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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] [MESH Headings] [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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Hayward JA, Tian S, Tachedjian G. GALV-KoRV-related retroviruses in diverse Australian and African rodent species. Virus Evol 2024; 10:veae061. [PMID: 39175839 PMCID: PMC11341202 DOI: 10.1093/ve/veae061] [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: 02/27/2024] [Revised: 06/12/2024] [Accepted: 07/26/2024] [Indexed: 08/24/2024] Open
Abstract
The enigmatic origins and transmission events of the gibbon ape leukemia virus (GALV) and its close relative the koala retrovirus (KoRV) have been a source of enduring debate. Bats and rodents are each proposed as major reservoirs of interspecies transmission, with ongoing efforts to identify additional animal hosts of GALV-KoRV-related retroviruses. In this study, we identified nine rodent species as novel hosts of GALV-KoRV-related retroviruses. Included among these hosts are two African rodents, revealing the first appearance of this clade beyond the Australian and Southeast Asian region. One of these African rodents, Mastomys natalensis, carries an endogenous GALV-KoRV-related retrovirus that is fully intact and potentially still infectious. Our findings support the hypothesis that rodents are the major carriers of GALV-KoRV-related retroviruses.
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Affiliation(s)
- Joshua A Hayward
- Life Sciences Discipline, Burnet Institute, 85 Commercial Rd, Melbourne, VIC 3004, Australia
- Department of Microbiology, Monash University, Wellington Rd, Clayton, VIC 3168, Australia
| | - Shuoshuo Tian
- Life Sciences Discipline, Burnet Institute, 85 Commercial Rd, Melbourne, VIC 3004, Australia
| | - Gilda Tachedjian
- Life Sciences Discipline, Burnet Institute, 85 Commercial Rd, Melbourne, VIC 3004, Australia
- Department of Microbiology, Monash University, Wellington Rd, Clayton, VIC 3168, Australia
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, VIC 3000, Australia
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3
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Liao BY, Weng MP, Chang TY, Chang AYF, Ching YH, Wu CH. Degeneration of the Olfactory System in a Murid Rodent that Evolved Diurnalism. Mol Biol Evol 2024; 41:msae037. [PMID: 38376543 PMCID: PMC10906987 DOI: 10.1093/molbev/msae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/03/2024] [Accepted: 02/13/2024] [Indexed: 02/21/2024] Open
Abstract
In mammalian research, it has been debated what can initiate an evolutionary tradeoff between different senses, and the phenomenon of sensory tradeoff in rodents, the most abundant mammalian clade, is not evident. The Nile rat (Arvicanthis niloticus), a murid rodent, recently adapted to a diurnal niche through an evolutionary acquisition of daylight vision with enhanced visual acuity. As such, this model provides an opportunity for a cross-species investigation where comparative morphological and multi-omic analyses of the Nile rat are made with its closely related nocturnal species, e.g. the mouse (Mus musculus) and the rat (Rattus norvegicus). Thus, morphological examinations were performed, and evolutionary reductions in relative sizes of turbinal bone surfaces, the cribriform plate, and the olfactory bulb were discovered in Nile rats. Subsequently, we compared multiple murid genomes, and profiled olfactory epithelium transcriptomes of mice and Nile rats at various ages with RNA sequencing. The results further demonstrate that, in comparison with mouse olfactory receptor (OR) genes, Nile rat OR genes have experienced less frequent gain, more frequent loss, and more frequent expression reduction during their evolution. Furthermore, functional degeneration of coding sequences in the Nile rat lineage was found in OR genes, yet not in other genes. Taken together, these results suggest that acquisition of improved vision in the Nile rat has been accompanied by degeneration of both olfaction-related anatomical structures and OR gene repertoires, consistent with the hypothesis of an olfaction-vision tradeoff initiated by the switch from a nocturnal to a diurnal lifestyle in mammals.
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Affiliation(s)
- Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Meng-Pin Weng
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Ting-Yan Chang
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Andrew Ying-Fei Chang
- Institute of Population Health Sciences, National Health Research Institutes, Taiwan, Republic of China
| | - Yung-Hao Ching
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Taiwan, Republic of China
| | - Chia-Hwa Wu
- Laboratory Animal Center, National Health Research Institutes, Taiwan, Republic of China
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4
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Piwczyński M, Granjon L, Trzeciak P, Carlos Brito J, Oana Popa M, Daba Dinka M, Johnston NP, Boratyński Z. Unraveling phylogenetic relationships and species boundaries in the arid adapted Gerbillus rodents (Muridae: Gerbillinae) by RAD-seq data. Mol Phylogenet Evol 2023; 189:107913. [PMID: 37659480 DOI: 10.1016/j.ympev.2023.107913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023]
Abstract
Gerbillus is one of the most speciose genera among rodents, with ca. 51 recognized species. Previous attempts to reconstruct the evolutionary history of Gerbillus mainly relied on the mitochondrial cyt-b marker as a source of phylogenetic information. In this study, we utilize RAD-seq genomic data from 37 specimens representing 11 species to reconstruct the phylogenetic tree for Gerbillus, applying concatenation and coalescence methods. We identified four highly supported clades corresponding to the traditionally recognized subgenera: Dipodillus, Gerbillus, Hendecapleura and Monodia. Only two uncertain branches were detected in the resulting trees, with one leading to diversification of the main lineages in the genus, recognized by quartet sampling analysis as uncertain due to possible introgression. We also examined species boundaries for four pairs of sister taxa, including potentially new species from Morocco, using SNAPP. The results strongly supported a speciation model in which all taxa are treated as separate species. The dating analyses confirmed the Plio-Pleistocene diversification of the genus, with the uncertain branch coinciding with the beginning of aridification of the Sahara at the the Plio-Pleistocene boundary. This study aligns well with the earlier analyses based on the cyt-b marker, reaffirming its suitability as an adequate marker for estimating genetic diversity in Gerbillus.
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Affiliation(s)
- Marcin Piwczyński
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland.
| | - Laurent Granjon
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Université de Montpellier, Montpellier, France
| | - Paulina Trzeciak
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland
| | - José Carlos Brito
- CIBIO-InBio, Research Center in Biodiversity and Genetic Resources, University of Porto, Campus de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Madalina Oana Popa
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland; "Stejarul" Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Alexandru cel Bun 6, RO-610004, Piatra Neamţ, Romania
| | - Mergi Daba Dinka
- Department of Ecology and Biogeography, Nicolaus Copernicus University in Toruń, Lwowska 1, PL-87-100 Toruń, Poland
| | - Nikolas P Johnston
- School of Life Sciences, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia; Centre for Sustainable Ecosystem Solutions, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Northfields Ave, Wollongong, NSW 2500, Australia
| | - Zbyszek Boratyński
- CIBIO-InBio, Research Center in Biodiversity and Genetic Resources, University of Porto, Campus de Vairão, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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Thomas GWC, Hughes JJ, Kumon T, Berv JS, Nordgren CE, Lampson M, Levine M, Searle JB, Good JM. The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555178. [PMID: 37693498 PMCID: PMC10491188 DOI: 10.1101/2023.08.28.555178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.
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Affiliation(s)
- Gregg W. C. Thomas
- Division of Biological Sciences, University of Montana, Missoula, MT, 59801
- Informatics Group, Harvard University, Cambridge, MA, 02138
| | - Jonathan J. Hughes
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, 92521
| | - Tomohiro Kumon
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Jacob S. Berv
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109
| | - C. Erik Nordgren
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Michael Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Mia Levine
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, MT, 59801
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Xu Y, Hu J, Shi Z, Chen W, Zhou J, Zhang B, Yong F, Khanal L, Jiang X, Chen Z. Integrative systematics and evolutionary history of Berylmys bowersi (Mammalia, Rodentia, Muridae). Ecol Evol 2023; 13:e10234. [PMID: 37408634 PMCID: PMC10318578 DOI: 10.1002/ece3.10234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 07/07/2023] Open
Abstract
The Bower's Berylmys (Berylmys bowersi) is one of the largest rodent species with a wide distribution range in southern China and the Indochinese Peninsula. The taxonomy and evolutionary history of the B. bowersi is still controversial and confusing. In this study, we used two mitochondrial (Cyt b and COI) and three nuclear (GHR, IRBP, and RAG1) genes to estimate the phylogeny, divergence times, and biogeographic history of B. bowersi. We also explored morphological variations among the specimens collected across China. Our phylogenetic analyses indicated that the traditional B. bowersi contains at least two species: B. bowersi and B. latouchei. Berylmys latouchei was considered a junior synonym of B. bowersi distributed in eastern China, which is confirmed to be distinguishable at specific level because of its larger size, relatively larger and whiter hind feet, and several cranial traits. The estimated split of B. bowersi and B. latouchei was at the early Pleistocene (ca. 2.00 Mya), which might be the outcome of the combined effects of climate change in the early Pleistocene and isolation by the Minjiang River. Our results highlight the Wuyi Mountains in northern Fujian, China, as a glacial refugia during the Pleistocene and call for more intensive surveys and systematic revisions of small mammals in eastern China.
