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Besson ME, Pépin M, Metral PA. Lassa Fever: Critical Review and Prospects for Control. Trop Med Infect Dis 2024; 9:178. [PMID: 39195616 PMCID: PMC11359316 DOI: 10.3390/tropicalmed9080178] [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: 07/21/2024] [Revised: 08/10/2024] [Accepted: 08/12/2024] [Indexed: 08/29/2024] Open
Abstract
Lassa Fever is a deadly viral haemorrhagic disease, causing annually several hundreds of deaths in West Africa. This zoonotic disease is primarily transmitted to humans by rodents of the genus Mastomys, even though other rodents reportedly carry the Lassa virus, while secondary interhuman transmission accounts for approximately 20% of cases. Although this disease has been endemic in rural zones of Nigeria, Sierra Leone, Liberfia, and Guinea for hundreds of years, it is also characterised by epidemic outbreaks in the dry season, responsible for heavy death tolls. No licensed vaccine or satisfying treatment is currently available. Disease management is hindered by the incomplete knowledge of the epidemiology and distribution of the disease, resulting from an inadequate health and surveillance system. Additional scientific constraints such as the genetic diversity of the virus and the lack of understanding of the mechanisms of immune protection complexify the development of a vaccine. The intricate socio-economic context in the affected regions, and the lack of monetary incentive for drug development, allow the disease to persist in some of West Africa's poorest communities. The increase in the number of reported cases and in the fatality rate, the expansion of the endemic area, as well as the threat Lassa Fever represents internationally should urge the global community to work on the disease control and prevention. The disease control requires collaborative research for medical countermeasures and tailored public health policies. Lassa Fever, created by the interconnection between animals, humans, and ecosystems, and embedded in an intricate social context, should be addressed with a 'One Health' approach. This article provides an overview of Lassa Fever, focusing on Nigeria, and discusses the perspectives for the control of disease.
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Affiliation(s)
- Marianne E. Besson
- Department of Public Health, Royal Veterinary College, London NW1 0TU, UK
| | - Michel Pépin
- Department of Virology and Infectiology, VetAgro Sup Lyon University, 69280 Marcy L’Etoile, France;
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2
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Bohler F, Cashman K, Wilkinson E, Johnson JC, Rosenke K, Shamblin J, Hensley L, Honko A, Shaia C. An atlas of gross and histologic lesions and immunohistochemical immunoreactivity during the temporal progression of aerosolized Lassa virus induced hemorrhagic fever in cynomolgus macaques. Front Cell Infect Microbiol 2024; 14:1341891. [PMID: 38404292 PMCID: PMC10884106 DOI: 10.3389/fcimb.2024.1341891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/15/2024] [Indexed: 02/27/2024] Open
Abstract
Lassa virus (LASV) causes an acute multisystemic hemorrhagic fever in humans known as Lassa fever, which is endemic in several African countries. This manuscript focuses on the progression of disease in cynomolgus macaques challenged with aerosolized LASV and serially sampled for the development and progression of gross and histopathologic lesions. Gross lesions were first noted in tissues on day 6 and persisted throughout day 12. Viremia and histologic lesions were first noted on day 6 commencing with the pulmonary system and hemolymphatic system and progressing at later time points to include all systems. Immunoreactivity to LASV antigen was first observed in the lungs of one macaque on day 3 and appeared localized to macrophages with an increase at later time points to include immunoreactivity in all organ systems. Additionally, this manuscript will serve as a detailed atlas of histopathologic lesions and disease progression for comparison to other animal models of aerosolized Arenaviral disease.
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Affiliation(s)
- Forrest Bohler
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, Division of Intramural Research, National Institutes of Health (NIH), Hamilton, MT, United States
| | - Kathleen Cashman
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD, United States
| | - Eric Wilkinson
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD, United States
| | - Joshua C. Johnson
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD, United States
| | - Kyle Rosenke
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, Division of Intramural Research, National Institutes of Health (NIH), Hamilton, MT, United States
| | - Josh Shamblin
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD, United States
| | - Lisa Hensley
- Zoonotic and Emerging Disease Research Unit, United States Department of Agriculture (USDA), Manhattan, KS, United States
| | - Anna Honko
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD, United States
| | - Carl Shaia
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, Division of Intramural Research, National Institutes of Health (NIH), Hamilton, MT, United States
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3
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Cuypers LN, Gryseels S, Van Houtte N, Baird SJE, Sabuni CA, Katakweba AS, van den Burg SRM, Bryja J, Leirs H, Goüy de Bellocq J. Subspecific rodent taxa as the relevant host taxonomic level for mammarenavirus host specificity. Virology 2023; 581:116-127. [PMID: 36958216 DOI: 10.1016/j.virol.2023.02.014] [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: 12/22/2022] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/10/2023]
Abstract
Mastomys natalensis-borne mammarenaviruses appear specific to subspecific M. natalensis taxa rather than to the whole species. Yet mammarenaviruses carried by M. natalensis are known to spill over and jump hosts in northern sub-Saharan Africa. Phylogeographic studies increasingly show that, like M. natalensis, small mammals in sub-Saharan Africa are often genetically structured into several subspecific taxa. Other mammarenaviruses may thus also form virus-subspecific host taxon associations. To investigate this, and if mammarenaviruses carried by M. natalensis in southern Africa are less prone to spill-over, we screened 1225 non-M. natalensis samples from Tanzania where many small mammal taxa meet. We found mammarenavirus RNA in 6 samples. Genetic/genomic characterisation confirmed they were not spill-over from M. natalensis. We detected host jumps among rodent tribe members and an association between mammarenaviruses and subspecific taxa of Mus minutoides and Grammomys surdaster, indicating host genetic structure may be crucial to understand virus distribution and host specificity.
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Affiliation(s)
- Laura N Cuypers
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.
| | - Sophie Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium; OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000, Brussels, Belgium
| | - Natalie Van Houtte
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Stuart J E Baird
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic
| | - Christopher A Sabuni
- Institute of Pest Management, Sokoine University of Agriculture, P.O. Box 3110 Chuo Kikuu, Morogoro, Tanzania
| | - Abdul S Katakweba
- Institute of Pest Management, Sokoine University of Agriculture, P.O. Box 3110 Chuo Kikuu, Morogoro, Tanzania
| | - Sebastiaan R M van den Burg
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic; Department of Botany and Zoology, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Herwig Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic
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4
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Dianat M, Voet I, Ortiz D, Goüy de Bellocq J, Cuypers LN, Kryštufek B, Bureš M, Čížková D, Bryjová A, Bryja J, Nicolas V, Konečný A. Cryptic diversity of Crocidura shrews in the savannahs of Eastern and Southern Africa. Mol Phylogenet Evol 2023; 180:107708. [PMID: 36657626 DOI: 10.1016/j.ympev.2023.107708] [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: 11/03/2022] [Revised: 01/07/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023]
Abstract
Crocidura (Eulipotyphla, Soricidae) is the most species-rich genus among mammals, with high cryptic diversity and complicated taxonomy. The hirta-flavescens group of Crocidura represents the most abundant and widespread shrews in savannahs of eastern and southern Africa, making them a suitable phylogeographical model for assessing the role of paleoclimatic changes on current biodiversity in open African habitats. We present the first comprehensive study on the phylogeography, evolutionary history, geographical distribution, systematics, and taxonomy of the group, using the integration of mitochondrial, genome-wide (ddRAD sequencing), morphological and morphometrical data collected from specimens over most of the known geographic distribution. Our genomic data confirmed the monophyly of this group and its sister relationship with the olivieri group of Crocidura. There is a substantial genetic variation within the hirta-flavescens group, with three highly supported clades showing parapatric distribution and which can be distinguished morphologically: C. hirta, distributed in both the Zambezian and Somali-Masai bioregions, C. flavescens, known from South Africa and south-western Zambia, and C. cf. flavescens, which is known to occur only in central and western Tanzania. Morphometric data revealed relatively minor differences between C. hirta and C. cf. flavescens, but they differ in the colouration of the pelage. Diversification of the hirta-flavescens group has most likely happened during phases of grassland expansion and contraction during Plio-Pleistocene climatic cycles. Eastern African Rift system, rivers, and the distinctiveness of Zambezian and Somali-Masai bioregions seem to have also shaped the pattern of their diversity, which is very similar to sympatric rodent species living in open habitats. Finally, we review the group's taxonomy and propose to revalidate C. bloyeti, currently a synonym of C. hirta, including the specimens treated as C. cf. flavescens.
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Affiliation(s)
- Malahat Dianat
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Kvetna 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic.
| | - Inessa Voet
- Institut de Systematique, Evolution, Biodiversite (ISYEB), Museum national d'Histoire naturelle, CNRS, Sorbonne Universite, EPHE, Universite des Antilles, CP51, 75005 Paris, France
| | - David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Kvetna 8, 603 65 Brno, Czech Republic
| | - Laura N Cuypers
- Evolutionary Ecology Group, Department of Biology, University of Antwerp,Universiteitsplein 1, 2610 Antwerp, Belgium
| | | | - Michal Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Dagmar Čížková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Kvetna 8, 603 65 Brno, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Kvetna 8, 603 65 Brno, Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Kvetna 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Violaine Nicolas
- Institut de Systematique, Evolution, Biodiversite (ISYEB), Museum national d'Histoire naturelle, CNRS, Sorbonne Universite, EPHE, Universite des Antilles, CP51, 75005 Paris, France
| | - Adam Konečný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
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5
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Historical demography and climatic niches of the Natal multimammate mouse (Mastomys natalensis) in the Zambezian region. Mamm Biol 2023. [DOI: 10.1007/s42991-023-00346-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
AbstractThe Natal multimammate mouse (Mastomys natalensis) is the most widespread rodent species in sub-Saharan Africa, often studied as an agricultural pest and reservoir of viruses. Its mitochondrial (Mt) phylogeny revealed six major lineages parapatrically distributed across open habitats of sub-Saharan Africa. In this study we used 1949 sequences of the mitochondrial cytochrome b gene to elaborate on distribution and evolutionary history of three Mt lineages inhabiting the open habitats of the Zambezian region (corresponding roughly to the African savannas south of the Equator). We describe in more detail contact zones between the lineages—their location and extent of co-occurrence within localities—and infer past population trends. The estimates are interpreted in the light of climatic niche models. The lineages underwent reduction in effective population size during the last glacial, but they spread widely after that: two of them after the last glacial maximum and the last one in mid-Holocene. The centers of expansion, i.e., possible long-term savanna refugia, were estimated to lie close to the Eastern Arc Mountains and lakes of the Great African Rift, geomorphological structures likely to have had long-term influence on geographical distribution of the lineages. Environmental niche modeling shows climate could also affect the broad scale distribution of the lineages but is unlikely to explain the narrow width of the contact zones. The intraspecific Mt differentiation of M. natalensis echoes phylogeographic patterns observed in multiple co-distributed mammal species, which suggests the mammal communities in the region are shaped by the same long-term processes.
