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Martins ALP, Dias FCR, Oliveira EL, Rodrigues GAV, de Avelar GF, de Melo FCSA, Costa KLC, da Matta SLP. Testicular histomorphometric patterns and spermatogenesis dynamics of Oecomys bicolor tomes, 1860 (Rodentia: Cricetidae). Anat Histol Embryol 2024; 53:e13062. [PMID: 38837469 DOI: 10.1111/ahe.13062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 04/10/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024]
Abstract
Although the order Rodentia does not present a high risk of extinction compared to mammals as a whole, several families demonstrate high levels of threat and/or data deficiency, therefore highlighting the need for targeted research and the application of ecological and reproductive data to the development of conservation actions. The order Rodentia, the largest among mammals, includes 9 families, and the family Cricetidae is the most diverse of the Brazilian rodents. In Brazil, 12 of the 16 genera of Oecomys are found. Oecomys bicolor is known in Brazil as the 'arboreal rat' and is, found in dry, deciduous and tropical forests. The mean body weight of Oecomys bicolor was 35.8 g and the gonadal, tubular and epithelial somatic indexes were, 0.53%, 0.47% and 0.37%, respectively. Seminiferous tubules volume density was 89.72% and the mitotic and meiotic indexes corresponded to 8.59 and 2.45 cells, respectively, and the yield of spermatogenesis was 23.83 cells. The intertubular compartment represented 10.28% of the testis parenchyma and around 5% of the interstitial space was occupied by Leydig cells, whose number per gram of testis was 11.10 × 107 cells. By evaluating the biometric and histomorphometric characteristics of the testis, there is evidence that this species has a high investment in reproduction. Due to the high contribution of the seminiferous epithelium and the intertubular compartment in this species, compared to the others of the same family, it is possible to infer that the species Oecomys bicolor has a promiscuous reproductive behaviour.
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Sgarlata GM, Rasolondraibe E, Salmona J, Le Pors B, Ralantoharijaona T, Rakotonanahary A, Jan F, Manzi S, Iribar A, Zaonarivelo JR, Volasoa Andriaholinirina N, Rasoloharijaona S, Chikhi L. The genomic diversity of the Eliurus genus in northern Madagascar with a putative new species. Mol Phylogenet Evol 2024; 193:107997. [PMID: 38128795 DOI: 10.1016/j.ympev.2023.107997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Madagascar exhibits extraordinarily high level of species richness and endemism, while being severely threatened by habitat loss and fragmentation (HL&F). In front of these threats to biodiversity, conservation effort can be directed, for instance, in the documentation of species that are still unknown to science, or in investigating how species respond to HL&F. The tufted-tail rats genus (Eliurus spp.) is the most speciose genus of endemic rodents in Madagascar, with 13 described species, which occupy two major habitat types: dry or humid forests. The large species diversity and association to specific habitat types make the Eliurus genus a suitable model for investigating species adaptation to new environments, as well as response to HL&F (dry vs humid). In the present study, we investigated Eliurus spp. genomic diversity across northern Madagascar, a region covered by both dry and humid fragmented forests. From the mitochondrial DNA (mtDNA) and nuclear genomic (RAD-seq) data of 124 Eliurus individuals sampled in poorly studied forests of northern Madagascar, we identified an undescribed Eliurus taxon (Eliurus sp. nova). We tested the hypothesis of a new Eliurus species using several approaches: i) DNA barcoding; ii) phylogenetic inferences; iii) species delimitation tests based on the Multi-Species Coalescent (MSC) model, iv) genealogical divergence index (gdi); v) an ad-hoc test of isolation-by-distance within versus between sister-taxa, vi) comparisons of %GC content patterns and vii) morphological analyses. All analyses support the recognition of the undescribed lineage as a putative distinct species. In addition, we show that Eliurus myoxinus, a species known from the dry forests of western Madagascar, is, surprisingly, found mostly in humid forests in northern Madagascar. In conclusion, we discuss the implications of such findings in the context of Eliurus species evolution and diversification, and use the distribution of northern Eliurus species as a proxy for reconstructing past changes in forest cover and vegetation type in northern Madagascar.
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Affiliation(s)
| | - Emmanuel Rasolondraibe
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar.
| | - Jordi Salmona
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal; Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - Barbara Le Pors
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Tantely Ralantoharijaona
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Ando Rakotonanahary
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar.
| | - Fabien Jan
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Sophie Manzi
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - Amaia Iribar
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
| | - John Rigobert Zaonarivelo
- Département des Sciences de la Nature et de l'Environnement, Université d'Antsiranana, 201 Antsiranana, Madagascar.
| | | | - Solofonirina Rasoloharijaona
- Département de Biologie Animale et Ecologie, Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal; Centre de Recherche sur la Biodiversité et l'Environnement (CRBE),Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 -Paul Sabatier (UT3), Toulouse, France.
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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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Salazar-Bravo J, Tinoco N, Zeballos H, Brito J, Arenas-Viveros D, Marín-C D, Ramírez-Fernández JD, Percequillo AR, Lee, Jr. TE, Solari S, Colmenares-Pinzon J, Nivelo C, Rodríguez Herrera B, Merino W, Medina CE, Murillo-García O, Pardiñas UF. Systematics and diversification of the Ichthyomyini (Cricetidae, Sigmodontinae) revisited: evidence from molecular, morphological, and combined approaches. PeerJ 2023; 11:e14319. [PMID: 36655048 PMCID: PMC9841913 DOI: 10.7717/peerj.14319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 10/09/2022] [Indexed: 01/15/2023] Open
Abstract
Ichthyomyini, a morphologically distinctive group of Neotropical cricetid rodents, lacks an integrative study of its systematics and biogeography. Since this tribe is a crucial element of the Sigmodontinae, the most speciose subfamily of the Cricetidae, we conducted a study that includes most of its recognized diversity (five genera and 19 species distributed from southern Mexico to northern Bolivia). For this report we analyzed a combined matrix composed of four molecular markers (RBP3, GHR, RAG1, Cytb) and 56 morphological traits, the latter including 15 external, 14 cranial, 19 dental, five soft-anatomical and three postcranial features. A variety of results were obtained, some of which are inconsistent with the currently accepted classification and understanding of the tribe. Ichthyomyini is retrieved as monophyletic, and it is divided into two main clades that are here recognized as subtribes: one to contain the genus Anotomys and the other composed by the remaining genera. Neusticomys (as currently recognized) was found to consist of two well supported clades, one of which corresponds to the original concept of Daptomys. Accordingly, we propose the resurrection of the latter as a valid genus to include several species from low to middle elevations and restrict Neusticomys to several highland forms. Numerous other revisions are necessary to reconcile the alpha taxonomy of ichthyomyines with our phylogenetic results, including placement of the Cajas Plateau water rat (formerly Chibchanomys orcesi) in the genus Neusticomys (sensu stricto), and the recognition of at least two new species (one in Neusticomys, one in Daptomys). Additional work is necessary to confirm other unanticipated results, such as the non-monophyletic nature of Rheomys and the presence of a possible new genus and species from Peru. Our results also suggest that ichthyomyines are one of the main Andean radiations of sigmodontine cricetids, with an evolutionary history dating to the Late Miocene and subsequent cladogenesis during the Pleistocene.
