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Kujawska M, Raulo A, Millar M, Warren F, Baltrūnaitė L, Knowles SCL, Hall LJ. Bifidobacterium castoris strains isolated from wild mice show evidence of frequent host switching and diverse carbohydrate metabolism potential. ISME COMMUNICATIONS 2022; 2:20. [PMID: 37938745 PMCID: PMC9723756 DOI: 10.1038/s43705-022-00102-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 01/30/2022] [Accepted: 02/09/2022] [Indexed: 11/09/2023]
Abstract
Members of the gut microbiota genus Bifidobacterium are widely distributed human and animal symbionts believed to exert beneficial effects on their hosts. However, in-depth genomic analyses of animal-associated species and strains are somewhat lacking, particularly in wild animal populations. Here, to examine patterns of host specificity and carbohydrate metabolism capacity, we sequenced whole genomes of Bifidobacterium isolated from wild-caught small mammals from two European countries (UK and Lithuania). Members of Bifidobacterium castoris, Bifidobacterium animalis and Bifodobacterium pseudolongum were detected in wild mice (Apodemus sylvaticus, Apodemus agrarius and Apodemus flavicollis), but not voles or shrews. B. castoris constituted the most commonly recovered Bifidobacterium (78% of all isolates), with the majority of strains only detected in a single population, although populations frequently harboured multiple co-circulating strains. Phylogenetic analysis revealed that the mouse-associated B. castoris clades were not specific to a particular location or host species, and their distribution across the host phylogeny was consistent with regular host shifts rather than host-microbe codiversification. Functional analysis, including in vitro growth assays, suggested that mouse-derived B. castoris strains encoded an extensive arsenal of carbohydrate-active enzymes, including putative novel glycosyl hydrolases such as chitosanases, along with genes encoding putative exopolysaccharides, some of which may have been acquired via horizontal gene transfer. Overall, these results provide a rare genome-level analysis of host specificity and genomic capacity among important gut symbionts of wild animals, and reveal that Bifidobacterium has a labile relationship with its host over evolutionary time scales.
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Affiliation(s)
- Magdalena Kujawska
- Gut Microbes & Health, Quadram Institute Biosciences, Norwich Research Park, Norwich, UK
- Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Aura Raulo
- Department of Zoology, University of Oxford, Mansfield Road, Oxford, UK
| | - Molly Millar
- Food Innovation and Health, Quadram Institute Biosciences, Norwich Research Park, Norwich, UK
| | - Fred Warren
- Food Innovation and Health, Quadram Institute Biosciences, Norwich Research Park, Norwich, UK
| | | | - Sarah C L Knowles
- Department of Zoology, University of Oxford, Mansfield Road, Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, Hatfield, Herfordshire, UK
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Biosciences, Norwich Research Park, Norwich, UK.
- Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK.
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Sex Differences in Mouse Exploratory Behaviour to Fel d 1, a Cat ABP-Like Protein. Animals (Basel) 2021; 11:ani11113149. [PMID: 34827881 PMCID: PMC8614430 DOI: 10.3390/ani11113149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/23/2021] [Accepted: 11/03/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Fel d 1 is a cat secreted protein, known as the main cat allergen, that is abundantly released and found in their habitat. Cats are one of the main predators of rodents and have been historically used to control rodent populations in human habitats. We assumed that laboratory mice, as a model of wild mice, would be able to detect and avoid this abundant cat molecule as a mechanism to increase chances of survival. In our study, we compared mice exploratory behaviours facing Fel d 1, a fox faeces molecule (TMT) as a positive control, and a negative control (purified water). We found that mice did not avoid Fel d 1 as we expected; however, male mice remained in the area with Fel d 1 longer than females. These results give interesting insights about how sexes can react differently to a predator stimulus and give support to the use of both sexes in behavioural studies, and more precisely in predator-prey interactions research Abstract Fel d 1 is a cat protein abundantly released and found in their habitat and is closely related to mouse androgen-binding proteins (ABPs). We hypothesized that mice have developed chemical communication mechanisms to detect and avoid this protein. We tested purified natural Fel d 1, a fox faeces molecule (TMT) as a positive control, and a negative control (purified water) in three different mouse groups (n = 14 each) to evaluate exploratory behaviour and stress responses. The mice did not show clear avoidance or stress responses to Fel d 1. Our results demonstrated a sex-treatment interaction for Fel d 1, with males spending more time in the areas treated with Fel d 1 than in the untreated areas (p = 0.018). This sex-treated area interaction was also not observed for either the blank or TMT. These results suggest that Fel d 1 from domestic cats could be recognized differently by male and female mice. These sex differences could be linked to the sexual role of ABP proteins and the ABP-like characteristics of Fel d 1.
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Olgun Karacan G, Çolak R, Çolak E. The roles of possible geographic barriers and geological events on the phylogeographic structure of the Eastern broad toothed field mouse ( Apodemus mystacinus). MAMMALIA 2021. [DOI: 10.1515/mammalia-2020-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The Eastern broad toothed field mouse, Apodemus mystacinus, is a rodent species distributed in Turkey, the Middle East, and a few Aegean Islands. The aim of this study is to analyse the phylogeographic structure of A. mystacinus and possible causes of its differentiation, on the basis of mitochondrial and nuclear DNA sequences using a large number of new samples from Turkey. In this context, partial mitochondrial sequences of cytochrome b (Cytb), control region (D-loop) and a nuclear interphotoreceptor retinoid-binding protein (IRBP) gene were used to reveal the geographical differentiation among A. mystacinus populations and the validity of its subspecies. The estimated divergence times revealed that the first separation of A. mystacinus into three distinct groups (subspecies of A. mystacinus: A. m. mystacinus, A. m. smyrnensis, and A. m. euxinus) begun 0.641 Mya. The possible physical barriers in Anatolia such as high mountains and rivers could interrupt the gene flow between A. mystacinus populations. The results of the present study indicated that A. mystacinus might have used the high rocky areas along the Anatolian Diagonal as a dispersal way. Moreover, mitochondrial data in this study suggested for the first time that A. m. rhodius is synonymous with the nominative subspecies A. m. mystacinus.
