions that the human Lassa fever endemic area has not expanded to the rest of sub-Saharan Africa.
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Affiliation(s)
- Sophie Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- * E-mail:
| | - Stuart J. E. Baird
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Research Facility Studenec, Brno, Czech Republic
| | - Benny Borremans
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Rhodes Makundi
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Herwig Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Joëlle Goüy de Bellocq
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Research Facility Studenec, Brno, Czech Republic
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36
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Heine S, Dar-Nimrod I, Cheung B, Proulx T. Essentially Biased. ADVANCES IN EXPERIMENTAL SOCIAL PSYCHOLOGY 2017. [DOI: 10.1016/bs.aesp.2016.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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37
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Leaché AD, Grummer JA, Miller M, Krishnan S, Fujita MK, Böhme W, Schmitz A, Lebreton M, Ineich I, Chirio L, Ofori-boateng C, Eniang EA, Greenbaum E, Rödel MO, Wagner P. Bayesian inference of species diffusion in the West African Agama agama species group (Reptilia, Agamidae). SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1238018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Adam D. Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195-1800, USA
| | - Jared A. Grummer
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195-1800, USA
| | - Michael Miller
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195-1800, USA
| | - Sneha Krishnan
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195-1800, USA
| | - Matthew K. Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Wolfgang Böhme
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, D53113, Bonn, Germany
| | - Andreas Schmitz
- Natural History Museum of Geneva, Department of Herpetology and Ichthyology, C.P. 6434, CH-1211, Geneva 6, Switzerland
| | - Matthew Lebreton
- Muséum National d'Histoire Naturelle & Sorbonne Universités, Département Systématique et Évolution (Reptiles), ISyEB (Institut de Systématique, Évolution, Biodiversité, UMR 7205 CNRS/UPMC/EPHE/MNHN), Paris, France
| | - Ivan Ineich
- Muséum National d'Histoire Naturelle & Sorbonne Universités, Département Systématique et Évolution (Reptiles), ISyEB (Institut de Systématique, Évolution, Biodiversité, UMR 7205 CNRS/UPMC/EPHE/MNHN), Paris, France
| | - Laurent Chirio
- Muséum National d'Histoire Naturelle & Sorbonne Universités, Département Systématique et Évolution (Reptiles), ISyEB (Institut de Systématique, Évolution, Biodiversité, UMR 7205 CNRS/UPMC/EPHE/MNHN), Paris, France
| | | | - Edem A. Eniang
- Department of Forestry and Wildlife, University of Uyo, Akwa Ibom State, Nigeria
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, 500 West University Ave., El Paso, TX, 79968, USA
| | - Mark-Oliver Rödel
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, 10115, Berlin, Germany
| | - Philipp Wagner
- Zoologische Staatssammlung München, Münchhausenstr. 21, D81247, München, Germany
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38
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de Manuel M, Kuhlwilm M, Frandsen P, Sousa VC, Desai T, Prado-Martinez J, Hernandez-Rodriguez J, Dupanloup I, Lao O, Hallast P, Schmidt JM, Heredia-Genestar JM, Benazzo A, Barbujani G, Peter BM, Kuderna LFK, Casals F, Angedakin S, Arandjelovic M, Boesch C, Kühl H, Vigilant L, Langergraber K, Novembre J, Gut M, Gut I, Navarro A, Carlsen F, Andrés AM, Siegismund HR, Scally A, Excoffier L, Tyler-Smith C, Castellano S, Xue Y, Hvilsom C, Marques-Bonet T. Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science 2016; 354:477-481. [PMID: 27789843 DOI: 10.1126/science.aag2602] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 12/13/2022]
Abstract
Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that chimpanzee population substructure makes genetic information a good predictor of geographic origin at country and regional scales. Multiple lines of evidence suggest that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200,000 and 550,000 years ago, probably with subsequent spread into Nigeria-Cameroon chimpanzees. Together with another, possibly more recent contact (after 200,000 years ago), bonobos contributed less than 1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution.