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Affiliation(s)
- Jorge Salazar-Bravo
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States,Instituto de Ecologia, Universidad Mayor de San Andrés, La Paz, Bolivia,Instituto Nacional de Biodiversidad, Quito, Ecuador
| | - Nicolás Tinoco
- Museo de Zoología Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | | | - Jorge Brito
- Instituto Nacional de Biodiversidad, Quito, Ecuador
| | | | - David Marín-C
- Colección Teriológica, Universidad de Antioquia, Medellin, Colombia
| | | | - Alexandre R. Percequillo
- Escola Superior de Agricultura “Luiz de Queiroz”, Departamento de Ciências Biológicas, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Thomas E. Lee, Jr.
- Department of Biology, Abilene Christian University, Abilene, Texas, United States
| | - Sergio Solari
- Instituto de Biología, Universidad de Antioquia, Medellin, Antioquia, Colombia
| | - Javier Colmenares-Pinzon
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States,Grupo de Estudios en Biodiversidad, Escuela de Biología, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
| | - Carlos Nivelo
- Museo de Zoologia, Escuela de Biología, Universidad del Azuay, Cuenca, Ecuador,Instituto de Diversidad y Evolución Austral, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Chubut, Argentina
| | | | - William Merino
- Escuela de Biología, Universidad de El Salvador, San Salvador, San Salvador, El Salvador
| | - Cesar E. Medina
- Museo de Historia Natural, Universidad Nacional de San Agustin, Arequipa, Arequipa, Peru
| | - Oscar Murillo-García
- Departamento de Biología, Universidad del Valle, Cali, Valle del Cauca, Colombia
| | - Ulyses F.J. Pardiñas
- Instituto Nacional de Biodiversidad, Quito, Ecuador,Instituto de Diversidad y Evolución Austral, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Chubut, Argentina
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Bentz EJ, Ophir AG. Chromosome-scale genome assembly of the African giant pouched rat (Cricetomys ansorgei) and evolutionary analysis reveals evidence of olfactory specialization. Genomics 2022; 114:110521. [PMID: 36351561 DOI: 10.1016/j.ygeno.2022.110521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/07/2022]
Abstract
The Southern giant pouched rat, Cricetomys ansorgei, is a large rodent best known for its ability to detect landmines using its impressive sense of smell. Their powerful chemosensory abilities enable subtle discrimination of chemical social signals, and female pouched rats demonstrate a unique reproductive physiology hypothesized to be mediated by pheromonal mechanisms. Thus, C. ansorgei represents a novel mammalian model for chemosensory physiology, social behavior, and pheromonal control of reproductive physiology. We present the first chromosome-scale genomic sequence of the pouched rat encoding 22,671 protein coding genes, including 1571 olfactory receptors, and provide a glance into the evolutionary history of this species. Functional enrichment analysis reveals genetic expansions specific to the pouched rat are enriched for functions related to olfactory specialization. Overall, this assembly is of reference-quality, and will serve as a useful and informative genomic sequence on which we can confidently base future molecular research involving the pouched rat.
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Affiliation(s)
- Ehren J Bentz
- Department of Psychology, Cornell University, Ithaca, NY, USA.
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Abstract
SignificancePhylogenies are the basis of many ecological and evolutionary studies. However, zokor phylogeny and speciation patterns are heavily debated. This study disentangled the phylogeny and speciation of zokors genomically. Six species of the Eospalax were separated into high-altitude E. baileyi and E. smithi and the rest four low-altitude species by recent Qinghai-Tibet Plateau uplift 3.6 million y ago. E. rothschildi and E. smithi speciated south of the Qinling-Huaihe Line, where refuges were supplied during glaciation. Introgression and incomplete lineage sorting led to the complex phylogeny of zokors. Genomic islands were formed due to ancient polymorphisms and divergence hitchhiking. This study concluded that climatic, geological, and tectonic events shaped the phylogeny and speciation of zokors in China.
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8
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Bussi Y, Kapon R, Reich Z. Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy. PLoS One 2021; 16:e0258693. [PMID: 34648558 PMCID: PMC8516232 DOI: 10.1371/journal.pone.0258693] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/02/2021] [Indexed: 12/24/2022] Open
Abstract
Information theoretic approaches are ubiquitous and effective in a wide variety of bioinformatics applications. In comparative genomics, alignment-free methods, based on short DNA words, or k-mers, are particularly powerful. We evaluated the utility of varying k-mer lengths for genome comparisons by analyzing their sequence space coverage of 5805 genomes in the KEGG GENOME database. In subsequent analyses on four k-mer lengths spanning the relevant range (11, 21, 31, 41), hierarchical clustering of 1634 genus-level representative genomes using pairwise 21- and 31-mer Jaccard similarities best recapitulated a phylogenetic/taxonomic tree of life with clear boundaries for superkingdom domains and high subtree similarity for named taxons at lower levels (family through phylum). By analyzing ~14.2M prokaryotic genome comparisons by their lowest-common-ancestor taxon levels, we detected many potential misclassification errors in a curated database, further demonstrating the need for wide-scale adoption of quantitative taxonomic classifications based on whole-genome similarity.
