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Šumbera R, Uhrová M, Montoya-Sanhueza G, Bryjová A, Bennett NC, Mikula O. Genetic diversity of the largest African mole-rat genus, Bathyergus. one, two or four species? Mol Phylogenet Evol 2024; 199:108157. [PMID: 39029550 DOI: 10.1016/j.ympev.2024.108157] [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: 04/26/2024] [Revised: 07/01/2024] [Accepted: 07/14/2024] [Indexed: 07/21/2024]
Abstract
Recent advances in sequencing technology and phylogenetic methods allow us to solve puzzling taxonomic questions using detailed analyses of genetic diversity of populations and gene flow between them. The genus of solitary-living dune mole-rat, Bathyergus, is quite unique among six genera of African mole-rats. The animals are by far the largest and the only scratch digging mole-rat genus possessing a skull less adapted to digging, grooved upper incisors, and more surface locomotor activity. Most authors recognize two species of dune mole-rats, B. suillus and B. janetta, but according to others, the genus is monotypic. In addition, recent molecular studies have revealed cryptic genetic diversity and suggested the existence of up to four species. In our study, we used mitochondrial and genome-wide nuclear data collected throughout the distribution of the genus to investigate the number of species. In agreement with previous studies, we found Bathyergus to be differentiated into several distinct lineages, but we also found evidence for a degree of gene flow between some of them. Furthermore, we confirmed that B. janetta is nested within B. suillus, making the latter paraphyletic and we documented an instance of local mitochondrial introgression between these two nominal species. Phylogeographic structure of the genus was found to be very shallow. Although traditionally dated to the Miocene, we found the first split within the genus to be much younger estimated to 0.82 Ma before present. Genealogical distinctiveness of some lineages was very low, and the coancestry matrix showed extensive sharing of closely related haplotypes throughout the genus. Accordingly, Infomap clustering on the matrix showed all populations to form a single cluster. Overall, our study tends to support the existence of only one species of Bathyergus namely, B. suillus. Environmental niche modelling confirmed its dependence on sandy soils and the preference for soils with relatively high carbon content. Bayesian skyline plots indicate recent population decline in the janetta lineage, probably related to global environmental change.
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Affiliation(s)
- R Šumbera
- Department of Zoology, Faculty of Sciences, University of South Bohemia in České Budějovice, Czech Republic.
| | - M Uhrová
- Department of Zoology, Faculty of Sciences, University of South Bohemia in České Budějovice, Czech Republic
| | - G Montoya-Sanhueza
- Department of Zoology, Faculty of Sciences, University of South Bohemia in České Budějovice, Czech Republic; Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile (UACh), Valdivia, Chile
| | - A Bryjová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - N C Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, South Africa
| | - O Mikula
- Department of Zoology, Faculty of Sciences, University of South Bohemia in České Budějovice, Czech Republic; Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
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2
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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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3
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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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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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Krásová J, Mikula O, Bryja J, Baptista NL, António T, Aghová T, Šumbera R. Biogeography of Angolan rodents: The first glimpse based on phylogenetic evidence. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Jarmila Krásová
- Department of Zoology Faculty of Science University of South Bohemia České Budějovice Czech Republic
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
| | - Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences Brno Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - Ninda L. Baptista
- Instituto Superior de Ciências da Educação da Huíla (ISCED‐Huíla) Lubango Angola
- CIBIO‐InBIO Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto Vairão Portugal
- Faculdade de Ciências Universidade do Porto Porto Portugal
| | - Telmo António
- Instituto Superior de Ciências da Educação da Huíla (ISCED‐Huíla) Lubango Angola
| | - Tatiana Aghová
- Centre of OncocytogenomicsInstitute of Medical Biochemistry and Laboratory DiagnosticsGeneral University Hospital and First Faculty of MedicineCharles University Prague Czech Republic
| | - Radim Šumbera
- Department of Zoology Faculty of Science University of South Bohemia České Budějovice Czech Republic
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6
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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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7
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Krásová J, Mikula O, Šumbera R, Horáková S, Robovský J, Kostin DS, Martynov AA, Lavrenchenko LA, Bryja J. The Rufous Sengi is not
Elephantulus
—Multilocus reconstruction of evolutionary history of sengis from the subfamily Macroscelidinae. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12460] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Jarmila Krásová
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
- Department of Zoology Faculty of Science University of South Bohemia České Budějovice Czech Republic
| | - Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
| | - Radim Šumbera
- Department of Zoology Faculty of Science University of South Bohemia České Budějovice Czech Republic
| | - Sylvie Horáková
- Department of Zoology Faculty of Science University of South Bohemia České Budějovice Czech Republic
| | - Jan Robovský
- Department of Zoology Faculty of Science University of South Bohemia České Budějovice Czech Republic
| | - Danila S. Kostin
- A. N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences Moscow Russia
| | - Aleksey A. Martynov
- A. N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences Moscow Russia
| | - Leonid A. Lavrenchenko
- A. N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences Moscow Russia
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
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8
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Couvreur TL, Dauby G, Blach‐Overgaard A, Deblauwe V, Dessein S, Droissart V, Hardy OJ, Harris DJ, Janssens SB, Ley AC, Mackinder BA, Sonké B, Sosef MS, Stévart T, Svenning J, Wieringa JJ, Faye A, Missoup AD, Tolley KA, Nicolas V, Ntie S, Fluteau F, Robin C, Guillocheau F, Barboni D, Sepulchre P. Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna. Biol Rev Camb Philos Soc 2021; 96:16-51. [PMID: 32924323 PMCID: PMC7821006 DOI: 10.1111/brv.12644] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/30/2022]
Abstract
Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.