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Affiliation(s)
- Marc de Manuel
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Martin Kuhlwilm
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Peter Frandsen
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark. Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
| | - Vitor C Sousa
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tariq Desai
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Javier Prado-Martinez
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Isabelle Dupanloup
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Oscar Lao
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Pille Hallast
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK. Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Joshua M Schmidt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - José María Heredia-Genestar
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
| | - Benjamin M Peter
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Lukas F K Kuderna
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Ferran Casals
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Samuel Angedakin
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Hjalmar Kühl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Kevin Langergraber
- School of Human Evolution and Social Change and Institute of Human Origins, Arizona State University, Tempe, AZ 85287, USA
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Marta Gut
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Ivo Gut
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Arcadi Navarro
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain
| | - Frands Carlsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Hans R Siegismund
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Aylwyn Scally
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Laurent Excoffier
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Sergi Castellano
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Christina Hvilsom
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark.
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain.
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Kuhlwilm M, de Manuel M, Nater A, Greminger MP, Krützen M, Marques-Bonet T. Evolution and demography of the great apes. Curr Opin Genet Dev 2016; 41:124-129. [PMID: 27716526 DOI: 10.1016/j.gde.2016.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 09/03/2016] [Accepted: 09/12/2016] [Indexed: 01/27/2023]
Abstract
The great apes are the closest living relatives of humans. Chimpanzees and bonobos group together with humans, while gorillas and orangutans are more divergent from humans. Here, we review insights into their evolution pertaining to the topology of species and subspecies and the reconstruction of their demography based on genome-wide variation. These advances have only become possible recently through next-generation sequencing technologies. Given the close relationship to humans, they provide an important evolutionary context for human genetics.
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Affiliation(s)
- Martin Kuhlwilm
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Alexander Nater
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Maja P Greminger
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
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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.
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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
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Oetjens MT, Shen F, Emery SB, Zou Z, Kidd JM. Y-Chromosome Structural Diversity in the Bonobo and Chimpanzee Lineages. Genome Biol Evol 2016; 8:2231-40. [PMID: 27358426 PMCID: PMC4987114 DOI: 10.1093/gbe/evw150] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The male-specific regions of primate Y-chromosomes (MSY) are enriched for multi-copy genes highly expressed in the testis. These genes are located in large repetitive sequences arranged as palindromes, inverted-, and tandem repeats termed amplicons. In humans, these genes have critical roles in male fertility and are essential for the production of sperm. The structure of human and chimpanzee amplicon sequences show remarkable difference relative to the remainder of the genome, a difference that may be the result of intense selective pressure on male fertility. Four subspecies of common chimpanzees have undergone extended periods of isolation and appear to be in the early process of subspeciation. A recent study found amplicons enriched for testis-expressed genes on the primate X-chromosome the target of hard selective sweeps, and male-fertility genes on the Y-chromosome may also be the targets of selection. However, little is understood about Y-chromosome amplicon diversity within and across chimpanzee populations. Here, we analyze nine common chimpanzee (representing three subspecies: Pan troglodytes schweinfurthii, Pan troglodytes ellioti, and Pan troglodytes verus) and two bonobo (Pan paniscus) male whole-genome sequences to assess Y ampliconic copy-number diversity across the Pan genus. We observe that the copy number of Y chromosome amplicons is variable among chimpanzees and bonobos, and identify several lineage-specific patterns, including variable copy number of azoospermia candidates RBMY and DAZ. We detect recurrent switchpoints of copy-number change along the ampliconic tracts across chimpanzee populations, which may be the result of localized genome instability or selective forces.