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Affiliation(s)
- Yifan Xu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of Education, School of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Jiangxiao Hu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of Education, School of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Zifan Shi
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of Education, School of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
| | - Wenwen Chen
- School of Resources and Environmental EngineeringAnhui UniversityHefeiChina
| | - Jiajun Zhou
- Zhejiang Forest Resources Monitoring CenterHangzhouChina
| | - Baowei Zhang
- School of Life SciencesAnhui UniversityHefeiChina
| | - Fan Yong
- Nanjing Institute of Environmental SciencesMinistry of Ecology and EnvironmentNanjingChina
| | - Laxman Khanal
- Central Department of Zoology, Institute of Science and TechnologyTribhuvan UniversityKathmanduNepal
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Zhongzheng Chen
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co‐founded by Anhui Province and Ministry of Education, School of Ecology and EnvironmentAnhui Normal UniversityWuhuChina
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
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7
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Lin JL, Fang X, Li JX, Chen ZW, Wu WK, Guo XX, Liu NJ, Huang JF, Chen FY, Wang LJ, Xu B, Martin C, Chen XY, Huang JQ. Dirigent gene editing of gossypol enantiomers for toxicity-depleted cotton seeds. NATURE PLANTS 2023; 9:605-615. [PMID: 36928775 DOI: 10.1038/s41477-023-01376-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Axial chirality of biaryls can generate varied bioactivities. Gossypol is a binaphthyl compound made by cotton plants. Of its two axially chiral isomers, (-)-gossypol is the bioactive form in mammals and has antispermatogenic activity, and its accumulation in cotton seeds poses health concerns. Here we identified two extracellular dirigent proteins (DIRs) from Gossypium hirsutum, GhDIR5 and GhDIR6, which impart the hemigossypol oxidative coupling into (-)- and (+)-gossypol, respectively. To reduce cotton seed toxicity, we disrupted GhDIR5 by genome editing, which eliminated (-)-gossypol but had no effects on other phytoalexins, including (+)-gossypol, that provide pest resistance. Reciprocal mutagenesis identified three residues responsible for enantioselectivity. The (-)-gossypol-forming DIRs emerged later than their enantiocomplementary counterparts, from tandem gene duplications that occurred shortly after the cotton genus diverged. Our study offers insight into how plants control enantiomeric ratios and how to selectively modify the chemical spectra of cotton plants and thereby improve crop quality.
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Affiliation(s)
- Jia-Ling Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xin Fang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jian-Xu Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Wen-Kai Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Xiang Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ning-Jing Liu
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Jia-Fa Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fang-Yan Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ling-Jian Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Baofu Xu
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | | | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China.
| | - Jin-Quan Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
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Montgelard C, Muller T, Arnal V, Maree S, Taylor PJ, Sands AF, Robinson TJ, Matthee CA. Diversification and evolutionary history of the African laminated-toothed rats (Rodentia, Otomyini). Mol Phylogenet Evol 2023; 183:107779. [PMID: 37019420 DOI: 10.1016/j.ympev.2023.107779] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/23/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023]
Abstract
The African continent was subjected to periodic climatic shifts during the Pliocene and Pleistocene. These habitat changes greatly affected the evolutionary processes and tempo of diversification in numerous, widely distributed mammals. The Otomyini (Family Muridae) comprises three African rodent genera, Parotomys, Otomys and Myotomys, characterized by unique laminated-shaped molars. Species within this tribe generally prefer open-habitat and show low dispersal capabilities, with previous studies suggesting that their diversification was closely associated with climatic oscillations over the last four million years. Our phylogenetic reconstructions, based on three mitochondrial (mtDNA) genes (Cytb, COI and 12S) and four nuclear introns (EF, SPTBN, MGF and THY), identified eight major genetic clades that are distributed across southern, eastern and western Africa. Our data permit the re-examination of the taxonomic status of the three genera as well as the previously proposed mesic-arid dichotomy of the 10 South African species. Moreover, multiple mtDNA species delimitation methods incorporating 168 specimens estimated the number of Otomyini species to be substantially higher than the ∼30 recognized, suggesting that the current taxonomy will necessitate an integrative approach to delimit extant species diversity within the Otomyini. The data suggests that the origin of the tribe can be dated back to ∼5.7 million years ago (Ma) in southern Africa. The distribution and phylogenetic associations among the eight major otomyine evolutionary lineages can best be explained by several waves of northward colonization from southern Africa, complemented by independent reversed dispersals from eastern back to southern Africa at different time periods. There is strong support for the hypothesis that the radiation, dispersion, and diversification of the otomyine rodents is closely linked to recent Plio-Pleistocene climatic oscillations.
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Prevalence of Pathogenic Leptospira spp. in Non-Volant Small Mammals of Hutan Lipur Sekayu, Terengganu, Malaysia. Pathogens 2022; 11:pathogens11111300. [PMID: 36365051 PMCID: PMC9693538 DOI: 10.3390/pathogens11111300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/03/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Leptospirosis is an important zoonotic disease that is transmitted worldwide through infected small mammals such as rodents. In Malaysia, there is a paucity of information on the animal reservoirs that are responsible for leptospirosis transmission, with only a few studies focusing on leptospirosis risk in recreational areas. Therefore, in this study we characterized the species composition and the prevalence of pathogenic Leptospira spp. in non-volant small mammals of Hutan Lipur Sekayu, Terengganu. We performed ten trapping sessions totaling 3000 trappings between September 2019 and October 2020. Kidney samples from captured individuals were extracted for the PCR detection of pathogenic Leptospira spp. Overall, we captured 45 individuals from 8 species (1.56% successful trapping effort), with 9 individuals testing positive for pathogenic Leptospira, that is, a 20% (n = 9/45) prevalence rate. Rattus tiomanicus (n = 22) was the most dominant captured species and had the highest positive individual with pathogenic Leptospira (44.4%, n = 4/9). Despite the low successful trapping effort in this study, the results show the high diversity of non-volant small mammals in Hutan Lipur Sekayu, and that they could also maintain and transmit pathogenic Leptospira.
