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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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Montoya-Sanhueza G, Bennett NC, Šumbera R. Functional and morphological divergence in the forelimb musculoskeletal system of scratch-digging subterranean mammals (Rodentia: Bathyergidae). J Anat 2024. [PMID: 38760952 DOI: 10.1111/joa.14058] [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: 07/12/2023] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/20/2024] Open
Abstract
Whether the forelimb-digging apparatus of tooth-digging subterranean mammals has similar levels of specialization as compared to scratch-diggers is still unknown. We assessed the scapular morphology and forelimb musculature of all four solitary African mole rats (Bathyergidae): two scratch-diggers, Bathyergus suillus and Bathyergus janetta, and two chisel-tooth diggers, Heliophobius argenteocinereus and Georychus capensis. Remarkable differences were detected: Bathyergus have more robust neck, shoulder, and forearm muscles as compared to the other genera. Some muscles in Bathyergus were also fused and often showing wider attachment areas to bones, which correlate well with its more robust and larger scapula, and its wider and medially oriented olecranon. This suggests that shoulder, elbow, and wrist work in synergy in Bathyergus for generating greater out-forces and that the scapula and proximal ulna play fundamental roles as pivots to maximize and accommodate specialized muscles for better (i) glenohumeral and scapular stabilization, (ii) powerful shoulder flexion, (iii) extension of the elbow and (iv) flexion of the manus and digits. Moreover, although all bathyergids showed a similar set of muscles, Heliophobius lacked the m. tensor fasciae antebrachii (aiding with elbow extension and humeral retraction), and Heliophobius and Georychus lacked the m. articularis humeri (aiding with humeral adduction), indicating deeper morphogenetic differences among digging groups and suggesting a relatively less specialized scratch-digging ability. Nevertheless, Heliophobius and Bathyergus shared some similar adaptations allowing scratch-digging. Our results provide new information about the morphological divergence within this family associated with the specialization to distinct functions and digging behaviors, thus contributing to understand the mosaic of adaptations emerging in phylogenetically and ecologically closer subterranean taxa. This and previous anatomical studies on the Bathyergidae will provide researchers with a substantial basis on the form and function of the musculoskeletal system for future kinematic investigations of digging behavior, as well as to define potential indicators of scratch-digging ability.
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Affiliation(s)
- Germán Montoya-Sanhueza
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Nigel C Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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Hrabina P, Pernerová L, Suchomel J, Robovský J. Utility of cytochrome c oxidase I for the deciphering of unstable phylogeny and taxonomy of gorals, genus Nemorhaedus Hamilton Smith, 1827 (Bovidae, Ovibovina). Zookeys 2023; 1181:81-110. [PMID: 38313159 PMCID: PMC10838175 DOI: 10.3897/zookeys.1181.108019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/04/2023] [Indexed: 02/06/2024] Open
Abstract
Gorals represent ungulate mammals of the Palearctic and Indo-Malayan realms that face habitat destruction and intense hunting pressure. Their classification has been the subject of various (mainly genetic) assessments in the last decade, but some results are conflicting, hampering some conservation-based decisions. Genetic sampling of gorals has increased considerably in recent years, at least for mitochondrial (mt) DNA. Results based on two mt genes (cytochrome b and the D-loop) are currently available. Still, the utility of cytochrome oxidase subunit I remains unanalysed, even though it belongs among the gene markers that enable a correct species identification in mammals. This study examines phylogenetic relationships and species delimitation in gorals using all currently available cytochrome oxidase subunit I sequences, including the not yet analysed goral population from Pakistan. Our results of various phylogenetic approaches, such as maximum parsimony, likelihood and Bayesian inference, and exploration of species boundaries via species delimitation support the validity of six species of goral, namely N.baileyi, N.caudatus, N.cranbrooki, N.evansi, N.goral, and N.griseus. This result accords well with results based on other mt genes, especially the cytochrome b from the highly exhaustive data sampling. Our study also summarises common sources of errors in the assessment of goral phylogeny and taxonomy and highlights future priorities in understanding goral diversification.