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Affiliation(s)
- Gül Olgun Karacan
- Department of Medical Services and Techniques , Vocational School of Health Services, Aksaray University , Aksaray 68100 , Turkey
| | - Reyhan Çolak
- Department of Biology , Faculty of Science, Ankara University , Ankara , Turkey
| | - Ercüment Çolak
- Department of Biology , Faculty of Science, Ankara University , Ankara , Turkey
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Hu TL, Cheng F, Xu Z, Chen ZZ, Yu L, Ban Q, Li CL, Pan T, Zhang BW. Molecular and morphological evidence for a new species of the genus Typhlomys (Rodentia: Platacanthomyidae). Zool Res 2021; 42:100-107. [PMID: 33258336 PMCID: PMC7840448 DOI: 10.24272/j.issn.2095-8137.2020.132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In this study, we reassessed the taxonomic position of Typhlomys (Rodentia: Platacanthomyidae) from Huangshan, Anhui, China, based on morphological and molecular evidence. Results suggested that Typhlomys is comprised of up to six species, including four currently recognized species ( Typhlomys cinereus, T. chapensis, T. daloushanensis, and T. nanus), one unconfirmed candidate species, and one new species ( Typhlomys huangshanensis sp. nov.). Morphological analyses further supported the designation of the Huangshan specimens found at mid-elevations in the southern Huangshan Mountains (600 m to 1 200 m a.s.l.) as a new species.
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Affiliation(s)
- Ting-Li Hu
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Feng Cheng
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biology and Biochemistry, University Potsdam, Potsdam, Brandenburg 14476, Germany
| | - Zhen Xu
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Zhong-Zheng Chen
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241000, China. E-mail:
| | - Lei Yu
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China.,International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Hefei, Anhui 230601, China
| | - Qian Ban
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Chun-Lin Li
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui 230601, China
| | - Tao Pan
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Bao-Wei Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China.,International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology, Hefei, Anhui 230601, China. E-mail:
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Amshokova A, Tembotova F, Kononenko E. Assessment differentiation degree cryptic species of the genus Apodemus in the Northern Caucasus based on non-metric cranial characters. BIO WEB OF CONFERENCES 2021. [DOI: 10.1051/bioconf/20213500004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A phenetic analysis of non-metric cranial traits of two genetically identified cryptic species of the genus Apodemus in different ecological conditions of the North Caucasus was carried out. The maximum distance obtained between cryptic species did not exceed the level of subspecies differences. The phenetic distance between A. uralensis and A. flavicollis, which inhabit symbiotopically and sympatrically in the Western Caucasus, is almost 2 times lower. The smaller value of phenetic differences is probably related to the habitat of both species in similar land-scapebiotopic and climatic conditions, which contributes to the development of phenotypic similarity. In general, the obtained results indicate weak morphological differentiation of the studied species according to the studied phenetic characters (cranial foramen), although according to the results of molecular genetic analysis of the cyt b gene site, the genetic distance between the studied taxa is 10% and corresponds to the level of interspecific differences. Based on the above, reliable diagnosis of the studied species in the Caucasus is possible only by molecular genetic methods.
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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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Orekhova NYA. Hepatic effects of low-dose rate radiation in natural mouse populations ( Apodemus uralensis and Apodemus agrarius): comparative interspecific analysis. Int J Radiat Biol 2020; 96:1038-1050. [PMID: 32412327 DOI: 10.1080/09553002.2020.1770362] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Hypothesis: Natural mouse populations in radioactive contamination zone provide adequate information about dose loads and biological effects for 'non-human biota'. The comparative analysis of the responses of different species of mice allows us to reveal the possible variation in the effects of low-dose rate radiation relative to the ecological-physiological and functional-metabolic features of the species.Materials and methods: Objects of study - two sympatric rodent species [pygmy wood mouse (Apodemus uralensis Pallas, 1811) and striped field mouse (Apodemus agrarius Pallas, 1771)] caught on the territory of the East-Ural radioactive trace (EURT). The EURT zone is consequence the Kyshtym accident in South Urals in 1957. Nowadays, the main dose-forming radionuclide is β-emitting 90Sr. The individual dose rate of impacted mice caused by internal exposure to 90Sr varied from 0.021 to 0.152 mGy/day. The baseline functional-metabolic characteristics of the liver were researched: protein-, lipid-, and glycogen-synthesizing processes; glycolysis; aerobic synthesis of ATP; lipid peroxidation; and the H2O2-scavenging enzymatic status; and the functional activity of the genome.Results: The hepatic shifts for impacted populations are amplified with increasing dose rate of irradiation, regardless of which species is considered. But, the response of closely related species of rodents to irradiation is different both in the vector and the level (in A. agrarius sample was 2 time higher than that for A. uralensis).Conclusion: The radiation-induced hepatic shifts in A. uralensis from the EURT area correspond to the chronic response under stressful environmental conditions. The impacted population of A. agrarius can be considered the more reactive species to the radiation burden, demonstrating an acute effect. The interspecies contrast in the radiation response is associated with the original interspecies differences (background rodents' samples in 28 km from the impact study site), and also the degree of residency of the species in the impact plots.
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Affiliation(s)
- Natal Ya A Orekhova
- Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, Russia
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Chevret P, Renaud S, Helvaci Z, Ulrich RG, Quéré J, Michaux JR. Genetic structure, ecological versatility, and skull shape differentiation in
Arvicola
water voles (Rodentia, Cricetidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pascale Chevret
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558 CNRS Université Claude Bernard Lyon 1Université de Lyon Villeurbanne France
| | - Sabrina Renaud
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558 CNRS Université Claude Bernard Lyon 1Université de Lyon Villeurbanne France
| | - Zeycan Helvaci
- Conservation Genetics Laboratory Institut de Botanique Liège Belgium
| | - Rainer G. Ulrich
- Institute of Novel and Emerging Infectious Diseases Friedrich‐Loeffler‐Institut Federal Research Institute for Animal Health Greifswald ‐ Insel Riems Germany
| | - Jean‐Pierre Quéré
- Centre de Biologie et Gestion des Populations (INRA/IRD/Cirad/Montpellier SupAgro)Campus International de Baillarguet Montferrier‐sur‐Lez Cedex France
| | - Johan R. Michaux
- Conservation Genetics Laboratory Institut de Botanique Liège Belgium
- CIRAD/INRA UMR117 ASTRECampus International de Baillarguet Montpellier Cedex France
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Martin Cerezo ML, Kucka M, Zub K, Chan YF, Bryk J. Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq. BMC Genomics 2020; 21:241. [PMID: 32183700 PMCID: PMC7079423 DOI: 10.1186/s12864-020-6603-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 02/21/2020] [Indexed: 02/08/2023] Open
Abstract
Background Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context. Results Here we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise FST<0.086. Conclusion Our study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.