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Mammarenavirus Genetic Diversity and Its Biological Implications. Curr Top Microbiol Immunol 2023; 439:265-303. [PMID: 36592249 DOI: 10.1007/978-3-031-15640-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Members of the family Arenaviridae are classified into four genera: Antennavirus, Hartmanivirus, Mammarenavirus, and Reptarenavirus. Reptarenaviruses and hartmaniviruses infect (captive) snakes and have been shown to cause boid inclusion body disease (BIBD). Antennaviruses have genomes consisting of 3, rather than 2, segments, and were discovered in actinopterygian fish by next-generation sequencing but no biological isolate has been reported yet. The hosts of mammarenaviruses are mainly rodents and infections are generally asymptomatic. Current knowledge about the biology of reptarenaviruses, hartmaniviruses, and antennaviruses is very limited and their zoonotic potential is unknown. In contrast, some mammarenaviruses are associated with zoonotic events that pose a threat to human health. This review will focus on mammarenavirus genetic diversity and its biological implications. Some mammarenaviruses including lymphocytic choriomeningitis virus (LCMV) are excellent experimental model systems for the investigation of acute and persistent viral infections, whereas others including Lassa (LASV) and Junin (JUNV) viruses, the causative agents of Lassa fever (LF) and Argentine hemorrhagic fever (AHF), respectively, are important human pathogens. Mammarenaviruses were thought to have high degree of intra-and inter-species amino acid sequence identities, but recent evidence has revealed a high degree of mammarenavirus genetic diversity in the field. Moreover, closely related mammarenavirus can display dramatic phenotypic differences in vivo. These findings support a role of genetic variability in mammarenavirus adaptability and pathogenesis. Here, we will review the molecular biology of mammarenaviruses, phylogeny, and evolution, as well as the quasispecies dynamics of mammarenavirus populations and their biological implications.
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Abstract
Individuals living in endemic hotspots of Lassa fever have recurrent exposure to Lassa virus (LASV) via spillover from the primary host reservoir Mastomys natalensis. Despite M. natalensis being broadly distributed across sub-Saharan Africa, Lassa fever is only found in West Africa. In recent years, new LASV reservoirs have been identified. Erudition of rodent habitats, reproduction and fecundity, movement patterns, and spatial preferences are essential to institute preventative measures against Lassa fever. Evolutionary insights have also added to our knowledge of closely related mammarenavirus distribution amongst rodents throughout the continent.
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Affiliation(s)
- Allison R Smither
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA.
| | - Antoinette R Bell-Kareem
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, USA
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8
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Klitting R, Kafetzopoulou LE, Thiery W, Dudas G, Gryseels S, Kotamarthi A, Vrancken B, Gangavarapu K, Momoh M, Sandi JD, Goba A, Alhasan F, Grant DS, Okogbenin S, Ogbaini-Emovo E, Garry RF, Smither AR, Zeller M, Pauthner MG, McGraw M, Hughes LD, Duraffour S, Günther S, Suchard MA, Lemey P, Andersen KG, Dellicour S. Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades. Nat Commun 2022; 13:5596. [PMID: 36167835 PMCID: PMC9515147 DOI: 10.1038/s41467-022-33112-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 09/02/2022] [Indexed: 01/27/2023] Open
Abstract
Lassa fever is a severe viral hemorrhagic fever caused by a zoonotic virus that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate and land use changes could affect the endemic area of this virus, currently limited to parts of West Africa. By exploring the environmental data associated with virus occurrence using ecological niche modelling, we show how temperature, precipitation and the presence of pastures determine ecological suitability for virus circulation. Based on projections of climate, land use, and population changes, we find that regions in Central and East Africa will likely become suitable for Lassa virus over the next decades and estimate that the total population living in ecological conditions that are suitable for Lassa virus circulation may drastically increase by 2070. By analysing geotagged viral genomes using spatially-explicit phylogeography and simulating virus dispersal, we find that in the event of Lassa virus being introduced into a new suitable region, its spread might remain spatially limited over the first decades.
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Affiliation(s)
- Raphaëlle Klitting
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Liana E. Kafetzopoulou
- grid.5596.f0000 0001 0668 7884Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium ,grid.424065.10000 0001 0701 3136Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Wim Thiery
- grid.8767.e0000 0001 2290 8069Department of Hydrology and Hydraulic Engineering, Vrije Universiteit Brussel, Brussels, Belgium
| | - Gytis Dudas
- grid.6441.70000 0001 2243 2806Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Sophie Gryseels
- grid.5284.b0000 0001 0790 3681Evolutionary Ecology group, Department of Biology, University of Antwerp, 2610 Antwerp, Belgium ,grid.20478.390000 0001 2171 9581Vertebrate group, Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | - Anjali Kotamarthi
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Bram Vrancken
- grid.5596.f0000 0001 0668 7884Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Karthik Gangavarapu
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Mambu Momoh
- grid.442296.f0000 0001 2290 9707Eastern Technical University of Sierra Leone, Kenema, Sierra Leone ,grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - John Demby Sandi
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Augustine Goba
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Foday Alhasan
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone
| | - Donald S. Grant
- grid.463455.50000 0004 1799 2069Viral Hemorrhagic Fever Program, Kenema Government Hospital, Ministry of Health and Sanitation, Kenema, Sierra Leone ,grid.442296.f0000 0001 2290 9707College of Medicine and Allied Health Sciences, University of Sierra Leone, Kenema, Sierra Leone
| | - Sylvanus Okogbenin
- grid.508091.5Irrua Specialist Teaching Hospital, Irrua, Nigeria ,grid.411357.50000 0000 9018 355XFaculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | | | - Robert F. Garry
- grid.265219.b0000 0001 2217 8588Department of Microbiology and Immunology, Tulane University, School of Medicine, New Orleans, LA 70112 USA ,grid.505518.c0000 0004 5901 1919Zalgen Labs, LCC, Frederick, MD 21703 USA ,grid.475149.aGlobal Virus Network (GVN), Baltimore, MD 21201 USA
| | - Allison R. Smither
- grid.265219.b0000 0001 2217 8588Department of Microbiology and Immunology, Tulane University, School of Medicine, New Orleans, LA 70112 USA
| | - Mark Zeller
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Matthias G. Pauthner
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Michelle McGraw
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Laura D. Hughes
- grid.214007.00000000122199231Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Sophie Duraffour
- grid.424065.10000 0001 0701 3136Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany ,grid.452463.2German Center for Infection Research (DZIF), Partner site Hamburg–Lübeck–Borstel–Riems, Hamburg, Germany
| | - Stephan Günther
- grid.424065.10000 0001 0701 3136Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany ,grid.452463.2German Center for Infection Research (DZIF), Partner site Hamburg–Lübeck–Borstel–Riems, Hamburg, Germany
| | - Marc A. Suchard
- grid.19006.3e0000 0000 9632 6718Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Philippe Lemey
- grid.5596.f0000 0001 0668 7884Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium
| | - Kristian G. Andersen
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA ,grid.214007.00000000122199231Scripps Research Translational Institute, La Jolla, CA 92037 USA
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven - University of Leuven, Leuven, Belgium. .,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, 1050, Bruxelles, Belgium.
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9
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Rocha JL, Vaz Pinto P, Siegismund HR, Meyer M, Jansen van Vuuren B, Veríssimo L, Ferrand N, Godinho R. African climate and geomorphology drive evolution and ghost introgression in sable antelope. Mol Ecol 2022; 31:2968-2984. [PMID: 35305042 DOI: 10.1111/mec.16427] [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: 09/10/2020] [Revised: 02/13/2022] [Accepted: 03/04/2022] [Indexed: 11/27/2022]
Abstract
The evolutionary history of African ungulates has been largely explained in the light of Pleistocene climatic oscillations and the way these influenced the distribution of vegetation types, leading to range expansions and/or isolation in refugia. In contrast, comparatively fewer studies have addressed the continent's environmental heterogeneity and the role played by its geomorphological barriers. In this study, we performed a range-wide analysis of complete mitogenomes of sable antelope (Hippotragus niger) to explore how these different factors may have contributed as drivers of evolution in South-Central Africa. Our results supported two sympatric and deeply divergent mitochondrial lineages in west Tanzanian sables, which can be explained as the result of introgressive hybridization of a mitochondrial ghost lineage from an archaic, as-yet-undefined, congener. Phylogeographic subdivisions into three main lineages suggest that sable diversification may not have been solely driven by climatic events affecting populations differently across a continental scale. Often in interplay with climate, geomorphological features have also clearly shaped the species' patterns of vicariance, where the East Africa Rift System and the Eastern Arc Mountains acted as geological barriers. Subsequent splits among southern populations may be linked to rearrangements in the Zambezi system, possibly framing the most recent time when the river attained its current drainage profile. This work underscores how the use of comprehensive mitogenomic datasets on a model species with a wide geographic distribution can contribute to a much-enhanced understanding of environmental, geomorphological, and evolutionary patterns in Africa throughout the Quaternary.
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Affiliation(s)
- Joana L Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
| | - Pedro Vaz Pinto
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,TwinLab CIBIO/ISCED, Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola.,Fundação Kissama, Rua Joaquim Capango 49, Luanda, Angola
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Bettine Jansen van Vuuren
- Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Luís Veríssimo
- Fundação Kissama, Rua Joaquim Capango 49, Luanda, Angola
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,TwinLab CIBIO/ISCED, Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,TwinLab CIBIO/ISCED, Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, 2006, South Africa
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10
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Mapaco L, Crespin L, Rodrigues D, Gouy de Bellocq J, Bryja J, Bourgarel M, Missé D, Caron A, Fafetine J, Cappelle J, Liégeois F. Detection and genetic diversity of Mopeia virus in Mastomys natalensis from different habitats in the Limpopo National Park, Mozambique. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105204. [PMID: 34999003 DOI: 10.1016/j.meegid.2022.105204] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/15/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
Mammarenaviruses have been a growing concern for public health in Africa since the 1970s when Lassa virus cases in humans were first described in west Africa. In southern Africa, a single outbreak of Lujo virus was reported to date in South Africa in 2008 with a case fatality rate of 80%. The natural reservoir of Lassa virus is Mastomys natalensis while for the Lujo virus the natural host has yet to be identified. Mopeia virus was described for the first time in M. natalensis in the central Mozambique in 1977 but few studies have been conducted in the region. In this study, rodents were trapped between March and November 2019in villages, croplands fields and mopane woodland forest. The aim was to assess the potential circulation and to evaluate the genetic diversity of mammarenaviruses in M. natalensis trapped in the Limpopo National Park and its buffer zone in Massingir district, Mozambique. A total of 534 M. natalensis were screened by RT-PCR and the overall proportion of positive individuals was 16.9%. No significant differences were detected between the sampled habitats (χ2 = 0.018; DF = 1; p = 0.893). The Mopeia virus (bootstrap value 91%) was the Mammarenavirus circulating in the study area sites, forming a specific sub-clade with eight different sub-clusters. We concluded that Mopeia virus circulates in all habitats investigated and it forms a different sub-clade to the one reported in central Mozambique in 1977.
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Affiliation(s)
- Lourenço Mapaco
- Agrarian Research Institute of Mozambique, Directorate of Animal Sciences, IIAM, P. O. Box 1922, Maputo, Mozambique; ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France; CIRAD, UMR ASTRE, Montpellier, France
| | - Laurent Crespin
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122 Saint-Genès-Champanelle, France; Université Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280 Marcy-L'Etoile, France
| | - Dércio Rodrigues
- Agrarian Research Institute of Mozambique, Directorate of Animal Sciences, IIAM, P. O. Box 1922, Maputo, Mozambique
| | - Joelle Gouy de Bellocq
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
| | | | - Dorothée Missé
- MIVEGEC, University of Montpellier, IRD, CNRS, 34394 Montpellier, France
| | - Alexandre Caron
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France; Veterinary Faculty, UEM, P. O. Box 257, Maputo, Mozambique
| | - Jose Fafetine
- Veterinary Faculty, UEM, P. O. Box 257, Maputo, Mozambique
| | - Julien Cappelle
- ASTRE, Univ Montpellier, CIRAD, INRA, Montpellier, France; CIRAD, UMR ASTRE, Montpellier, France.
| | - Florian Liégeois
- MIVEGEC, University of Montpellier, IRD, CNRS, 34394 Montpellier, France; Faculty of Veterinary Science, University of Zimbabwe, P.O. Box MP167, Harare, Zimbabwe.
