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Chen JT, Zhan JB, Zhu MC, Li KJ, Liu MQ, Hu B, Cai K, Xiong HR, Chen SL, Tan WL, Chen LJ, Hou W. Diversity and genetic characterization of orthohantavirus from small mammals and humans during 2012-2022 in Hubei Province, Central China. Acta Trop 2024; 249:107046. [PMID: 37866727 DOI: 10.1016/j.actatropica.2023.107046] [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: 07/15/2023] [Revised: 10/03/2023] [Accepted: 10/19/2023] [Indexed: 10/24/2023]
Abstract
Hemorrhagic fever with renal syndrome (HFRS) is a significant public health problem in Hubei Province, China, where a novel strain of orthohantavirus, HV004, was reported in 2012. However, no systematic study has investigated the prevalence and variation of orthohantavirus in rodents and humans. Herein, 2137 small mammals were collected from ten HFRS epidemic areas in Hubei Province from 2012 to 2022, and 143 serum samples from patients with suspected hemorrhagic fever were collected from two hospitals from 2017 to 2021. Orthohantavirus RNA was recovered from 134 lung tissue samples from five rodent species, with a 6.27 % prevalence, and orthohantavirus was detected in serum samples from 25 patients. Genetic analyses revealed that orthohantavirus hantanense (HTNV), orthohantavirus seoulense (SEOV), and orthohantavirus dabieshanense (DBSV) are co-circulating in rodents in Hubei, and HTNV and SEOV were identified in patient serum. Phylogenetic analysis showed that most of the HTNV sequences were clustered with HV004, indicating that HV004-like orthohantavirus was the main HNTV subtype in rodents. Two genetic reassortments and six recombination events were observed in Hubei orthohantaviruses. In summary, this study identified the diversity of orthohantaviruses circulating in Hubei over the past decade, with the HV004-like subtype being the main genotype in rodents and patients. These findings highlight the need for continued attention and focus on orthohantaviruses, especially concerning newly identified strains.
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Affiliation(s)
- Jin-Tao Chen
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Jian-Bo Zhan
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control & Prevention, 6 Zhuodaoquan Road, Wuhan, Hubei 430079, China
| | - Ming-Chao Zhu
- Department of Clinical Laboratory, The First People's Hospital of Tianmen, 1 Jingling Renming Road, Tianmen, Hubei 431700, China
| | - Kai-Ji Li
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Man-Qing Liu
- Division of Virology, Wuhan Center for Disease Control & Prevention, 288 Machang Road, Wuhan, Hubei 430015, China
| | - Bin Hu
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control & Prevention, 6 Zhuodaoquan Road, Wuhan, Hubei 430079, China
| | - Kun Cai
- Institute of Health Inspection and Testing, Hubei Provincial Center for Disease Control & Prevention, 6 Zhuodaoquan Road, Wuhan, Hubei 430079, China
| | - Hai-Rong Xiong
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Shu-Liang Chen
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China
| | - Wei-Long Tan
- Department of Infection Disease, Nanjing Bioengineering (Gene) Technology Center for Medicines, 293 Zhongshan East Road, Nanjing, Jiangsu 210002, China
| | - Liang-Jun Chen
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China.
| | - Wei Hou
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Provincial Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China; School of Public Health, Wuhan University, 185 Donghu Road, Wuhan, Hubei 430071, China; School of Ecology and Environment, Tibet University, 36 Jiangsu Road, Lhasa 850000, China.
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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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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: 0] [Impact Index Per Article: 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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Côrte-Real JV, Baldauf HM, Melo-Ferreira J, Abrantes J, Esteves PJ. Evolution of Guanylate Binding Protein ( GBP) Genes in Muroid Rodents (Muridae and Cricetidae) Reveals an Outstanding Pattern of Gain and Loss. Front Immunol 2022; 13:752186. [PMID: 35222365 PMCID: PMC8863968 DOI: 10.3389/fimmu.2022.752186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/20/2022] [Indexed: 01/05/2023] Open
Abstract
Guanylate binding proteins (GBPs) are paramount in the host immunity by providing defense against invading pathogens. Multigene families related to the immune system usually show that the duplicated genes can either undergo deletion, gain new functions, or become non-functional. Here, we show that in muroids, the Gbp genes followed an unusual pattern of gain and loss of genes. Muroids present a high diversity and plasticity regarding Gbp synteny, with most species presenting two Gbp gene clusters. The phylogenetic analyses revealed seven different Gbps groups. Three of them clustered with GBP2, GBP5 and GBP6 of primates. Four new Gbp genes that appear to be exclusive to muroids were identified as Gbpa, b, c and d. A duplication event occurred in the Gbpa group in the common ancestor of Muridae and Cricetidae (~20 Mya), but both copies were deleted from the genome of Mus musculus, M. caroli and Cricetulus griseus. The Gbpb gene emerged in the ancestor of Muridae and Cricetidae and evolved independently originating Gbpb1 in Muridae, Gbpb2 and Gbpb3 in Cricetidae. Since Gbpc appears only in three species, we hypothesize that it was present in the common ancestor and deleted from most muroid genomes. The second Gbp gene cluster, Gbp6, is widespread across all muroids, indicating that this cluster emerged before the Muridae and Cricetidae radiation. An expansion of Gbp6 occurred in M. musculus and M. caroli probably to compensate the loss of Gbpa and b. Gbpd is divided in three groups and is present in most muroids suggesting that a duplication event occurred in the common ancestor of Muridae and Cricetidae. However, in Grammomys surdaster and Mus caroli, Gbpd2 is absent, and in Arvicanthis niloticus, Gbpd1 appears to have been deleted. Our results further demonstrated that primate GBP1, GBP3 and GBP7 are absent from the genome of muroids and showed that the Gbp gene annotations in muroids were incorrect. We propose a new classification based on the phylogenetic analyses and the divergence between the groups. Extrapolations to humans based on functional studies of muroid Gbps should be re-evaluated. The evolutionary analyses of muroid Gbp genes provided new insights about the evolution and function of these genes.
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Affiliation(s)
- João Vasco Côrte-Real
- Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Vairão, Portugal.,Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU) München, Munich, Germany.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Research Center in Biodiversity and Genetic Resources (CIBIO), Vairão, Portugal
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU) München, Munich, Germany
| | - José Melo-Ferreira
- Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Research Center in Biodiversity and Genetic Resources (CIBIO), Vairão, Portugal
| | - Joana Abrantes
- Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Research Center in Biodiversity and Genetic Resources (CIBIO), Vairão, Portugal
| | - Pedro José Esteves
- Research Center in Biodiversity and Genetic Resources (CIBIO-InBIO), University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Research Center in Biodiversity and Genetic Resources (CIBIO), Vairão, Portugal.,Center of Investigation in Health Technologies (CITS), CESPU, Gandra, Portugal
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5
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Terray L, Denys C, Goodman SM, Soarimalala V, Lalis A, Cornette R. Skull morphological evolution in Malagasy endemic Nesomyinae rodents. PLoS One 2022; 17:e0263045. [PMID: 35120158 PMCID: PMC8815910 DOI: 10.1371/journal.pone.0263045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/11/2022] [Indexed: 11/22/2022] Open
Abstract
Madagascar is a large island to the south-east of Africa and in many ways continental in size and ecological complexity. Here we aim to define how skull morphology of an endemic and monophyletic clade of rodents (sub-family Nesomyinae), that show considerable morphological variation, have evolved and how their disparity is characterized in context of the geographical and ecological complexity of the island. We performed a two-dimensional geometric morphometric analysis on 370 dorsal and 399 ventral skull images of 19 species (comprising all nine extant endemic genera) and tested the influence of three ecological parameters (climate, locomotor habitat and nychthemeral cycle) in a phylogenetic context on size and shape. The results indicate that skull shape appears to importantly reflect phylogeny, whereas skull size does not carry a significant phylogenetic signal. Skull shape is significantly influenced by climate while, skull size is not impacted by any of the ecological factors tested, which is controversial to expectations in an insular context. In conclusion, Nesomyinae must have evolved under unusual types of local constraints, preventing this radiation from demonstrating strong ecological release.