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Affiliation(s)
- Maria Luisa Martin Cerezo
- School of Applied Sciences, University of Huddersfield, Quennsgate, Huddersfield, UK.,AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Department of Zoology, Linköping University, Linköping, Sweden
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Karol Zub
- The Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | | | - Jarosław Bryk
- School of Applied Sciences, University of Huddersfield, Quennsgate, Huddersfield, UK.
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Okulova NM, Bogdanov AS, Baskevich MI, Orlov VN, Antonets NV, Popova YV, Lavrenchenko LA. Skull Sizes and Proportions in Western Palearctic Wood Mice (Sylvaemus, Muridae, Rodentia) from Eastern Europe: 1. Interspecific Variability. BIOL BULL+ 2019. [DOI: 10.1134/s1062359019080107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ge D, Feijó A, Cheng J, Lu L, Liu R, Abramov AV, Xia L, Wen Z, Zhang W, Shi L, Yang Q. Evolutionary history of field mice (Murinae: Apodemus), with emphasis on morphological variation among species in China and description of a new species. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractMice of the genus Apodemus are widely distributed across Eurasia. Several species of this genus are hosts of important zoonotic diseases and parasites. The evolutionary history and dispersal routes of these mice remain unclear and the distribution of these species in China was poorly explored in previous studies. We here investigate the divergence times and historical geographical evolution of Apodemus and study the taxonomy of species in China by integrating molecular and morphological data. The crown age of this genus is dated to the Late Miocene, approximately 9.84 Mya. Western and Central Asia were inferred as the most likely ancestral area of this genus. Moreover, we recognize nine living species of Apodemus in China: Apodemus uralensis, A. agrarius, A. chevrieri, A. latronum, A. peninsulae, A. draco, A. ilex, A. semotus and A. nigrus sp. nov., the last from the highlands (elevation > 1984 m) of Fanjing Mountain in Guizhou Province and Jinfo Mountain in Chongqing Province. This new species diverged from A. draco, A. semotus and A. ilex approximately 4.53 Mya. The discovery of A. nigrus highlights the importance of high mountains as refugia and ‘isolated ecological islands’ for temperate species in south-eastern China.
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Affiliation(s)
- Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 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
| | - Rongrong 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
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia
- Joint Russian–Vietnamese Tropical Research and Technological Centre, Hanoi, Vietnam
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | | | - Lei Shi
- Fanjingshan National Nature Reserve, Tongren, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
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Czarnomska SD, Niedziałkowska M, Borowik T, Jędrzejewska B. Winter temperature correlates with mtDNA genetic structure of yellow-necked mouse population in NE Poland. PLoS One 2019; 14:e0216361. [PMID: 31067251 PMCID: PMC6505929 DOI: 10.1371/journal.pone.0216361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/18/2019] [Indexed: 11/19/2022] Open
Abstract
We analysed a fragment (247 bp) of cytochrome b of mitochondrial DNA sequenced using 353 samples of yellow-necked mice Apodemus flavicollis trapped in seven forests and along three woodlot transects in north-eastern Poland. Our aims were to identify the phylogeographic pattern and mtDNA structure of the population and to evaluate the role of environmental conditions in shaping the spatial pattern of mtDNA diversity. We found out that three European haplogroups occurred sympatrically in north-eastern Poland. Inferences based on mtDNA haplotype distribution and frequency defined five subpopulations. The mtDNA-based structure of mice significantly correlated with winter temperature: frequency of Haplogroup 1 was positively, and that of Haplogroup 3 negatively correlated to mean temperature of January in the year of trapping. Synthesis of the published pan-European data on the species phylogeography also showed that the possibly 'thermophilous' Haplogroup 1 has the westernmost occurrence, whereas the more 'cold-resistant' Haplogroup 3 occurs much further to north-east than the other haplogroups. The observed patter may be a byproduct of the tight coevolution with nuclear genes, as we have earlier found that - in mice population in NE Poland - the spatial pattern of nuclear DNA was best explained by January temperature. Alternatively, the observed association of mitochondrial genetic variation with temperature is possible to be adaptive as cytochrome b is involved in the process of ATP production via oxidative phosphorylation.
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Affiliation(s)
| | | | - Tomasz Borowik
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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Matur F, Yanchukov A, Çolak F, Sözen M. Two major clades of blind mole rats (Nannospalax sp.) revealed by mtDNA and microsatellite genotyping in Western and Central Turkey. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2018.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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14
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Motokawa M, Wu Y, Harada M, Shintaku Y, Jiang XL, Li YC. Karyotypes of field mice of the genus Apodemus (Mammalia: Rodentia) from China. Zool Res 2018; 39:348-355. [PMID: 29872031 PMCID: PMC6102681 DOI: 10.24272/j.issn.2095-8137.2018.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/03/2018] [Indexed: 11/11/2022] Open
Abstract
Karyotypes of four Chinese species of field mice of the genus Apodemus were examined, including Apodemus chevrieri (diploid chromosome number, 2n=48, fundamental number of autosomal arms, FNa=56), A. draco (2n=48, FNa=48), A. ilex (2n=48, FNa=48), and A. latronum (2n=48, FNa=48). Karyotypes of A. chevrieri, A. draco, and A. ilex are reported here for the first time, providing useful information for their species taxonomy. Determining the karyotypes of all species of Apodemus in Asia, both in this and previous studies, provides a solid overview of the chromosome evolution and species differentiation of the genus in East Asia. In addition to allopatric speciation, chromosome rearrangements likely played an important role in the formation of the four Apodemus species groups as well as speciation within each group in East Asia. For example, increased centromeric heterochromatin in A. latronum may have contributed to the post-mating reproductive isolation from the A. draco-A. ilex-A. semotus clade.