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Affiliation(s)
- Yuval Bussi
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ruti Kapon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Reich
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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Guo YT, Zhang J, Xu DM, Tang LZ, Liu Z. Phylogenomic relationships and molecular convergences to subterranean life in rodent family Spalacidae. Zool Res 2021; 42:671-674. [PMID: 34490760 PMCID: PMC8455469 DOI: 10.24272/j.issn.2095-8137.2021.240] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
All extant species in the rodent family Spalacidae are subterranean and have evolved various traits for underground life. However, the phylogenomic relationships among its three subfamilies (Myospalacinae, Spalacinae, and Rhizomyinae) and the molecular basis underlying their adaptations to underground life remain poorly understood. Here, we inferred the phylogenomic relationships among these subfamilies based on de novo sequencing the genome of the hoary bamboo rat ( Rhizomys pruinosus). Analyses showed that ~50% of the identified 11 028 one-to-one orthologous protein-coding genes and the concatenated sequences of these orthologous genes strongly supported a sister relationship between Myospalacinae and Rhizomyinae. The three subfamilies diversified from each other within ~2 million years. Compared with the non-subterranean controls with similar divergence dates, the spalacids shared more convergent genes with the African subterranean mole-rats at the genomic scale due to more rapid protein sequence evolution. Furthermore, these convergent genes were enriched in the functional categories of carboxylic acid transport, vascular morphogenesis, and response to oxidative stress, which are closely associated with adaptations to the hypoxic-hypercapnic underground environment. Our study presents a well-supported phylogenomic relationship among the three subfamilies of Spalacidae and offers new insights into the molecular adaptations of spalacids living underground.
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Affiliation(s)
- Yuan-Ting Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Jia Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Dong-Ming Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Li-Zhou Tang
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, China. E-mail:
| | - Zhen Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
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Evolution Towards Fossoriality and Morphological Convergence in the Skull of Spalacidae and Bathyergidae (Rodentia). J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09550-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Maestri R, Duarte L. Evoregions: Mapping shifts in phylogenetic turnover across biogeographic regions. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Renan Maestri
- Departamento de Ecologia Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Leandro Duarte
- Departamento de Ecologia Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
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12
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Baskevich MI, Bogdanov AS, Khlyap LA, Malygin VM, Oparin ML, Sapelnikov SF, Sheftel BI. Phylogeny and Differentiation of Sibling-Species Sicista of the Group Betulina (Rodentia, Dipodoidea): Results of Analysis of a Fragment of the IRBP Gene of Nuclear DNA Variability. BIOL BULL+ 2020. [DOI: 10.1134/s1062359020050027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Species and genetic diversity of Bandicota (Murinae, Rodentia) from Myanmar based on mitochondrial and nuclear gene sequences. MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00491-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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Zou Y, Xu M, Ren S, Liang N, Han C, Nan X, Shi J. Taxonomy and phylogenetic relationship of zokors. J Genet 2020. [DOI: 10.1007/s12041-020-01200-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Hamidi K, Darvish J, Behnam-Rassouli M. The Role of Postcranial Skeleton Morphology in Species Identification and Phylogeny Inferences: Gerbillinae (Rodentia: Muridae) as a Case Study. MAMMAL STUDY 2020. [DOI: 10.3106/ms2019-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Kordiyeh Hamidi
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Jamshid Darvish
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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Freeman AR, Ophir AG, Sheehan MJ. The giant pouched rat (Cricetomys ansorgei) olfactory receptor repertoire. PLoS One 2020; 15:e0221981. [PMID: 32240170 PMCID: PMC7117715 DOI: 10.1371/journal.pone.0221981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 03/06/2020] [Indexed: 12/12/2022] Open
Abstract
For rodents, olfaction is essential for locating food, recognizing mates and competitors, avoiding predators, and navigating their environment. It is thought that rodents may have expanded olfactory receptor repertoires in order to specialize in olfactory behavior. Despite being the largest clade of mammals and depending on olfaction relatively little work has documented olfactory repertoires outside of conventional laboratory species. Here we report the olfactory receptor repertoire of the African giant pouched rat (Cricetomys ansorgei), a Muroid rodent distantly related to mice and rats. The African giant pouched rat is notable for its large cortex and olfactory bulbs relative to its body size compared to other sympatric rodents, which suggests anatomical elaboration of olfactory capabilities. We hypothesized that in addition to anatomical elaboration for olfaction, these pouched rats might also have an expanded olfactory receptor repertoire to enable their olfactory behavior. We examined the composition of the olfactory receptor repertoire to better understand how their sensory capabilities have evolved. We identified 1145 intact olfactory genes, and 260 additional pseudogenes within 301 subfamilies from the African giant pouched rat genome. This repertoire is similar to mice and rats in terms of size, pseudogene percentage and number of subfamilies. Analyses of olfactory receptor gene trees revealed that the pouched rat has 6 expansions in different subfamilies compared to mice, rats and squirrels. We identified 81 orthologous genes conserved among 4 rodent species and an additional 147 conserved genes within the Muroid rodents. The orthologous genes shared within Muroidea suggests that there may be a conserved Muroid-specific olfactory receptor repertoire. We also note that the description of this repertoire can serve as a complement to other studies of rodent olfaction, as the pouched rat is an outgroup within Muroidea. Thus, our data suggest that African giant pouched rats are capable of both natural and trained olfactory behaviors with a typical Muriod olfactory receptor repertoire.
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Affiliation(s)
- Angela R. Freeman
- Department of Psychology, Cornell University, Ithaca, NY, United States of America
- * E-mail:
| | - Alexander G. Ophir
- Department of Psychology, Cornell University, Ithaca, NY, United States of America
| | - Michael J. Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, United States of America
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Franco‐Sierra ND, Díaz‐Nieto JF. Rapid mitochondrial genome sequencing based on Oxford Nanopore Sequencing and a proxy for vertebrate species identification. Ecol Evol 2020; 10:3544-3560. [PMID: 32274008 PMCID: PMC7141017 DOI: 10.1002/ece3.6151] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/09/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023] Open
Abstract
Molecular information is crucial for species identification when facing challenging morphology-based specimen identifications. The use of DNA barcodes partially solves this problem, but in some cases when PCR is not an option (i.e., primers are not available, problems in reaction standardization), amplification-free approaches could be an optimal alternative. Recent advances in DNA sequencing, like the MinION device from Oxford Nanopore Technologies (ONT), allow to obtain genomic data with low laboratory and technical requirements, and at a relatively low cost. In this study, we explore ONT sequencing for molecular species identification from a total DNA sample obtained from a neotropical rodent and we also test the technology for complete mitochondrial genome reconstruction via genome skimming. We were able to obtain "de novo" the complete mitogenome of a specimen from the genus Melanomys (Cricetidae: Sigmodontinae) with average depth coverage of 78X using ONT-only data and by combining multiple assembly routines. Our pipeline for an automated species identification was able to identify the sample using unassembled sequence data (raw) in a reasonable computing time, which was substantially reduced when a priori information related to the organism identity was known. Our findings suggest ONT sequencing as a suitable candidate to solve species identification problems in metazoan nonmodel organisms and generate complete mtDNA datasets.