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Affiliation(s)
- Léa Terray
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, CP 51, Paris, France
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, CP 51, Paris, France
- * E-mail:
| | - Steven M. Goodman
- Field Museum of Natural History, Chicago, IL, United States of America
- Association Vahatra, Antananarivo, Madagascar
| | - Voahangy Soarimalala
- Association Vahatra, Antananarivo, Madagascar
- Institut des Sciences et Techniques de l’Environnement, University of Fianarantsoa, Fianarantsoa, Madagascar
| | - Aude Lalis
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, CP 51, Paris, France
| | - Raphaël Cornette
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, CP 51, Paris, France
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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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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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He D, Hu J, Yang R, Zeng B, Yang D, Li D, Zhang M, Yang M, Ni Q, Ning R, Fan X, Li X, Mao X, Li Y. Evolutionary analysis of chemokine CXCL16 and its receptor CXCR6 in murine rodents. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 109:103718. [PMID: 32360411 DOI: 10.1016/j.dci.2020.103718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
The chemokine CXCL16 and its receptor CXCR6 are implicated in various physiological and pathological processes in cooperative and/or stand-alone fashions. Despite the significance of rodent animal models in elucidating the function and clinical relevance of the chemokine and its receptor, the evolutionary characterization of these molecules remains deficient for this taxon to a certain extent. In this study, we implemented a comparison of synonymous and nonsynonymous variation rates in combination with the maximum likelihood (ML) analysis and Tajima's test to evaluate the interspecific and intraspecific evolutions of CXCL16 and CXCR6 in murine rodents. Our results indicate that adaptive selection has frequently contributed to genetic diversity of both CXCL16 and CXCR6 in the murine lineage that is asynchronous with a relative dependence between these genes. This signature is radically different from the lineage-specific and concordant adaptive diversity of the primate homologues of these genes, which was reported in a previous study. The diversity identified in the present study shed further light on molecular strategies against the challenges towards CXCL16 and CXCR6.
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Affiliation(s)
- Dan He
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Jia Hu
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Rongrong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Bo Zeng
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Diyan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Mingyao Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Qingyong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Ruihong Ning
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Xiaolan Fan
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Xiaoyan Li
- Beijing Anzhen Hospital, Capital Medical University, Beijing, People's Republic of China; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Capital Medical University, Ministry of Education, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, People's Republic of China
| | - Xueping Mao
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China
| | - Yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Wenjiang, People's Republic of China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, People's Republic of China.
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9
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Roycroft EJ, Moussalli A, Rowe KC. Phylogenomics Uncovers Confidence and Conflict in the Rapid Radiation of Australo-Papuan Rodents. Syst Biol 2019; 69:431-444. [DOI: 10.1093/sysbio/syz044] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 06/12/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
The estimation of robust and accurate measures of branch support has proven challenging in the era of phylogenomics. In data sets of potentially millions of sites, bootstrap support for bifurcating relationships around very short internal branches can be inappropriately inflated. Such overestimation of branch support may be particularly problematic in rapid radiations, where phylogenetic signal is low and incomplete lineage sorting severe. Here, we explore this issue by comparing various branch support estimates under both concatenated and coalescent frameworks, in the recent radiation Australo-Papuan murine rodents (Muridae: Hydromyini). Using nucleotide sequence data from 1245 independent loci and several phylogenomic inference methods, we unequivocally resolve the majority of genus-level relationships within Hydromyini. However, at four nodes we recover inconsistency in branch support estimates both within and among concatenated and coalescent approaches. In most cases, concatenated likelihood approaches using standard fast bootstrap algorithms did not detect any uncertainty at these four nodes, regardless of partitioning strategy. However, we found this could be overcome with two-stage resampling, that is, across genes and sites within genes (using -bsam GENESITE in IQ-TREE). In addition, low confidence at recalcitrant nodes was recovered using UFBoot2, a recent revision to the bootstrap protocol in IQ-TREE, but this depended on partitioning strategy. Summary coalescent approaches also failed to detect uncertainty under some circumstances. For each of four recalcitrant nodes, an equivalent (or close to equivalent) number of genes were in strong support ($>$ 75% bootstrap) of both the primary and at least one alternative topological hypothesis, suggesting notable phylogenetic conflict among loci not detected using some standard branch support metrics. Recent debate has focused on the appropriateness of concatenated versus multigenealogical approaches to resolving species relationships, but less so on accurately estimating uncertainty in large data sets. Our results demonstrate the importance of employing multiple approaches when assessing confidence and highlight the need for greater attention to the development of robust measures of uncertainty in the era of phylogenomics.
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Affiliation(s)
- Emily J Roycroft
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Department of Science, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
| | - Adnan Moussalli
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Department of Science, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
| | - Kevin C Rowe
- School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
- Department of Science, Museums Victoria, GPO Box 666, Melbourne, VIC 3001, Australia
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10
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Cramb J, Price GJ, Hocknull SA. Short-tailed mice with a long fossil record: the genus Leggadina (Rodentia: Muridae) from the Quaternary of Queensland, Australia. PeerJ 2018; 6:e5639. [PMID: 30258727 PMCID: PMC6152458 DOI: 10.7717/peerj.5639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/27/2018] [Indexed: 11/25/2022] Open
Abstract
The genus Leggadina (colloquially known as ‘short-tailed mice’) is a common component of Quaternary faunas of northeastern Australia. They represent a member of the Australian old endemic murid radiation that arrived on the continent sometime during the late Cenozoic. Here we describe two new species of extinct Leggadina from Quaternary cave deposits as well as additional material of the extinct Leggadina macrodonta. Leggadina irvini sp. nov. recovered from Middle-Upper (late) Pleistocene cave deposits near Chillagoe, northeastern Queensland, is the biggest member of the genus, being substantially larger than any other species so far described. Leggadina webbi sp. nov. from Middle Pleistocene cave deposits at Mount Etna, central eastern Queensland, shares features with the oldest species of the genus, the Early Pleistocene L. gregoriensis. Based on the current palaeoecological interpretation of the type locality, L. webbi, represents the only member of the genus that inhabited rainforest. The succession of Leggadina species through the late Quaternary suggests an ecological replacement of the extinct large-bodied L. irvini with the extant, small-bodied L. lakedownesis at Chillagoe. At Mt. Etna, the extinct rainforest species L. webbi is replaced with the extant xeric-adapted L. forresti during the latest Middle Pleistocene. This replacement is associated with a mid-Pleistocene shift towards progressive intensifying seasonal and arid climates. Our study adds to the growing list of small-bodied faunal extinctions during the late Quaternary of northern Australia.