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11
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Cuypers LN, Sabuni C, Šumbera R, Aghová T, Lišková E, Leirs H, Baird SJE, Goüy de Bellocq J, Bryja J. Biogeographical Importance of the Livingstone Mountains in Southern Tanzania: Comparative Genetic Structure of Small Non-volant Mammals. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.742851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Livingstone Mountains (LM; also known as the Kipengere Range) found in south-western Tanzania at the northern end of Lake Nyasa are an important region for understanding the biogeography of Eastern Africa. The two branches of the East African Rift Valley meet here and the mountains might represent stepping stones for colonization and migration between different parts of the Eastern Afromontane Biodiversity Hotspot (especially the link between the Eastern Arc Mountains, EAM, and the Southern Rift Mountains, SRM), as well as an efficient barrier to gene flow for taxa living in drier savannahs in lower elevations. Here we combine new mitochondrial sequence data from 610 recently sampled rodents and shrews with available georeferenced genetic data (3538 specimens) from southern Tanzania, northern Malawi/Zambia and northern Mozambique and compare the spatial genetic structure among different taxa. There is no universal phylogeographic pattern in taxa preferring humid montane habitats. For some of them, the Makambako Gap acts as a barrier between the SRM and the EAM, but other taxa can bridge this gap. Barriers within the EAM (frequently) and within the SRM (sometimes) appear more important. The Rukwa rift between the SRM and the ARM is an important barrier that perhaps can only be crossed by taxa that are not that strictly tied to humid montane environments. For mammals living in lower-elevation savannah-like habitats, the LM can act as a strict barrier to gene flow, and together with the Ufipa Plateau, Lake Nyasa and the EAM create a very similar phylogeographic pattern with three recognizable genetic groups in most savannah-dwellers. The Livingstone Mountains thus appear to be one of the most important biogeographic crossroads in Eastern Africa.
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12
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Metabolomic Alteration in the Plasma of Wild Rodents Environmentally Exposed to Lead: A Preliminary Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19010541. [PMID: 35010801 PMCID: PMC8744629 DOI: 10.3390/ijerph19010541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/24/2021] [Accepted: 01/01/2022] [Indexed: 01/27/2023]
Abstract
Lead poisoning is often considered a traditional disease; however, the specific mechanism of toxicity remains unclear. The study of Pb-induced alterations in cellular metabolic pathways is important to understand the biological response and disorders associated with environmental exposure to lead. Metabolomics studies have recently been paid considerable attention to understand in detail the biological response to lead exposure and the associated toxicity mechanisms. In the present study, wild rodents collected from an area contaminated with lead (N = 18) and a control area (N = 10) were investigated. This was the first ever experimental metabolomic study of wildlife exposed to lead in the field. While the levels of plasma phenylalanine and isoleucine were significantly higher in a lead-contaminated area versus the control area, hydroxybutyric acid was marginally significantly higher in the contaminated area, suggesting the possibility of enhancement of lipid metabolism. In the interregional least-absolute shrinkage and selection operator (lasso) regression model analysis, phenylalanine and isoleucine were identified as possible biomarkers, which is in agreement with the random forest model. In addition, in the random forest model, glutaric acid, glutamine, and hydroxybutyric acid were selected. In agreement with previous studies, enrichment analysis showed alterations in the urea cycle and ATP-binding cassette transporter pathways. Although regional rodent species bias was observed in this study, and the relatively small sample size should be taken into account, the present results are to some extent consistent with those of previous studies on humans and laboratory animals.
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13
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Hánová A, Konečný A, Mikula O, Bryjová A, Šumbera R, Bryja J. Diversity, distribution, and evolutionary history of the most studied African rodents, multimammate mice of the genus
Mastomys
: An overview after a quarter of century of using DNA sequencing. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Alexandra Hánová
- Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Brno Czech Republic
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - Adam Konečný
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - Ondřej Mikula
- Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Brno Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Brno Czech Republic
| | - Radim Šumbera
- Department of Zoology Faculty of Science University of South Bohemia České Budějovice Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Brno Czech Republic
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
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14
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Grobbelaar AA, Jardine J, Burt FJ, Shepherd AJ, Shepherd SP, Leman PA, Kemp A, Braack LEO, Weyer J, Paweska JT, Swanepoel R. Mammarenaviruses of Rodents, South Africa and Zimbabwe. Emerg Infect Dis 2021; 27:3092-3102. [PMID: 34808083 PMCID: PMC8632164 DOI: 10.3201/eid2712.211088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We conducted a survey for group-specific indirect immunofluorescence antibody to mammarenaviruses by using Lassa fever and Mopeia virus antigens on serum specimens of 5,363 rodents of 33 species collected in South Africa and Zimbabwe during 1964-1994. Rodents were collected for unrelated purposes or for this study and stored at -70°C. We found antibody to be widely distributed in the 2 countries; antibody was detected in serum specimens of 1.2%-31.8% of 14 species of myomorph rodents, whereas 19 mammarenavirus isolates were obtained from serum specimens and viscera of 4 seropositive species. Phylogenetic analysis on the basis of partial nucleoprotein sequences indicates that 14 isolates from Mastomys natalensis, the Natal multimammate mouse, were Mopeia virus, whereas Merino Walk virus was characterized as a novel virus in a separate study. The remaining 4 isolates from 3 rodent species potentially constitute novel viruses pending full characterization.
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15
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Wozniak DM, Riesle-Sbarbaro SA, Kirchoff N, Hansen-Kant K, Wahlbrink A, Stern A, Lander A, Hartmann K, Krasemann S, Kurth A, Prescott J. Inoculation route-dependent Lassa virus dissemination and shedding dynamics in the natural reservoir - Mastomys natalensis. Emerg Microbes Infect 2021; 10:2313-2325. [PMID: 34792436 PMCID: PMC8654411 DOI: 10.1080/22221751.2021.2008773] [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] [Indexed: 02/08/2023]
Abstract
Lassa virus (LASV), a Risk Group-4 zoonotic haemorrhagic fever virus, affects sub-Saharan African countries. Lassa fever, caused by LASV, results in thousands of annual deaths. Although decades have elapsed since the identification of the Natal multimammate mouse (Mastomys natalensis) as a natural reservoir of LASV, little effort has been made to characterize LASV infection in its reservoir. The natural route of infection and transmission of LASV within M. natalensis remains unknown, and the clinical impact of LASV in M. natalensis is mostly undescribed. Herein, using an outbred colony of M. natalensis, we investigate the replication and dissemination dynamics of LASV in this reservoir following various inoculation routes. Inoculation with LASV, regardless of route, resulted in a systemic infection and accumulation of abundant LASV-RNA in many tissues. LASV infection in the Natal multimammate mice was subclinical, however, clinical chemistry values were transiently altered and immune infiltrates were observed histologically in lungs, spleens and livers, indicating a minor disease with coordinated immune responses are elicited, controlling infection. Intranasal infection resulted in unique virus tissue dissemination dynamics and heightened LASV shedding, compared to subcutaneous inoculation. Our study provides important insights into LASV infection in its natural reservoir using a contemporary infection system, demonstrating that specific inoculation routes result in disparate dissemination outcomes, suggesting intranasal inoculation is important in the maintenance of LASV in the natural reservoir, and emphasizes that selection of the appropriate inoculation route is necessary to examine aspects of viral replication, transmission and responses to zoonotic viruses in their natural reservoirs.
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Affiliation(s)
- D M Wozniak
- ZBS5-Biosafety Level-4 Laboratory, Robert Koch-Institute, Berlin, Germany
| | | | - N Kirchoff
- ZBS5-Biosafety Level-4 Laboratory, Robert Koch-Institute, Berlin, Germany
| | - K Hansen-Kant
- ZBS5-Biosafety Level-4 Laboratory, Robert Koch-Institute, Berlin, Germany
| | - A Wahlbrink
- ZBS5-Biosafety Level-4 Laboratory, Robert Koch-Institute, Berlin, Germany
| | - A Stern
- ZBS5-Biosafety Level-4 Laboratory, Robert Koch-Institute, Berlin, Germany
| | - A Lander
- ZBS5-Biosafety Level-4 Laboratory, Robert Koch-Institute, Berlin, Germany
| | - K Hartmann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - S Krasemann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - A Kurth
- ZBS5-Biosafety Level-4 Laboratory, Robert Koch-Institute, Berlin, Germany
| | - J Prescott
- ZBS5-Biosafety Level-4 Laboratory, Robert Koch-Institute, Berlin, Germany
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16
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Uhrová M, Mikula O, Bennett NC, Van Daele P, Piálek L, Bryja J, Visser JH, Jansen van Vuuren B, Šumbera R. Species limits and phylogeographic structure in two genera of solitary African mole-rats Georychus and Heliophobius. Mol Phylogenet Evol 2021; 167:107337. [PMID: 34757170 DOI: 10.1016/j.ympev.2021.107337] [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: 04/22/2021] [Revised: 10/19/2021] [Accepted: 10/27/2021] [Indexed: 11/28/2022]
Abstract
African mole-rats (Bathyergidae) are an intensively studied family of subterranean rodents including three highly social and three solitary genera. Although their phylogenetic interrelations are clear, genetic diversity and the number of species within each genus is much less certain. Among the solitary genera, Heliophobius and Georychus were for a long time considered as monotypic, but molecular studies demonstrated strong phylogeographic structure within each genus and proposed that they represent complexes of cryptic species. The present study re-evaluates their internal genetic/phylogenetic structure using a combination of methodological approaches. We generated datasets of one mitochondrial and six specifically selected nuclear markers as well as of a large number of double digest restriction site associated (ddRAD) loci and then applied species delimitation analyses based on the multispecies coalescent model or clustering on co-ancestry matrices. The population structure was largely congruent across all analyses, but the methods differed in their resolution scale when determining distinct gene pools. While the multispecies coalescent model distinguished five Georychus and between eleven to thirteen Heliophobius gene pools in both Sanger sequenced and ddRAD loci, two clustering algorithms revealed significantly finer or coarser structure in ddRAD based co-ancestry matrices. Tens of clusters were distinguished by fineRADstructure and one (in Georychus) or two clusters (in Heliophobius) by Infomap. The divergence dating of the bathyergid phylogeny estimated that diversification within both genera coincided with the onset of the Pleistocene and was likely driven by repeated large-scale climatic changes. Based on this updated genetic evidence, we suggest recognizing one species of Georychus and two species of Heliophobius, corresponding to a northern and southern major lineage, separated by the Eastern Arc Mountains. Yet, the final taxonomic revision should await integrated evidence stemming from e.g.. morphological, ecological, or behavioral datasets.