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Affiliation(s)
- Nicolás D. Franco‐Sierra
- Grupo de investigación en Biodiversidad, Evolución y Conservación (BEC)Departamento de Ciencias Biológicas, Escuela de CienciasUniversidad EAFITMedellínColombia
| | - Juan F. Díaz‐Nieto
- Grupo de investigación en Biodiversidad, Evolución y Conservación (BEC)Departamento de Ciencias Biológicas, Escuela de CienciasUniversidad EAFITMedellínColombia
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Potapova EG. Morphological Specificity of the Auditory Capsule of Sciurid (Sciuridae, Rodentia). BIOL BULL+ 2020. [DOI: 10.1134/s1062359019070094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Diversification and evolutionary history of brush-tailed mice, Calomyscidae (Rodentia), in southwestern Asia. ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-019-00426-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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de Córdova JF, Nivelo-Villavicencio C, Reyes-Puig C, Pardiñas UF, Brito J. A new species of crab-eating rat of the genus Ichthyomys, from Ecuador (Rodentia, Cricetidae, Sigmodontinae). MAMMALIA 2019. [DOI: 10.1515/mammalia-2019-0022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Based on two adult specimens collected in the Río León (Azuay, Ecuador), we describe a new highland species of a small crab-eating rat of the genus Ichthyomys Thomas (Rodentia, Cricetidae, Ichthyomyini). It is distinguishable from Ichthyomys hydrobates (Winge, 1891), the species phenetically closest to it, by its smaller size, bicolored tail (unicolored in I. hydrobates), broad and heavily fringed hindfoot (narrower and moderately fringed in I. hydrobates), and several craniodental traits (e.g. rostrum short broad; nasals anteriorly truncated; interorbital region narrow; supraorbital margins smoothly rounded; supraorbital foramina small, zygomatic plate very narrow; incisors opisthodont; length of M3 half that of M2). The new species occurs in the western Andes in southern Ecuador and is allopatric with Ichthyomys stolzmanni Thomas, 1893, which also has a bicolored tail but is larger. The new species brings the number of Ecuadorean Ichthyomys to four, Ecuador thus becoming the country with the greatest diversity of Ichthyomyini (four genera and eight species).
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Affiliation(s)
- Javier Fernández de Córdova
- Laboratorio de Ecoacústica , Escuela de Biología de la Universidad del Azuay , Cuenca , 0101981 , Ecuador
- Facultad de Ciencias Exactas , Universidad de Buenos Aires , Viamonte 430 , Ciudad Autónoma de Buenos Aires , Argentina
| | | | - Carolina Reyes-Puig
- Instituto de Diversidad Biológica Tropical iBOTROP, Museo de Zoología, Instituto BIOSFERA, Colegio de Ciencias Biológicas y Ambientales , Universidad San Francisco de Quito , Campus 15 Cumbayá, Casilla Postal 17-1200-841 , Quito , Ecuador
| | - Ulyses F.J. Pardiñas
- Instituto de Diversidad y Evolución Austral (IDEAus – CONICET) , Bv. Brown 2915, 9120 Puerto Madryn , Chubut , Argentina
- Instituto Nacional de Biodiversidad (INABIO) , Rumipamba 341 y Av. de los Shyris, casilla: 17-07-8976 , Quito , Ecuador
| | - Jorge Brito
- Instituto Nacional de Biodiversidad (INABIO) , Rumipamba 341 y Av. de los Shyris, casilla: 17-07-8976 , Quito , Ecuador
- Departamento de Biología, Facultad de Ciencias , Escuela Politécnica Nacional , Quito , Ecuador
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21
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HE Y, Hu S, Ge D, Yang Q, Connor T, Zhou C. Evolutionary history of Spalacidae inferred from fossil occurrences and molecular phylogeny. Mamm Rev 2019. [DOI: 10.1111/mam.12170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Ya HE
- Key Laboratory of Southwest China Wildlife Resources Conservation Institute of Ecology Institute of Rare Animals and Plants of School of Life Sciences China West Normal University Nanchong Sichuan 637009China
- Natural History Research Center Shanghai Natural History Museum Shanghai Science & Technology Museum Shanghai 200041China
| | - Shuzhan Hu
- Key Laboratory of Southwest China Wildlife Resources Conservation Institute of Ecology Institute of Rare Animals and Plants of School of Life Sciences China West Normal University Nanchong Sichuan 637009China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing 100101China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing 100101China
| | - Thomas Connor
- Department of Fisheries and Wildlife Michigan State University East Lansing Michigan48823USA
| | - Caiquan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation Institute of Ecology Institute of Rare Animals and Plants of School of Life Sciences China West Normal University Nanchong Sichuan 637009China
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22
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D’Elía G, Fabre PH, Lessa EP. Rodent systematics in an age of discovery: recent advances and prospects. J Mammal 2019. [DOI: 10.1093/jmammal/gyy179] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pierre-Henri Fabre
- Institut des Sciences de l’Evolution (ISEM, UMR 5554 CNRS-UM2-IRD), Université Montpellier, Montpellier Cedex 5, France
| | - Enrique P Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Guterres A, de Oliveira RC, Fernandes J, de Lemos ERS. The mystery of the phylogeographic structural pattern in rodent-borne hantaviruses. Mol Phylogenet Evol 2019; 136:35-43. [PMID: 30914396 DOI: 10.1016/j.ympev.2019.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 12/19/2022]
Abstract
Hantaviruses (order Bunyavirales, family Hantaviridae) are important zoonotic pathogens. Because of the great diversity of their reservoir hosts, hantaviruses are excellent models to evaluate the dynamics of virus-host co-evolution. To understand the mechanisms behind the evolutionary history of hantaviruses through virus-reservoir interactions, it is important to know how the radiation and diversity of hantaviruses occurred. In this paper, we evaluate the pattern of hantavirus diversification based on a complete S segment representing major groups of hantaviruses found in the Americas. Phylogenetic analyses revealed a high degree of phylogeographic structure and a surprising pattern of geographical distribution of New World hantaviruses. The available data suggest that hantaviruses related to the Arvicolinae rodent subfamily in North America probably emerged and initially adapted from a shared common ancestor of the Tula virus. The first clade of hantaviruses associated with Neotominae occupied a stem lineage, especially those that emerged in Central America or Mexico. Hantaviruses from Central America and Mexico found in Neotominae rodents spread northward and probably gave rise to the first phylogroup of hantaviruses associated with Sigmodontinae in North America. Two preferential host-switching transmissions in hantaviruses apparently gave rise to two different paraphyletic group in Neotominae and Sigmodontinae. Our study supports a probable epicenter of diversification in Central America and/or Mexico for hantaviruses related to both the Neotominae and Sigmodontinae subfamilies.