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Affiliation(s)
- Jonathan Cramb
- School of Earth and Environmental Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Gilbert J Price
- School of Earth and Environmental Sciences, University of Queensland, Brisbane, Queensland, Australia
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11
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Aghová T, Kimura Y, Bryja J, Dobigny G, Granjon L, Kergoat GJ. Fossils know it best: Using a new set of fossil calibrations to improve the temporal phylogenetic framework of murid rodents (Rodentia: Muridae). Mol Phylogenet Evol 2018; 128:98-111. [PMID: 30030180 DOI: 10.1016/j.ympev.2018.07.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 11/20/2022]
Abstract
Murid rodents (Rodentia: Muridae) represent the most diverse and abundant mammalian family. In this study, we provide a refined set of fossil calibrations which is used to reconstruct a dated phylogeny of the family using a multilocus dataset (six nuclear and nine mitochondrial gene fragments) encompassing 161 species representing 82 murid genera from four extant subfamilies (Deomyinae, Gerbillinae, Lophiomyinae and Murinae). In comparison with previous studies on murid or muroid rodents, our work stands out for the implementation of nine robust fossil constraints within the Muridae thanks to a thorough review of the fossil record. Before being assigned to specific nodes of the phylogeny, all potential fossil constraints were carefully assessed; they were also subjected to several cross-validation analyses. The resulting phylogeny is consistent with previous phylogenetic studies on murids, and recovers the monophyly of all sampled murid subfamilies and tribes. Based on nine controlled fossil calibrations, our inferred temporal timeframe indicates that the murid family likely originated in the course of the Early Miocene, 22.0-17.0 million years ago (Ma), and that most major lineages (i.e. tribes) started diversifying ca. 10 Ma. Historical biogeography analyses support the tropical origin for the family, with an initial internal split (vicariance event) between Afrotropical and Oriental (Indomalaya and Philippines) lineages. During the course of their diversification, the biogeographic pattern of murids is marked by several dispersal events toward the Australasian and the Palearctic regions. The Afrotropical region was also secondarily colonized at least three times from the Indomalaya, indicating that the latter region has acted as a major centre of diversification for the family.
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Affiliation(s)
- Tatiana Aghová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic; Department of Zoology, National Museum, Václavské náměstí 68, 115 79 Prague, Czech Republic.
| | - Yuri Kimura
- Department of Geology and Paleontology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba 305-0005, Ibaraki, Japan
| | - 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
| | - Gauthier Dobigny
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ. Montpellier, Montpellier, France; Ecole Polytechnique d'Abomey-Calavi, Abomey-Calavi University, 01BP2009 Cotonou, Benin
| | - Laurent Granjon
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | - Gael J Kergoat
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
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12
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Unraveling Deep Branches of the Sigmodontinae Tree (Rodentia: Cricetidae) in Eastern South America. J MAMM EVOL 2018. [DOI: 10.1007/s10914-018-9444-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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13
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Rowsey DM, Heaney LR, Jansa SA. Diversification rates of the "Old Endemic" murine rodents of Luzon Island, Philippines are inconsistent with incumbency effects and ecological opportunity. Evolution 2018; 72:1420-1435. [PMID: 29845633 DOI: 10.1111/evo.13511] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/18/2018] [Indexed: 12/31/2022]
Abstract
Diversity-dependent cladogenesis occurs when a colonizing lineage exhibits increasing interspecific competition as it ecologically diversifies. Repeated colonization of a region by closely related taxa may cause similar effects as species within each lineage compete with one another. This may be particularly relevant for secondary colonists, which could experience limited diversification due to competition with earlier, incumbent colonists over evolutionary time. We tested the hypothesis that an incumbent lineage may diminish the diversification of secondary colonists in two speciose clades of Philippine "Old Endemic" murine rodents-Phloeomyini and Chrotomyini-on the relatively old oceanic island of Luzon. Although phylogenetic analyses confirm the independent, noncontemporaneous colonization of Luzon by the ancestors of these two clades, we found no support for arrested diversification in either. Rather, it appears that diversification of both clades resulted from constant-rate processes that were either uniform or favored the secondary colonists (Chrotomyini), depending on the method used. Our results suggest that ecological incumbency has not played an important role in determining lineage diversification among Luzon murines, despite sympatric occurrence by constituent species within each lineage, and a substantial head start for the primary colonists.
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Affiliation(s)
- Dakota M Rowsey
- Bell Museum of Natural History, University of Minnesota, St. Paul, Minnesota 55108
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota 55108
| | - Lawrence R Heaney
- Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, Illinois 60605
| | - Sharon A Jansa
- Bell Museum of Natural History, University of Minnesota, St. Paul, Minnesota 55108
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota 55108
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14
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Pinheiro G, Prata DF, Araújo IM, Tiscornia G. The African spiny mouse ( Acomys spp.) as an emerging model for development and regeneration. Lab Anim 2018; 52:565-576. [PMID: 29699452 DOI: 10.1177/0023677218769921] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The African spiny mouse ( Acomys spp.) is an emerging animal model with remarkable biological characteristics that make it a subject of interest for a broad range of research fields. Typically a desert species adapted to a low-calorie diet, spiny mice develop diabetes-related symptoms when switched to high-energy diets. Spiny mice undergo relatively long gestation periods and have small litters of highly developed pups, making them an adequate model for late organogenesis and perinatal biology. Recently, they have been shown to have remarkable healing and regeneration capabilities, which make them unique among mammals. In this work, we describe our experience in housing a colony of African spiny mice and cover all basic aspects of feeding, maintenance and breeding for research purposes.
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Affiliation(s)
- Gonçalo Pinheiro
- 1 Center for Biomedical Research (CBMR), University of Algarve, Faro, Portugal.,2 Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal
| | - Diogo Filipe Prata
- 1 Center for Biomedical Research (CBMR), University of Algarve, Faro, Portugal.,2 Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal
| | - Inês Maria Araújo
- 1 Center for Biomedical Research (CBMR), University of Algarve, Faro, Portugal.,2 Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal.,3 Algarve Biomedical Center, University of Algarve, Faro, Portugal
| | - Gustavo Tiscornia
- 1 Center for Biomedical Research (CBMR), University of Algarve, Faro, Portugal.,3 Algarve Biomedical Center, University of Algarve, Faro, Portugal.,4 Clínica Eugin, Research and Innovation Department, Spain
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15
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Pahl T, McLennan HJ, Wang Y, Achmadi AS, Rowe KC, Aplin K, Breed WG. Sperm morphology of the Rattini – are the interspecific differences due to variation in intensity of intermale sperm competition? Reprod Fertil Dev 2018; 30:1434-1442. [DOI: 10.1071/rd17431] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/05/2018] [Indexed: 01/16/2023] Open
Abstract
It is widely accepted that in mammals a causal relationship exists between postcopulatory sexual selection and relative testes mass of the species concerned, but how much it determines sperm size and shape is debatable. Here we detailed for the largest murine rodent tribe, the Rattini, the interspecific differences in relative testes mass and sperm form. We found that residual testes mass correlates with sperm head apical hook length as well as its angle, together with tail length, and that within several lineages a few species have evolved highly divergent sperm morphology with a reduced or absent apical hook and shorter tail. Although most species have a relative testes mass of 1–4%, these derived sperm traits invariably co-occur in species with much smaller relative testes mass. We therefore suggest that high levels of intermale sperm competition maintain a sperm head with a long apical hook and long tail, whereas low levels of intermale sperm competition generally result in divergent sperm heads with a short or non-existent apical hook and shorter tail. We thus conclude that sexual selection is a major selective force in driving sperm head form and tail length in this large tribe of murine rodents.