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Affiliation(s)
| | - Feichen Shen
- Department of Human Genetics, University of Michigan Medical School
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School
| | - Zhengting Zou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School Department of Computational Medicine and Bioinformatics, University of Michigan Medical School
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Liu W, Sundararaman SA, Loy DE, Learn GH, Li Y, Plenderleith LJ, Ndjango JBN, Speede S, Atencia R, Cox D, Shaw GM, Ayouba A, Peeters M, Rayner JC, Hahn BH, Sharp PM. Multigenomic Delineation of Plasmodium Species of the Laverania Subgenus Infecting Wild-Living Chimpanzees and Gorillas. Genome Biol Evol 2016; 8:1929-39. [PMID: 27289102 PMCID: PMC4943199 DOI: 10.1093/gbe/evw128] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2016] [Indexed: 12/15/2022] Open
Abstract
Plasmodium falciparum, the major cause of malaria morbidity and mortality worldwide, is only distantly related to other human malaria parasites and has thus been placed in a separate subgenus, termed Laverania Parasites morphologically similar to P. falciparum have been identified in African apes, but only one other Laverania species, Plasmodium reichenowi from chimpanzees, has been formally described. Although recent studies have pointed to the existence of additional Laverania species, their precise number and host associations remain uncertain, primarily because of limited sampling and a paucity of parasite sequences other than from mitochondrial DNA. To address this, we used limiting dilution polymerase chain reaction to amplify additional parasite sequences from a large number of chimpanzee and gorilla blood and fecal samples collected at two sanctuaries and 30 field sites across equatorial Africa. Phylogenetic analyses of more than 2,000 new sequences derived from the mitochondrial, nuclear, and apicoplast genomes revealed six divergent and well-supported clades within the Laverania parasite group. Although two of these clades exhibited deep subdivisions in phylogenies estimated from organelle gene sequences, these sublineages were geographically defined and not present in trees from four unlinked nuclear loci. This greatly expanded sequence data set thus confirms six, and not seven or more, ape Laverania species, of which P. reichenowi, Plasmodium gaboni, and Plasmodium billcollinsi only infect chimpanzees, whereas Plasmodium praefalciparum, Plasmodium adleri, and Pladmodium blacklocki only infect gorillas. The new sequence data also confirm the P. praefalciparum origin of human P. falciparum.
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Affiliation(s)
- Weimin Liu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Sesh A Sundararaman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania Department of Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Dorothy E Loy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania Department of Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, United Kingdom
| | | | - Sheri Speede
- Sanaga-Yong Chimpanzee Rescue Center, IDA-Africa, Portland, Oregon
| | - Rebeca Atencia
- Tchimpounga Chimpanzee Rehabilitation Center, Pointe-Noire, Republic of the Congo
| | - Debby Cox
- Tchimpounga Chimpanzee Rehabilitation Center, Pointe-Noire, Republic of the Congo Africa Programmes, Jane Goodall Institute, Vienna, Virginia
| | - George M Shaw
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania Department of Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Ahidjo Ayouba
- UMI 233, Institut de Recherche pour le Développement (IRD), INSERM U1175, and University of Montpellier, France
| | - Martine Peeters
- UMI 233, Institut de Recherche pour le Développement (IRD), INSERM U1175, and University of Montpellier, France
| | - Julian C Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania Department of Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Paul M Sharp
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, United Kingdom
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Huntley JW, Voelker G. Cryptic diversity in Afro-tropical lowland forests: The systematics and biogeography of the avian genus Bleda. Mol Phylogenet Evol 2016; 99:297-308. [DOI: 10.1016/j.ympev.2016.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/28/2016] [Accepted: 04/02/2016] [Indexed: 01/18/2023]
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Takemoto H, Kawamoto Y, Furuichi T. How did bonobos come to range south of the congo river? Reconsideration of the divergence of Pan paniscus from other Pan populations. Evol Anthropol 2016; 24:170-84. [PMID: 26478139 DOI: 10.1002/evan.21456] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
While investigating the genetic structure in wild bonobos,(1) we realized that the widely accepted scenario positing that the Pleistocene appearance of the Congo River separated the common ancestor of chimpanzees (Pan troglodytes) and bonobos (P. paniscus) into two species is not supported by recent geographical knowledge about the formation of the Congo River. We explored the origin of bonobos using a broader biogeographical perspective by examining local faunas in the central African region. The submarine Congo River sediments and paleotopography of central Africa show that the Congo River has functioned as a geographical barrier for the last 34 million years. This evidence allows us to hypothesize that when the river was first formed, the ancestor of bonobos did not inhabit the current range of the species on the left bank of the Congo River but that, during rare times when the Congo River discharge decreased during the Pleistocene, one or more founder populations of ancestral Pan paniscus crossed the river to its left bank. The proposed scenario for formation of the Congo River and the corridor hypothesis for an ancestral bonobo population is key to understanding the distribution of great apes and their evolution.