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Affiliation(s)
- Alexandro Guterres
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
| | - Renata Carvalho de Oliveira
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Jorlan Fernandes
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Elba Regina Sampaio de Lemos
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
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Blankenship PA, Normann MC, Donaldson TN, Baumeister J, McNeal N, Grippo AJ, Wallace DG. Making waves: Comparing Morris water task performance in rats and prairie voles. Behav Brain Res 2018; 360:7-15. [PMID: 30472112 DOI: 10.1016/j.bbr.2018.11.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 11/26/2022]
Abstract
Spatial processing is a critical component for survival. This domain of information processing has been extensively studied in rats and mice. Limited work has examined the capacity of other rodent species, like the prairie vole (Microtus ochrogaster), to process spatial information. The Morris water task (MWT) is a classic spatial task that has been used to examine spatial cognition in rodents. This task involves an animal developing configural relationships between extra-maze cues and the location of a hidden platform to successfully escape from a pool of water. The current study compared performance in the MWT between rats and prairie voles. Rats were observed to outperform prairie voles in key aspects of the task including latency to find the platform, directness of swim paths to the platform, and degrees of heading error. These results may be attributed to potential interspecies differences in spatial cognition, stress reactivity, physiology, or motivation. This study provides the foundation for future work investigating the spatial cognition of prairie voles and the factors that contribute to water task performance in rodents.
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Affiliation(s)
| | - Marigny C Normann
- Psychology Department, Northern Illinois University, DeKalb, IL 60115-2892 USA
| | - Tia N Donaldson
- Psychology Department, Northern Illinois University, DeKalb, IL 60115-2892 USA
| | - Joanna Baumeister
- Psychology Department, Northern Illinois University, DeKalb, IL 60115-2892 USA
| | - Neal McNeal
- Psychology Department, Northern Illinois University, DeKalb, IL 60115-2892 USA
| | - Angela J Grippo
- Psychology Department, Northern Illinois University, DeKalb, IL 60115-2892 USA
| | - Douglas G Wallace
- Psychology Department, Northern Illinois University, DeKalb, IL 60115-2892 USA
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26
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Lee MJ, Lee D, Jung HS. Wound healing mechanism in Mongolian gerbil skin. Histochem Cell Biol 2018; 151:229-238. [DOI: 10.1007/s00418-018-1752-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2018] [Indexed: 12/18/2022]
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Wu Z, Liu B, Du J, Zhang J, Lu L, Zhu G, Han Y, Su H, Yang L, Zhang S, Liu Q, Jin Q. Discovery of Diverse Rodent and Bat Pestiviruses With Distinct Genomic and Phylogenetic Characteristics in Several Chinese Provinces. Front Microbiol 2018; 9:2562. [PMID: 30405596 PMCID: PMC6207626 DOI: 10.3389/fmicb.2018.02562] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/08/2018] [Indexed: 11/13/2022] Open
Abstract
Bats and rodents are widely distributed worldwide and can be native or intermediate reservoirs of many important zoonotic viruses. Pestiviruses are a group of virus species of the genus Pestivirus under the family Flaviviridae that can infect a wide variety of artiodactylous hosts, including swine and ruminants. Two classic types of pestiviruses, bovine viral diarrhea virus and classical swine fever virus, are important causative agents of mild-to-severe disease in bovine and swine hosts, respectively, and cause tremendous economic losses in these industries. Recent reports revealed that bats and rodents could also act as natural hosts of pestiviruses and an atypical porcine pestivirus, which cause disease in piglets, showed a close genetic relationship with a specific bat pestivirus, RaPestV-1. This study aimed to describe the detection and characterization of novel pestiviruses from bats and rodents in different locations by analyzing the available bat and rodent virome data from throughout China. Two bat pestivirus species and four rodent pestivirus species that are distinct from other known viruses were identified and sequenced. These viruses were identified from two bat species and four rodent species in different Chinese provinces. There were two distinct lineages present in these viruses, that differ from artiodactylous pestivirus. These findings expand our understanding of the genetic diversity of pestiviruses in bats and rodents and suggest the presence of a diverse set of pestiviruses in non-artiodactylous hosts. This study may provide new insight for the prevention of future viral disease outbreaks originating from bats and rodents.