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Affiliation(s)
- Masaharu Motokawa
- Kyoto University Museum, Kyoto University, Kyoto 606-8501, Japan; E-mail:
| | - Yi Wu
- Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou University, Guangzhou Guangdong 510006, China
| | - Masashi Harada
- Laboratory Animal Center, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan
| | - Yuta Shintaku
- Wildlife Research Center, Kyoto University, Sakyo, Kyoto 606-8203, Japan
- Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan
| | - Xue-Long Jiang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Yu-Chun Li
- Marine College, Shandong University (Weihai), Weihai Shandong 264209, China; E-mail:
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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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Yalkovskaya LE, Sibiryakov PA, Zykov SV. Genetic Variability in the Yellow-Necked Field Mouse (Sylvaemus flavicollis Melch., 1834, Muridae, Rodentia) at the Eastern Border of the Range. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418060157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Balasanyan V, Yavruyan E, Somerová B, Abramjan A, Landová E, Munclinger P, Frynta D. High Diversity of mtDNA Haplotypes Confirms Syntopic Occurrence of Two Field Mouse Species Apodemus uralensis and A. witherbyi (Muridae: Apodemus) in Armenia. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418060030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Mysteries of host switching: Diversification and host specificity in rodent-coccidia associations. Mol Phylogenet Evol 2018; 127:179-189. [PMID: 29753710 DOI: 10.1016/j.ympev.2018.05.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 11/21/2022]
Abstract
Recent studies show that host switching is much more frequent than originally believed and constitutes an important driver in evolution of host-parasite associations. However, its frequency and ecological mechanisms at the population level have been rarely investigated. We address this issue by analyzing phylogeny and population genetics of an extensive sample, from a broad geographic area, for commonly occurring parasites of the genus Eimeria within the abundant rodent genera Apodemus, Microtus and Myodes, using two molecular markers. At the most basal level, we demonstrate polyphyletic arrangement, i.e. multiple origin, of the rodent-specific clusters within the Eimeria phylogeny, and strong genetic/phylogenetic structure within these lineages determined at least partially by specificities to different host groups. However, a novel and the most important observation is a repeated occurrence of host switches among closely related genetic lineages which may become rapidly fixed. Within the studied model, this phenomenon applies particularly to the switches between the eimerians from Apodemus flavicollis/Apodemus sylvaticus and Apodemus agrarius groups. We show that genetic differentiation and isolation between A. flavicollis/A. sylvaticus and A. agrarius faunas is a secondary recent event and does not reflect host-parasite coevolutionary history. Rather, it provides an example of rapid ecology-based differentiation in the parasite population.
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Sozio G, Curini V, Pascucci I, Cammà C, Di Domenico M. A new fast real-time PCR method for the identification of three sibling Apodemus species ( A. sylvaticus, A. flavicollis, and A. alpicola) in Italy. Ecol Evol 2018; 8:4807-4814. [PMID: 29876059 PMCID: PMC5980278 DOI: 10.1002/ece3.4026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 01/31/2018] [Accepted: 02/26/2018] [Indexed: 11/23/2022] Open
Abstract
The identification of field mice Apodemus flavicollis, Apodemus sylvaticus, and Apodemus alpicola represents a challenge for field scientists due to their highly overlapping morphological traits and habitats. Here, we propose a new fast real-time PCR method to discriminate the three species by species-specific TaqMan assays. Primers and probes were designed based on the alignment of 54 cyt-b partial sequences from 25 different European countries retrieved from GenBank. TaqMan assays were then tested on 133 samples from three different areas of Italy. Real-time PCR analysis showed 92 samples classified as A. flavicollis, 13 as A. sylvaticus, and 28 as A. alpicola. We did not observe any double amplification and DNA sequencing confirmed species assignment obtained by the TaqMan assays. The method is implementable on different matrices (ear tissues, tail, and blood). It can be used on dead specimens or on alive animals with minimally invasive sampling, and given the high sensitivity, the assay may be also suitable for degraded or low-DNA samples. The method proved to work well to discriminate between the species analyzed. Furthermore, it gives clear results (amplified or not) and it does not require any postamplification handling of PCR product, reducing the time needed for the analyses and the risk of carryover contamination. It therefore represents a valuable tool for field ecologists, conservationists, and epidemiologists.
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Affiliation(s)
- Giulia Sozio
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise “G. Caporale”TeramoItaly
| | - Valentina Curini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise “G. Caporale”TeramoItaly
| | - Ilaria Pascucci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise “G. Caporale”TeramoItaly
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise “G. Caporale”TeramoItaly
| | - Marco Di Domenico
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise “G. Caporale”TeramoItaly
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Grigoryeva OO, Stakheev VV, Orlov VN. Mitochondrial Evidence of Refugial Distribution of the Pygmy Field Mouse Sylvaemus uralensis Pall. (Rodentia, Muridae) in the Northwestern Caucasus. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418030055] [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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21
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Urgoiti J, Muñoz A, Espelta JM, Bonal R. Distribution and space use of seed-dispersing rodents in central Pyrenees: implications for genetic diversity, conservation and plant recruitment. Integr Zool 2018; 13:307-318. [PMID: 29316239 DOI: 10.1111/1749-4877.12301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The function and conservation of many forest ecosystems depend on the distribution and diversity of the community of rodents that consume and disperse seeds. The habitat preferences and interactions are especially relevant in alpine systems where such granivorous rodents reach the southernmost limit of their distribution and are especially sensitive to global warming. We analyzed the community of granivorous rodents in the Pyrenees, one of the southernmost mountain ranges of Europe. Rodent species were identified by DNA with particular attention to the Apodemus species, which are prominent seed-dispersing rodents in Europe. We confirmed for the first time the presence of the yellow-necked mouse, Apodemus flavicollis, in central Pyrenees, a typical Eurosiberian species that reaches its southernmost distribution limit in this area. We also found the wood mouse, Apodemus sylvaticus, a related species more tolerant to Mediterranean environments. Both rodents were spatially segregated by altitude. A. sylvaticus was rare at high altitudes, which might cause the genetic differentiation between populations of the different valleys reported here. We also found other seed consumers like dormice, Elyomis quercinus, and voles, Myodes glareolus, with marked habitat preferences. We suggest that population isolation among valleys may increase the genetic diversity of rodents, like A. sylvaticus. We also highlight the potential threat that global warming may represent for species linked to high-altitude refuges at the southern edge of its distribution, like Apodemus flavicollis. Finally, we discuss how this threat may have a dimension in the conservation of alpine forests dispersed by these rodent populations.