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Affiliation(s)
- Petr Hrabina
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Zemědělská 1, Brno, 61300, Czech Republic Mendel University in Brno Brno Czech Republic
| | - Ludmila Pernerová
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic University of South Bohemia České Budějovice Czech Republic
| | - Josef Suchomel
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Zemědělská 1, Brno, 61300, Czech Republic Mendel University in Brno Brno Czech Republic
| | - Jan Robovský
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic University of South Bohemia České Budějovice Czech Republic
- Liberec Zoo, Lidové sady 425/1, Liberec, 46001, Czech Republic Liberec Zoo Liberec 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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Developmental Plasticity in the Ossification of the Proximal Femur of Heterocephalus glaber (Bathyergidae, Rodentia). J MAMM EVOL 2022. [DOI: 10.1007/s10914-022-09602-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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6
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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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Caspar KR, Heinrich A, Mellinghaus L, Gerhardt P, Begall S. Evoked auditory potentials from African mole-rats and coruros reveal disparity in subterranean rodent hearing. J Exp Biol 2021; 224:272630. [PMID: 34704596 DOI: 10.1242/jeb.243371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/22/2021] [Indexed: 12/28/2022]
Abstract
Hearing in subterranean rodents exhibits numerous peculiarities, including low sensitivity and restriction to a narrow range of comparatively low frequencies. Past studies provided two conflicting hypotheses explaining how these derived traits evolved: structural degeneration and adaptive specialization. To further elucidate this issue, we recorded auditory brainstem responses from three species of social subterranean rodents that differ in the degree of specialization to the underground habitat: the naked mole-rat (Heterocephalus glaber) and the Mashona mole-rat (Fukomys darlingi), which represent the ancient lineage of African mole-rats (Bathyergidae), and the coruro (Spalacopus cyanus), a South American rodent (Octodontidae) that adopted a subterranean lifestyle in more recent geological time. Additionally, we measured call amplitudes of social vocalizations to study auditory vocal coupling. We found elevated auditory thresholds and severe hearing range restrictions in the African mole-rats, with hearing in naked mole-rats tending to be more sensitive than in Mashona mole-rats, in which hearing notably deteriorated with increasing age. In contrast, hearing in coruros was similar to that of epigeic rodents, with its range extending into ultrasonic frequencies. However, as in the mole-rats, the coruros' region of best hearing was located at low frequencies close to 1 kHz. We argue that the auditory sensitivity of African mole-rats, although remarkably poor, has been underestimated by recent studies, whereas data on coruros conform to previous results. Considering the available evidence, we propose to be open to both degenerative and adaptive interpretations of hearing physiology in subterranean mammals, as each may provide convincing explanations for specific auditory traits observed.