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Affiliation(s)
- Zhiqiang Wu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiang Du
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Junpeng Zhang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Liang Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | | | - Yelin Han
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Haoxiang Su
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shuyi Zhang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Qiyong Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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28
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Kelly CD, Stoehr AM, Nunn C, Smyth KN, Prokop ZM. Sexual dimorphism in immunity across animals: a meta-analysis. Ecol Lett 2018; 21:1885-1894. [PMID: 30288910 DOI: 10.1111/ele.13164] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/16/2018] [Accepted: 09/03/2018] [Indexed: 01/03/2023]
Abstract
In animals, sex differences in immunity are proposed to shape variation in infection prevalence and intensity among individuals in a population, with females typically expected to exhibit superior immunity due to life-history trade-offs. We performed a systematic meta-analysis to investigate the magnitude and direction of sex differences in immunity and to identify factors that shape sex-biased immunocompetence. In addition to considering taxonomic and methodological effects as moderators, we assessed age-related effects, which are predicted to occur if sex differences in immunity are due to sex-specific resource allocation trade-offs with reproduction. In a meta-analysis of 584 effects from 124 studies, we found that females exhibit a significantly stronger immune response than do males, but the effect size is relatively small, and became non-significant after controlling for phylogeny. Female-biased immunity was more pronounced in adult than immature animals. More recently published studies did not report significantly smaller effect sizes. Among taxonomic and methodological subsets of the data, some of the largest effect sizes were in insects, further supporting previous suggestions that testosterone is not the only potential driver of sex differences in immunity. Our findings challenge the notion of pervasive biases towards female-biased immunity and the role of testosterone in driving these differences.
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Affiliation(s)
- Clint D Kelly
- Département des sciences biologiques, Université du Québec à Montréal, C.P. 8888, succursale Centre-Ville, Montreal, QC, H3C 3P8, Canada
| | - Andrew M Stoehr
- Department of Biological Sciences, Butler University, 4600 Sunset Avenue, Indianapolis, IN, USA
| | - Charles Nunn
- Department of Evolutionary Anthropology, Duke University, Science Drive, Durham, NC, 27708, USA.,Duke Global Health Institute, Duke University, Trent Drive, Durham, NC, 27710, USA
| | - Kendra N Smyth
- Department of Evolutionary Anthropology, Duke University, Science Drive, Durham, NC, 27708, USA.,University Program in Ecology, Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | - Zofia M Prokop
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
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29
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Wu Z, Lu L, Du J, Yang L, Ren X, Liu B, Jiang J, Yang J, Dong J, Sun L, Zhu Y, Li Y, Zheng D, Zhang C, Su H, Zheng Y, Zhou H, Zhu G, Li H, Chmura A, Yang F, Daszak P, Wang J, Liu Q, Jin Q. Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases. MICROBIOME 2018; 6:178. [PMID: 30285857 PMCID: PMC6171170 DOI: 10.1186/s40168-018-0554-9] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 09/05/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Rodents represent around 43% of all mammalian species, are widely distributed, and are the natural reservoirs of a diverse group of zoonotic viruses, including hantaviruses, Lassa viruses, and tick-borne encephalitis viruses. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases. RESULTS We used next-generation sequencing metagenomic analysis to survey for a range of mammalian viral families in rodents and other small animals of the orders Rodentia, Lagomorpha, and Soricomorpha in China. We sampled 3,055 small animals from 20 provinces and then outlined the spectra of mammalian viruses within these individuals and the basic ecological and genetic characteristics of novel rodent and shrew viruses among the viral spectra. Further analysis revealed that host taxonomy plays a primary role and geographical location plays a secondary role in determining viral diversity. Many viruses were reported for the first time with distinct evolutionary lineages, and viruses related to known human or animal pathogens were identified. Phylogram comparison between viruses and hosts indicated that host shifts commonly happened in many different species during viral evolutionary history. CONCLUSIONS These results expand our understanding of the viromes of rodents and insectivores in China and suggest that there is high diversity of viruses awaiting discovery in these species in Asia. These findings, combined with our previous bat virome data, greatly increase our knowledge of the viral community in wildlife in a densely populated country in an emerging disease hotspot.
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Affiliation(s)
- Zhiqiang Wu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
| | - Liang Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Jiang Du
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Li Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Xianwen Ren
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Bo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Jinyong Jiang
- Yunnan Institute of Parasitic Diseases, Puer, People's Republic of China
| | - Jian Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Jie Dong
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Lilian Sun
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Yafang Zhu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Yuhui Li
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Dandan Zheng
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Chi Zhang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Haoxiang Su
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Yuting Zheng
- Yunnan Institute of Parasitic Diseases, Puer, People's Republic of China
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Puer, People's Republic of China
| | | | | | | | - Fan Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | | | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China.
| | - Qiyong Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China.
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Baskevich MI, Bogdanov AS, Khlyap LA. Taxonomy and Phylogeny of Sibling-Species Sicista of the Group Caucasica and Their Position in the Genus Sicista (Rodentia, Dipodoidea) according to Sequencing of the IRBP Gene Fragment of Nuclear DNA. BIOL BULL+ 2018. [DOI: 10.1134/s1062359018050047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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Isotopic evidence for niche partitioning and the influence of anthropogenic disturbance on endemic and introduced rodents in central Madagascar. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2018; 105:44. [PMID: 29959538 DOI: 10.1007/s00114-018-1564-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/26/2018] [Accepted: 05/17/2018] [Indexed: 10/28/2022]
Abstract
We applied a multi-isotope approach to examine aspects of niche partitioning, competition, and mobility for rodents in the Central Highlands of Madagascar. Specifically, we used carbon (δ13C), nitrogen (δ15N), and strontium (87Sr/86Sr) isotope ratios in bone to investigate diet and mobility for endemic tufted tail rats (Eliurus spp.), and introduced black rats (Rattus rattus) and house mice (Mus musculus) within and outside a fragment of montane humid forest in the Ambohitantely Special Reserve. There was a clear spatial segregation in trapping success for different species: Eliurus was only in the forest interior and edge, Mus only outside of the fragment in a marsh and park housing complex, and Rattus in all habitats except the housing complex. We find only moderate support for mobility of rodents among habitats. Mus may routinely move between the marsh and housing complex. However, regular movement between the forest edge and interior, or between the forest fragment and surrounding grassland is not supported. Taxa appear to target different foods: Rattus tends to feed at a higher trophic level than Eliurus, and Mus consumes some C4 resources. To date, strontium isotopes have been underutilized in ecological research. Here, we show that they are highly complementary to carbon and nitrogen isotope data. Even in localities with relatively uniform underlying geology, it may be possible to distinguish individuals that regularly forage in different habitats.