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16
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Larsen BB, Cole KL, Worobey M. Ancient DNA provides evidence of 27,000-year-old papillomavirus infection and long-term codivergence with rodents. Virus Evol 2018; 4:vey014. [PMID: 29977605 PMCID: PMC6007503 DOI: 10.1093/ve/vey014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The long-term evolutionary history of many viral lineages is poorly understood. Novel sources of ancient DNA combined with phylogenetic analyses can provide insight into the time scale of virus evolution. Here we report viral sequences from ancient North American packrat middens. We screened samples up to 27,000-years old and found evidence of papillomavirus (PV) infection in Neotoma cinerea (Bushy-tailed packrat). Phylogenetic analysis placed the PV sequences in a clade with other previously published PV sequences isolated from rodents. Concordance between the host and virus tree topologies along with a correlation in branch lengths suggests a shared evolutionary history between rodents and PVs. Based on host divergence times, PVs have likely been circulating in rodents for at least 17 million years. These results have implications for our understanding of PV evolution and for further research with ancient DNA from Neotoma middens.
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Affiliation(s)
- Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St., Tucson, 85721 AZ, USA
| | - Kenneth L Cole
- Northern Arizona University, School of Earth Sciences and Environmental Sustainability, 525 S. Beaver St., Flagstaff, 86011 AZ, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St., Tucson, 85721 AZ, USA
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17
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Fabre PH, Reeve AH, Fitriana YS, Aplin KP, Helgen KM. A new species of Halmaheramys (Rodentia: Muridae) from Bisa and Obi Islands (North Maluku Province, Indonesia). J Mammal 2017. [DOI: 10.1093/jmammal/gyx160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Steppan SJ, Schenk JJ. Muroid rodent phylogenetics: 900-species tree reveals increasing diversification rates. PLoS One 2017; 12:e0183070. [PMID: 28813483 PMCID: PMC5559066 DOI: 10.1371/journal.pone.0183070] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 07/29/2017] [Indexed: 11/18/2022] Open
Abstract
We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily. Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene.
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Affiliation(s)
- Scott J. Steppan
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - John J. Schenk
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
- Department of Biology, Georgia Southern University, Statesboro, Georgia, United States of America
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19
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Camacho-Sanchez M, Leonard JA, Fitriana Y, Tilak MK, Fabre PH. The generic status of Rattus annandalei (Bonhote, 1903) (Rodentia, Murinae) and its evolutionary implications. J Mammal 2017. [DOI: 10.1093/jmammal/gyx081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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20
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Bellofiore N, Ellery SJ, Mamrot J, Walker DW, Temple-Smith P, Dickinson H. First evidence of a menstruating rodent: the spiny mouse (Acomys cahirinus). Am J Obstet Gynecol 2017; 216:40.e1-40.e11. [PMID: 27503621 DOI: 10.1016/j.ajog.2016.07.041] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/14/2016] [Accepted: 07/15/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Advances in research relating to menstruation and associated disorders (eg, endometriosis and premenstrual syndrome) have been hindered by the lack of an appropriate animal model. Menstruation, the cyclical shedding of the decidualized endometrium in the absence of pregnancy, is believed to be limited to 78 higher-order primates (human beings and Old World monkeys), 4 species of bat, and the elephant shrew. This represents only 1.5% of the known 5502 mammalian species and <0.09% of these are nonprimates. Thus, many aspects of menstruation remain poorly understood, limiting the development of effective treatments for women with menstrual disorders. Menstruation occurs as a consequence of progesterone priming of the endometrial stroma and a spontaneous decidual reaction. At the end of each infertile cycle as progesterone levels decline the uterus is unable to maintain this terminally differentiated stroma and the superficial endometrium is shed. True menstruation has never been reported in rodents. OBJECTIVE Here we describe the first observation of menstruation in a rodent, the spiny mouse (Acomys cahirinus). STUDY DESIGN Virgin female spiny mice (n = 14) aged 12-16 weeks were sampled through daily vaginal lavage for 2 complete reproductive cycles. Stage-specific collection of reproductive tissue and plasma was used for histology, prolactin immunohistochemistry, and enzyme-linked immunosorbent assay of progesterone (n = 4-5/stage of the menstrual cycle). Normally distributed data are reported as the mean ± SE and significant differences calculated using a 1-way analysis of variance. Nonnormal data are displayed as the median values of replicates (with interquartile range) and significant differences calculated using Kruskal-Wallis test. RESULTS Mean menstrual cycle length was 8.7 ± 0.4 days with red blood cells observed in the lavages over 3.0 ± 0.2 days. Cyclic endometrial shedding and blood in the vaginal canal concluding with each infertile cycle was confirmed in all virgin females. The endometrium was thickest during the luteal phase at 322.6 μm (254.8, 512.2), when plasma progesterone peaked at 102.1 ng/mL (70.1, 198.6) and the optical density for prolactin immunoreactivity was strongest (0.071 ± 0.01 arbitrary units). CONCLUSION The spiny mouse undergoes spontaneous decidualization, demonstrating for the first time menstruation in a rodent. The spiny mouse provides a readily accessible nonprimate model to study the mechanisms of menstrual shedding and repair, and may therefore be useful in furthering studies of human menstrual and pregnancy-associated disorders.
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21
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Sato JJ, Ohdachi SD, Echenique-Diaz LM, Borroto-Páez R, Begué-Quiala G, Delgado-Labañino JL, Gámez-Díez J, Alvarez-Lemus J, Nguyen ST, Yamaguchi N, Kita M. Molecular phylogenetic analysis of nuclear genes suggests a Cenozoic over-water dispersal origin for the Cuban solenodon. Sci Rep 2016; 6:31173. [PMID: 27498968 PMCID: PMC4976362 DOI: 10.1038/srep31173] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/13/2016] [Indexed: 11/09/2022] Open
Abstract
The Cuban solenodon (Solenodon cubanus) is one of the most enigmatic mammals and is an extremely rare species with a distribution limited to a small part of the island of Cuba. Despite its rarity, in 2012 seven individuals of S. cubanus were captured and sampled successfully for DNA analysis, providing new insights into the evolutionary origin of this species and into the origins of the Caribbean fauna, which remain controversial. We conducted molecular phylogenetic analyses of five nuclear genes (Apob, Atp7a, Bdnf, Brca1 and Rag1; total, 4,602 bp) from 35 species of the mammalian order Eulipotyphla. Based on Bayesian relaxed molecular clock analyses, the family Solenodontidae diverged from other eulipotyphlan in the Paleocene, after the bolide impact on the Yucatan Peninsula, and S. cubanus diverged from the Hispaniolan solenodon (S. paradoxus) in the Early Pliocene. The strikingly recent divergence time estimates suggest that S. cubanus and its ancestral lineage originated via over-water dispersal rather than vicariance events, as had previously been hypothesised.