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Banes GL, Galdikas BMF, Vigilant L. Reintroduction of confiscated and displaced mammals risks outbreeding and introgression in natural populations, as evidenced by orang-utans of divergent subspecies. Sci Rep 2016; 6:22026. [PMID: 26911345 PMCID: PMC4766574 DOI: 10.1038/srep22026] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/04/2016] [Indexed: 11/08/2022] Open
Abstract
Confiscated and displaced mammals are often taken to sanctuaries, where the explicit goal may be reintroduction to the wild. By inadvertently collecting animals from different source populations, however, such efforts risk reintroducing individuals that have not been in genetic contact for significant periods of time. Using genetic analyses and 44 years of data from Camp Leakey, an orang-utan rehabilitation site on Borneo, we determined the minimum extent to which orang-utans representing non-native, geographically and reproductively isolated taxa were reintroduced into the surrounding wild population. We found two reintroduced females were from a non-native subspecies, and have since produced at least 22 hybridized and introgressed descendants to date, of which at least 15 are living. Given that Bornean orang-utan subspecies are thought to have diverged from a common ancestor around 176,000 years ago, with marked differentiation over the last 80,000 years, we highlight the need for further evaluation of the effects of hybridizing orang-utans of different taxa--particularly in light of the ~1500 displaced orang-utans awaiting urgent reintroduction. As endangered mammals are increasing in number in sanctuaries worldwide, we stress the need for re-examination of historical reintroductions, to assess the extent and effects of de facto translocations in the past.
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Affiliation(s)
- Graham L. Banes
- Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, Pembroke Street, Cambridge, CB2 3QY, United Kingdom
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai 200031, People’s Republic of China
| | - Biruté M. F. Galdikas
- Department of Archaeology, Simon Fraser University, 8888 University Drive, Burnaby, B.C., V5A 1S6, Canada
| | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
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Petkova D, Novembre J, Stephens M. Visualizing spatial population structure with estimated effective migration surfaces. Nat Genet 2016; 48:94-100. [PMID: 26642242 PMCID: PMC4696895 DOI: 10.1038/ng.3464] [Citation(s) in RCA: 326] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 11/12/2015] [Indexed: 12/17/2022]
Abstract
Genetic data often exhibit patterns broadly consistent with 'isolation by distance'-a phenomenon where genetic similarity decays with geographic distance. In a heterogeneous habitat, this may occur more quickly in some regions than in others: for example, barriers to gene flow can accelerate differentiation between neighboring groups. We use the concept of 'effective migration' to model the relationship between genetics and geography. In this paradigm, effective migration is low in regions where genetic similarity decays quickly. We present a method to visualize variation in effective migration across a habitat from geographically indexed genetic data. Our approach uses a population genetic model to relate effective migration rates to expected genetic dissimilarities. We illustrate its potential and limitations using simulations and data from elephant, human and Arabidopsis thaliana populations. The resulting visualizations highlight important spatial features of population structure that are difficult to discern using existing methods for summarizing genetic variation.