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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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Timm RM, Pine RH, Hanson JD. A new species of Tanyuromys Pine, Timm, and Weksler, 2012 (Cricetidae: Oryzomyini), with comments on relationships within the Oryzomyini. J Mammal 2018. [DOI: 10.1093/jmammal/gyy042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Robert M Timm
- Department of Ecology and Evolutionary Biology & Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Ronald H Pine
- Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - J Delton Hanson
- RTLGenomics, Lubbock, TX, USA
- Department of Biology, Columbus State University, Columbus, GA, USA
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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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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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Khemiri H, Pimenta J, Amorim A, Chevret P, Nouira S, Lopes AM. Genetic diversity within two Tunisian wild jirds: Meriones shawi and Meriones libycus (Rodentia, Gerbillinae). AFRICAN ZOOLOGY 2017. [DOI: 10.1080/15627020.2016.1269612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Hanene Khemiri
- Laboratory of Animal Ecology, Department of Biology, Sciences Faculty of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - João Pimenta
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pascale Chevret
- Laboratoire de Biométrie et Biologie Evolutive – UMR CNRS 5558, Université Claude Bernard Lyon 1, Villeurbanne Cedex, France
| | - Saïd Nouira
- Laboratory of Animal Ecology, Department of Biology, Sciences Faculty of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Alexandra M Lopes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
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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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Ndiaye A, Chevret P, Dobigny G, Granjon L. Evolutionary systematics and biogeography of the arid habitat-adapted rodent genus Gerbillus
(Rodentia, Muridae): a mostly Plio-Pleistocene African history. J ZOOL SYST EVOL RES 2016. [DOI: 10.1111/jzs.12143] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arame Ndiaye
- BIOPASS; CBGP Campus de Bel-Air (UCAD/ISRA/CBGP), IRD; Dakar Sénégal
- Département de Biologie Animale; Faculté des Sciences et Techniques; Université Cheikh Anta Diop; Dakar Sénégal
| | - Pascale Chevret
- Laboratoire de Biométrie et Biologie Evolutive - UMR CNRS 5558; Université Claude Bernard Lyon 1; Villeurbanne Cedex France
| | - Gauthier Dobigny
- Institut de Recherche pour le Développement; Centre de Biologie pour la Gestion des Populations (CBGP, INRA/IRD/SUPAGRO/CIRAD); Montferrier-sur-Lez Cedex France
| | - Laurent Granjon
- Institut de Recherche pour le Développement; Centre de Biologie pour la Gestion des Populations (CBGP, INRA/IRD/SUPAGRO/CIRAD); Montferrier-sur-Lez Cedex France
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Christoff AU, Vieira EM, Oliveira LR, Gonçalves JW, Valiati VH, Tomasi PS. A new species ofJuliomys(Rodentia, Cricetidae, Sigmodontinae) from the Atlantic Forest of Southern Brazil. J Mammal 2016. [DOI: 10.1093/jmammal/gyw082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Mikula O, Šumbera R, Aghová T, Mbau JS, Katakweba AS, Sabuni CA, Bryja J. Evolutionary history and species diversity of African pouched mice (Rodentia: Nesomyidae:Saccostomus). ZOOL SCR 2016. [DOI: 10.1111/zsc.12179] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Ondřej Mikula
- Institute of Vertebrate Biology; Academy of Sciences of the Czech Republic; Brno Czech Republic
- Institute of Animal Physiology and Genetics; Academy of Sciences of the Czech Republic; Brno Czech Republic
| | - Radim Šumbera
- Department of Zoology; Faculty of Science; University of South Bohemia; České Budějovice Czech Republic
| | - Tatiana Aghová
- Institute of Vertebrate Biology; Academy of Sciences of the Czech Republic; Brno Czech Republic
- Department of Botany and Zoology; Faculty of Science; Masaryk University; Brno Czech Republic
| | - Judith S. Mbau
- College of Agriculture and Veterinary Sciences; University of Nairobi; Nairobi Kenya
| | - Abdul S. Katakweba
- Pest Management Center; Sokoine University of Agriculture; Morogoro Tanzania
| | | | - Josef Bryja
- Institute of Vertebrate Biology; Academy of Sciences of the Czech Republic; Brno Czech Republic
- Department of Botany and Zoology; Faculty of Science; Masaryk University; Brno Czech Republic
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Phukuntsi MA, Brettschneider H, Dalton DL, Kearney T, Badenhorst J, Kotze A. DNA barcoding for identification of cryptic species in the field and existing museum collections: a case study ofAethomysandMicaelamys(Rodentia: Muridae). AFRICAN ZOOLOGY 2016. [DOI: 10.1080/15627020.2016.1146084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Pereira AL, Malcher SM, Nagamachi CY, O’Brien PCM, Ferguson-Smith MA, Mendes-Oliveira AC, Pieczarka JC. Extensive Chromosomal Reorganization in the Evolution of New World Muroid Rodents (Cricetidae, Sigmodontinae): Searching for Ancestral Phylogenetic Traits. PLoS One 2016; 11:e0146179. [PMID: 26800516 PMCID: PMC4723050 DOI: 10.1371/journal.pone.0146179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 12/13/2015] [Indexed: 12/05/2022] Open
Abstract
Sigmodontinae rodents show great diversity and complexity in morphology and ecology. This diversity is accompanied by extensive chromosome variation challenging attempts to reconstruct their ancestral genome. The species Hylaeamys megacephalus–HME (Oryzomyini, 2n = 54), Necromys lasiurus—NLA (Akodontini, 2n = 34) and Akodon sp.–ASP (Akodontini, 2n = 10) have extreme diploid numbers that make it difficult to understand the rearrangements that are responsible for such differences. In this study we analyzed these changes using whole chromosome probes of HME in cross-species painting of NLA and ASP to construct chromosome homology maps that reveal the rearrangements between species. We include data from the literature for other Sigmodontinae previously studied with probes from HME and Mus musculus (MMU) probes. We also use the HME probes on MMU chromosomes for the comparative analysis of NLA with other species already mapped by MMU probes. Our results show that NLA and ASP have highly rearranged karyotypes when compared to HME. Eleven HME syntenic blocks are shared among the species studied here. Four syntenies may be ancestral to Akodontini (HME2/18, 3/25, 18/25 and 4/11/16) and eight to Sigmodontinae (HME26, 1/12, 6/21, 7/9, 5/17, 11/16, 20/13 and 19/14/19). Using MMU data we identified six associations shared among rodents from seven subfamilies, where MMU3/18 and MMU8/13 are phylogenetic signatures of Sigmodontinae. We suggest that the associations MMU2entire, MMU6proximal/12entire, MMU3/18, MMU8/13, MMU1/17, MMU10/17, MMU12/17, MMU5/16, MMU5/6 and MMU7/19 are part of the ancestral Sigmodontinae genome.