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Affiliation(s)
- Jun J. Sato
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
| | - Satoshi D. Ohdachi
- Institute of Low Temperature Science, Hokkaido University, Kita-19 Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Lazaro M. Echenique-Diaz
- Environmental Education Center, Miyagi University of Education, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-0845, Japan
| | | | - Gerardo Begué-Quiala
- Unidad Presupuestada Parque Nacional Alejandro de Humboldt (CITMA), Calle Abogado 14 e/ 12 y 13 Norte, Guantanamo 95200, Cuba
| | - Jorge L. Delgado-Labañino
- Estación Ecológica La Melba, Unidad Presupuestada Parque Nacional Alejandro de Humboldt, CITMA-Guantánamo, Cuba
| | - Jorgelino Gámez-Díez
- Estación Ecológica La Melba, Unidad Presupuestada Parque Nacional Alejandro de Humboldt, CITMA-Guantánamo, Cuba
| | - José Alvarez-Lemus
- Centro de Inspección y Control Ambiental (CICA), Ministerio de Ciencia, Tecnología y Medio Ambiente (CITMA), Cuba
| | - Son Truong Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Street, Cau Giay, Hanoi, Vietnam
| | - Nobuyuki Yamaguchi
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, PO Box 2713 Doha, Qatar
| | - Masaki Kita
- Graduate School of Pure and Applied Sciences and Tsukuba Research Center for Interdisciplinary Materials Science (TIMS), University of Tsukuba 1-1-1 Tennodai, Tsukuba 305-8571, Japan
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22
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Developmental genetics in emerging rodent models: case studies and perspectives. Curr Opin Genet Dev 2016; 39:182-186. [DOI: 10.1016/j.gde.2016.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/21/2016] [Accepted: 07/30/2016] [Indexed: 12/23/2022]
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23
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Martin SA, Alhajeri BH, Steppan SJ. Dietary adaptations in the teeth of murine rodents (Muridae): a test of biomechanical predictions. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12822] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Stephanie A. Martin
- Department of Biological Science; Florida State University; Tallahassee FL 32306-4295 USA
- Biology Department; Austin Community College; Austin TX USA
| | - Bader H. Alhajeri
- Department of Biological Sciences; Kuwait University; Safat 13110 Kuwait
| | - Scott J. Steppan
- Department of Biological Science; Florida State University; Tallahassee FL 32306-4295 USA
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Evidence of a complex phylogeographic structure in the Indomalayan pencil-tailed tree mouse Chiropodomys gliroides (Rodentia: Muridae) in eastern Indochina. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Lüke L, Tourmente M, Dopazo H, Serra F, Roldan ERS. Selective constraints on protamine 2 in primates and rodents. BMC Evol Biol 2016; 16:21. [PMID: 26801756 PMCID: PMC4724148 DOI: 10.1186/s12862-016-0588-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 01/12/2016] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Protamines are sperm nuclear proteins with a crucial role in chromatin condensation. Their function is strongly linked to sperm head morphology and male fertility. Protamines appear to be affected by a complex pattern of selective constraints. Previous studies showed that sexual selection affects protamine coding sequence and expression in rodents. Here we analyze selective constraints and post-copulatory sexual selection acting on protamine 2 (Prm2) gene sequences of 53 species of primates and rodents. We focused on possible differences in selective constraints between these two clades and on the two functional domains of PRM2 (cleaved- and mature-PRM2). We also assessed if and how changes in Prm2 coding sequence may affect sperm head dimensions. RESULTS The domain of Prm2 that is cleaved off during binding to DNA (cleaved-Prm2) was found to be under purifying selection in both clades, whereas the domain that remains bound to DNA (mature-Prm2) was found to be positively selected in primates and under relaxed constraint in rodents. Changes in cleaved-Prm2 coding sequence are significantly correlated to sperm head width and elongation in rodents. Contrary to expectations, a significant effect of sexual selection was not found on either domain or clade. CONCLUSIONS Mature-PRM2 may be free to evolve under less constraint due to the existence of PRM1 as a more conserved and functionally redundant copy. The cleaved-PRM2 domain seems to play an important role in sperm head shaping. However, sexual selection on its sequence may be difficult to detect until it is identified which sperm head phenotype (shape and size) confers advantages for sperm performance in different mammalian clades.
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Affiliation(s)
- Lena Lüke
- Reproductive Ecology and Biology Group, Museo Nacional de Ciencias Naturales (CSIC), c/Jose Gutierrez Abascal 2, 28006, Madrid, Spain.
| | - Maximiliano Tourmente
- Reproductive Ecology and Biology Group, Museo Nacional de Ciencias Naturales (CSIC), c/Jose Gutierrez Abascal 2, 28006, Madrid, Spain.
| | - Hernan Dopazo
- Department of Ecology, Genetics and Evolution, Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - François Serra
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Universitat Pompeu Fabra, Barcelona, Spain.
| | - Eduardo R S Roldan
- Reproductive Ecology and Biology Group, Museo Nacional de Ciencias Naturales (CSIC), c/Jose Gutierrez Abascal 2, 28006, Madrid, Spain.
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26
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Pagès M, Fabre PH, Chaval Y, Mortelliti A, Nicolas V, Wells K, Michaux JR, Lazzari V. Molecular phylogeny of South-East Asian arboreal murine rodents. ZOOL SCR 2015. [DOI: 10.1111/zsc.12161] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marie Pagès
- Unité de génétique de la conservation; Institut de Botanique; Université de Liège; 4000 Liège (Sart Tilman) Belgique
- INRA; UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro); Campus International de Baillarguet, CS 30016 34988 Montferrier-sur-Lez Cedex France
- Institut des Sciences de l’Évolution de Montpellier; Université de Montpellier; CNRS; IRD; EPHE; 34095 Montpellier France
| | - Pierre-Henri Fabre
- Harvard Museum of Comparative Zoology; 26 Oxford Street Cambridge MA 02138 USA
- Smithsonian Institution; PO Box 37012, MRC 108 Washington DC 20013-7012 USA
| | - Yannick Chaval
- INRA; UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro); Campus International de Baillarguet, CS 30016 34988 Montferrier-sur-Lez Cedex France
| | - Alessio Mortelliti
- Department of Wildlife, Fisheries, and Conservation Biology; University of Maine; 5755 Nutting Hall, Room 228 Orono ME 04469 USA
| | - Violaine Nicolas
- Institut de Systématique, Évolution, Biodiversité; ISYEB - UMR 7205, CNRS; MNHN; UPMC; EPHE; Muséum national d'Histoire naturelle; Sorbonne Universités 57 rue Cuvier, CP 51 75005 Paris France
| | - Konstans Wells
- Environmental Futures Research Institute; Griffith University; Brisbane Qld 4111 Australia
| | - Johan R. Michaux
- Unité de génétique de la conservation; Institut de Botanique; Université de Liège; 4000 Liège (Sart Tilman) Belgique
- CIRAD; TA C- 22/E - Campus international de Baillarguet 34398 Montpellier Cedex 5 France
| | - Vincent Lazzari
- Institut de paléoprimatologie; Paléontologie Humaine: Evolution et paléoenvironnements - UMR CNRS 7262 INEE; 86022 6 rue Michel Brunet Poitier France
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Missoup AD, Nicolas V, Eiseb S, Chung EK, Denys C. Phylogenetic position of the endemic Mount Oku rat,Lamottemys okuensis(Rodentia: Muridae), based on molecular and morphological data. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12361] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Alain Didier Missoup
- Department of Animal Biology Organisms; Faculty of Science; the University of Douala; PO Box: 24157 Douala Cameroon
- Institut de Systématique, Evolution, Biodiversité, ISYEB UMR 7205 - CNRS, MNHN, UPMC, EPHE, Museum National d'Histoire Naturelle; Sorbonne Universités; Paris France
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité, ISYEB UMR 7205 - CNRS, MNHN, UPMC, EPHE, Museum National d'Histoire Naturelle; Sorbonne Universités; Paris France
| | - Seth Eiseb
- University of Namibia; Private Bag 13301 Windhoek Namibia
| | | | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité, ISYEB UMR 7205 - CNRS, MNHN, UPMC, EPHE, Museum National d'Histoire Naturelle; Sorbonne Universités; Paris France
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28
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Esselstyn JA, Achmadi AS, Handika H, Rowe KC. A hog-nosed shrew rat (Rodentia: Muridae) from Sulawesi Island, Indonesia. J Mammal 2015. [DOI: 10.1093/jmammal/gyv093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Corrected placement of Mus-Rattus fossil calibration forces precision in the molecular tree of rodents. Sci Rep 2015; 5:14444. [PMID: 26411391 PMCID: PMC4585935 DOI: 10.1038/srep14444] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/14/2015] [Indexed: 12/03/2022] Open
Abstract
Time calibration derived from the fossil record is essential for molecular phylogenetic and evolutionary studies. Fossil mice and rats, discovered in the Siwalik Group of Pakistan, have served as one of the best-known fossil calibration points in molecular phylogenic studies. Although these fossils have been widely used as the 12 Ma date for the Mus/Rattus split or a more basal split, conclusive paleontological evidence for the nodal assignments has been absent. This study analyzes newly recognized characters that demonstrate lineage separation in the fossil record of Siwalik murines and examines the most reasonable nodal placement of the diverging lineages in a molecular phylogenetic tree by ancestral state reconstruction. Our specimen-based approach strongly indicates that Siwalik murines of the Karnimata clade are fossil members of the Arvicanthini-Otomyini-Millardini clade, which excludes Rattus and its relatives. Combining the new interpretation with the widely accepted hypothesis that the Progonomys clade includes Mus, the lineage separation event in the Siwalik fossil record represents the Mus/Arvicanthis split. Our test analysis on Bayesian age estimates shows that this new calibration point provides more accurate estimates of murine divergence than previous applications. Thus, we define this fossil calibration point and refine two other fossil-based points for molecular dating.