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Affiliation(s)
- Desislava Petkova
- Department of Statistics, The University of Chicago, Chicago, Illinois, USA
- Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - John Novembre
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Matthew Stephens
- Department of Statistics, The University of Chicago, Chicago, Illinois, USA
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
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Fuchs J, Bowie RC. Concordant genetic structure in two species of woodpecker distributed across the primary West African biogeographic barriers. Mol Phylogenet Evol 2015; 88:64-74. [DOI: 10.1016/j.ympev.2015.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 03/10/2015] [Accepted: 03/12/2015] [Indexed: 12/21/2022]
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Bataillon T, Duan J, Hvilsom C, Jin X, Li Y, Skov L, Glemin S, Munch K, Jiang T, Qian Y, Hobolth A, Wang J, Mailund T, Siegismund HR, Schierup MH. Inference of purifying and positive selection in three subspecies of chimpanzees (Pan troglodytes) from exome sequencing. Genome Biol Evol 2015; 7:1122-32. [PMID: 25829516 PMCID: PMC4419804 DOI: 10.1093/gbe/evv058] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We study genome-wide nucleotide diversity in three subspecies of extant chimpanzees using exome capture. After strict filtering, Single Nucleotide Polymorphisms and indels were called and genotyped for greater than 50% of exons at a mean coverage of 35× per individual. Central chimpanzees (Pan troglodytes troglodytes) are the most polymorphic (nucleotide diversity, θw = 0.0023 per site) followed by Eastern (P. t. schweinfurthii) chimpanzees (θw = 0.0016) and Western (P. t. verus) chimpanzees (θw = 0.0008). A demographic scenario of divergence without gene flow fits the patterns of autosomal synonymous nucleotide diversity well except for a signal of recent gene flow from Western into Eastern chimpanzees. The striking contrast in X-linked versus autosomal polymorphism and divergence previously reported in Central chimpanzees is also found in Eastern and Western chimpanzees. We show that the direction of selection statistic exhibits a strong nonmonotonic relationship with the strength of purifying selection S, making it inappropriate for estimating S. We instead use counts in synonymous versus nonsynonymous frequency classes to infer the distribution of S coefficients acting on nonsynonymous mutations in each subspecies. The strength of purifying selection we infer is congruent with the differences in effective sizes of each subspecies: Central chimpanzees are undergoing the strongest purifying selection followed by Eastern and Western chimpanzees. Coding indels show stronger selection against indels changing the reading frame than observed in human populations.
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Affiliation(s)
| | - Jinjie Duan
- Bioinformatics Research Centre, Aarhus University, Denmark
| | - Christina Hvilsom
- Science and Conservation, Copenhagen Zoo, Denmark Bioinformatics, University of Copenhagen, Denmark
| | | | | | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, Denmark
| | - Sylvain Glemin
- Institut des Sciences de l'Evolution, Universite Montpellier 2, France
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, Denmark
| | | | - Yu Qian
- Bioinformatics Research Centre, Aarhus University, Denmark
| | - Asger Hobolth
- Bioinformatics Research Centre, Aarhus University, Denmark
| | - Jun Wang
- BGI Shenzhen, China Section of Metabolic Genetics, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark The Department of Genetic Medicine, Faculty of Medicine and Princess Al Jawhara Albrahim Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia Department of Biology, University of Copenhagen, Denmark Macau University of Science and Technology, China
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, Denmark
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Mitchell MW, Locatelli S, Sesink Clee PR, Thomassen HA, Gonder MK. Environmental variation and rivers govern the structure of chimpanzee genetic diversity in a biodiversity hotspot. BMC Evol Biol 2015; 15:1. [PMID: 25608511 PMCID: PMC4314796 DOI: 10.1186/s12862-014-0274-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/15/2014] [Indexed: 11/13/2022] Open
Abstract