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Affiliation(s)
- M Uhrová
- Department of Zoology, Faculty of Sciences, University of South Bohemia
| | - O Mikula
- Department of Zoology, Faculty of Sciences, University of South Bohemia; Institute of Vertebrate Biology, Czech Academy of Sciences
| | - N C Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, 0002, South Africa
| | - P Van Daele
- Department of Zoology, Faculty of Sciences, University of South Bohemia
| | - L Piálek
- Department of Zoology, Faculty of Sciences, University of South Bohemia
| | - J Bryja
- Institute of Vertebrate Biology, Czech Academy of Sciences
| | - J H Visser
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, Johannesburg, South Africa; Department of Conservation and Marine Sciences, Cape Peninsula University of Technology, P.O. Box 652, Cape Town 8000, South Africa
| | - B Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - R Šumbera
- Department of Zoology, Faculty of Sciences, University of South Bohemia
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17
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Nicolas V, Mikula O, Lavrenchenko LA, Šumbera R, Bartáková V, Bryjová A, Meheretu Y, Verheyen E, Missoup AD, Lemmon AR, Moriarty Lemmon E, Bryja J. Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera. Mol Phylogenet Evol 2021; 163:107263. [PMID: 34273505 DOI: 10.1016/j.ympev.2021.107263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 11/25/2022]
Abstract
The tribe Praomyini is a diversified group including 64 species and eight extant rodent genera. They live in a broad spectrum of habitats across whole sub-Saharan Africa. Members of this tribe are often very abundant, they have a key ecological role in ecosystems, they are hosts of many potentially pathogenic microorganisms and comprise numerous agricultural pests. Although this tribe is well supported by both molecular and morphological data, its intergeneric relationships and the species contents of several genera are not yet fully resolved. Recent molecular data suggest that at least three genera in current sense are paraphyletic. However, in these studies the species sampling was sparse and the resolution of relationships among genera was poor, probably due to a fast radiation of the tribe dated to the Miocene and insufficient amount of genetic data. Here we used genomic scale data (395 nuclear loci = 610,965 bp long alignment and mitogenomes = 14,745 bp) and produced the first fully resolved species tree containing most major lineages of the Praomyini tribe (i.e. all but one currently delimited genera and major intrageneric clades). Results of a fossil-based divergence dating analysis suggest that the radiation started during the Messinian stage (ca. 7 Ma) and was likely linked to a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forests, while many others adapted to a broad spectrum of new open lowland and montane habitats that appeared at the beginning of Pliocene. Our analyses clearly confirmed the presence of three polyphyletic genera (Praomys, Myomyscus and Mastomys). We review current knowledge of these three genera and suggest corresponding taxonomic changes. To keep genera monophyletic, we propose taxonomic re-arrangements and delimit four new genera. Furthermore, we discovered a new highly divergent genetic lineage of Praomyini in southwestern Ethiopia, which is described as a new species and genus.
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Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Leonid A Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Veronika Bartáková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Yonas Meheretu
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Department of Biology and Institute of Mountain Research and Development, Mekelle University, Mekelle, Tigray, Ethiopia
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium; Evolutionary Ecology Group, Biology Department, University of Antwerp, 2020 Antwerp, Belgium
| | - Alain Didier Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, Douala, Cameroon
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4295, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic.
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18
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Těšíková J, Krásová J, Goüy de Bellocq J. Multiple Mammarenaviruses Circulating in Angolan Rodents. Viruses 2021; 13:982. [PMID: 34070551 PMCID: PMC8227972 DOI: 10.3390/v13060982] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 12/14/2022] Open
Abstract
Rodents are a speciose group of mammals with strong zoonotic potential. Some parts of Africa are still underexplored for the occurrence of rodent-borne pathogens, despite this high potential. Angola is at the convergence of three major biogeographical regions of sub-Saharan Africa, each harbouring a specific rodent community. This rodent-rich area is, therefore, strategic for studying the diversity and evolution of rodent-borne viruses. In this study we examined 290 small mammals, almost all rodents, for the presence of mammarenavirus and hantavirus RNA. While no hantavirus was detected, we found three rodent species positive for distinct mammarenaviruses with a particularly high prevalence in Namaqua rock rats (Micaelamys namaquensis). We characterised four complete virus genomes, which showed typical mammarenavirus organisation. Phylogenetic and genetic distance analyses revealed: (i) the presence of a significantly divergent strain of Luna virus in Angolan representatives of the ubiquitous Natal multimammate mouse (Mastomys natalensis), (ii) a novel Okahandja-related virus associated with the Angolan lineage of Micaelamys namaquensis for which we propose the name Bitu virus (BITV) and (iii) the occurrence of a novel Mobala-like mammarenavirus in the grey-bellied pygmy mouse (Mus triton) for which we propose the name Kwanza virus (KWAV). This high virus diversity in a limited host sample size and in a relatively small geographical area supports the idea that Angola is a hotspot for mammarenavirus diversity.
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Affiliation(s)
- Jana Těšíková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; (J.K.); (J.G.B.)
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Jarmila Krásová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; (J.K.); (J.G.B.)
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; (J.K.); (J.G.B.)
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic
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19
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Hansen F, Jarvis MA, Feldmann H, Rosenke K. Lassa Virus Treatment Options. Microorganisms 2021; 9:microorganisms9040772. [PMID: 33917071 PMCID: PMC8067676 DOI: 10.3390/microorganisms9040772] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 12/27/2022] Open
Abstract
Lassa fever causes an approximate 5000 to 10,000 deaths annually in West Africa and cases have been imported into Europe and the Americas, challenging public health. Although Lassa virus was first described over 5 decades ago in 1969, no treatments or vaccines have been approved to treat or prevent infection. In this review, we discuss current therapeutics in the development pipeline for the treatment of Lassa fever, focusing on those that have been evaluated in humans or animal models. Several treatments, including the antiviral favipiravir and a human monoclonal antibody cocktail, have shown efficacy in preclinical rodent and non-human primate animal models and have potential for use in clinical settings. Movement of the promising preclinical treatment options for Lassa fever into clinical trials is critical to continue addressing this neglected tropical disease.
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Affiliation(s)
- Frederick Hansen
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Michael A Jarvis
- The Vaccine Group Ltd., University of Plymouth, Plymouth PL4 8AA, UK
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Kyle Rosenke
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
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20
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Basinski AJ, Fichet-Calvet E, Sjodin AR, Varrelman TJ, Remien CH, Layman NC, Bird BH, Wolking DJ, Monagin C, Ghersi BM, Barry PA, Jarvis MA, Gessler PE, Nuismer SL. Bridging the gap: Using reservoir ecology and human serosurveys to estimate Lassa virus spillover in West Africa. PLoS Comput Biol 2021; 17:e1008811. [PMID: 33657095 PMCID: PMC7959400 DOI: 10.1371/journal.pcbi.1008811] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 03/15/2021] [Accepted: 02/17/2021] [Indexed: 01/07/2023] Open
Abstract
Forecasting the risk of pathogen spillover from reservoir populations of wild or domestic animals is essential for the effective deployment of interventions such as wildlife vaccination or culling. Due to the sporadic nature of spillover events and limited availability of data, developing and validating robust, spatially explicit, predictions is challenging. Recent efforts have begun to make progress in this direction by capitalizing on machine learning methodologies. An important weakness of existing approaches, however, is that they generally rely on combining human and reservoir infection data during the training process and thus conflate risk attributable to the prevalence of the pathogen in the reservoir population with the risk attributed to the realized rate of spillover into the human population. Because effective planning of interventions requires that these components of risk be disentangled, we developed a multi-layer machine learning framework that separates these processes. Our approach begins by training models to predict the geographic range of the primary reservoir and the subset of this range in which the pathogen occurs. The spillover risk predicted by the product of these reservoir specific models is then fit to data on realized patterns of historical spillover into the human population. The result is a geographically specific spillover risk forecast that can be easily decomposed and used to guide effective intervention. Applying our method to Lassa virus, a zoonotic pathogen that regularly spills over into the human population across West Africa, results in a model that explains a modest but statistically significant portion of geographic variation in historical patterns of spillover. When combined with a mechanistic mathematical model of infection dynamics, our spillover risk model predicts that 897,700 humans are infected by Lassa virus each year across West Africa, with Nigeria accounting for more than half of these human infections. The 2019 emergence of SARS-CoV-2 is a grim reminder of the threat animal-borne pathogens pose to human health. Even prior to SARS-CoV-2, the spillover of pathogens from animal reservoirs was a persistent problem, with pathogens such as Ebola, Nipah, and Lassa regularly but unpredictably causing outbreaks. Machine-learning models that anticipate when and where pathogen transmission from animals to humans is likely to occur would help guide surveillance efforts and preemptive countermeasures like information campaigns or vaccination programs. We develop a novel machine learning framework that uses datasets describing the distribution of a virus within its host and the range of its animal host, along with data on spatial patterns of human immunity, to infer rates of animal-to-human transmission across a region. By training the model on data from the animal host alone, our framework allows rigorous validation of spillover predictions using human data. We apply our framework to Lassa fever, a viral disease of West Africa that is spread to humans by rodents, and use the predictions to update estimates of Lassa virus infections in humans. Our results suggest that Nigeria is most at risk for the emergence of Lassa virus, and should be prioritized for outbreak-surveillance.
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Affiliation(s)
- Andrew J. Basinski
- Department of Mathematics, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
| | | | - Anna R. Sjodin
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Tanner J. Varrelman
- Bioinformatics and Computational Biology, University of Idaho, Moscow, Idaho, United States of America
| | - Christopher H. Remien
- Department of Mathematics, University of Idaho, Moscow, Idaho, United States of America
| | - Nathan C. Layman
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Brian H. Bird
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - David J. Wolking
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Corina Monagin
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Bruno M. Ghersi
- One Health Institute, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Peter A. Barry
- Center for Comparative Medicine, California National Primate Research Center, Department of Pathology and Laboratory Medicine, University of California, Davis, California, United States of America
| | - Michael A. Jarvis
- School of Biomedical and Healthcare Sciences, University of Plymouth, Plymouth, United Kingdom
| | - Paul E. Gessler
- College of Natural Resources, University of Idaho, Moscow, Idaho, United States of America
| | - Scott L. Nuismer
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
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21
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Eiseb SJ, Taylor PJ, Zeller U, Denys C, Nicolas V. Rapid peripatric speciation linked with drainage evolution in a rare African rodent,
Mastomys shortridgei
(Rodentia: Muridae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Seth J. Eiseb
- Department of Biological Sciences University of Namibia Windhoek Namibia
- National Museum of Namibia Windhoek Namibia
| | - Peter J. Taylor
- SARChI Chair on Biodiversity Value & Change in the Vhembe Biosphere Reserve & Core Team Member of Centre for Invasion Biology School of Mathematical & Natural Sciences University of Venda Thohoyandou South Africa
- Zoology & Entomology Department & Afromontane Research Unit University of the Free State Phuthaditjhaba South Africa
- National Geographic Okavango Wilderness ProjectWild Bird Trust Parktown South Africa
| | - Ulrich Zeller
- Lebenswissenschaftliche Fakultät Humboldt‐Universität zu Berlin Berlin Germany
| | - Christiane Denys
- Institut de Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRSSorbonne UniversitéEPHEUniversité des Antilles Paris France
| | - Violaine Nicolas
- Institut de Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRSSorbonne UniversitéEPHEUniversité des Antilles Paris France
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22
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Hánová A, Konečný A, Nicolas V, Denys C, Granjon L, Lavrenchenko LA, Šumbera R, Mikula O, Bryja J. Multilocus phylogeny of African striped grass mice (Lemniscomys): Stripe pattern only partly reflects evolutionary relationships. Mol Phylogenet Evol 2020; 155:107007. [PMID: 33160039 DOI: 10.1016/j.ympev.2020.107007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/20/2020] [Accepted: 10/29/2020] [Indexed: 12/18/2022]
Abstract
Murine rodents are one of the most evolutionary successful groups of extant mammals. They are also important for human as vectors and reservoirs of zoonoses and agricultural pests. Unfortunately, their fast and relatively recent diversification impedes our understanding of phylogenetic relationships and species limits of many murine taxa, including those with very conspicuous phenotype that has been frequently used for taxonomic purposes. One of such groups are the striped grass mice (genus Lemniscomys), distributed across sub-Saharan Africa in 11 currently recognized species. These are traditionally classified into three morphological groups according to different pelage colouration on the back: (a) L. barbarus group (three species) with several continuous pale longitudinal stripes; (b) L. striatus group (four species) with pale stripes diffused into short lines or dots; and (c) L. griselda group (four species) with a single mid-dorsal black stripe. Here we reconstructed the most comprehensive molecular phylogeny of the genus Lemniscomys to date, using the largest currently available multi-locus genetic dataset of all but two species. The results show four main lineages (=species complexes) with the distribution corresponding to the major biogeographical regions of Africa. Surprisingly, the four phylogenetic lineages are only in partial agreement with the morphological classification, suggesting that the single-stripe and/or multi-striped phenotypes evolved independently in multiple lineages. Divergence dating showed the split of Lemniscomys and Arvicanthis genera at the beginning of Pleistocene; most of subsequent speciation processes within Lemniscomys were affected by Pleistocene climate oscillations, with predominantly allopatric diversification in fragmented savanna biome. We propose taxonomic suggestions and directions for future research of this striking group of African rodents.