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Abstract
Only three species of fossil murine have been described to date in Australia even though they are often found in fossil deposits and can be highly useful in understanding environmental change over time. Until now the genus Leggadina, a group of short-tailed mice that is particularly well adapted to an arid environment, was only known from two extant species: L. forresti and L. lakedownensis. Here two new fossil species of the genus are described from sites in northwestern Queensland. Leggadina gregoriensis sp. nov. comes from the Early Pleistocene Rackham’s Roost Site in the Riversleigh World Heritage Area and Leggadina macrodonta sp. nov. is from the Plio-Pleistocene Site 5C at Floraville Station. The evolution of the genus Leggadina and the lineage’s response to palaeoecological factors is considered. Taphonomy of the two fossil deposits is examined and shows marked differences in both faunal composition of the assemblages and preservation. Description of L. gregoriensis and L. macrodonta extends the known temporal range of the Leggadina lineage by over 2 million years.
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Affiliation(s)
- Ada J Klinkhamer
- School of Biological, Earth and Environmental Sciences, University of New South Wales , NSW , Australia
| | - Henk Godthelp
- School of Biological, Earth and Environmental Sciences, University of New South Wales , NSW , Australia
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31
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Alhajeri BH, Hunt OJ, Steppan SJ. Molecular systematics of gerbils and deomyines (Rodentia: Gerbillinae, Deomyinae) and a test of desert adaptation in the tympanic bulla. J ZOOL SYST EVOL RES 2015. [DOI: 10.1111/jzs.12102] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Bader H. Alhajeri
- Department of Biological Science; Florida State University; Tallahassee FL USA
- Department of Biological Sciences; Kuwait University; Safat Kuwait
| | - Ondreia J. Hunt
- Department of Biological Science; Florida State University; Tallahassee FL USA
- Eastern Virginia Medical School; Norfolk VA USA
| | - Scott J. Steppan
- Department of Biological Science; Florida State University; Tallahassee FL USA
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32
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Balakirev AE, Abramov AV, Rozhnov VV. Phylogenetic relationships in the Niviventer-Chiromyscus complex (Rodentia, Muridae) inferred from molecular data, with description of a new species. Zookeys 2014; 451:109-36. [PMID: 25493050 PMCID: PMC4258623 DOI: 10.3897/zookeys.451.7210] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 09/03/2014] [Indexed: 12/05/2022] Open
Abstract
Based on molecular data for mitochondrial (Cyt b, COI) and nuclear (IRBP, GHR) genes, and morphological examinations of museum specimens, we examined diversity, species boundaries, and relationships within and between the murine genera Chiromyscus and Niviventer. Phylogenetic patterns recovered demonstrate that Niviventer sensu lato is not monophyletic but instead includes Chiromyscuschiropus, the only previously recognized species of Chiropus. To maintain the genera Niviventer and Chiropus as monophyletic lineages, the scope and definition of the genus Chiromyscus is revised to include at least three distinct species: Chiromyscuschiropus (the type species of Chiromyscus), Chiromyscuslangbianis (previously regarded as a species of Niviventer), and a new species, described in this paper under the name Chiromyscusthomasi sp. n.
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Affiliation(s)
- Alexander E. Balakirev
- Joint Russian-Vietnamese Tropical Research and Technological Centre, Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- A.N. Severtsov’s Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia
| | - Alexei V. Abramov
- Joint Russian-Vietnamese Tropical Research and Technological Centre, Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, Saint Petersburg 199034, Russia
| | - Viatcheslav V. Rozhnov
- Joint Russian-Vietnamese Tropical Research and Technological Centre, Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- A.N. Severtsov’s Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia
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Lobban KD, Lovegrove BG, Rakotondravony D. The energetics of a Malagasy rodent, Macrotarsomys ingens (Nesomyinae): a test of island and zoogeographical effects on metabolism. J Comp Physiol B 2014; 184:1077-89. [DOI: 10.1007/s00360-014-0853-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/22/2014] [Accepted: 08/05/2014] [Indexed: 11/24/2022]
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Abstract
Laelaps giganteus and Laelaps muricola (Mesostigmata; Laelapidae) are widespread and locally abundant host generalists on small mammals in southern Africa. The large host range and complex life history of these ectoparasites may allude to possible intraspecific cryptic diversity in these taxa. To assess genetic and morphological diversity in L. giganteus and L. muricola, we sampled 228 rodents at eight localities in South Africa. This sample included nine previously recorded host species and on these, L. muricola was only recorded from Mastomys natalensis and Micaelamys namaquensis while L. giganteus was found on Rhabdomys dilectus and Lemniscomys rosalia. Phylogenetic analyses of partial mtDNA cytochrome oxidase subunit I (COI) and nuclear ITS1 data strongly supported the recognition of L. giganteus and L. muricola, a scenario partly supported by the Tropomyosin intron. Strong support for evolutionary distinct lineages within L. giganteus is found: L. giganteus lineage 1 is confined to R. dilectus and L. giganteus lineage 2 is confined to L. rosalia. These host specific monophyletic lineages were also separated by 9.84% mtDNA sequence divergence and 3.44% nuclear DNA sequence divergence. Since quantitative morphometric analyses were not congruent with these findings, these two lineages more than likely represent cryptic species.