Background The mechanisms that underlie the diversification of tropical animals remain poorly understood, but new approaches that combine geo-spatial modeling with spatially explicit genetic data are providing fresh insights on this topic. Data about the diversification of tropical mammals remain particularly sparse, and vanishingly few opportunities exist to study endangered large mammals that increasingly exist only in isolated pockets. The chimpanzees of Cameroon represent a unique opportunity to examine the mechanisms that promote genetic differentiation in tropical mammals because the region is home to two chimpanzee subspecies: Pan troglodytes ellioti and P. t. trogolodytes. Their ranges converge in central Cameroon, which is a geographically, climatically and environmentally complex region that presents an unparalleled opportunity to examine the roles of rivers and/or environmental variation in influencing the evolution of chimpanzee populations. Results We analyzed microsatellite genotypes and mtDNA HVRI sequencing data from wild chimpanzees sampled at a fine geographic scale across Cameroon and eastern Nigeria using a spatially explicit approach based upon Generalized Dissimilarity Modeling. Both the Sanaga River and environmental variation were found to contribute to driving separation of the subspecies. The importance of environmental variation differed among subspecies. Gene-environment associations were weak in P. t. troglodytes, whereas environmental variation was found to play a much larger role in shaping patterns of genetic differentiation in P. t. ellioti. Conclusions We found that both the Sanaga River and environmental variation likely play a role in shaping patterns of chimpanzee genetic diversity. Future studies using single nucleotide polymorphism (SNP) data are necessary to further understand how rivers and environmental variation contribute to shaping patterns of genetic variation in chimpanzees. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0274-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew W Mitchell
- Department of Biology, Drexel University, Philadelphia 19104, Pennsylvania, USA.
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Sesink Clee PR, Abwe EE, Ambahe RD, Anthony NM, Fotso R, Locatelli S, Maisels F, Mitchell MW, Morgan BJ, Pokempner AA, Gonder MK. Chimpanzee population structure in Cameroon and Nigeria is associated with habitat variation that may be lost under climate change. BMC Evol Biol 2015; 15:2. [PMID: 25608567 PMCID: PMC4314735 DOI: 10.1186/s12862-014-0275-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/15/2014] [Indexed: 01/23/2023] Open
Abstract
Background The Nigeria-Cameroon chimpanzee (Pan troglodytes ellioti) is found in the Gulf of Guinea biodiversity hotspot located in western equatorial Africa. This subspecies is threatened by habitat fragmentation due to logging and agricultural development, hunting for the bushmeat trade, and possibly climate change. Although P. t. ellioti appears to be geographically separated from the neighboring central chimpanzee (P. t. troglodytes) by the Sanaga River, recent population genetics studies of chimpanzees from across this region suggest that additional factors may also be important in their separation. The main aims of this study were: 1) to model the distribution of suitable habitat for P. t. ellioti across Cameroon and Nigeria, and P. t. troglodytes in southern Cameroon, 2) to determine which environmental factors best predict their optimal habitats, and 3) to compare modeled niches and test for their levels of divergence from one another. A final aim of this study was to examine the ways that climate change might impact suitable chimpanzee habitat across the region under various scenarios. Results Ecological niche models (ENMs) were created using the software package Maxent for the three populations of chimpanzees that have been inferred to exist in Cameroon and eastern Nigeria: (i) P. t. troglodytes in southern Cameroon, (ii) P. t. ellioti in northwestern Cameroon, and (iii) P. t. ellioti in central Cameroon. ENMs for each population were compared using the niche comparison test in ENMtools, which revealed complete niche divergence with very little geographic overlap of suitable habitat between populations. Conclusions These findings suggest that a positive relationship may exist between environmental variation and the partitioning of genetic variation found in chimpanzees across this region. ENMs for each population were also projected under three different climate change scenarios for years 2020, 2050, and 2080. Suitable habitat of P. t. ellioti in northwest Cameroon / eastern Nigeria is expected to remain largely unchanged through 2080 in all considered scenarios. In contrast, P. t. ellioti in central Cameroon, which represents half of the population of this subspecies, is expected to experience drastic reductions in its ecotone habitat over the coming century. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0275-z) contains supplementary material, which is available to authorized users.
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