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Affiliation(s)
- Jon Urgoiti
- CREAF, Cerdanyola del Vallés, Catalonia, Spain
| | - Alberto Muñoz
- Department of Didactics of Experimental Sciences, Faculty of Education, University Complutense of Madrid, Madrid, Spain
| | | | - Raúl Bonal
- Forest Research Group, INDEHESA, University of Extremadura, Plasencia, Spain.,DITEG Research Group, University of Castilla-La Mancha, Toledo, Spain.,Research group of Genetic and Cultural Biodiversity, Research centre for Cinegetic Resources (CSIC-UCLM-JCCM), Ciudad Real, Spain
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23
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Genetic evidence supporting the taxonomic separation of the Arabian and Northwest African subspecies of the desert hedgehog ( Paraechinus aethiopicus ). Gene 2017; 620:54-65. [DOI: 10.1016/j.gene.2017.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/30/2017] [Accepted: 04/07/2017] [Indexed: 11/21/2022]
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Honda A, Choijookhuu N, Izu H, Kawano Y, Inokuchi M, Honsho K, Lee AR, Nabekura H, Ohta H, Tsukiyama T, Ohinata Y, Kuroiwa A, Hishikawa Y, Saitou M, Jogahara T, Koshimoto C. Flexible adaptation of male germ cells from female iPSCs of endangered Tokudaia osimensis. SCIENCE ADVANCES 2017; 3:e1602179. [PMID: 28508054 PMCID: PMC5429033 DOI: 10.1126/sciadv.1602179] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/27/2017] [Indexed: 06/07/2023]
Abstract
In mammals, the Y chromosome strictly influences the maintenance of male germ cells. Almost all mammalian species require genetic contributors to generate testes. An endangered species, Tokudaia osimensis, has a unique sex chromosome composition XO/XO, and genetic differences between males and females have not been confirmed. Although a distinctive sex-determining mechanism may exist in T. osimensis, it has been difficult to examine thoroughly in this rare animal species. To elucidate the discriminative sex-determining mechanism in T. osimensis and to find a strategy to prevent its possible extinction, we have established induced pluripotent stem cells (iPSCs) and derived interspecific chimeras using mice as the hosts and recipients. Generated iPSCs are considered to be in the so-called "true naïve" state, and T. osimensis iPSCs may contribute as interspecific chimeras to several different tissues and cells in live animals. Surprisingly, female T. osimensis iPSCs not only contributed to the female germ line in the interspecific mouse ovary but also differentiated into spermatocytes and spermatids that survived in the adult interspecific mouse testes. Thus, T. osimensis cells have high sexual plasticity through which female somatic cells can be converted to male germline cells. These findings suggest flexibility in T. osimensis cells, which can adapt their germ cell sex to the gonadal niche. The probable reduction of the extinction risk of an endangered species through the use of iPSCs is indicated by this study.
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Affiliation(s)
- Arata Honda
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
- RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Narantsog Choijookhuu
- Department of Histochemistry and Cell Biology, Department of Anatomy, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Haruna Izu
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Yoshihiro Kawano
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Mizuho Inokuchi
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
- Division of Bio-Resources, Frontier Science Research Center, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Kimiko Honsho
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Ah-Reum Lee
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Hiroki Nabekura
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Hiroshi Ohta
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomoyuki Tsukiyama
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Yasuhide Ohinata
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Asato Kuroiwa
- Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Yoshitaka Hishikawa
- Department of Histochemistry and Cell Biology, Department of Anatomy, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Japan Science and Technology Agency (JST), Exploratory Research for Advanced Technology (ERATO), Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takamichi Jogahara
- Division of Bio-Resources, Frontier Science Research Center, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Chihiro Koshimoto
- Division of Bio-Resources, Frontier Science Research Center, University of Miyazaki, Miyazaki 889-1692, Japan
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Knitlová M, Horáček I. Late Pleistocene-Holocene paleobiogeography of the genus Apodemus in Central Europe. PLoS One 2017; 12:e0173668. [PMID: 28282422 PMCID: PMC5345881 DOI: 10.1371/journal.pone.0173668] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/25/2017] [Indexed: 11/20/2022] Open
Abstract
Wood mice of the genus Apodemus are an essential component of small mammal communities throughout Europe. Molecular data suggest the postglacial colonization of current ranges from south European glacial refugia, different in particular species. Yet, details on the course of colonization and Holocene history of particular species are not available, partly because of a lack of reliable criteria for species identification in the fossil record. Using a sample of extant species, we analyzed variation patterns and between-species overlaps for a large set of metric and non-metric dental variables and established the criteria enabling the reliable species identification of fragmentary fossil material. The corresponding biometrical analyses were undertaken with fossil material of the genus (2528 items, 747 MNI) from 22 continuous sedimentary series in the Czech Republic and Slovakia, from LGM to Recent. In Central Europe, the genus is invariantly absent in LGM assemblages but regularly appears during the Late Vistulian. All the earliest records belong to A. flavicollis, the species clearly predominating in the fossil record until the Late Holocene. A. uralensis accompanied it in all regions until the late Boreal when disappeared from the fossil record (except for Pannonia). A few items identified as A. sylvaticus had already appeared in the early Holocene assemblages, first in the western part of the region, yet the regular appearance of the species is mostly in the post-Neolithic age. A. agrarius appeared sparsely from the Boreal with a maximum frequency during the post-Neolithic period. The results conform well to the picture suggested by molecular phylogeography but demonstrate considerable differences among particular species in dynamic of the range colonization. Further details concerning Holocene paleobiogeography of individual species in the medium latitude Europe are discussed.
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Affiliation(s)
- Markéta Knitlová
- Department of Zoology, Charles University, Viničná 7, Praha 2, Czech Republic
| | - Ivan Horáček
- Department of Zoology, Charles University, Viničná 7, Praha 2, Czech Republic
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Ruiz-García M, Chacón D, Plese T, Schuler I, Shostell JM. Mitogenomics phylogenetic relationships of the current sloth's genera and species (Bradypodidae and Megalonychidae). Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:281-299. [PMID: 28129732 DOI: 10.1080/24701394.2016.1275602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We sequenced the complete mitogenome of 39 sloths (19 Bradypus variegatus, 4 B. tridactylus, 1 B. pygmaeus, 1 B. torquatus, 4 Choloepus didactylus, and 10 C. hoffmanni). A Bayesian tree (BI) indicated a temporal split between Bradypus and Choloepus around 31 million years ago (MYA, Oligocene) and the other major splits within each genera during the Miocene and Pliocene. A haplotype network (MJN) estimated a lower temporal split between the sloth genera (around 23.5 MYA). Both methods detected the ancestor of B. torquatus as the first to diverge within Bradypus (21 for BI and 19 MJN), followed by that of the ancestor of B. tridactylus. The split of B. pygmaeus from the common ancestor with B. variegatus was around 12 MYA (BI) or 4.3 MYA (MJN). The splits among the previous populations of B. variegatus began around 8 MYA (BI) or 3.6 MYA (MJN). The trans-Andean population was the first to diverge from the remaining cis-Andean populations of B. variegatus. The genetic differentiation of the trans-Andean B. variegatus population relative to the cis-Andean B. variegatus is similar to that found for different species of sloths. The mitogenomic analysis resolved the differentiation of C. hoffmanni from the C. didactylus individuals of the Guiana Shield. However, one C. didactylus from the Colombian Amazon specimen was inside the C. hoffmanni clade. This could be the first example of possible natural hybridization in the Amazon of both Choloepus taxa or the existence of un-differentiable phenotypes of these two species in some Amazonian areas.