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10
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Lövy M, Boratyński Z, Okrouhlík J, Svačinová L, Meheretu Y, Šumbera R. Alternative highland adaptations: organ masses and fur insulation in Afroalpine rodents. J Zool (1987) 2022. [DOI: 10.1111/jzo.13028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- M. Lövy
- Department of Zoology, Faculty of Science University of South Bohemia České Budějovice Czech Republic
| | - Z. Boratyński
- BIOPOLIS, CIBIO/InBio, Research Centre in Biodiversity and Genetic Resources University of Porto Vairão Portugal
| | - J. Okrouhlík
- Department of Zoology, Faculty of Science University of South Bohemia České Budějovice Czech Republic
| | - L. Svačinová
- Department of Zoology, Faculty of Science University of South Bohemia České Budějovice Czech Republic
| | - Y. Meheretu
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
- Department of Biology and Institute of Mountain Research & Development Mekelle University Mekelle Ethiopia
- Department of Wildlife, Fish & Environmental Studies Swedish University of Agricultural Sciences Umeå Sweden
| | - R. Šumbera
- Department of Zoology, Faculty of Science University of South Bohemia České Budějovice Czech Republic
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11
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Roycroft E, Fabre PH, MacDonald AJ, Moritz C, Moussalli A, Rowe KC. New Guinea uplift opens ecological opportunity across a continent. Curr Biol 2022; 32:4215-4224.e3. [PMID: 36057260 DOI: 10.1016/j.cub.2022.08.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 12/14/2022]
Abstract
Sahul unites the world's largest and highest tropical island and the oldest and most arid continent on the backdrop of dynamic environmental conditions. Massive geological uplift in New Guinea is predicted to have acted as a species pump from the late Miocene onward, but the impact of this process on biogeography and diversification remains untested across Sahul as a whole. To address this, we reconstruct the assembly of a recent and diverse radiation of rodents (Murinae: Hydromyini) spanning New Guinea, Australia, and oceanic islands. Using phylogenomic data from 270 specimens, including many recently extinct and highly elusive species, we find that the orogeny and expansion of New Guinea opened ecological opportunity and triggered diversification across a continent. After a single over-water colonization from Asia ca. 8.5 Ma, ancestral Hydromyini were restricted to the tropical rainforest of proto-New Guinea for 3.5 million years. Following a shift in diversification coincident with the orogeny of New Guinea ca. 5 Ma and subsequent colonization of Australia, transitions between geographic regions (n = 24) and biomes (n = 34) become frequent. Recurrent over-water colonization between mainland and islands demonstrate how islands can play a substantial role in the assembly of continental fauna. Our results are consistent with a model of increased ecological opportunity across Sahul following major geological uplift in New Guinea ca. 5 Ma, with sustained diversification facilitated by over-water colonization from the Pleistocene to present. We show how geological processes, biome transitions, and over-water colonization collectively drove the diversification of an expansive continental radiation.
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Affiliation(s)
- Emily Roycroft
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia; Sciences Department, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia; Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia.
| | - Pierre-Henri Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS-IRD-UM), Université de Montpellier, Place E. Bataillon, CC 064, 34095 Montpellier Cedex 5, France; Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Anna J MacDonald
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia; The John Curtin School of Medical Research, The Australian National University, Acton, ACT 2601, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Adnan Moussalli
- Sciences Department, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
| | - Kevin C Rowe
- Sciences Department, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
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12
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Rowsey DM, Duya MRM, Ibañez JC, Jansa SA, Rickart EA, Heaney LR. A new genus and species of shrew-like mouse (Rodentia: Muridae) from a new center of endemism in eastern Mindanao, Philippines. J Mammal 2022; 103:1259-1277. [PMID: 36660555 PMCID: PMC9841421 DOI: 10.1093/jmammal/gyac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/13/2022] [Indexed: 01/17/2023] Open
Abstract
The Philippine archipelago hosts an exceptional diversity of murid rodents that have diversified following several independent colonization events. Here, we report the discovery of a new species of rodent from Mt. Kampalili on eastern Mindanao Island. Molecular and craniodental analyses reveal this species as a member of a Philippine "New Endemic" clade consisting of Tarsomys, Limnomys, and Rattus everetti (tribe Rattini). This new species of "shrew-mouse" is easily distinguished from its relatives in both craniodental and external characteristics including a long, narrow snout; small eyes and ears; short, dark, dense fur dorsally and ventrally; stout body with a tapering, visibly haired tail shorter than head and body length; stout forepaws; bulbous and nearly smooth braincase; narrow, tapering rostrum; short incisive foramina; slender mandible; and narrow, slightly opisthodont incisors. This new genus and species of murid rodent illustrates that murids of the tribe Rattini have exhibited greater species and morphological diversification within the Philippines than previously known and provides evidence that Mt. Kampalili represents a previously unrecognized center of mammalian endemism on Mindanao Island that is deserving of conservation action.
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Affiliation(s)
| | - Mariano Roy M Duya
- Institute of Biology, University of the Philippines–Diliman, Quezon City, Philippines
| | - Jayson C Ibañez
- Philippine Eagle Foundation, Philippine Eagle Center, Malagos, Baguio District Davao City, Philippines
| | - Sharon A Jansa
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Eric A Rickart
- Natural History Museum of Utah, University of Utah, Salt Lake City, Utah, USA
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13
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Kostin DS, Martynov AA, Lebedev VS, Zemlemerova ED, Gromov AR, Lavrenchenko LA. Position of the ammodile and the origin of Gerbillinae (Rodentia): Out of the Horn of Africa? ZOOL SCR 2022. [DOI: 10.1111/zsc.12553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- 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
| | | | - Elena D. Zemlemerova
- 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
| | - Leonid A. Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow Russia
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14
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Komarova VA, Mugue NS, Kostin DS, Lavrenchenko LA. Uncovering the diversity of endemic Ethiopian fauna: complete mitochondrial genomes of four Lophuromys species (Rodentia, Muridae). Mitochondrial DNA B Resour 2022; 7:1001-1004. [PMID: 35756435 PMCID: PMC9225773 DOI: 10.1080/23802359.2022.2079435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Complete mitochondrial genomes of four species of Ethiopian speckled brush-furred rats Lophuromys (L. chrysopus, L. menageshae, L. melanonyx, and L. simensis) were assembled for the first time. We provide data concerning the sequencing, assembly, and annotation of the obtained mitogenomes; compare two widely used circular-genome annotation tools (MITOS and MitoZ), and discuss relevant points concerning relationships within both Ethiopian Lophuromys and the Muridae family.
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Affiliation(s)
- Valeria A. Komarova
- Laboratory of Mammalian Microevolution, A.N. Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - Nikolai S. Mugue
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, Moscow, Russia
| | - Danila S. Kostin
- Laboratory of Mammalian Microevolution, A.N. Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
| | - Leonid A. Lavrenchenko
- Laboratory of Mammalian Microevolution, A.N. Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
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15
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Balmori-de la Puente A, Ventura J, Miñarro M, Somoano A, Hey J, Castresana J. Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola. Sci Rep 2022; 12:4065. [PMID: 35260719 PMCID: PMC8904462 DOI: 10.1038/s41598-022-07877-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/21/2022] [Indexed: 01/18/2023] Open
Abstract
Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus Arvicola, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of A. scherman present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, A. amphibius, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species.
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Affiliation(s)
- Alfonso Balmori-de la Puente
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003, Barcelona, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain.,Àrea de Recerca en Petits Mamífers, Granollers Museum of Natural Sciences, Palaudàries, 102, 08402, Granollers, Barcelona, Spain
| | - Marcos Miñarro
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Ctra AS-267, PK 19, 33300, Villaviciosa, Asturias, Spain
| | - Aitor Somoano
- Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), Ctra AS-267, PK 19, 33300, Villaviciosa, Asturias, Spain
| | - Jody Hey
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37, 08003, Barcelona, Spain.
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16
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Description of the Type Specimen of the Extinct Tenerife Giant Rat (Canariomys bravoi). J MAMM EVOL 2022. [DOI: 10.1007/s10914-021-09594-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Renom P, de-Dios T, Civit S, Llovera L, Sánchez-Gracia A, Lizano E, Rando JC, Marquès-Bonet T, Kergoat GJ, Casanovas-Vilar I, Lalueza-Fox C. Genetic data from the extinct giant rat from Tenerife (Canary Islands) points to a recent divergence from mainland relatives. Biol Lett 2021; 17:20210533. [PMID: 34932923 PMCID: PMC8692034 DOI: 10.1098/rsbl.2021.0533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Evolution of vertebrate endemics in oceanic islands follows a predictable pattern, known as the island rule, according to which gigantism arises in originally small-sized species and dwarfism in large ones. Species of extinct insular giant rodents are known from all over the world. In the Canary Islands, two examples of giant rats, †Canariomys bravoi and †Canariomys tamarani, endemic to Tenerife and Gran Canaria, respectively, disappeared soon after human settlement. The highly derived morphological features of these insular endemic rodents hamper the reconstruction of their evolutionary histories. We have retrieved partial nuclear and mitochondrial data from †C. bravoi and used this information to explore its evolutionary affinities. The resulting dated phylogeny confidently places †C. bravoi within the African grass rat clade (Arvicanthis niloticus). The estimated divergence time, 650 000 years ago (95% higher posterior densities: 373 000–944 000), points toward an island colonization during the Günz–Mindel interglacial stage. †Canariomys bravoi ancestors would have reached the island via passive rafting and then underwent a yearly increase of mean body mass calculated between 0.0015 g and 0.0023 g; this corresponds to fast evolutionary rates (in darwins (d), ranging from 7.09 d to 2.78 d) that are well above those observed for non-insular mammals.