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Affiliation(s)
| | - Gilles Dauby
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - Anne Blach‐Overgaard
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Vincent Deblauwe
- Center for Tropical Research (CTR), Institute of the Environment and SustainabilityUniversity of California, Los Angeles (UCLA)Los AngelesCA90095U.S.A.
- International Institute of Tropical Agriculture (IITA)YaoundéCameroon
| | | | - Vincent Droissart
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Oliver J. Hardy
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - David J. Harris
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghU.K.
| | | | - Alexandra C. Ley
- Institut für Geobotanik und Botanischer GartenUniversity Halle‐WittenbergNeuwerk 21Halle06108Germany
| | | | - Bonaventure Sonké
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
| | | | - Tariq Stévart
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Jens‐Christian Svenning
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Jan J. Wieringa
- Naturalis Biodiversity CenterDarwinweg 2Leiden2333 CRThe Netherlands
| | - Adama Faye
- Laboratoire National de Recherches sur les Productions Végétales (LNRPV)Institut Sénégalais de Recherches Agricoles (ISRA)Route des Hydrocarbures, Bel Air BP 1386‐ CP18524DakarSenegal
| | - Alain D. Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of ScienceUniversity of DoualaPO Box 24157DoualaCameroon
| | - Krystal A. Tolley
- South African National Biodiversity InstituteKirstenbosch Research CentrePrivate Bag X7, ClaremontCape Town7735South Africa
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandPrivate Bag 3Wits2050South Africa
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHEUniversité des AntillesCP51, 57 rue CuvierParis75005France
| | - Stéphan Ntie
- Département de Biologie, Faculté des SciencesUniversité des Sciences et Techniques de MasukuFrancevilleBP 941Gabon
| | - Frédiéric Fluteau
- Institut de Physique du Globe de Paris, CNRSUniversité de ParisParisF‐75005France
| | - Cécile Robin
- CNRS, Géosciences Rennes, UMR6118University of RennesRennes35042France
| | | | - Doris Barboni
- CEREGE, Aix‐Marseille University, CNRS, IRD, Collège de France, INRA, Technopole Arbois MéditerranéeBP80Aix‐en‐Provence cedex413545France
| | - Pierre Sepulchre
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA‐CNRS‐UVSQUniversité Paris‐SaclayGif‐sur‐YvetteF‐91191France
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9
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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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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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11
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Joordens JC, Feibel CS, Vonhof HB, Schulp AS, Kroon D. Relevance of the eastern African coastal forest for early hominin biogeography. J Hum Evol 2019; 131:176-202. [DOI: 10.1016/j.jhevol.2019.03.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/25/2022]
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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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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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Ostfeld JK, Keesing F. Impacts of large mammals on movements of the pouched mouse (
Saccostomus mearnsi
) in central Kenya. Afr J Ecol 2018. [DOI: 10.1111/aje.12549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Fernandez Blanco MV, Cassini GH, Bona P. Skull ontogeny of extant caimans: a three-dimensional geometric morphometric approach. ZOOLOGY 2018; 129:69-81. [DOI: 10.1016/j.zool.2018.06.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 06/15/2018] [Accepted: 06/18/2018] [Indexed: 01/10/2023]
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16
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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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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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