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Affiliation(s)
- Manuel Ruiz-García
- a Departamento de Biología, Facultad de Ciencias , Pontificia Universidad Javeriana , Bogotá , DC , Colombia
| | - Diego Chacón
- a Departamento de Biología, Facultad de Ciencias , Pontificia Universidad Javeriana , Bogotá , DC , Colombia
| | | | - Ingrid Schuler
- a Departamento de Biología, Facultad de Ciencias , Pontificia Universidad Javeriana , Bogotá , DC , Colombia
| | - Joseph Mark Shostell
- c Math, Science and Technology Department , University of Minnesota Crookston , Crookston , MN , USA
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Herman JS, Jóhannesdóttir F, Jones EP, McDevitt AD, Michaux JR, White TA, Wójcik JM, Searle JB. Post-glacial colonization of Europe by the wood mouse,Apodemus sylvaticus: evidence of a northern refugium and dispersal with humans. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12882] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jeremy S. Herman
- National Museums of Scotland; Chambers Street Edinburgh EH1 1JF UK
| | - Fríđa Jóhannesdóttir
- Department of Ecology and Evolutionary Biology; Cornell University; Corson Hall Ithaca NY 14853-2701 USA
| | | | - Allan D. McDevitt
- Ecosystems and Environment Research Centre; School of Environment and Life Sciences; University of Salford; Salford M5 4WT UK
- Mammal Research Institute; Polish Academy of Sciences; 17-230 Białowieża Poland
| | - Johan R. Michaux
- Unité de génétique de la conservation; Institut de Botanique; Université de Liège; 4000 Liège Belgique
| | - Thomas A. White
- Department of Ecology and Evolutionary Biology; Cornell University; Corson Hall Ithaca NY 14853-2701 USA
- Lancaster Environment Centre; Lancaster University; Lancaster LA1 4YQ UK
| | - Jan M. Wójcik
- Mammal Research Institute; Polish Academy of Sciences; 17-230 Białowieża Poland
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology; Cornell University; Corson Hall Ithaca NY 14853-2701 USA
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Genetic instability and aging under the scrutiny of comparative biology: a meta-analysis of spontaneous micronuclei frequency. Mech Ageing Dev 2016; 156:34-41. [DOI: 10.1016/j.mad.2016.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/08/2016] [Accepted: 04/10/2016] [Indexed: 12/17/2022]
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29
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Buckley M, Gu M, Shameer S, Patel S, Chamberlain AT. High-throughput collagen fingerprinting of intact microfaunal remains; a low-cost method for distinguishing between murine rodent bones. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:805-12. [PMID: 27408951 PMCID: PMC4831026 DOI: 10.1002/rcm.7483] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/07/2015] [Accepted: 12/13/2015] [Indexed: 05/19/2023]
Abstract
RATIONALE Microfaunal skeletal remains can be sensitive indicators of the contemporary ecosystem in which they are sampled and are often recovered in owl pellets in large numbers. Species identification of these remains can be obtained using a range of morphological criteria established for particular skeletal elements, but typically dominated by a reliance on cranial characters. However, this can induce biases under different environmental and taphonomic conditions. The aim of this research was to develop a high-throughput method of objectively identifying rodent remains from archaeological deposits using collagen fingerprinting, most notably the identification of rats from other myomorph rodents as a means to identify disturbances in the archaeofauna through the presence of invasive taxa not contemporary with the archaeological deposits. METHODS Collagen was extracted from complete microfaunal skeletal remains in such a manner as to leave the bones morphologically intact (i.e., weaker concentration of acid than previously used over shorter length of time). Acid-soluble collagen was then ultrafiltered into ammonium bicarbonate and digested with trypsin prior to dilution in the MALDI matrix and acquisition of peptide mass fingerprints using a matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometer. RESULTS Collagen fingerprinting was able to distinguish between Rattus, Mus, Apodemus and Micromys at the genus level; at the species level, R. rattus and R. norvegicus could be separated whereas A. flavicollis and A. sylvaticus could not. A total of 12,317 archaeological microvertebrate samples were screened for myomorph signatures but none were found to be invasive rats (Rattus) or mice (Mus). Of the contemporary murine fauna, no harvest mice (Micromys) were identified and only 24 field mouse (Apodemus) discovered. CONCLUSIONS As a result, no evidence of recent bioturbation could be inferred from the faunal remains of these archaeological deposits. More importantly this work presents a method for high-throughput screening of specific taxa and is the first application of collagen fingerprinting to microfaunal remains of archaeological specimens.