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Affiliation(s)
- Pere Renom
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain.,University of Tartu, Institute of Genomics, Estonian Biocentre, Tartu 51010, Estonia
| | - Sergi Civit
- Departament of Genetics, Microbiology and Statistics-Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona 08028, Spain
| | - Laia Llovera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain
| | - Alejandro Sánchez-Gracia
- Departament of Genetics, Microbiology and Statistics-Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona 08028, Spain
| | - Esther Lizano
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona 08193, Spain
| | - Juan Carlos Rando
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, La Laguna 38206, Tenerife, Spain
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona 08193, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona 08010, Spain.,CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08036, Spain
| | - Gael J Kergoat
- CBGP, INRAE, IRD, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Isaac Casanovas-Vilar
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona 08193, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona 08003, Spain
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18
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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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19
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Pradhan N, Norris RW, Decher J, Peterhans JK, Gray CR, Bauer G, Carleton MD, Kilpatrick CW. Phylogenetic relationships and biogeography of the Hybomys division (Muridae: Murinae: Arvicanthini), rodents endemic to Africa's rainforests. JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.21034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Nelish Pradhan
- Department of Biology, University of Vermont, Burlington, USA; e-mail: ,
| | - Ryan W. Norris
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University at Lima, Lima, USA; e-mail: ,
| | - Jan Decher
- Mammal Section, Zoological Research Museum Alexander Koenig, Bonn, Germany; e-mail:
| | | | | | - George Bauer
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University at Lima, Lima, USA; e-mail: ,
| | - Michael D. Carleton
- Department of Vertebrate Zoology, Mammal Division, National Museum of Natural History, Washington, USA; e-mail:
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20
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Ge D, Feijó A, Wen Z, Abramov AV, Lu L, Cheng J, Pan S, Ye S, Xia L, Jiang X, Vogler AP, Yang Q. Demographic History and Genomic Response to Environmental Changes in a Rapid Radiation of Wild Rats. Mol Biol Evol 2021; 38:1905-1923. [PMID: 33386846 PMCID: PMC8097305 DOI: 10.1093/molbev/msaa334] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha, which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste, and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species.
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Affiliation(s)
- Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia.,Joint Russian-Vietnamese Tropical Research and Technological Centre, Hanoi, Vietnam
| | - Liang Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Shengkai Pan
- CAS Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Sicheng Ye
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
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21
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Nicolas V, Mikula O, Lavrenchenko LA, Šumbera R, Bartáková V, Bryjová A, Meheretu Y, Verheyen E, Missoup AD, Lemmon AR, Moriarty Lemmon E, Bryja J. Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera. Mol Phylogenet Evol 2021; 163:107263. [PMID: 34273505 DOI: 10.1016/j.ympev.2021.107263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 11/25/2022]
Abstract
The tribe Praomyini is a diversified group including 64 species and eight extant rodent genera. They live in a broad spectrum of habitats across whole sub-Saharan Africa. Members of this tribe are often very abundant, they have a key ecological role in ecosystems, they are hosts of many potentially pathogenic microorganisms and comprise numerous agricultural pests. Although this tribe is well supported by both molecular and morphological data, its intergeneric relationships and the species contents of several genera are not yet fully resolved. Recent molecular data suggest that at least three genera in current sense are paraphyletic. However, in these studies the species sampling was sparse and the resolution of relationships among genera was poor, probably due to a fast radiation of the tribe dated to the Miocene and insufficient amount of genetic data. Here we used genomic scale data (395 nuclear loci = 610,965 bp long alignment and mitogenomes = 14,745 bp) and produced the first fully resolved species tree containing most major lineages of the Praomyini tribe (i.e. all but one currently delimited genera and major intrageneric clades). Results of a fossil-based divergence dating analysis suggest that the radiation started during the Messinian stage (ca. 7 Ma) and was likely linked to a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forests, while many others adapted to a broad spectrum of new open lowland and montane habitats that appeared at the beginning of Pliocene. Our analyses clearly confirmed the presence of three polyphyletic genera (Praomys, Myomyscus and Mastomys). We review current knowledge of these three genera and suggest corresponding taxonomic changes. To keep genera monophyletic, we propose taxonomic re-arrangements and delimit four new genera. Furthermore, we discovered a new highly divergent genetic lineage of Praomyini in southwestern Ethiopia, which is described as a new species and genus.
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Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Leonid A Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Veronika Bartáková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Yonas Meheretu
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Department of Biology and Institute of Mountain Research and Development, Mekelle University, Mekelle, Tigray, Ethiopia
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium; Evolutionary Ecology Group, Biology Department, University of Antwerp, 2020 Antwerp, Belgium
| | - Alain Didier Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, Douala, Cameroon
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4295, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37, Brno, Czech Republic.
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22
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Museum genomics reveals the rapid decline and extinction of Australian rodents since European settlement. Proc Natl Acad Sci U S A 2021; 118:2021390118. [PMID: 34183409 DOI: 10.1073/pnas.2021390118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Australia has the highest historically recorded rate of mammalian extinction in the world, with 34 terrestrial species declared extinct since European colonization in 1788. Among Australian mammals, rodents have been the most severely affected by these recent extinctions; however, given a sparse historical record, the scale and timing of their decline remain unresolved. Using museum specimens up to 184 y old, we generate genomic-scale data from across the entire assemblage of Australian hydromyine rodents (i.e., eight extinct species and their 42 living relatives). We reconstruct a phylogenomic tree for these species spanning ∼5.2 million years, revealing a cumulative total of 10 million years (>10%) of unique evolutionary history lost to extinction within the past ∼150 y. We find no evidence for reduced genetic diversity in extinct species just prior to or during decline, indicating that their extinction was extremely rapid. This suggests that populations of extinct Australian rodents were large prior to European colonization, and that genetic diversity does not necessarily protect species from catastrophic extinction. In addition, comparative analyses suggest that body size and biome interact to predict extinction and decline, with larger species more likely to go extinct. Finally, we taxonomically resurrect a species from extinction, Gould's mouse (Pseudomys gouldii Waterhouse, 1839), which survives as an island population in Shark Bay, Western Australia (currently classified as Pseudomys fieldi Waite, 1896). With unprecedented sampling across a radiation of extinct and living species, we unlock a previously inaccessible historical perspective on extinction in Australia. Our results highlight the capacity of collections-based research to inform conservation and management of persisting species.