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35
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Li J, Zheng X, Cai Y, Zhang X, Yang M, Yue B, Li J. DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China. Mol Ecol Resour 2014; 15:153-67. [PMID: 24838015 DOI: 10.1111/1755-0998.12279] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/24/2014] [Accepted: 05/07/2014] [Indexed: 12/25/2022]
Abstract
Identification of rodents is very difficult mainly due to high similarities in morphology and controversial taxonomy. In this study, mitochondrial cytochrome oxidase subunit I (COI) was used as DNA barcode to identify the Murinae and Arvicolinae species distributed in China and to facilitate the systematics studies of Rodentia. In total, 242 sequences (31 species, 11 genera) from Murinae and 130 sequences (23 species, 6 genera) from Arvicolinae were investigated, of which 90 individuals were novel. Genetic distance, threshold method, tree-based method, online BLAST and BLOG were employed to analyse the data sets. There was no obvious barcode gap. The average K2P distance within species and genera was 2.10% and 12.61% in Murinae, and 2.86% and 11.80% in Arvicolinae, respectively. The optimal threshold was 5.62% for Murinae and 3.34% for Arvicolinae. All phylogenetic trees exhibited similar topology and could distinguish 90.32% of surveyed species in Murinae and 82.60% in Arvicolinae with high support values. BLAST analyses yielded similar results with identification success rates of 92.15% and 93.85% for Murinae and Arvicolinae, respectively. BLOG successfully authenticated 100% of detected species except Leopoldamys edwardsi based on the latest taxonomic revision. Our results support the species status of recently recognized Micromys erythrotis, Eothenomys tarquinius and E. hintoni and confirm the important roles of comprehensive taxonomy and accurate morphological identification in DNA barcoding studies. We believe that, when proper analytic methods are applied or combined, DNA barcoding could serve as an accurate and effective species identification approach for Murinae and Arvicolinae based on a proper taxonomic framework.
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Affiliation(s)
- Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610065, China
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36
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Bannikova AA, Lebedev VS, Abramov AV, Rozhnov VV. Contrasting evolutionary history of hedgehogs and gymnures (Mammalia: Erinaceomorpha) as inferred from a multigene study. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12299] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anna A. Bannikova
- Lomonosov Moscow State University; Vorobievy Gory 119991 Moscow Russia
| | - Vladimir S. Lebedev
- Zoological Museum; Moscow State University; B.Nikitskaya 6 125009 Moscow Russia
| | - Alexei V. Abramov
- Zoological Institute; Russian Academy of Sciences; Universitetskaya nab. 1 199034 St. Petersburg Russia
| | - Viatcheslav V. Rozhnov
- A.N. Severtsov Institute of Ecology and Evolution; Russian Academy of Sciences; Leninskii pr. 33 Moscow Russia
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37
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Achmadi AS, Esselstyn JA, Rowe KC, Maryanto I, Abdullah MT. Phylogeny, diversity, and biogeography of Southeast Asian spiny rats (Maxomys). J Mammal 2013. [DOI: 10.1644/13-mamm-a-092.1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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38
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Fabre PH, Pagès M, Musser GG, Fitriana YS, Fjeldså J, Jennings A, Jønsson KA, Kennedy J, Michaux J, Semiadi G, Supriatna N, Helgen KM. A new genus of rodent from Wallacea (Rodentia: Muridae: Murinae: Rattini), and its implication for biogeography and Indo-Pacific Rattini systematics. Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12061] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Pierre-Henri Fabre
- Center for Macroecology, Evolution and Climate (CMEC, Department of Biology), Zoological Museum; University of Copenhagen; Universitetsparken 15 DK-2100 Copenhagen Denmark
| | - Marie Pagès
- Laboratoire de génétique des microorganismes; Université de Liège; 4000 Liège Belgique
- INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro); Campus International de Baillarguet; CS 30016 34988 Montferrier-sur-Lez Cedex France
| | - Guy G. Musser
- Division of Vertebrate Zoology (Mammalogy); American Museum of Natural History; New York NY 10024 USA
| | - Yuli S. Fitriana
- Museum Zoologicum Bogoriense; Research Center For Biology; Indonesian Institute of Sciences (LIPI); Jl.Raya Jakarta-Bogor Km.46 Cibinong 16911 Indonesia
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate (CMEC, Department of Biology), Zoological Museum; University of Copenhagen; Universitetsparken 15 DK-2100 Copenhagen Denmark
| | - Andy Jennings
- Muséum National d'Histoire Naturelle; Département Systématique et Evolution CP 51; 57 Rue Cuvier 75231 Paris France
| | - Knud A. Jønsson
- Center for Macroecology, Evolution and Climate (CMEC, Department of Biology), Zoological Museum; University of Copenhagen; Universitetsparken 15 DK-2100 Copenhagen Denmark
| | - Jonathan Kennedy
- Center for Macroecology, Evolution and Climate (CMEC, Department of Biology), Zoological Museum; University of Copenhagen; Universitetsparken 15 DK-2100 Copenhagen Denmark
| | - Johan Michaux
- INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro); Campus International de Baillarguet; CS 30016 34988 Montferrier-sur-Lez Cedex France
| | - Gono Semiadi
- Museum Zoologicum Bogoriense; Research Center For Biology; Indonesian Institute of Sciences (LIPI); Jl.Raya Jakarta-Bogor Km.46 Cibinong 16911 Indonesia
| | - Nanang Supriatna
- Museum Zoologicum Bogoriense; Research Center For Biology; Indonesian Institute of Sciences (LIPI); Jl.Raya Jakarta-Bogor Km.46 Cibinong 16911 Indonesia
| | - Kristofer M. Helgen
- National Museum of Natural History; Smithsonian. Institution; P.O. Box 37012 MRC 108 Washington DC 20013-7012 USA
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Schenk JJ, Rowe KC, Steppan SJ. Ecological Opportunity and Incumbency in the Diversification of Repeated Continental Colonizations by Muroid Rodents. Syst Biol 2013; 62:837-64. [DOI: 10.1093/sysbio/syt050] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- John J. Schenk
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA; and 2Museum Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
| | - Kevin C. Rowe
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA; and 2Museum Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
| | - Scott J. Steppan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA; and 2Museum Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
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Hautier L, Bennett NC, Viljoen H, Howard L, Milinkovitch MC, Tzika AC, Goswami A, Asher RJ. PATTERNS OF OSSIFICATION IN SOUTHERN VERSUS NORTHERN PLACENTAL MAMMALS. Evolution 2013; 67:1994-2010. [DOI: 10.1111/evo.12071] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 01/31/2013] [Indexed: 12/01/2022]
Affiliation(s)
- Lionel Hautier
- Department of Zoology; University of Cambridge; Downing St. Cambridge CB2 3EJ United Kingdom
| | - Nigel C. Bennett
- Department of Zoology and Entomology; University of Pretoria; Pretoria 0002 South Africa
| | - Hermien Viljoen
- Department of Zoology and Entomology; University of Pretoria; Pretoria 0002 South Africa
| | - Lauren Howard
- Science Facilities Department; British Museum of Natural History; Cromwell Road London SW7 5BD United Kingdom
| | - Michel C. Milinkovitch
- Laboratory of Artificial and Natural Evolution; Department of Genetics & Evolution; Sciences III Building; 30 Quai Ernest-Ansermet 1211 Geneva Switzerland
| | - Athanasia C. Tzika
- Laboratory of Artificial and Natural Evolution; Department of Genetics & Evolution; Sciences III Building; 30 Quai Ernest-Ansermet 1211 Geneva Switzerland
| | - Anjali Goswami
- Department of Genetics, Evolution, and Environment and Department of Earth Sciences; University College London; Wolfson House to Darwin Building; Gower Street London WC1E 6BT United Kingdom
| | - Robert J. Asher
- Department of Zoology; University of Cambridge; Downing St. Cambridge CB2 3EJ United Kingdom
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42
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Dlugosz EM, Chappell MA, Meek TH, Szafrańska P, Zub K, Konarzewski M, Jones JH, Bicudo E, Nespolo RF, Careau V, Garland T. Phylogenetic analysis of mammalian maximal oxygen consumption during exercise. J Exp Biol 2013; 216:4712-21. [DOI: 10.1242/jeb.088914] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Summary
We compiled published values of mammalian maximum oxygen consumption during exercise (VO2max) and supplemented these data with new measurements of VO2max for the largest rodent (capybara), 20 species of smaller-bodied rodents, two species of weasels, and one small marsupial. Many of the new data were obtained with running-wheel respirometers instead of the treadmill systems used in most previous measurements of mammalian VO2max. We used both conventional and phylogenetically informed allometric regression models to analyze VO2max of 77 ‘species’ (including subspecies or separate populations within species) in relation to body size, phylogeny, diet, and measurement method. Both body mass and allometrically mass-corrected VO2max showed highly significant phylogenetic signal (i.e., related species tended to resemble each other). The Akaike Information Criterion corrected for sample size was used to compare 27 candidate models predicting VO2max (all of which included body mass). In addition to mass, the two best-fitting models (cumulative Akaike weight = 0.93) included dummy variables coding for three species previously shown to have high VO2max (pronghorn, horse, and a bat), and incorporated a transformation of the phylogenetic branch lengths under an Ornstein-Uhlenbeck model of residual variation (thus indicating phylogenetic signal in the residuals). We found no statistical difference between wheel- and treadmill-elicited values, and diet had no predictive ability for VO2max. Averaged across all models, the allometric scaling exponent was 0.839, with 95% confidence limits of 0.795 and 0.883, which does not provide support for a scaling exponent of 0.67, 0.75 or unity.