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Affiliation(s)
- Adenilson Leão Pereira
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brasil
| | - Stella Miranda Malcher
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brasil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brasil
- CNPq Researcher, Brasília, Brasil
| | - Patricia Caroline Mary O’Brien
- Cambridge Resource Center for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Center for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, ICB, Universidade Federal do Pará, Belém, Pará, Brasil
- CNPq Researcher, Brasília, Brasil
- * E-mail:
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Li Q, Wang X. Into Tibet: An Early Pliocene Dispersal of Fossil Zokor (Rodentia: Spalacidae) from Mongolian Plateau to the Hinterland of Tibetan Plateau. PLoS One 2015; 10:e0144993. [PMID: 26658457 PMCID: PMC4678110 DOI: 10.1371/journal.pone.0144993] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 11/25/2015] [Indexed: 11/19/2022] Open
Abstract
This paper reports the fossil zokors (Myospalacinae) collected from the lower Pliocene (~4.4 Ma) of Zanda Basin, southwestern Tibet, which is the first record in the hinterland of Tibetan Plateau within the Himalayan Range. Materials include 29 isolated molars belonging to Prosiphneus eriksoni (Schlosser, 1924) by having characters including large size, highly fused roots, upper molars of orthomegodont type, m1 anterior cap small and centrally located, and first pair of m1 reentrants on opposing sides, high crowns, and high value of dentine tract parameters. Based on the cladistics analysis, all seven species of Prosiphneus and P. eriksoni of Zanda form a monophyletic clade. P. eriksoni from Zanda, on the other hand, is nearly the terminal taxon of this clade. The appearance of P. eriksoni in Zanda represents a significant dispersal in the early Pliocene from its center of origin in north China and Mongolian Plateau, possibly via the Hol Xil-Qiangtang hinterland in northern Tibet. The fast evolving zokors are highly adapted to open terrains at a time when regional climates had become increasingly drier in the desert zones north of Tibetan Plateau during the late Miocene to Pliocene. The occurrence of this zokor in Tibet thus suggests a rather open steppe environment. Based on fossils of large mammals, we have formulated an “out of Tibet” hypothesis that suggests earlier and more primitive large mammals from the Pliocene of Tibet giving rise to the Ice Age megafauna. However, fossil records for large mammals are still too poor to evaluate whether they have evolved from lineages endemic to the Tibetan Plateau or were immigrants from outside. The superior record of small mammals is in a better position to address this question. With relatively dense age intervals and numerous localities in much of northern Asia, fossil zokors provide the first example of an “into Tibet” scenario–earlier and more primitive taxa originated from outside of the Tibetan Plateau and the later the lineage became extinct in southwestern Tibet.
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Affiliation(s)
- Qiang Li
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China
- * E-mail:
| | - Xiaoming Wang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- Department of Vertebrate Paleontology, Natural History Museum of Los Angeles County, Los Angeles, California, United States of America
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Alhajeri BH, Schenk JJ, Steppan SJ. Ecomorphological diversification following continental colonization in muroid rodents (Rodentia: Muroidea). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12695] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Bader H. Alhajeri
- Department of Biological Science; Florida State University; Tallahassee FL 32306-4295 USA
- Department of Biological Sciences; Kuwait University; Safat 13110 Kuwait
| | - John J. Schenk
- Department of Biological Science; Florida State University; Tallahassee FL 32306-4295 USA
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA 70118-5698 USA
| | - Scott J. Steppan
- Department of Biological Science; Florida State University; Tallahassee FL 32306-4295 USA
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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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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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Two novel mitogenomes of Dipodidae species and phylogeny of Rodentia inferred from the complete mitogenomes. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.04.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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50
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Wolf G, Yang P, Füchtbauer AC, Füchtbauer EM, Silva AM, Park C, Wu W, Nielsen AL, Pedersen FS, Macfarlan TS. The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses. Genes Dev 2015; 29:538-54. [PMID: 25737282 PMCID: PMC4358406 DOI: 10.1101/gad.252767.114] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Endogenous retroviruses (ERVs) are epigenetically silenced during development, yet the cellular factors recognizing ERVs in a sequence-specific manner remain elusive. Wolf et al. find that ZFP809 initiates the silencing of ERVs in a sequence-specific manner via recruitment of heterochromatin-inducing complexes. ERV reactivation is accompanied by an epigenetic shift from repressive to active histone modifications. ZFP809 is required to initiate ERV silencing during embryonic development but becomes largely dispensable in somatic tissues. Retroviruses have been invading mammalian germlines for millions of years, accumulating in the form of endogenous retroviruses (ERVs) that account for nearly one-tenth of the mouse and human genomes. ERVs are epigenetically silenced during development, yet the cellular factors recognizing ERVs in a sequence-specific manner remain elusive. Here we demonstrate that ZFP809, a member of the Krüppel-associated box zinc finger protein (KRAB-ZFP) family, initiates the silencing of ERVs in a sequence-specific manner via recruitment of heterochromatin-inducing complexes. ZFP809 knockout mice display highly elevated levels of ZFP809-targeted ERVs in somatic tissues. ERV reactivation is accompanied by an epigenetic shift from repressive to active histone modifications but only slight destabilization of DNA methylation. Importantly, using conditional alleles and rescue experiments, we demonstrate that ZFP809 is required to initiate ERV silencing during embryonic development but becomes largely dispensable in somatic tissues. Finally, we show that the DNA-binding specificity of ZFP809 is evolutionarily conserved in the Muroidea superfamily of rodents and predates the endogenization of retroviruses presently targeted by ZFP809 in Mus musculus. In sum, these data provide compelling evidence that ZFP809 evolved to recognize foreign DNA and establish histone modification-based epigenetic silencing of ERVs.
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Affiliation(s)
- Gernot Wolf
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Peng Yang
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Annette C Füchtbauer
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Andreia M Silva
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Chungoo Park
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Warren Wu
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Anders L Nielsen
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Finn S Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA;
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