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Affiliation(s)
- Alexandra Hánová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
| | - Adam Konečný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France.
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France.
| | - Laurent Granjon
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, 755 avenue du Campus Agropolis, CS 30016, 34988 Montferrier-sur-Lez cedex, France.
| | - Leonid A Lavrenchenko
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia.
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic.
| | - Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic.
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
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23
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Calvignac-Spencer S, Kouadio L, Couacy-Hymann E, Sogoba N, Rosenke K, Davison AJ, Leendertz F, Jarvis MA, Feldmann H, Ehlers B. Multiple DNA viruses identified in multimammate mouse (Mastomys natalensis) populations from across regions of sub-Saharan Africa. Arch Virol 2020; 165:2291-2299. [PMID: 32754877 PMCID: PMC7497350 DOI: 10.1007/s00705-020-04738-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/17/2020] [Indexed: 11/29/2022]
Abstract
The multimammate mouse (Mastomys natalensis; M. natalensis) serves as the main reservoir for the zoonotic arenavirus Lassa virus (LASV), and this has led to considerable investigation into the distribution of LASV and other related arenaviruses in this host species. In contrast to the situation with arenaviruses, the presence of other viruses in M. natalensis remains largely unexplored. In this study, herpesviruses and polyomaviruses were identified and partially characterized by PCR methods, sequencing, and phylogenetic analysis. In tissues sampled from M. natalensis populations in Côte d'Ivoire and Mali, six new DNA viruses (four betaherpesviruses, one gammaherpesvirus and one polyomavirus) were identified. Phylogenetic analysis based on glycoprotein B amino acid sequences showed that the herpesviruses clustered with cytomegaloviruses and rhadinoviruses of multiple rodent species. The complete circular genome of the newly identified polyomavirus was amplified by PCR. Amino acid sequence analysis of the large T antigen or VP1 showed that this virus clustered with a known polyomavirus from a house mouse (species Mus musculus polyomavirus 1). These two polyomaviruses form a clade with other rodent polyomaviruses, and the newly identified virus represents the third known polyomavirus of M. natalensis. This study represents the first identification of herpesviruses and the discovery of a novel polyomavirus in M. natalensis. In contrast to arenaviruses, we anticipate that these newly identified viruses represent a low zoonotic risk due to the normally highly restricted specificity of members of these two DNA virus families to their individual mammalian host species.
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Affiliation(s)
| | - Léonce Kouadio
- LANADA/Central Laboratory for Animal Diseases, Bingerville, Côte d'Ivoire.,P3 "Epidemiology of Highly Pathogenic Microorganisms", Robert Koch-Institute, Berlin, Germany
| | | | - Nafomon Sogoba
- Faculty of Medicine and Odontostomatology, Malaria Research and Training Center, International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Kyle Rosenke
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Fabian Leendertz
- P3 "Epidemiology of Highly Pathogenic Microorganisms", Robert Koch-Institute, Berlin, Germany
| | - Michael A Jarvis
- School of Biomedical Sciences, University of Plymouth, Plymouth, UK.,The Vaccine Group Ltd, Plymouth, UK
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Bernhard Ehlers
- Division 12 "Measles, Mumps, Rubella, and Viruses Affecting Immunocompromised Patients", Robert Koch Institut, Berlin, Germany.
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24
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Kostin DS, Martynov AA, Komarova VA, Alexandrov DY, Yihune M, Kasso M, Bryja J, Lavrenchenko LA. Rodents of Choke Mountain and surrounding areas (Ethiopia): the Blue Nile gorge as a strong biogeographic barrier. JOURNAL OF VERTEBRATE BIOLOGY 2020. [DOI: 10.25225/jvb.20016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Danila S. Kostin
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia; e-mail:
| | - Aleksey A. Martynov
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia; e-mail:
| | - Valeria A. Komarova
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia; e-mail:
| | - Dmitriy Yu. Alexandrov
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia; e-mail:
| | - Mesele Yihune
- Addis Ababa University, Department of Zoological Sciences, Addis Ababa, Ethiopia
| | | | - Josef Bryja
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
| | - Leonid A. Lavrenchenko
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia; e-mail:
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25
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De Bellocq JG, Bryjová A, Martynov AA, Lavrenchenko LA. Dhati Welel virus, the missing mammarenavirus of the widespread Mastomys natalensis. JOURNAL OF VERTEBRATE BIOLOGY 2020. [DOI: 10.25225/jvb.20018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Joëlle Goüy De Bellocq
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic; e-mail: ,
| | - Anna Bryjová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic; e-mail: ,
| | - Aleksey A. Martynov
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia; e-mail: ,
| | - Leonid A. Lavrenchenko
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia; e-mail: ,
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26
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Cuypers LN, Baird SJE, Hánová A, Locus T, Katakweba AS, Gryseels S, Bryja J, Leirs H, Goüy de Bellocq J. Three arenaviruses in three subspecific natal multimammate mouse taxa in Tanzania: same host specificity, but different spatial genetic structure? Virus Evol 2020; 6:veaa039. [PMID: 33033629 PMCID: PMC7532547 DOI: 10.1093/ve/veaa039] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Mastomys natalensis is widespread in sub-Saharan Africa and hosts several arenavirus species, including the pathogenic zoonotic Lassa virus in West Africa. Mitochondrial lineages sub-divide the range of M. natalensis and have been associated with cryptic structure within the species. To test specificity of arenaviruses to hosts carrying these lineages, we screened 1772 M. natalensis in a large area of Tanzania where three mitochondrial lineages meet. We detected fifty-two individuals that were positive for one of three arenaviruses: Gairo, Morogoro, and Luna virus. This is the first record of Luna virus in Tanzania. We confirmed the specificity of each arenavirus to a distinct host mitochondrial lineage except for three cases in one locality at the centre of a host hybrid zone. No arenaviruses were detected in a large part of the study area. Morogoro and Gairo virus showed differences in prevalence (Morogoro virus lower than Gairo virus) and in genetic structure (Morogoro virus more structured than Gairo virus). However, both viruses have genetic neighbourhood size estimates of the same order of magnitude as Lassa virus. While differences in arenavirus and/or host evolutionary and ecological dynamics may exist, Tanzanian arenaviruses could be suited to model Lassa virus dynamics in M. natalensis.
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Affiliation(s)
- Laura N Cuypers
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Stuart J E Baird
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Alexandra Hánová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic.,Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Tatjana Locus
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Abdul S Katakweba
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Sophie Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic.,Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Herwig Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
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27
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Population structure of Lassa Mammarenavirus in West Africa. Viruses 2020; 12:v12040437. [PMID: 32294960 PMCID: PMC7232344 DOI: 10.3390/v12040437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/07/2020] [Accepted: 04/10/2020] [Indexed: 01/01/2023] Open
Abstract
Lassa mammarenavirus (LASV) is the etiologic agent of Lassa fever. In endemic regions in West Africa, LASV genetic diversity tends to cluster by geographic area. Seven LASV lineages are recognized, but the role of viral genetic determinants on disease presentation in humans is uncertain. We investigated the geographic structure and distribution of LASV in West Africa. We found strong spatial clustering of LASV populations, with two major east–west and north–south diversity gradients. Analysis of ancestry components indicated that known LASV lineages diverged from an ancestral population that most likely circulated in Nigeria, although alternative locations, such as Togo, cannot be excluded. Extant sequences carrying the largest contribution of this ancestral population include the prototype Pinneo strain, the Togo isolates, and a few viruses isolated in Nigeria. The LASV populations that experienced the strongest drift circulate in Mali and the Ivory Coast. By focusing on sequences form a single LASV sublineage (IIg), we identified an ancestry component possibly associated with protection from a fatal disease outcome. Although the same ancestry component tends to associate with lower viral loads in plasma, the small sample size requires that these results are treated with extreme caution.
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28
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Olayemi A, Fichet-Calvet E. Systematics, Ecology, and Host Switching: Attributes Affecting Emergence of the Lassa Virus in Rodents across Western Africa. Viruses 2020; 12:E312. [PMID: 32183319 PMCID: PMC7150792 DOI: 10.3390/v12030312] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022] Open
Abstract
Ever since it was established that rodents serve as reservoirs of the zoonotic Lassa virus (LASV), scientists have sought to answer the questions: which populations of rodents carry the virus? How do fluctuations in LASV prevalence and rodent abundance influence Lassa fever outbreaks in humans? What does it take for the virus to adopt additional rodent hosts, proliferating what already are devastating cycles of rodent-to-human transmission? In this review, we examine key aspects of research involving the biology of rodents that affect their role as LASV reservoirs, including phylogeography, demography, virus evolution, and host switching. We discuss how this knowledge can help control Lassa fever and suggest further areas for investigation.
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Affiliation(s)
- Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, Ile Ife HO220005, Nigeria;
| | - Elisabeth Fichet-Calvet
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
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29
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Hardin A, Nevonen KA, Eckalbar WL, Carbone L, Ahituv N. Comparative Genomic Characterization of the Multimammate Mouse Mastomys coucha. Mol Biol Evol 2020; 36:2805-2812. [PMID: 31424545 PMCID: PMC6878952 DOI: 10.1093/molbev/msz188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Mastomys are the most widespread African rodent and carriers of various diseases such as the plague or Lassa virus. In addition, mastomys have rapidly gained a large number of mammary glands. Here, we generated a genome, variome, and transcriptomes for Mastomys coucha. As mastomys diverged at similar times from mouse and rat, we demonstrate their utility as a comparative genomic tool for these commonly used animal models. Furthermore, we identified over 500 mastomys accelerated regions, often residing near important mammary developmental genes or within their exons leading to protein sequence changes. Functional characterization of a noncoding mastomys accelerated region, located in the HoxD locus, showed enhancer activity in mouse developing mammary glands. Combined, our results provide genomic resources for mastomys and highlight their potential both as a comparative genomic tool and for the identification of mammary gland number determining factors.