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Cross-species transmission in the speciation of the currently known murinae-associated hantaviruses. J Virol 2012; 86:11171-82. [PMID: 22855492 DOI: 10.1128/jvi.00021-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
To gain more insight into the phylogeny of Dabieshan virus (DBSV), carried by Niviventer confucianus and other Murinae-associated hantaviruses, genome sequences of novel variants of DBSV were recovered from Niviventer rats trapped in the mountainous areas of Wenzhou, China. Genetic analyses show that all known genetic variants of DBSV, including the ones identified in this study, are distinct from other Murinae-associated hantaviruses. DBSV variants show geographic clustering and high intraspecies diversity. The data suggest that DBSV is a distinct species in the genus Hantavirus. Interestingly, DBSV shows the highest sequence identity to Hantaan virus (HTNV), with a >7% difference in the sequences of the N, GPC, and L proteins, while N. confucianus is more closely related to Rattus norvegicus (the host of Seoul virus [SEOV]) than to Apodemus agrarius (the host of HTNV and Saaremaa virus [SAAV]). Further genetic analyses of all known Murinae-associated hantaviruses (both established and tentative species) show that many of them, including DBSV, may have originated from host switching. The estimation of evolutionary rates and divergence time supports the role of cross-species transmission in the evolution of Murinae-associated hantaviruses. The detection of positive selection suggests that genetic drift may contribute to the speciation of Murinae-associated hantaviruses and that adaptation has a role as well.
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Balakirev AE, Abramov AV, Tikhonov AN, Rozhnov VV. Molecular phylogeny of the Dacnomys division (Rodentia, Muridae): the taxonomic positions of Saxatilomys and Leopoldamys. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2012; 445:251-254. [PMID: 22945528 DOI: 10.1134/s0012496612040096] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Indexed: 06/01/2023]
Affiliation(s)
- A E Balakirev
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
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Fabre PH, Hautier L, Dimitrov D, Douzery EJP. A glimpse on the pattern of rodent diversification: a phylogenetic approach. BMC Evol Biol 2012; 12:88. [PMID: 22697210 PMCID: PMC3532383 DOI: 10.1186/1471-2148-12-88] [Citation(s) in RCA: 300] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 05/14/2012] [Indexed: 11/17/2022] Open
Abstract
Background Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia. Results Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56% and 81% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation. Conclusions The present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes.
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Affiliation(s)
- Pierre-Henri Fabre
- Center for Macroecology, Evolution and Climate (CMEC, Department of Biology), Zoological Museum, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
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Chen WC, Hao HB, Sun ZY, Liu Y, Liu SY, Yue BS. Phylogenetic position of the genus Proedromys (Arvicolinae, Rodentia): Evidence from nuclear and mitochondrial DNA. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Chen XP, Yu J, Li MH, Zhao GY, Wang W, Guo WP, Deng XZ, Zhang Y, Fu ZF, Qin XC, Zhang YZ. Pathogenicity of a natural reassortant hantavirus CGRn9415 in newborn rats and newborn mice. J Gen Virol 2012; 93:1017-1022. [DOI: 10.1099/vir.0.038703-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To better understand the pathogenicity and infectivity of a natural reassortant CGRn9415 generated from Hantaan virus (HTNV) and Seoul virus (SEOV), CGRn9415, HTNV 76–118 and SEOV L99 were used to infect newborn Kunming (KM) mice and newborn Wistar rats. In KM mice, there was no statistical difference between the death rate with CGRn9415 and that of L99, while 76–118 killed all mice even at low dosage; CGRn9415 killed all infected rats similar to L99 at the dosage of 105 f.f.u., while no death occurred in rats infected with 76–118 even as high as 2×105 f.f.u., suggesting that the reassortant CGRn9415 possesses similar pathogenicity as L99. Furthermore, the reassortant CGRn9415 could establish a persistent infection in both KM mice and Wistar rats more easily than 76–118 or L99. These data suggest that the reassorted hantavirus behaves more like SEOV as far as the pathogenicity is concerned.
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Affiliation(s)
- Xiao-Ping Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
| | - Juan Yu
- Medical Institute of Nanjing Army, Nanjing, PR China
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
| | - Ming-Hui Li
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
| | - Gao-Yu Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
| | - Wen Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
| | - Wen-Ping Guo
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
| | | | - Yun Zhang
- Medical Institute of Nanjing Army, Nanjing, PR China
| | - Zhen F. Fu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, 430070 Wuhan, PR China
- Department of Pathology, University of Georgia, Athens, GA 30602, USA
| | - Xin-Cheng Qin
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
| | - Yong-Zhen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Liuzi 5, 102206 Beijing, PR China
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Upham NS, Patterson BD. Diversification and biogeography of the Neotropical caviomorph lineage Octodontoidea (Rodentia: Hystricognathi). Mol Phylogenet Evol 2012; 63:417-29. [DOI: 10.1016/j.ympev.2012.01.020] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 11/14/2011] [Accepted: 01/20/2012] [Indexed: 11/29/2022]
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Missoup AD, Nicolas V, Wendelen W, Keming E, Bilong Bilong CF, Couloux A, Atanga E, Hutterer R, Denys C. Systematics and diversification of Praomys species (Rodentia: Muridae) endemic to the Cameroon Volcanic Line (West Central Africa). ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2012.00541.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Zhang Q, Xia L, Kimura Y, Shenbrot G, Zhang Z, Ge D, Yang Q. Tracing the Origin and Diversification of Dipodoidea (Order: Rodentia): Evidence from Fossil Record and Molecular Phylogeny. Evol Biol 2012. [DOI: 10.1007/s11692-012-9167-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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