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23
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Mitogenomics and Evolutionary History of Rodent Whipworms ( Trichuris spp.) Originating from Three Biogeographic Regions. Life (Basel) 2021; 11:life11060540. [PMID: 34207698 PMCID: PMC8228637 DOI: 10.3390/life11060540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/03/2021] [Accepted: 06/06/2021] [Indexed: 11/30/2022] Open
Abstract
Trichuris spp. is a widespread nematode which parasitizes a wide range of mammalian hosts including rodents, the most diverse mammalian order. However, genetic data on rodent whipworms are still scarce, with only one published whole genome (Trichuris muris) despite an increasing demand for whole genome data. We sequenced the whipworm mitogenomes from seven rodent hosts belonging to three biogeographic regions (Palearctic, Afrotropical, and Indomalayan), including three previously described species: Trichuris cossoni, Trichurisarvicolae, and Trichurismastomysi. We assembled and annotated two complete and five almost complete mitogenomes (lacking only the long non-coding region) and performed comparative genomic and phylogenetic analyses. All the mitogenomes are circular, have the same organisation, and consist of 13 protein-coding, 2 rRNA, and 22 tRNA genes. The phylogenetic analysis supports geographical clustering of whipworm species and indicates that T. mastomysi found in Eastern Africa is able to infect multiple closely related rodent hosts. Our results are informative for species delimitation based on mitochondrial markers and could be further used in studies on phylogeny, phylogeography, and population genetics of rodent whipworms
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24
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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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25
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Roycroft E, Achmadi A, Callahan CM, Esselstyn JA, Good JM, Moussalli A, Rowe KC. Molecular Evolution of Ecological Specialisation: Genomic Insights from the Diversification of Murine Rodents. Genome Biol Evol 2021; 13:6275684. [PMID: 33988699 PMCID: PMC8258016 DOI: 10.1093/gbe/evab103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2021] [Indexed: 12/15/2022] Open
Abstract
Adaptive radiations are characterized by the diversification and ecological differentiation of species, and replicated cases of this process provide natural experiments for understanding the repeatability and pace of molecular evolution. During adaptive radiation, genes related to ecological specialization may be subject to recurrent positive directional selection. However, it is not clear to what extent patterns of lineage-specific ecological specialization (including phenotypic convergence) are correlated with shared signatures of molecular evolution. To test this, we sequenced whole exomes from a phylogenetically dispersed sample of 38 murine rodent species, a group characterized by multiple, nested adaptive radiations comprising extensive ecological and phenotypic diversity. We found that genes associated with immunity, reproduction, diet, digestion, and taste have been subject to pervasive positive selection during the diversification of murine rodents. We also found a significant correlation between genome-wide positive selection and dietary specialization, with a higher proportion of positively selected codon sites in derived dietary forms (i.e., carnivores and herbivores) than in ancestral forms (i.e., omnivores). Despite striking convergent evolution of skull morphology and dentition in two distantly related worm-eating specialists, we did not detect more genes with shared signatures of positive or relaxed selection than in a nonconvergent species comparison. Although a small number of the genes we detected can be incidentally linked to craniofacial morphology or diet, protein-coding regions are unlikely to be the primary genetic basis of this complex convergent phenotype. Our results suggest a link between positive selection and derived ecological phenotypes, and highlight specific genes and general functional categories that may have played an integral role in the extensive and rapid diversification of murine rodents.
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Affiliation(s)
- Emily Roycroft
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia.,Sciences Department, Museums Victoria, Melbourne, Victoria, Australia.,Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australian Capital Territory, Australia
| | - Anang Achmadi
- Museum Zoologicum Bogoriense, Research Center for Biology, Cibinong, Jawa Barat, Indonesia
| | - Colin M Callahan
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Jacob A Esselstyn
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, USA.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Los Angeles, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA.,Wildlife Biology Program, University of Montana, Missoula, Montana, USA
| | - Adnan Moussalli
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia.,Sciences Department, Museums Victoria, Melbourne, Victoria, Australia
| | - Kevin C Rowe
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia.,Sciences Department, Museums Victoria, Melbourne, Victoria, Australia
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26
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Komarova VA, Kostin DS, Bryja J, Mikula O, Bryjová A, Čížková D, Šumbera R, Meheretu Y, Lavrenchenko LA. Complex reticulate evolution of speckled brush-furred rats (Lophuromys) in the Ethiopian centre of endemism. Mol Ecol 2021; 30:2349-2365. [PMID: 33738874 DOI: 10.1111/mec.15891] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 01/04/2023]
Abstract
The Ethiopian highlands represent a remarkable biodiversity 'hot spot' with a very high number of endemic species, even among vertebrates. Ethiopian representatives of a species complex of speckled brush-furred rats (Lophuromys flavopunctatus sensu lato) inhabit highland habitats ranging from low-elevation forests to Afroalpine grasslands. These may serve as a suitable model for understanding evolutionary processes leading to high genetic and ecological diversity in montane biodiversity hot spots. Here, we analyse the most comprehensive genetic data set of this group, comprising 315 specimens (all nine putative Ethiopian Lophuromys taxa sampled across most of their distribution ranges) genotyped at one mitochondrial and four nuclear markers, and thousands of SNPs from ddRAD sequencing. We performed phylogenetic analyses, delimited species and mapped their distribution and estimated divergence time between species (under the species-tree framework) and mitochondrial lineages. We found significant incongruence between mitochondrial and nuclear phylogenies, most probably caused by multiple interspecific introgression events. We discuss alternative scenarios of Ethiopian Lophuromys evolution, from retention of ancestral polymorphism to hybridization upon secondary contact of partially reproductively isolated lineages leading to reticulate evolution. Finally, we use the diversity of the speckled brush-furred rats for the description of the main biogeographic patterns in the fauna of the Ethiopian highlands.
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Affiliation(s)
- Valeria A Komarova
- 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
| | - 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
| | - Ondřej Mikula
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Dagmar Čížková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Yonas Meheretu
- Department of Biology and Institute of Mountain Research and Development, Mekelle University, Mekelle, Tigray, Ethiopia
| | - Leonid A Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
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27
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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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28
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Kimura Y, Flynn LJ, Jacobs LL. Tempo and Mode: Evidence on a Protracted Split From a Dense Fossil Record. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.642814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Fossil records generally inform paleobiologists about extinct taxa and rates of evolution measured at the scale of millions of years. Good records that are densely sampled through time can reveal species level details such as longevity in local sections. Yet fossil data normally do not address details of lineage microevolution because the density through time of lineage sampling is insufficient to perceive patterns at a precision finer than 106 years in most cases. This study concerns details of a splitting event in the evolution of murine rodents, an event for which multiple fossil samples dated to a precision of 105 years fortuitously document the tempo and mode of origin of sister species, the stems of two extant tribes of mice. Evolution of early Murinae in the northern part of the biogeographically restricted Indian subcontinent between 11.6 and 10.5 Ma involved cladogenesis of two crown taxa, the extant tribes Murini and Arvicanthini. Large samples of fossil rodent teeth document their divergence from a common morphological pool. Definitive basal Murini and Arvicanthini at 10.5 Ma are similar in size and differ by subtle features of the dentition. Those features occur sporadically in the common pool of older fossil teeth at 11.2, 11.4, and 11.6 Ma as inconsistent polymorphisms. Interpreted as a single lineage in the 11.6–11.2 Ma interval, variability of this abundant murine incorporated the roots of the two crown tribes. The pattern through time suggests morphological stasis for several hundred thousand years prior to splitting. This special case informs us on one example of evolution and shows that the tempo of splitting evolution in some cases may be measured in hundreds of thousands of years, followed by stasis once daughter species have differentiated morphologically.
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29
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Cissé OH, Ma L, Dekker JP, Khil PP, Youn JH, Brenchley JM, Blair R, Pahar B, Chabé M, Van Rompay KKA, Keesler R, Sukura A, Hirsch V, Kutty G, Liu Y, Peng L, Chen J, Song J, Weissenbacher-Lang C, Xu J, Upham NS, Stajich JE, Cuomo CA, Cushion MT, Kovacs JA. Genomic insights into the host specific adaptation of the Pneumocystis genus. Commun Biol 2021; 4:305. [PMID: 33686174 PMCID: PMC7940399 DOI: 10.1038/s42003-021-01799-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/04/2021] [Indexed: 11/21/2022] Open
Abstract
Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans. Cissé, Ma et al. utilize genomic data from Pneumocystis species infecting macaques, rabbit, dogs and rats to investigate the molecular basis of host specificity in Pneumocystis. Their analyses provide insight to the specific adaptations enabling the infection of humans by P. jirovecii.