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Affiliation(s)
- Aaron Hardin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR
| | - Walter L Eckalbar
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
| | - Lucia Carbone
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR.,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR.,Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR.,Division of Genetics, Oregon National Primate Research Center, Beaverton, OR
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA
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30
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Mikula O, Nicolas V, Boratyński Z, Denys C, Dobigny G, Fichet-Calvet E, Gagaré S, Hutterer R, Nimo-Paintsil SC, Olayemi A, Bryja J. Commensalism outweighs phylogeographical structure in its effect on phenotype of a Sudanian savanna rodent. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blz184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The murid rodent Praomys daltoni is widespread in Sudanian savanna and woodlands of West Africa, and previous study of mitochondrial DNA variability suggested that it encompasses the phenotypically (small, grey-bellied) and ecologically (commensal) distinct form, Praomys derooi. Here, we comprehensively examined the genetic and morphological diversity within the complex. Six mitochondrial lineages showed a fine-scale phylogeographical pattern, whereas delimitation based on nuclear loci pooled four of them into a single widespread unit. A newly discovered lineage from southern Mauritania stands apart from the rest of the complex and might represent an unrecognized species. At the same time, the internal position of P. derooi (C2 mitochondrial lineage) was confirmed by the multilocus analysis. The magnitude of genetic distances between major phylogeographical lineages was typical for interspecific divergence in other clades of Praomys, despite the little differences among them in morphology (skull and upper molar row shapes). The most pronounced morphological shift was associated with a transition to commensalism, especially in P. derooi, but also in other lineages. This makes the whole complex a suitable model for the study of phenotypic novelty, the evolution of commensalism and conditions for ecological speciation.
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Affiliation(s)
- Ondřej Mikula
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Violaine Nicolas
- Muséum National d’Histoire Naturelle, Institute of Systematics and Evolution of the Biodiversity, UMR7205 CNRS-MNHN-UPMC-EPHE-Sorbonne University, Paris, France
| | - Zbyszek Boratyński
- CIBIO-InBIO Associate Laboratory, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Christiane Denys
- Muséum National d’Histoire Naturelle, Institute of Systematics and Evolution of the Biodiversity, UMR7205 CNRS-MNHN-UPMC-EPHE-Sorbonne University, Paris, France
| | - Gauthier Dobigny
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
- Ecole Polytechnique d’Abomey-Calavi, Abomey-Calavi University, Cotonou, Benin
| | | | - Sama Gagaré
- Centre Régional Agrhymet, Département Formation Recherche, Niamey, Niger
| | - Rainer Hutterer
- Zoologisches Forschungsinstitut und Museum Alexander Koenig, Bonn, Germany
| | | | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
| | - Josef Bryja
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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31
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Bryja J, Meheretu Y, Šumbera R, Lavrenchenko LA. Annotated checklist, taxonomy and distribution of rodents in Ethiopia. FOLIA ZOOLOGICA 2019. [DOI: 10.25225/fozo.030.2019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Josef Bryja
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic; e-mail:
| | - Yonas Meheretu
- Department of Biology and Institute of Mountain Research & Development, Mekelle University, Ethiopia; e-mail:
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic; e-mail:
| | - Leonid A. Lavrenchenko
- A. N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia; e-mail:
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Petružela J, Bryja J, Bryjová A, Katakweba A, Sabuni C, Baird SJE, de Bellocq JG. Evolutionary history of Pneumocystis fungi in their African rodent hosts. INFECTION GENETICS AND EVOLUTION 2019; 75:103934. [PMID: 31247340 DOI: 10.1016/j.meegid.2019.103934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/17/2019] [Accepted: 06/20/2019] [Indexed: 02/08/2023]
Abstract
Pneumocystis is a genus of parasitic fungi infecting lung tissues in a wide range of mammal species, displaying a strong host specificity and patterns of co-speciation with their hosts. However, a recent study on Asiatic murids challenged these patterns reporting several Pneumocystis lineages/species shared by different host species or even genera in the Rattini and Murini tribes. Here we screened lung samples of 27 species of African rodents from five families for the presence of Pneumocystis DNA. Using reconstructed multi-locus phylogenies of both hosts and parasites, we tested the hypothesis of their co-evolution. We found that Pneumocystis is widespread in African rodents, detected in all but seven screened host species, with species-level prevalence ranging from 5.9 to 100%. Several host species carry pairs of highly divergent Pneumocystis lineages/species. The retrieved co-phylogenetic signal was highly significant (p = .0017). We found multiple co-speciations, sorting events and two host-shift events, which occurred between Murinae and Deomyinae hosts. Comparison of genetic distances suggests higher substitution rates for Pneumocystis relative to the rodent hosts on neutral loci and slower rates on selected ones. We discuss life-history traits and population dynamics factors which could explain the observed results.
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Affiliation(s)
- Jan Petružela
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Faculty of Science, Department of Botany and Zoology, Masaryk University, Brno, Czech Republic.
| | - Josef Bryja
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Faculty of Science, Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Abdul Katakweba
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Christopher Sabuni
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Stuart J E Baird
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Joëlle Goüy de Bellocq
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Aghová T, Palupčíková K, Šumbera R, Frynta D, Lavrenchenko LA, Meheretu Y, Sádlová J, Votýpka J, Mbau JS, Modrý D, Bryja J. Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny. BMC Evol Biol 2019; 19:69. [PMID: 30832573 PMCID: PMC6399835 DOI: 10.1186/s12862-019-1380-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 02/01/2019] [Indexed: 01/02/2023] Open
Abstract
Background Spiny mice of the genus Acomys are distributed mainly in dry open habitats in Africa and the Middle East, and they are widely used as model taxa for various biological disciplines (e.g. ecology, physiology and evolutionary biology). Despite their importance, large distribution and abundance in local communities, the phylogeny and the species limits in the genus are poorly resolved, and this is especially true for sub-Saharan taxa. The main aims of this study are (1) to reconstruct phylogenetic relationships of Acomys based on the largest available multilocus dataset (700 genotyped individuals from 282 localities), (2) to identify the main biogeographical divides in the distribution of Acomys diversity in dry open habitats in Afro-Arabia, (3) to reconstruct the historical biogeography of the genus, and finally (4) to estimate the species richness of the genus by application of the phylogenetic species concept. Results The multilocus phylogeny based on four genetic markers shows presence of five major groups of Acomys called here subspinosus, spinosissimus, russatus, wilsoni and cahirinus groups. Three of these major groups (spinosissimus, wilsoni and cahirinus) are further sub-structured to phylogenetic lineages with predominantly parapatric distributions. Combination of alternative species delimitation methods suggests the existence of 26 molecular operational taxonomic units (MOTUs), potentially corresponding to separate species. The highest genetic diversity was found in Eastern Africa. The origin of the genus Acomys is dated to late Miocene (ca. 8.7 Ma), when the first split occurred between spiny mice of eastern (Somali-Masai) and south-eastern (Zambezian) savannas. Further diversification, mostly in Plio-Pleistocene, and the current distribution of Acomys were influenced by the interplay of global climatic factors (e.g., Messinian salinity crisis, intensification of Northern Hemisphere glaciation) with local geomorphology (mountain chains, aridity belts, water bodies). Combination of divergence dating, species distribution modelling and historical biogeography analysis suggests repeated “out-of-East-Africa” dispersal events into western Africa, the Mediterranean region and Arabia. Conclusions The genus Acomys is very suitable model for historical phylogeographic and biogeographic reconstructions of dry non-forested environments in Afro-Arabia. We provide the most thorough phylogenetic reconstruction of the genus and identify major factors that influenced its evolutionary history since the late Miocene. We also highlight the urgent need of integrative taxonomic revision of east African taxa. Electronic supplementary material The online version of this article (10.1186/s12862-019-1380-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- T Aghová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65, Brno, Czech Republic. .,Department of Zoology, National Museum, 115 79, Prague, Czech Republic.
| | - K Palupčíková
- Department of Zoology, Faculty of Science, Charles University, 128 44, Prague, Czech Republic
| | - R Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05, České Budějovice, Czech Republic
| | - D Frynta
- Department of Zoology, Faculty of Science, Charles University, 128 44, Prague, Czech Republic
| | - L A Lavrenchenko
- A. N. Severtsov Institute of Ecology and Evolution RAS, 119071, Moscow, Russia
| | - Y Meheretu
- Department of Biology and Institute of Mountain Research and Development, Mekelle University, P.O. Box 3102, Mekelle, Tigray, Ethiopia
| | - J Sádlová
- Department of Parasitology, Faculty of Science, Charles University, 128 44, Prague, Czech Republic
| | - J Votýpka
- Department of Parasitology, Faculty of Science, Charles University, 128 44, Prague, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
| | - J S Mbau
- Department of Land Resource Management and Agricultural Technology, College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya
| | - D Modrý
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic.,Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, 612 42, Brno, Czech Republic
| | - J Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65, Brno, Czech Republic.,Department of Botany and Zoology, Faculty of Science, Masaryk University, 602 00, Brno, Czech Republic
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Pontremoli C, Forni D, Sironi M. Arenavirus genomics: novel insights into viral diversity, origin, and evolution. Curr Opin Virol 2019; 34:18-28. [DOI: 10.1016/j.coviro.2018.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/18/2022]
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Differentiation underground: Range-wide multilocus genetic structure of the silvery mole-rat does not support current taxonomy based on mitochondrial sequences. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Sabuni C, Aghová T, Bryjová A, Šumbera R, Bryja J. Biogeographic implications of small mammals from Northern Highlands in Tanzania with first data from the volcanic Mount Kitumbeine. MAMMALIA 2018. [DOI: 10.1515/mammalia-2017-0069] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractSmall terrestrial mammals and their biogeographical affinities were studied on Mount Kitumbeine, one of the little known volcanoes in the Gregory Rift Valley (northern Tanzania). In June, 2015, a total of 10 species, two insectivores and eight rodents, were recorded during a short-time sampling in two high altitude habitats. Taxonomic identification was based on genetic data allowing zoogeographic interpretations. For most of the taxa, there was a clear link with fauna of the northern part of the Eastern Arc Mountains, but there were also species with their core distributions in the Albertine Rift Mountains (Crocidura montis) as well as taxa endemic to the volcanic Northern Highlands (e.g. Hanang or Ngorongoro), such asLophuromys makundiand probablyOtomys angoniensis. Comparison of genotyped small mammals from Kitumbeine and neighboring hills with previously collected data revealed the first genetically confirmed Tanzanian records of two species (C. montisandLophuromys stanleyi) and one species (Lophuromys sabunii) is reported for the first time from Zambia. The present study thus showed that, even in such well-studied areas like northern Tanzania, a basic faunistic survey of mammals can still bring interesting results stressing the need to study biota in small and poorly known areas.
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Mazoch V, Mikula O, Bryja J, Konvičková H, Russo IR, Verheyen E, Šumbera R. Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion. MAMMALIA 2018. [DOI: 10.1515/mammalia-2017-0001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Abstract
Murid rodents of the genus Aethomys are one of the most common rodents in drier habitats in sub-Saharan Africa. Among them, the red veld rat Aethomys chrysophilus is the most widespread species with the core distribution located in the Zambezian bioregion. In this study, we describe phylogeographic structure of the species and estimate its age from a time-calibrated phylogeny of the genus. Seven parapatric clades were identified in the mitochondrial cytochrome b phylogeny, where some of the distributions of these clades have been separated by previously described biogeographical divides (Zambezi-Kafue river system, Rukwa Rift and the Eastern Arc Mountains). One internal clade corresponded to populations previously described as a distinct species, Aethomys ineptus. The whole A. chrysophilus complex was estimated to be 1.3 (0.5–2.4) Mya old, with A. ineptus originating 0.7 (0.1–1.4) Mya before present. The internal position of A. ineptus was also recovered in phylogenetic reconstruction based on two nuclear genes and thus it is not a consequence of mitochondrial introgression. In addition, we analyzed skull form variation across the species’ distributional range and found no significant difference between A. ineptus and the rest of A. chrysophilus complex.