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Affiliation(s)
- Kai R Caspar
- Department of General Zoology, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - Alexandra Heinrich
- Department of General Zoology, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - Lea Mellinghaus
- Department of General Zoology, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - Patricia Gerhardt
- Institute of Physiology, Faculty of Medicine, University of Duisburg-Essen, 45147 Essen, Germany
| | - Sabine Begall
- Department of General Zoology, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
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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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Onditi KO, Demos TC, Kerbis Peterhans J, Chen ZZ, Bryja J, Lavrenchenko LA, Musila S, Verheyen E, Van de Perre F, Akaibe BD, de la Sancha NU, Jiang XL. Historical biogeography, systematics, and integrative taxonomy of the non-Ethiopian speckled pelage brush-furred rats (Lophuromys flavopunctatus group). BMC Ecol Evol 2021; 21:89. [PMID: 34011264 PMCID: PMC8132446 DOI: 10.1186/s12862-021-01813-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/19/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) have been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity and evolution. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys. RESULTS The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subgenus Lophuromys (L. sikapusi group and L. flavopunctatus group). The L. flavopunctatus group comprised the speckled-pelage brush-furred Lophuromys endemic to Ethiopia (Ethiopian L. flavopunctatus members [ETHFLAVO]) and the non-Ethiopian ones (non-Ethiopian L. flavopunctatus members [NONETHFLAVO]) in deeply nested relationships. There were distinctly geographically structured mtDNA clades among the NONETHFLAVO, which were incongruous with the nuclear tree where several clades were unresolved. The morphometric datasets did not systematically assign samples to meaningful taxonomic units or agree with the mtDNA clades. The divergence dating and ancestral range reconstructions showed the NONETHFLAVO colonized the current ranges over two independent dispersal events out of Ethiopia in the early Pleistocene. CONCLUSION The phylogenetic associations and divergence times of the L. flavopunctatus group support the hypothesis that paleoclimatic impacts and ecosystem refugia during the Pleistocene impacted the evolutionary radiation of these rodents. The overlap in craniodental variation between distinct mtDNA clades among the NONETHFLAVO suggests unraveling underlying ecomorphological drivers is key to reconciling taxonomically informative morphological characters. The genus Lophuromys requires a taxonomic reassessment based on extensive genomic evidence to elucidate the patterns and impacts of genetic isolation at clade contact zones.
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Affiliation(s)
- Kenneth Otieno Onditi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
- Mammal Section, Zoology Department, National Museums of Kenya, Nairobi, Kenya
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Nairobi, Kenya
| | - Terrence C Demos
- Science & Education, Field Museum of Natural History, Chicago, USA
| | - Julian Kerbis Peterhans
- Science & Education, Field Museum of Natural History, Chicago, USA
- College of Arts and Sciences, Roosevelt University, Chicago, USA
| | - Zhong-Zheng Chen
- Collaborative Innovation Centre of Recovery and Reconstruction of Degraded Ecosystems in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Anhui, China
| | - 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
| | - Leonid A Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Science, Moscow, Russia
| | - Simon Musila
- Mammal Section, Zoology Department, National Museums of Kenya, Nairobi, Kenya
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Nairobi, Kenya
| | - Erik Verheyen
- Operational Direction Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, Brussels, Belgium
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Frederik Van de Perre
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Benjamin Dudu Akaibe
- Department of Ecology and Animal Resource Management, Faculty of Science, Biodiversity Monitoring Centre, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Noé U de la Sancha
- Science & Education, Field Museum of Natural History, Chicago, USA
- Department of Biological Sciences, Chicago State University, Chicago, USA
| | - Xue-Long Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
- Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Nairobi, Kenya.
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Evolution Towards Fossoriality and Morphological Convergence in the Skull of Spalacidae and Bathyergidae (Rodentia). J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09550-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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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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Braude S, Holtze S, Begall S, Brenmoehl J, Burda H, Dammann P, Marmol D, Gorshkova E, Henning Y, Hoeflich A, Höhn A, Jung T, Hamo D, Sahm A, Shebzukhov Y, Šumbera R, Miwa S, Vyssokikh MY, Zglinicki T, Averina O, Hildebrandt TB. Surprisingly long survival of premature conclusions about naked mole‐rat biology. Biol Rev Camb Philos Soc 2020; 96:376-393. [DOI: 10.1111/brv.12660] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Stan Braude