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Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA.,Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Pavel P Khil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA.,Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Jung-Ho Youn
- Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Robert Blair
- Tulane National Primate Research Center, Tulane University, New Orleans, LA, USA
| | - Bapi Pahar
- Tulane National Primate Research Center, Tulane University, New Orleans, LA, USA
| | - Magali Chabé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Rebekah Keesler
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Antti Sukura
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Vanessa Hirsch
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Geetha Kutty
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yueqin Liu
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Li Peng
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jun Song
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nathan S Upham
- Arizona State University, School of Life Sciences, Tempe, ARI, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology and Institute for Integrative Genome Biology, University of California, Riverside, Riverside-California, Riverside, CA, USA
| | - Christina A Cuomo
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Melanie T Cushion
- Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
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30
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Izquierdo-Rico MJ, Moros-Nicolás C, Pérez-Crespo M, Laguna-Barraza R, Gutiérrez-Adán A, Veyrunes F, Ballesta J, Laudet V, Chevret P, Avilés M. ZP4 Is Present in Murine Zona Pellucida and Is Not Responsible for the Specific Gamete Interaction. Front Cell Dev Biol 2021; 8:626679. [PMID: 33537315 PMCID: PMC7848090 DOI: 10.3389/fcell.2020.626679] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
Mammalian eggs are surrounded by an extracellular matrix called the zona pellucida (ZP). This envelope participates in processes such as acrosome reaction induction, sperm binding, protection of the oviductal embryo, and may be involved in speciation. In eutherian mammals, this coat is formed of three or four glycoproteins (ZP1-ZP4). While Mus musculus has been used as a model to study the ZP for more than 35 years, surprisingly, it is the only eutherian species in which the ZP is formed of three glycoproteins Zp1, Zp2, and Zp3, Zp4 being a pseudogene. Zp4 was lost in the Mus lineage after it diverged from Rattus, although it is not known when precisely this loss occurred. In this work, the status of Zp4 in several murine rodents was tested by phylogenetic, molecular, and proteomic analyses. Additionally, assays of cross in vitro fertilization between three and four ZP rodents were performed to test the effect of the presence of Zp4 in murine ZP and its possible involvement in reproductive isolation. Our results showed that Zp4 pseudogenization is restricted to the subgenus Mus, which diverged around 6 MYA. Heterologous in vitro fertilization assays demonstrate that a ZP formed of four glycoproteins is not a barrier for the spermatozoa of species with a ZP formed of three glycoproteins. This study identifies the existence of several mouse species with four ZPs that can be considered suitable for use as an experimental animal model to understand the structural and functional roles of the four ZP proteins in other species, including human.
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Affiliation(s)
- Mª José Izquierdo-Rico
- Department of Cell Biology and Histology, Faculty of Medicine, University of Murcia, Murcia, Spain
- Institute for Biomedical Research of Murcia (IMIB-Arrixaca), Murcia, Spain
- International Excellence Campus for Higher Education and Research “Campus Mare Nostrum”, Murcia, Spain
| | - Carla Moros-Nicolás
- Department of Cell Biology and Histology, Faculty of Medicine, University of Murcia, Murcia, Spain
- Institute for Biomedical Research of Murcia (IMIB-Arrixaca), Murcia, Spain
- International Excellence Campus for Higher Education and Research “Campus Mare Nostrum”, Murcia, Spain
| | - Míriam Pérez-Crespo
- Department of Animal Reproduction, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Madrid, Spain
| | - Ricardo Laguna-Barraza
- Department of Animal Reproduction, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Madrid, Spain
| | - Alfonso Gutiérrez-Adán
- Department of Animal Reproduction, Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Madrid, Spain
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution, UMR5554 CNRS/Université Montpellier/IRD/EPHE, Montpellier, France
| | - José Ballesta
- Department of Cell Biology and Histology, Faculty of Medicine, University of Murcia, Murcia, Spain
- Institute for Biomedical Research of Murcia (IMIB-Arrixaca), Murcia, Spain
- International Excellence Campus for Higher Education and Research “Campus Mare Nostrum”, Murcia, Spain
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Pascale Chevret
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, CNRS, Université de Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Manuel Avilés
- Department of Cell Biology and Histology, Faculty of Medicine, University of Murcia, Murcia, Spain
- Institute for Biomedical Research of Murcia (IMIB-Arrixaca), Murcia, Spain
- International Excellence Campus for Higher Education and Research “Campus Mare Nostrum”, Murcia, Spain
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31
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Mikula O, Nicolas V, Šumbera R, Konečný A, Denys C, Verheyen E, Bryjová A, Lemmon AR, Moriarty Lemmon E, Bryja J. Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini). Mol Phylogenet Evol 2021; 157:107069. [PMID: 33421615 DOI: 10.1016/j.ympev.2021.107069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 01/09/2023]
Abstract
The tribe Arvicanthini (Muridae: Murinae) is a highly diversified group of rodents (ca. 100 species) and with 18 African genera (plus one Asiatic) represents probably the most successful adaptive radiation of extant mammals in Africa. They colonized a broad spectrum of habitats (from rainforests to semi-deserts) in whole sub-Saharan Africa and their members often belong to most abundant parts of mammal communities. Despite intensive efforts, the phylogenetic relationships among major lineages (i.e. genera) remained obscured, which was likely caused by the intensive radiation of the group, dated to the Late Miocene. Here we used genomic scale data (377 nuclear loci; 581,030 bp) and produced the first fully resolved species tree containing all currently delimited genera of the tribe. Mitogenomes were also extracted, and while the results were largely congruent, there was less resolution at basal nodes of the mitochondrial phylogeny. Results of a fossil-based divergence dating analysis suggest that the African radiation started early after the colonization of Africa by a single arvicanthine ancestor from Asia during the Messinian stage (ca. 7 Ma), and was likely linked with a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forest, while many others successfully colonized broad spectrum of new open habitats (e.g. savannas, wetlands or montane moorlands) that appeared at the beginning of Pliocene. One lineage even evolved partially arboricolous life style in savanna woodlands, which allowed them to re-colonize equatorial forests. We also discuss delimitation of genera in Arvicanthini and propose corresponding taxonomic changes.
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Affiliation(s)
- Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, 602 00 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
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Adam Konečný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium; Evolutionary Ecology Group, Biology Department, University of Antwerp, 2020 Antwerp, Belgium
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4295, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic.
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Nations JA, Mount GG, Morere SM, Achmadi AS, Rowe KC, Esselstyn JA. Locomotory mode transitions alter phenotypic evolution and lineage diversification in an ecologically rich clade of mammals. Evolution 2021; 75:376-393. [PMID: 33370843 DOI: 10.1111/evo.14156] [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: 04/30/2020] [Revised: 12/04/2020] [Accepted: 12/20/2020] [Indexed: 11/30/2022]
Abstract
The relationship between organismal function and form is a cornerstone of biology because functional diversity is key to generating and maintaining ecological diversity. Morphological changes often occur in unison with behavioral or ecological transitions, and this process may foster diversification, but alternately could trap a species on an adaptive peak. We estimated the most comprehensive phylogenetic hypothesis of Murinae, a young (∼15 million years) and diverse (∼700 species) clade of mammals. We then tested for correlated evolution among four morphological traits with potential links to locomotor modes (Arboreal, General, Terrestrial, and Amphibious), then investigated the effects of locomotion on morphological and lineage diversification. We found unique combinations of trait values for each locomotor mode, including strong covariance between the tail and hindfoot lengths of specialized Arboreal and ecologically flexible General species. Low diversification rates and long branch lengths suggest that specialized lineages represent stable evolutionary "cul-de-sacs." General species, characterized by the classic "rat-like" body plan and broad locomotor abilities, have narrow optimal trait values and slow phenotypic evolution, but high lineage diversification rates. Our findings suggest that versatile, generalist forms act as seeds of species diversity and morphological specialization, which together build ecologically diverse radiations.
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Affiliation(s)
- Jonathan A Nations
- Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Genevieve G Mount
- Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Sara M Morere
- Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, Louisiana, 70803
| | - Anang S Achmadi
- Museum Zoologicum Bogoriense, Research Centre for Biology, Cibinong, Jawa Barat, 16911, Indonesia
| | - Kevin C Rowe
- Sciences Department, Museums Victoria, Melbourne, Victoria, 3001, Australia
| | - Jacob A Esselstyn
- Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
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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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Marcy AE, Guillerme T, Sherratt E, Rowe KC, Phillips MJ, Weisbecker V. Australian Rodents Reveal Conserved Cranial Evolutionary Allometry across 10 Million Years of Murid Evolution. Am Nat 2020; 196:755-768. [PMID: 33211559 DOI: 10.1086/711398] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractAmong vertebrates, placental mammals are particularly variable in the covariance between cranial shape and body size (allometry), with rodents being a major exception. Australian murid rodents allow an assessment of the cause of this anomaly because they radiated on an ecologically diverse continent notably lacking other terrestrial placentals. Here, we use 3D geometric morphometrics to quantify species-level and evolutionary allometries in 38 species (317 crania) from all Australian murid genera. We ask whether ecological opportunity resulted in greater allometric diversity compared with other rodents or whether conserved allometry suggests intrinsic constraints and/or stabilizing selection. We also assess whether cranial shape variation follows the proposed rule of craniofacial evolutionary allometry (CREA), whereby larger species have relatively longer snouts and smaller braincases. To ensure we could differentiate parallel versus nonparallel species-level allometric slopes, we compared the slopes of rarefied samples across all clades. We found exceedingly conserved allometry and CREA-like patterns across the 10-million-year split between Mus and Australian murids. This could support both intrinsic-constraint and stabilizing-selection hypotheses for conserved allometry. Large-bodied frugivores evolved faster than other species along the allometric trajectory, which could suggest stabilizing selection on the shape of the masticatory apparatus as body size changes.