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38
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Petružela J, Šumbera R, Aghová T, Bryjová A, Katakweba AS, Sabuni CA, Chitaukali WN, Bryja J. Spiny mice of the Zambezian bioregion – phylogeny, biogeography and ecological differentiation within the Acomys spinosissimus complex. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.03.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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39
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Mairal M, Sanmartín I, Herrero A, Pokorny L, Vargas P, Aldasoro JJ, Alarcón M. Geographic barriers and Pleistocene climate change shaped patterns of genetic variation in the Eastern Afromontane biodiversity hotspot. Sci Rep 2017; 7:45749. [PMID: 28397796 PMCID: PMC5387718 DOI: 10.1038/srep45749] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/02/2017] [Indexed: 12/02/2022] Open
Abstract
The Eastern African Afromontane forest is getting increased attention in conservation studies because of its high endemicity levels and shrinking geographic distribution. Phylogeographic studies have found evidence of high levels of genetic variation structured across the Great Rift System. Here, we use the epiphytic plant species Canarina eminii to explore causal explanations for this pattern. Phylogeographic analyses were undertaken using plastid regions and AFLP fragments. Population genetic analyses, Statistical Parsimony, and Bayesian methods were used to infer genetic diversity, genealogical relationships, structure, gene flow barriers, and the spatiotemporal evolution of populations. A strong phylogeographic structure was found, with two reciprocally monophyletic lineages on each side of the Great Rift System, high genetic exclusivity, and restricted gene flow among mountain ranges. We explain this pattern by topographic and ecological changes driven by geological rifting in Eastern Africa. Subsequent genetic structure is attributed to Pleistocene climatic changes, in which sky-islands acted as long-term refuges and cradles of genetic diversity. Our study highlights the importance of climate change and geographic barriers associated with the African Rift System in shaping population genetic patterns, as well as the need to preserve the high levels of exclusive and critically endangered biodiversity harboured by current patches of the Afromontane forest.
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Affiliation(s)
- Mario Mairal
- Real Jardín Botánico (RJB-CSIC), 28014 Madrid, Spain
| | | | | | - Lisa Pokorny
- Royal Botanic Gardens, Kew (RBGK), Richmond, Surrey, TW9 3DS, UK
| | - Pablo Vargas
- Real Jardín Botánico (RJB-CSIC), 28014 Madrid, Spain
| | - Juan J Aldasoro
- Instituto Botánico de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Spain.,Universidad Rey Juan Carlos, Móstoles, Spain
| | - Marisa Alarcón
- Instituto Botánico de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Spain
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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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Olayemi A, Obadare A, Oyeyiola A, Igbokwe J, Fasogbon A, Igbahenah F, Ortsega D, Asogun D, Umeh P, Vakkai I, Abejegah C, Pahlman M, Becker-Ziaja B, Günther S, Fichet-Calvet E. Arenavirus Diversity and Phylogeography of Mastomys natalensis Rodents, Nigeria. Emerg Infect Dis 2016; 22:694-7. [PMID: 26982388 PMCID: PMC4806934 DOI: 10.3201/eid2204.150155] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mastomys natalensis rodents are natural hosts for Lassa virus
(LASV). Detection of LASV in 2 mitochondrial phylogroups of the rodent near the Niger
and Benue Rivers in Nigeria underlines the potential for LASV emergence in fresh
phylogroups of this rodent. A Mobala-like sequence was also detected in eastern
Nigeria.
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42
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Russo IRM, Sole CL, Barbato M, von Bramann U, Bruford MW. Landscape determinants of fine-scale genetic structure of a small rodent in a heterogeneous landscape (Hluhluwe-iMfolozi Park, South Africa). Sci Rep 2016; 6:29168. [PMID: 27406468 PMCID: PMC4942783 DOI: 10.1038/srep29168] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/13/2016] [Indexed: 12/05/2022] Open
Abstract
Small mammals provide ecosystem services, acting, for example, as pollinators and seed dispersers. In addition, they are also disease reservoirs that can be detrimental to human health and they can also act as crop pests. Knowledge of their dispersal preferences is therefore useful for population management and landscape planning. Genetic data were used alongside landscape data to examine the influence of the landscape on the demographic connectedness of the Natal multimammate mouse (Mastomys natalensis) and to identify landscape characteristics that influence the genetic structure of this species across a spatially and temporally varying environment. The most significant landscape features shaping gene flow were aspect, vegetation cover, topographic complexity (TC) and rivers, with western facing slopes, topographic complexity and rivers restricting gene flow. In general, thicket vegetation was correlated with increased gene flow. Identifying features of the landscape that facilitate movement/dispersal in M. natalensis potentially has application for other small mammals in similar ecosystems. As the primary reservoir host of the zoonotic Lassa virus, a landscape genetics approach may have applications in determining areas of high disease risk to humans. Identifying these landscape features may also be important in crop management due to damage by rodent pests.
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Affiliation(s)
- Isa-Rita M Russo
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX United Kingdom
| | - Catherine L Sole
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield, 0028 South Africa
| | - Mario Barbato
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX United Kingdom
| | - Ullrich von Bramann
- Technische Universität Braunschweig, Institut für Geosysteme und Bioindikation, Langer Kamp 19c, Braunschweig, 38106 Germany
| | - Michael W Bruford
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX United Kingdom
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Gryseels S, Goüy de Bellocq J, Makundi R, Vanmechelen K, Broeckhove J, Mazoch V, Šumbera R, Zima J, Leirs H, Baird SJE. Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow. J Evol Biol 2016; 29:1952-1967. [PMID: 27306876 DOI: 10.1111/jeb.12919] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 06/14/2016] [Indexed: 01/03/2023]
Abstract
Special conditions are required for genetic differentiation to arise at a local geographical scale in the face of gene flow. The Natal multimammate mouse, Mastomys natalensis, is the most widely distributed and abundant rodent in sub-Saharan Africa. A notorious agricultural pest and a natural host for many zoonotic diseases, it can live in close proximity to humans and appears to compete with other rodents for the synanthropic niche. We surveyed its population genetic structure across a 180-km transect in central Tanzania along which the landscape varied between agricultural land in a rural setting and natural woody vegetation, rivers, roads and a city (Morogoro). We sampled M. natalensis across 10 localities and genotyped 15 microsatellite loci from 515 individuals. Hierarchical STRUCTURE analyses show a K-invariant pattern distinguishing Morogoro suburbs (located in the centre of the transect) from nine surrounding rural localities. Landscape connectivity analyses in Circuitscape and comparison of rainfall patterns suggest that neither geographical isolation nor natural breeding asynchrony could explain the genetic differentiation of the urban population. Using the isolation-with-migration model implemented in IMa2, we inferred that a split between suburban and rural populations would have occurred recently (<150 years ago) with higher urban effective population density consistent with an urban source to rural sink of effective migration. The observed genetic differentiation of urban multimammate mice is striking given the uninterrupted distribution of the animal throughout the landscape and the high estimates of effective migration (2Ne M = 3.0 and 29.7), suggesting a strong selection gradient across the urban boundary.
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Affiliation(s)
- S Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium.
| | - J Goüy de Bellocq
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium.,Institute of Vertebrate Biology, Research Facility Studenec, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - R Makundi
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - K Vanmechelen
- Computational Modelling and Programming, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - J Broeckhove
- Computational Modelling and Programming, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - V Mazoch
- Department of Zoology, University of South Bohemia, České Budějovice, Czech Republic
| | - R Šumbera
- Department of Zoology, University of South Bohemia, České Budějovice, Czech Republic
| | - J Zima
- Institute of Vertebrate Biology, Research Facility Studenec, Academy of Sciences of the Czech Republic, Brno, Czech Republic.,Department of Zoology, University of South Bohemia, České Budějovice, Czech Republic
| | - H Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - S J E Baird
- Institute of Vertebrate Biology, Research Facility Studenec, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Redding DW, Moses LM, Cunningham AA, Wood J, Jones KE. Environmental-mechanistic modelling of the impact of global change on human zoonotic disease emergence: a case study of Lassa fever. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12549] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- David W. Redding
- Centre for Biodiversity and Environment Research; Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
| | - Lina M. Moses
- Department of Microbiology and Immunology; Tulane University; New Orleans Louisiana USA
| | - Andrew A. Cunningham
- Institute of Zoology; Zoological Society of London; Regent's Park London NW1 4RY UK
| | - James Wood
- Department of Veterinary Medicine; Disease Dynamics Unit; University of Cambridge; Cambridge UK
| | - Kate E. Jones
- Centre for Biodiversity and Environment Research; Department of Genetics, Evolution and Environment; University College London; Gower Street London WC1E 6BT UK
- Institute of Zoology; Zoological Society of London; Regent's Park London NW1 4RY UK
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McDonough MM, Šumbera R, Mazoch V, Ferguson AW, Phillips CD, Bryja J. Multilocus phylogeography of a widespread savanna-woodland-adapted rodent reveals the influence of Pleistocene geomorphology and climate change in Africa's Zambezi region. Mol Ecol 2015; 24:5248-66. [DOI: 10.1111/mec.13374] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 08/27/2015] [Accepted: 09/01/2015] [Indexed: 02/04/2023]
Affiliation(s)
- Molly M. McDonough
- Department of Biological Sciences; Texas Tech University; Lubbock TX USA
- National Museum of Natural History; Smithsonian Institution; Washington DC USA
| | - Radim Šumbera
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Vladimír Mazoch
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Adam W. Ferguson
- Department of Biological Sciences; Texas Tech University; Lubbock TX USA
| | - Caleb D. Phillips
- Department of Biological Sciences; Texas Tech University; Lubbock TX USA
- Research and Testing Laboratory; Lubbock TX USA
| | - Josef Bryja
- Institute of Vertebrate Biology; Academy of Sciences of the Czech Republic; Brno Czech Republic
- Department of Botany and Zoology; Faculty of Science; Masaryk University; Brno Czech Republic
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Jacquet F, Denys C, Verheyen E, Bryja J, Hutterer R, Kerbis Peterhans JC, Stanley WT, Goodman SM, Couloux A, Colyn M, Nicolas V. Phylogeography and evolutionary history of the Crocidura olivieri complex (Mammalia, Soricomorpha): from a forest origin to broad ecological expansion across Africa. BMC Evol Biol 2015; 15:71. [PMID: 25900417 PMCID: PMC4422046 DOI: 10.1186/s12862-015-0344-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 03/30/2015] [Indexed: 12/18/2022] Open
Abstract
Background This study aims to reconstruct the evolutionary history of African shrews referred to the Crocidura olivieri complex. We tested the respective role of forest retraction/expansion during the Pleistocene, rivers (allopatric models), ecological gradients (parapatric model) and anthropogenic factors in explaining the distribution and diversification within this species complex. We sequenced three mitochondrial and four nuclear markers from 565 specimens encompassing the known distribution of the complex, i.e. from Morocco to Egypt and south to Mozambique. We used Bayesian phylogenetic inference, genetic structure analyses and divergence time estimates to assess the phylogenetic relationships and evolutionary history of these animals. Results The C. olivieri complex (currently composed of C. olivieri, C. fulvastra, C. viaria and C. goliath) can be segregated into eight principal geographical clades, most exhibiting parapatric distributions. A decrease in genetic diversity was observed between central and western African clades and a marked signal of population expansion was detected for a broadly distributed clade occurring across central and eastern Africa and portions of Egypt (clade IV). The main cladogenesis events occurred within the complex between 1.37 and 0.48 Ma. Crocidura olivieri sensu stricto appears polyphyletic and C. viaria and C. fulvastra were not found to be monophyletic. Conclusions Climatic oscillations over the Pleistocene probably played a major role in shaping the genetic diversity within this species complex. Different factors can explain their diversification, including Pleistocene forest refuges, riverine barriers and differentiation along environmental gradients. The earliest postulated members of the complex originated in central/eastern Africa and the first radiations took place in rain forests of the Congo Basin. A dramatic shift in the ecological requirements in early members of the complex, in association with changing environments, took place sometime after 1.13 Ma. Some lineages then colonized a substantial portion of the African continent, including a variety of savannah and forest habitats. The low genetic divergence of certain populations, some in isolated localities, can be explained by their synanthropic habits. This study underlines the need to revise the taxonomy of the C. olivieri complex. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0344-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- François Jacquet
- Institut de Systématique, Évolution, Biodiversité, ISYEB UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP 51, 75005, Paris, France.