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Rubtsov NB, Karamysheva TV, Bogdanov AS, Kartavtseva IV, Bochkarev MN, Iwasa MA. Comparative analysis of DNA homology in pericentric regions of chromosomes of wood mice from genera Apodemus and Sylvaemus. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415120091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Genetic isolation of Korean populations of Apodemus peninsulae (Rodentia: Muridae) from their neighboring populations. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0331-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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32
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Phylogenetic analyses of the harvest mouse, Micromys minutus (Rodentia: Muridae) based on the complete mitogenome sequences. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Phylogenetic Relationships of Apodemus Kaup, 1829 (Rodentia: Muridae) Species in the Eastern Mediterranean Inferred from Mitochondrial DNA, with Emphasis on Iranian Species. J MAMM EVOL 2015. [DOI: 10.1007/s10914-015-9294-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Zaleśny G, Hildebrand J, Paziewska-Harris A, Behnke JM, Harris PD. Heligmosomoides neopolygyrus Asakawa & Ohbayashi, 1986, a cryptic Asian nematode infecting the striped field mouse Apodemus agrarius in Central Europe. Parasit Vectors 2014; 7:457. [PMID: 25303901 PMCID: PMC4198666 DOI: 10.1186/s13071-014-0457-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 09/20/2014] [Indexed: 12/31/2022] Open
Abstract
Background Heligmosomoides polygyrus is a widespread gastro-intestinal nematode infecting wild Apodemus (wood mice) throughout Europe. Using molecular and morphological evidence, we review the status of Heligmosomoides from Apodemus agrarius in Poland previously considered to be an outlying clade of H. polygyrus, to further resolve the status of the laboratory model species, H. bakeri. Methods Morphological analysis of the male bursa and the synlophe, and molecular analyses of concatenated nuclear (28S rDNA, ITS1 and ITS2) and mitochondrial (CO1 and cytb) genes, of Heligmosomoides collected from Apodemus agrarius from two sites in Poland and comparison with related heligmosomids from voles and mice in Eurasia. Results Heligmosomoides neopolygyrus, a heligmosomid nematode from Apodemus species from China and Japan, is recognised for the first time in western Europe infecting Apodemus agrarius in Poland. It can be distinguished from H. polygyrus by the filiform externo-dorsal rays of the male copulatory bursa and the small, equally distributed longitudinal crêtes on the body. Specimens from A. agrarius are 20% different at ribosomal (ITS1 and ITS2) nuclear loci, and 10% different at the mitochondrial cytb locus from H. polygyrus, and in phylogenetic analyses group with the vole-infecting genus Heligmosomum. Conclusions Despite morphological similarity, H. neopolygyrus is only distantly related to H. polygyrus from western European Apodemus, and may be more closely related to vole-infecting taxa. It was brought into Europe by the recent rapid migration of the host mice. Inclusion of H. neopolygyrus in phylogenies makes it clear that Heligmosomoides is paraphyletic, with the pika-infecting Ohbayashinema and the vole-infecting Heligmosomum nesting within it. Clarification of the European status of H. neopolygyrus also allows H. bakeri, the laboratory model species, to be seen as a terminal sister clade to H. polygyrus, rather than as an internal clade of the latter taxon. Electronic supplementary material The online version of this article (doi:10.1186/s13071-014-0457-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Grzegorz Zaleśny
- Department of Invertebrate Systematics and Ecology, Institute of Biology, Wrocław University of Environmental and Life Sciences, ul. Kożuchowska 5b, 51-631, Wrocław, Poland.
| | - Joanna Hildebrand
- Department of Parasitology, Institute of Genetics and Microbiology, University of Wrocław, ul. Przybyszewskiego 63, 51-148, Wrocław, Poland.
| | - Anna Paziewska-Harris
- KIT Biomedical Research, Royal Tropical Institute, Meibergdreef 39, 1105 AZ, Amsterdam, the Netherlands.
| | - Jerzy M Behnke
- School of Life Sciences, University of Nottingham, NG2 7RD, Nottingham, UK.
| | - Philip D Harris
- Natural History Museum, University of Oslo, P.O. Box 1172, N-0562, Oslo, Norway.
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Balakirev AE, Abramov AV, Rozhnov VV. Phylogenetic relationships in the Niviventer-Chiromyscus complex (Rodentia, Muridae) inferred from molecular data, with description of a new species. Zookeys 2014; 451:109-36. [PMID: 25493050 PMCID: PMC4258623 DOI: 10.3897/zookeys.451.7210] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 09/03/2014] [Indexed: 12/05/2022] Open
Abstract
Based on molecular data for mitochondrial (Cyt b, COI) and nuclear (IRBP, GHR) genes, and morphological examinations of museum specimens, we examined diversity, species boundaries, and relationships within and between the murine genera Chiromyscus and Niviventer. Phylogenetic patterns recovered demonstrate that Niviventer sensu lato is not monophyletic but instead includes Chiromyscuschiropus, the only previously recognized species of Chiropus. To maintain the genera Niviventer and Chiropus as monophyletic lineages, the scope and definition of the genus Chiromyscus is revised to include at least three distinct species: Chiromyscuschiropus (the type species of Chiromyscus), Chiromyscuslangbianis (previously regarded as a species of Niviventer), and a new species, described in this paper under the name Chiromyscusthomasi sp. n.
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Affiliation(s)
- Alexander E. Balakirev
- Joint Russian-Vietnamese Tropical Research and Technological Centre, Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- A.N. Severtsov’s Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia
| | - Alexei V. Abramov
- Joint Russian-Vietnamese Tropical Research and Technological Centre, Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, Saint Petersburg 199034, Russia
| | - Viatcheslav V. Rozhnov
- Joint Russian-Vietnamese Tropical Research and Technological Centre, Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- A.N. Severtsov’s Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii pr. 33, Moscow 119071, Russia
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Abramov AV, Balakirev AE, Rozhnov VV. An enigmatic pygmy dormouse: molecular and morphological evidence for the species taxonomic status of Typhlomys chapensis (Rodentia: Platacanthomyidae). Zool Stud 2014. [DOI: 10.1186/s40555-014-0034-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Jojić V, Bugarski-Stanojević V, Blagojević J, Vujošević M. Discrimination of the sibling species Apodemus flavicollis and A. sylvaticus (Rodentia, Muridae). ZOOL ANZ 2014. [DOI: 10.1016/j.jcz.2014.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Lin LK, Ma GC, Chen TH, Lin WH, Lee DJ, Wen PY, Wu SH, Chen M. Genomic analyses of the Formosan harvest mouse (Micromys minutus) and comparisons to the brown Norway rat (Rattus norvegicus) and the house mouse (Mus musculus). ZOOLOGY 2013; 116:307-15. [PMID: 24028897 DOI: 10.1016/j.zool.2013.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 06/13/2013] [Accepted: 07/13/2013] [Indexed: 10/26/2022]
Abstract
The harvest mouse, Micromys minutus (MMIN), has a very wide range of distribution (from the British Isles across the Euroasian continent to Japan and Taiwan). We studied an isolated population of MMIN in Taiwan, which is at the southeastern margin of the species' geographic distribution, and compared its genetic complement with those of the same species previously reported from other geographic locations and with two model rodent species, the house mouse (Mus musculus) and the brown Norway rat (Rattus norvegicus). The diploid number (2N) of MMIN was 68, consistent with that reported for other populations. However, variations were noted in the fundamental number (FN) and the shape and banding patterns of the individual chromosomes among populations. The FN of MMIN was estimated to be 72, including 2 bi-armed autosomes, 31 one-armed autosomes, and one pair of one-armed sex chromosomes. Here, we propose the first ideogram for MMIN. C-banding, Ag-NOR, and the locations of 18S rRNA gene sequences (MMIN chromosomes no. 10, 14, 19, 29, 31, 33, and X) mapped by fluorescence in situ hybridization (FISH) are also reported. Additionally, we compared the 18S rDNA sequences and performed cross-species X chromosome painting (FISH) for M. minutus, M. musculus, and R. norvegicus. The results indicate that both genetic elements are rather conserved across species. Thus, implications for the phylogenetic position of Micromys were limited.