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Mizerovská D, Mikula O, Meheretu Y, Bartáková V, Bryjová A, Kostin DS, Šumbera R, Lavrenchenko LA, Bryja J. Integrative taxonomic revision of the Ethiopian endemic rodent genus Stenocephalemys (Muridae: Murinae: Praomyini) with the description of two new species. JOURNAL OF VERTEBRATE BIOLOGY 2020. [DOI: 10.25225/jvb.20031] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Daniela Mizerovská
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; e-mail: , , , ,
| | - Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; e-mail: , , , ,
| | - Yonas Meheretu
- Department of Biology and Institute of Mountain Research and Development, Mekelle University, Mekelle, Ethiopia; e-mail:
| | - Veronika Bartáková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; e-mail: , , , ,
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; e-mail: , , , ,
| | - Danila S. Kostin
- A. N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia; 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: ,
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; e-mail: , , , ,
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Molecular characterization of Acomys louisae from Somaliland: a deep divergence and contrasting genetic patterns in a rift zone. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00045-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Nicolas V, Gerbault-Seureau M, Delapre A, Bed'Hom B. Small mammal inventory in the Lama forest reserve (south Benin), with new cytogenetical data. JOURNAL OF VERTEBRATE BIOLOGY 2020. [DOI: 10.25225/jvb.20009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 57 rue Cuvier, 75005 Paris, France; e-mail: , michele.gerbault-seur
| | - Michèle Gerbault-Seureau
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 57 rue Cuvier, 75005 Paris, France; e-mail: , michele.gerbault-seur
| | - Arnaud Delapre
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 57 rue Cuvier, 75005 Paris, France; e-mail: , michele.gerbault-seur
| | - Bertrand Bed'Hom
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 57 rue Cuvier, 75005 Paris, France; e-mail: , michele.gerbault-seur
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Martin Cerezo ML, Kucka M, Zub K, Chan YF, Bryk J. Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq. BMC Genomics 2020; 21:241. [PMID: 32183700 PMCID: PMC7079423 DOI: 10.1186/s12864-020-6603-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 02/21/2020] [Indexed: 02/08/2023] Open
Abstract
Background Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context. Results Here we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise FST<0.086. Conclusion Our study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.
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Affiliation(s)
- Maria Luisa Martin Cerezo
- School of Applied Sciences, University of Huddersfield, Quennsgate, Huddersfield, UK.,AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Department of Zoology, Linköping University, Linköping, Sweden
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Karol Zub
- The Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | | | - Jarosław Bryk
- School of Applied Sciences, University of Huddersfield, Quennsgate, Huddersfield, UK.
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Dianat M, Darvish J, Aliabadian M, Siahsarvie R, Krystufek B, Nicolas V. Systematics and evolution of the libyan jird based on molecular and morphometric data. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Malahat Dianat
- Department of Biology, Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
| | - Jamshid Darvish
- Department of Biology, Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
| | - Mansour Aliabadian
- Department of Biology, Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
| | - Roohollah Siahsarvie
- Department of Biology, Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
- Rodentology Research Department, Institute of Applied Zoology, Faculty of Sciences Ferdowsi University of Mashhad Mashhad Iran
| | | | - Violaine Nicolas
- Institut de Systematique, Evolution, Biodiversite, ISYEB‐UMR 7205‐CNRS, MNHN, UPMC EPHE, Museum National d’Histoire Naturelle, Sorbonne Universites Paris France
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40
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Magalhaes ILF, Azevedo GHF, Michalik P, Ramírez MJ. The fossil record of spiders revisited: implications for calibrating trees and evidence for a major faunal turnover since the Mesozoic. Biol Rev Camb Philos Soc 2020; 95:184-217. [PMID: 31713947 DOI: 10.1111/brv.12559] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 01/24/2023]
Abstract
Studies in evolutionary biology and biogeography increasingly rely on the estimation of dated phylogenetic trees using molecular clocks. In turn, the calibration of such clocks is critically dependent on external evidence (i.e. fossils) anchoring the ages of particular nodes to known absolute ages. In recent years, a plethora of new fossil spiders, especially from the Mesozoic, have been described, while the number of studies presenting dated spider phylogenies based on fossil calibrations increased sharply. We critically evaluate 44 of these studies, which collectively employed 67 unique fossils in 180 calibrations. Approximately 54% of these calibrations are problematic, particularly regarding unsupported assignment of fossils to extant clades (44%) and crown (rather than stem) dating (9%). Most of these cases result from an assumed equivalence between taxonomic placement of fossils and their phylogenetic position. To overcome this limitation, we extensively review the literature on fossil spiders, with a special focus on putative synapomorphies and the phylogenetic placement of fossil species with regard to their importance for calibrating higher taxa (families and above) in the spider tree of life. We provide a curated list including 41 key fossils intended to be a basis for future estimations of dated spider phylogenies. In a second step, we use a revised set of 23 calibrations to estimate a new dated spider tree of life based on transcriptomic data. The revised placement of key fossils and the new calibrated tree are used to resolve a long-standing debate in spider evolution - we tested whether there has been a major turnover in the spider fauna between the Mesozoic and Cenozoic. At least 17 (out of 117) extant families have been recorded from the Cretaceous, implying that at least 41 spider lineages in the family level or above crossed the Cretaeous-Paleogene (K-Pg) boundary. The putative phylogenetic affinities of families known only from the Mesozoic suggest that at least seven Cretaceous families appear to have no close living relatives and might represent extinct lineages. There is no unambiguous fossil evidence of the retrolateral tibial apophysis clade (RTA-clade) in the Mesozoic, although molecular clock analyses estimated the major lineages within this clade to be at least ∼100 million years old. Our review of the fossil record supports a major turnover showing that the spider faunas in the Mesozoic and the Cenozoic are very distinct at high taxonomic levels, with the Mesozoic dominated by Palpimanoidea and Synspermiata, while the Cenozoic is dominated by Araneoidea and RTA-clade spiders.
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Affiliation(s)
- Ivan L F Magalhaes
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
| | - Guilherme H F Azevedo
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
| | - Peter Michalik
- Zoologisches Institut und Museum, Universität Greifswald, Loitzer Straβe 26, Greifswald, D-17489, Germany
| | - Martín J Ramírez
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
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Mikula O, Nicolas V, Boratyński Z, Denys C, Dobigny G, Fichet-Calvet E, Gagaré S, Hutterer R, Nimo-Paintsil SC, Olayemi A, Bryja J. Commensalism outweighs phylogeographical structure in its effect on phenotype of a Sudanian savanna rodent. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blz184] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The murid rodent Praomys daltoni is widespread in Sudanian savanna and woodlands of West Africa, and previous study of mitochondrial DNA variability suggested that it encompasses the phenotypically (small, grey-bellied) and ecologically (commensal) distinct form, Praomys derooi. Here, we comprehensively examined the genetic and morphological diversity within the complex. Six mitochondrial lineages showed a fine-scale phylogeographical pattern, whereas delimitation based on nuclear loci pooled four of them into a single widespread unit. A newly discovered lineage from southern Mauritania stands apart from the rest of the complex and might represent an unrecognized species. At the same time, the internal position of P. derooi (C2 mitochondrial lineage) was confirmed by the multilocus analysis. The magnitude of genetic distances between major phylogeographical lineages was typical for interspecific divergence in other clades of Praomys, despite the little differences among them in morphology (skull and upper molar row shapes). The most pronounced morphological shift was associated with a transition to commensalism, especially in P. derooi, but also in other lineages. This makes the whole complex a suitable model for the study of phenotypic novelty, the evolution of commensalism and conditions for ecological speciation.