| | - Christiane Denys
- Institut de Systématique, Évolution, Biodiversité, ISYEB UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP 51, 75005, Paris, France.
| | - Erik Verheyen
- Royal Belgian Institute of Natural Sciences, Operational Direction Taxonomy and Phylogeny, Molecular Laboratory, Vautierstraat 29, 1000, Brussels, Belgium. .,Biology Department, University of Antwerpen, Evolutionary Ecology Group, Groenenborgerlaan 171, 2020, Antwerpen, Belgium.
| | - Josef Bryja
- Institute of Vertebrate Biology ASCR, Academy of Sciences of the Czech Republic, Květná 8, 603 65, Brno, Czech Republic. .,Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic.
| | - Rainer Hutterer
- Zoologisches Forschungmuseum Alexander Koenig, Adenauerallee 160, D-53113, Bonn, Germany.
| | - Julian C Kerbis Peterhans
- College of Professional Studies, Roosevelt University, 430 S Michigan Avenue, Chicago, IL, 60605, USA. .,Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA.
| | - William T Stanley
- Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA.
| | - Steven M Goodman
- Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA. .,Association Vahatra, BP 3972, Antananarivo, 101, Madagascar.
| | - Arnaud Couloux
- Génoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, 91057, Evry Cedex, France.
| | - Marc Colyn
- Université de Rennes 1, CNRS, UMR 6553 Ecobio, Station Biologique, 35380, Paimpont, France.
| | - Violaine Nicolas
- Institut de Systématique, Évolution, Biodiversité, ISYEB UMR 7205 - CNRS, MNHN, UPMC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP 51, 75005, Paris, France.
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Bryja J, Mikula O, Šumbera R, Meheretu Y, Aghová T, Lavrenchenko LA, Mazoch V, Oguge N, Mbau JS, Welegerima K, Amundala N, Colyn M, Leirs H, Verheyen E. Pan-African phylogeny of Mus (subgenus Nannomys) reveals one of the most successful mammal radiations in Africa. BMC Evol Biol 2014; 14:256. [PMID: 25496476 PMCID: PMC4280006 DOI: 10.1186/s12862-014-0256-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 11/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rodents of the genus Mus represent one of the most valuable biological models for biomedical and evolutionary research. Out of the four currently recognized subgenera, Nannomys (African pygmy mice, including the smallest rodents in the world) comprises the only original African lineage. Species of this subgenus became important models for the study of sex determination in mammals and they are also hosts of potentially dangerous pathogens. Nannomys ancestors colonized Africa from Asia at the end of Miocene and Eastern Africa should be considered as the place of their first radiation. In sharp contrast with this fact and despite the biological importance of Nannomys, the specimens from Eastern Africa were obviously under-represented in previous studies and the phylogenetic and distributional patterns were thus incomplete. RESULTS We performed comprehensive genetic analysis of 657 individuals of Nannomys collected at approximately 300 localities across the whole sub-Saharan Africa. Phylogenetic reconstructions based on mitochondrial (CYTB) and nuclear (IRBP) genes identified five species groups and three monotypic ancestral lineages. We provide evidence for important cryptic diversity and we defined and mapped the distribution of 27 molecular operational taxonomic units (MOTUs) that may correspond to presumable species. Biogeographical reconstructions based on data spanning all of Africa modified the previous evolutionary scenarios. First divergences occurred in Eastern African mountains soon after the colonization of the continent and the remnants of these old divergences still occur there, represented by long basal branches of M. (previously Muriculus) imberbis and two undescribed species from Ethiopia and Malawi. The radiation in drier lowland habitats associated with the decrease of body size is much younger, occurred mainly in a single lineage (called the minutoides group, and especially within the species M. minutoides), and was probably linked to aridification and climatic fluctuations in middle Pliocene/Pleistocene. CONCLUSIONS We discovered very high cryptic diversity in African pygmy mice making the genus Mus one of the richest genera of African mammals. Our taxon sampling allowed reliable phylogenetic and biogeographic reconstructions that (together with detailed distributional data of individual MOTUs) provide a solid basis for further evolutionary, ecological and epidemiological studies of this important group of rodents.
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Affiliation(s)
- Josef Bryja
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Research Facility Studenec, Studenec 122, 675 02, Koněšín, Czech Republic.
| | - Ondřej Mikula
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
| | - Yonas Meheretu
- Department of Biology, College of Natural and Computational Sciences, Mekelle University, Tigray, Ethiopia.
| | - Tatiana Aghová
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | | | - Vladimír Mazoch
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
| | | | - Judith S Mbau
- College of Agriculture and Veterinary Sciences, University of Nairobi, Nairobi, Kenya.
| | - Kiros Welegerima
- Department of Biology, College of Natural and Computational Sciences, Mekelle University, Tigray, Ethiopia.
| | - Nicaise Amundala
- University of Kisangani, Eastern Province, Kisangani, DR, Congo.
| | - Marc Colyn
- CNRS UMR 6552/53, Université de Rennes 1, Station Biologique, Paimpont, France.
| | - Herwig Leirs
- Evolutionary Ecology Group, Biology Department, University of Antwerp, Antwerpen, Belgium.
| | - Erik Verheyen
- Evolutionary Ecology Group, Biology Department, University of Antwerp, Antwerpen, Belgium.
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, Brussels, Belgium.
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Sands AF, Matthee S, Mfune JKE, Matthee CA. The influence of life history and climate driven diversification on the mtDNA phylogeographic structures of two southern AfricanMastomysspecies (Rodentia: Muridae: Murinae). Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12397] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Arthur F. Sands
- Evolutionary Genomics Group; Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - Sonja Matthee
- Department of Conservation Ecology and Entomology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
| | - John K. E. Mfune
- Department of Biological Sciences; University of Namibia; Windhoek Namibia
| | - Conrad A. Matthee
- Evolutionary Genomics Group; Department of Botany and Zoology; Stellenbosch University; Private Bag X1 Matieland 7602 South Africa
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Visser JH, Bennett NC, Jansen van Vuuren B. Local and regional scale genetic variation in the Cape dune mole-rat, Bathyergus suillus. PLoS One 2014; 9:e107226. [PMID: 25229558 PMCID: PMC4167993 DOI: 10.1371/journal.pone.0107226] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Accepted: 08/14/2014] [Indexed: 11/18/2022] Open
Abstract
The distribution of genetic variation is determined through the interaction of life history, morphology and habitat specificity of a species in conjunction with landscape structure. While numerous studies have investigated this interplay of factors in species inhabiting aquatic, riverine, terrestrial, arboreal and saxicolous systems, the fossorial system has remained largely unexplored. In this study we attempt to elucidate the impacts of a subterranean lifestyle coupled with a heterogeneous landscape on genetic partitioning by using a subterranean mammal species, the Cape dune mole-rat (Bathyergus suillus), as our model. Bathyergus suillus is one of a few mammal species endemic to the Cape Floristic Region (CFR) of the Western Cape of South Africa. Its distribution is fragmented by rivers and mountains; both geographic phenomena that may act as geographical barriers to gene-flow. Using two mitochondrial fragments (cytochrome b and control region) as well as nine microsatellite loci, we determined the phylogeographic structure and gene-flow patterns at two different spatial scales (local and regional). Furthermore, we investigated genetic differentiation between populations and applied Bayesian clustering and assignment approaches to our data. Nearly every population formed a genetically unique entity with significant genetic structure evident across geographic barriers such as rivers (Berg, Verlorenvlei, Breede and Gourits Rivers), mountains (Piketberg and Hottentots Holland Mountains) and with geographic distance at both spatial scales. Surprisingly, B. suillus was found to be paraphyletic with respect to its sister species, B. janetta-a result largely overlooked by previous studies on these taxa. A systematic revision of the genus Bathyergus is therefore necessary. This study provides a valuable insight into how the biology, life-history and habitat specificity of animals inhabiting a fossorial system may act in concert with the structure of the surrounding landscape to influence genetic distinctiveness and ultimately speciation.
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Affiliation(s)
- Jacobus H. Visser
- Department of Zoology, University of Johannesburg, Auckland Park, South Africa
| | - Nigel C. Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
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Dobigny G, Tatard C, Gauthier P, Ba K, Duplantier JM, Granjon L, Kergoat GJ. Mitochondrial and nuclear genes-based phylogeography of Arvicanthis niloticus (Murinae) and sub-Saharan open habitats pleistocene history. PLoS One 2013; 8:e77815. [PMID: 24223730 PMCID: PMC3815218 DOI: 10.1371/journal.pone.0077815] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 09/05/2013] [Indexed: 11/19/2022] Open
Abstract
A phylogeographic study was conducted on the Nile grass rat, Arvicanthis niloticus, a rodent species that is tightly associated with open grasslands from the Sudano-Sahelian regions. Using one mitochondrial (cytochrome b) and one nuclear (intron 7 of Beta Fibrinogen) gene, robust patterns were retrieved that clearly show that (i) the species originated in East Africa concomitantly with expanding grasslands some 2 Ma, and (ii) four parapatric and genetically well-defined lineages differentiated essentially from East to West following Pleistocene bioclimatic cycles. This strongly points towards allopatric genetic divergence within savannah refuges during humid episodes, then dispersal during arid ones; secondary contact zones would have then stabilized around geographic barriers, namely, Niger River and Lake Chad basins. Our results pertinently add to those obtained for several other African rodent as well as non-rodent species that inhabit forests, humid zones, savannahs and deserts, all studies that now allow one to depict a more comprehensive picture of the Pleistocene history of the continent south of the Sahara. In particular, although their precise location remains to be determined, at least three Pleistocene refuges are identified within the West and Central African savannah biome.
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Affiliation(s)
- Gauthier Dobigny
- IRD, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Campus de Baillarguet, Montferrier-sur-Lez, France
- Centre Régional Agrhymet, Rive Droite, Niamey, Niger
| | - Caroline Tatard
- Inra, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Campus de Baillarguet, Montferrier-sur-Lez, France
| | - Philippe Gauthier
- IRD, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Campus de Baillarguet, Montferrier-sur-Lez, France
| | - Khalilou Ba
- IRD, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Dakar, Senegal
| | - Jean-Marc Duplantier
- IRD, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Campus de Baillarguet, Montferrier-sur-Lez, France
| | - Laurent Granjon
- IRD, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Campus de Baillarguet, Montferrier-sur-Lez, France
- IRD, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Dakar, Senegal
| | - Gael J. Kergoat
- Inra, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Campus de Baillarguet, Montferrier-sur-Lez, France
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