- Biology Department Washington University, One Brookings Drive St. Louis MO 63130 U.S.A
| | - Susanne Holtze
- Department of Reproduction Management Leibniz‐Institute for Zoo and Wildlife Research Berlin 10315 Germany
| | - Sabine Begall
- Department of General Zoology, Faculty of Biology University of Duisburg‐Essen, Universitätsstr Essen 45147 Germany
| | - Julia Brenmoehl
- Institute for Genome Biology Leibniz‐Institute for Farm Animal Biology Dummerstorf 18196 Germany
| | - Hynek Burda
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences Czech University of Life Sciences Praha 16500 Czech Republic
| | - Philip Dammann
- Department of General Zoology, Faculty of Biology University of Duisburg‐Essen, Universitätsstr Essen 45147 Germany
- University Hospital Essen Hufelandstr Essen 45141 Germany
| | - Delphine Marmol
- Molecular Physiology Research Unit (URPhyM), NARILIS University of Namur Namur 5000 Belgium
| | - Ekaterina Gorshkova
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova str. 32 Moscow 119991 Russia
- Faculty of Biology Lomonosov Moscow State University Moscow 119991 Russia
| | - Yoshiyuki Henning
- University Hospital Essen Hufelandstr Essen 45141 Germany
- Institute of Physiology Department of General Zoology University of Duisburg Essen Germany
| | - Andreas Hoeflich
- Division Signal Transduction Institute for Genome Biology, Leibniz‐Institute for Farm Animal Biology, FBN Dummerstorf, Wilhelm‐Stahl‐Allee 2 Dummerstorf 18196 Germany
| | - Annika Höhn
- Department of Molecular Toxicology German Institute of Human Nutrition (DIfE) Potsdam‐Rehbrücke Nuthetal 14558 Germany
- German Center for Diabetes Research (DZD) München‐Neuherberg 85764 Germany
| | - Tobias Jung
- Department of Molecular Toxicology German Institute of Human Nutrition (DIfE) Potsdam‐Rehbrücke Nuthetal 14558 Germany
| | - Dania Hamo
- Charité ‐ Universitätsmedizin Berlin Berlin Institute of Health Center for Regenerative Therapies (BCRT) Berlin 13353 Germany
- German Rheumatism Research Centre Berlin (DRFZ) Berlin 10117 Germany
| | - Arne Sahm
- Computational Biology Group Leibniz Institute on Aging – Fritz Lipmann Institute Jena 07745 Germany
| | - Yury Shebzukhov
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilova str. 32 Moscow 119991 Russia
- Charité ‐ Universitätsmedizin Berlin Berlin Institute of Health Center for Regenerative Therapies (BCRT) Berlin 13353 Germany
| | - Radim Šumbera
- Faculty of Science University of South Bohemia České Budějovice 37005 Czech Republic
| | - Satomi Miwa
- Biosciences Institute, Edwardson building, Campus for Ageing and Vitality Newcastle University Newcastle upon Tyne NE4 5PL U.K
| | - Mikhail Y. Vyssokikh
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow 119991 Russia
| | - Thomas Zglinicki
- Biosciences Institute, Edwardson building, Campus for Ageing and Vitality Newcastle University Newcastle upon Tyne NE4 5PL U.K
| | - Olga Averina
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow 119991 Russia
| | - Thomas B. Hildebrandt
- Department of Reproduction Management Leibniz‐Institute for Zoo and Wildlife Research Berlin 10315 Germany
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13
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Zemlemerova ED, Kostin DS, Lebedev VS, Martynov AA, Gromov AR, Alexandrov DY, Lavrenchenko LA. Genetic diversity of the naked mole‐rat (
Heterocephalus glaber). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elena D. Zemlemerova
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Danila S. Kostin
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | | | - Aleksey A. Martynov
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Anton R. Gromov
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Dmitry Yu. Alexandrov
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
| | - Leonid A. Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
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Horáková S, Šumbera R, Sovová J, Robovský J. The penial and bacular morphology of the solitary silvery mole-rat (Heliophobius argenteocinereus, Bathyergidae) from Malawi and evolutionary patterns across the African mole-rat family. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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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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16
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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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17
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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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Šumbera R. Thermal biology of a strictly subterranean mammalian family, the African mole-rats (Bathyergidae, Rodentia) - a review. J Therm Biol 2019; 79:166-189. [DOI: 10.1016/j.jtherbio.2018.11.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 12/12/2022]
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19
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Matur F, Yanchukov A, Çolak F, Sözen M. Two major clades of blind mole rats (Nannospalax sp.) revealed by mtDNA and microsatellite genotyping in Western and Central Turkey. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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