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Affiliation(s)
- Ondřej Mikula
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Violaine Nicolas
- Muséum National d’Histoire Naturelle, Institute of Systematics and Evolution of the Biodiversity, UMR7205 CNRS-MNHN-UPMC-EPHE-Sorbonne University, Paris, France
| | - Zbyszek Boratyński
- CIBIO-InBIO Associate Laboratory, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Christiane Denys
- Muséum National d’Histoire Naturelle, Institute of Systematics and Evolution of the Biodiversity, UMR7205 CNRS-MNHN-UPMC-EPHE-Sorbonne University, Paris, France
| | - Gauthier Dobigny
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
- Ecole Polytechnique d’Abomey-Calavi, Abomey-Calavi University, Cotonou, Benin
| | | | - Sama Gagaré
- Centre Régional Agrhymet, Département Formation Recherche, Niamey, Niger
| | - Rainer Hutterer
- Zoologisches Forschungsinstitut und Museum Alexander Koenig, Bonn, Germany
| | | | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
| | - Josef Bryja
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
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Nicolas V, Fabre PH, Bryja J, Denys C, Verheyen E, Missoup AD, Olayemi A, Katuala P, Dudu A, Colyn M, Kerbis Peterhans J, Demos T. The phylogeny of the African wood mice (Muridae, Hylomyscus) based on complete mitochondrial genomes and five nuclear genes reveals their evolutionary history and undescribed diversity. Mol Phylogenet Evol 2019; 144:106703. [PMID: 31816395 DOI: 10.1016/j.ympev.2019.106703] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/22/2019] [Accepted: 12/05/2019] [Indexed: 11/26/2022]
Abstract
Wood mice of the genus Hylomyscus, are small-sized rodents widely distributed in lowland and montane rainforests in tropical Africa, where they can be locally abundant. Recent morphological and molecular studies have increased the number of recognized species from 8 to 18 during the last 15 years. We used complete mitochondrial genomes and five nuclear genes to infer the number of candidate species within this genus and depict its evolutionary history. In terms of gene sampling and geographical and taxonomic coverage, this is the most comprehensive review of the genus Hylomyscus to date. The six species groups (aeta, alleni, anselli, baeri, denniae and parvus) defined on morphological grounds are monophyletic. Species delimitation analyses highlight undescribed diversity within this genus: perhaps up to 10 taxa need description or elevation from synonymy, pending review of type specimens. Our divergence dating and biogeographical analyses show that diversification of the genus occurred after the end of the Miocene and is closely linked to the history of the African forest. The formation of the Rift Valley combined with the declining global temperatures during the Late Miocene caused the fragmentation of the forests and explains the first split between the denniae group and remaining lineages. Subsequently, periods of increased climatic instability during Plio-Pleistocene probably resulted in elevated diversification in both lowland and montane forest taxa.
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Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France.
| | - Pierre-Henri Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS-IRD-UM), Université de Montpellier, Place E. Bataillon CC 064 - 34095, Montpellier Cedex 5, France
| | - 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
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium
| | - Alain Didier Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, Douala, Cameroon
| | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile Ife, Nigeria
| | - Pionus Katuala
- Animal Ecology and Resource Management, Laboratory (LEGERA), University of Kisangani, B.P. 2012, Kisangani, Congo
| | - Akaibe Dudu
- Animal Ecology and Resource Management, Laboratory (LEGERA), University of Kisangani, B.P. 2012, Kisangani, Congo
| | - Marc Colyn
- Université de Rennes 1, CNRS, UMR 6553 Ecobio, Station Biologique, 35380 Paimpont, France
| | - Julian Kerbis Peterhans
- Science & Education, Field Museum of Natural History, 60605 Chicago, IL, USA; College of Arts & Sciences, Roosevelt University, 430 S Michigan, Chicago, IL 60605, USA
| | - Terrence Demos
- College of Arts & Sciences, Roosevelt University, 430 S Michigan, Chicago, IL 60605, USA
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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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Nations JA, Heaney LR, Demos TC, Achmadi AS, Rowe KC, Esselstyn JA. A simple skeletal measurement effectively predicts climbing behaviour in a diverse clade of small mammals. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractArboreal locomotion allows access to above-ground resources and might have fostered the diversification of mammals. Nevertheless, simple morphological measurements that consistently correlate with arboreality remain indefinable. As such, the climbing habits of many species of mammals, living and extinct, remain speculative. We collected quantitative data on the climbing tendencies of 20 species of murine rodents, an ecologically and morphologically diverse clade. We leveraged Bayesian phylogenetic mixed models (BPMMs), incorporating intraspecific variation and phylogenetic uncertainty, to determine which, if any, traits (17 skeletal indices) predict climbing frequency. We used ordinal BPMMs to test the ability of the indices to place 48 murine species that lack quantitative climbing data into three qualitative locomotor categories (terrestrial, general and arboreal). Only two indices (both measures of relative digit length) accurately predict locomotor styles, with manus digit length showing the best fit. Manus digit length has low phylogenetic signal, is largely explained by locomotor ecology and might effectively predict locomotion across a multitude of small mammals, including extinct species. Surprisingly, relative tail length, a common proxy for locomotion, was a poor predictor of climbing. In general, detailed, quantitative natural history data, such as those presented here, are needed to enhance our understanding of the evolutionary and ecological success of clades.
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Affiliation(s)
- Jonathan A Nations
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | | | | | - Anang S Achmadi
- Museum Zoologicum Bogoriense, Research Centre for Biology, Cibinong, Jawa Barat, Indonesia
| | - Kevin C Rowe
- Sciences Department, Museum Victoria, Melbourne, VIC, Australia
| | - Jacob A Esselstyn
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
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Zhang B, Jiang X. The complete mitochondrial genome of marmoset rats Hapalomys delacouri (Rodentia: Muridae). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2525-2526. [PMID: 33365611 PMCID: PMC7687551 DOI: 10.1080/23802359.2019.1627938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The marmoset rats (Hapalomys delacouri) is a rarely investigated rodent. It occupies important ecological niche and phylogenetic position. The complete mitochondrial genome of H. delacouri was determined for the first time by long PCR and second-generation sequencing. The results showed that the entire mitogenome of H. delacouri was 16,316 bp long (deposited in GenBank with accession number MK850463). The gene order and orientation were the same as the most rodent. Only tRNALys (TTT) and tRNASer (AGN) of 22 transfer RNAs showed atypical cloverleaf structures, lacking a dihydrouridine (DHU) arm. The newly added H. delacouri mitogenome will benefit population genetic and phylogenetic studies in the rodent.
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Affiliation(s)
- Bin Zhang
- Department of Anatomy and Neurobiology, Biology Postdoctoral Workstation, School of Basic Medical Sciences, Central South University, Changsha, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
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Bryja J, Colangelo P, Lavrenchenko LA, Meheretu Y, Šumbera R, Bryjová A, Verheyen E, Leirs H, Castiglia R. Diversity and evolution of African Grass Rats (Muridae:
Arvicanthis
)—From radiation in East Africa to repeated colonization of northwestern and southeastern savannas. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12290] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- 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
| | - Paolo Colangelo
- National Research Council Institute of Agro‐environmental and Forest Biology (CNR‐IBAF) Rome Italy
| | - Leonid A. Lavrenchenko
- A.N.Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences Moscow Russia
| | - Yonas Meheretu
- Department of Biology, Institute of Mountain Research and Development Mekelle University Mekelle Ethiopia
| | - Radim Šumbera
- Department of Zoology, Faculty of Science University of South Bohemia České Budějovice Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
| | - Erik Verheyen
- Operational Direction Taxonomy and Phylogeny Royal Belgian Institute for Natural Sciences Brussels Belgium
- Evolutionary Ecology Group, Biology Department University of Antwerp Antwerp Belgium
| | - Herwig Leirs
- Evolutionary Ecology Group, Biology Department University of Antwerp Antwerp Belgium
| | - Riccardo Castiglia
- Department of Biology and Biotechnology “Charles Darwin” Sapienza University of Rome Rome Italy
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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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