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Affiliation(s)
- Liang-Kong Lin
- Department of Life Sciences, Tunghai University, Taichung, Taiwan
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Šandera M, Albrecht T, Stopka P. Variation in apical hook length reflects the intensity of sperm competition in murine rodents. PLoS One 2013; 8:e68427. [PMID: 23844198 PMCID: PMC3700964 DOI: 10.1371/journal.pone.0068427] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 05/30/2013] [Indexed: 11/18/2022] Open
Abstract
Background Post-copulatory sexual selection has been shown to shape morphology of male gametes. Both directional and stabilizing selection on sperm phenotype have been documented in vertebrates in response to sexual promiscuity. Methodology Here we investigated the degree of variance in apical hook length and tail length in six taxa of murine rodents. Conclusions Tail sperm length and apical hook length were positively associated with relative testis mass, our proxy for levels of sperm competition, thus indicating directional post-copulatory selection on sperm phenotypes. Moreover, our study shows that increased levels of sperm competition lead to the reduction of variance in the hook length, indicating stabilizing selection. Hence, the higher risk of sperm competition affects increasing hook length together with decreasing variance in the hook length. Species-specific post-copulatory sexual selection likely optimizes sperm morphology.
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Affiliation(s)
- Martin Šandera
- Biocev group, Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Tomáš Albrecht
- Biocev group, Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Pavel Stopka
- Biocev group, Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- * E-mail:
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Bugarski-Stanojević V, Blagojević J, Adnađević T, Jovanović V, Vujošević M. Identification of the sibling species Apodemus sylvaticus and Apodemus flavicollis (Rodentia, Muridae)—Comparison of molecular methods. ZOOL ANZ 2013. [DOI: 10.1016/j.jcz.2012.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Dlugosz EM, Chappell MA, Meek TH, Szafrańska P, Zub K, Konarzewski M, Jones JH, Bicudo E, Nespolo RF, Careau V, Garland T. Phylogenetic analysis of mammalian maximal oxygen consumption during exercise. J Exp Biol 2013; 216:4712-21. [DOI: 10.1242/jeb.088914] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Summary
We compiled published values of mammalian maximum oxygen consumption during exercise (VO2max) and supplemented these data with new measurements of VO2max for the largest rodent (capybara), 20 species of smaller-bodied rodents, two species of weasels, and one small marsupial. Many of the new data were obtained with running-wheel respirometers instead of the treadmill systems used in most previous measurements of mammalian VO2max. We used both conventional and phylogenetically informed allometric regression models to analyze VO2max of 77 ‘species’ (including subspecies or separate populations within species) in relation to body size, phylogeny, diet, and measurement method. Both body mass and allometrically mass-corrected VO2max showed highly significant phylogenetic signal (i.e., related species tended to resemble each other). The Akaike Information Criterion corrected for sample size was used to compare 27 candidate models predicting VO2max (all of which included body mass). In addition to mass, the two best-fitting models (cumulative Akaike weight = 0.93) included dummy variables coding for three species previously shown to have high VO2max (pronghorn, horse, and a bat), and incorporated a transformation of the phylogenetic branch lengths under an Ornstein-Uhlenbeck model of residual variation (thus indicating phylogenetic signal in the residuals). We found no statistical difference between wheel- and treadmill-elicited values, and diet had no predictive ability for VO2max. Averaged across all models, the allometric scaling exponent was 0.839, with 95% confidence limits of 0.795 and 0.883, which does not provide support for a scaling exponent of 0.67, 0.75 or unity.
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Galan M, Pagès M, Cosson JF. Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples. PLoS One 2012; 7:e48374. [PMID: 23144869 PMCID: PMC3492341 DOI: 10.1371/journal.pone.0048374] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 09/25/2012] [Indexed: 11/18/2022] Open
Abstract
Rodentia is the most diverse order among mammals, with more than 2,000 species currently described. Most of the time, species assignation is so difficult based on morphological data solely that identifying rodents at the specific level corresponds to a real challenge. In this study, we compared the applicability of 100 bp mini-barcodes from cytochrome b and cytochrome c oxidase 1 genes to enable rodent species identification. Based on GenBank sequence datasets of 115 rodent species, a 136 bp fragment of cytochrome b was selected as the most discriminatory mini-barcode, and rodent universal primers surrounding this fragment were designed. The efficacy of this new molecular tool was assessed on 946 samples including rodent tissues, feces, museum samples and feces/pellets from predators known to ingest rodents. Utilizing next-generation sequencing technologies able to sequence mixes of DNA, 1,140 amplicons were tagged, multiplexed and sequenced together in one single 454 GS-FLX run. Our method was initially validated on a reference sample set including 265 clearly identified rodent tissues, corresponding to 103 different species. Following validation, 85.6% of 555 rodent samples from Europe, Asia and Africa whose species identity was unknown were able to be identified using the BLASTN program and GenBank reference sequences. In addition, our method proved effective even on degraded rodent DNA samples: 91.8% and 75.9% of samples from feces and museum specimens respectively were correctly identified. Finally, we succeeded in determining the diet of 66.7% of the investigated carnivores from their feces and 81.8% of owls from their pellets. Non-rodent species were also identified, suggesting that our method is sensitive enough to investigate complete predator diets. This study demonstrates how this molecular identification method combined with high-throughput sequencing can open new realms of possibilities in achieving fast, accurate and inexpensive species identification.
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Affiliation(s)
- Maxime Galan
- Institut national de la recherche agronomique, Joint Research Unit Centre de Biologie pour la Gestion des Populations (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, Montferrier-sur-Lez, France.
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Ledevin R, Quéré JP, Michaux JR, Renaud S. Can tooth differentiation help to understand species coexistence? The case of wood mice in China. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/j.1439-0469.2012.00666.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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The Y chromosome of the Okinawa spiny rat, Tokudaia muenninki, was rescued through fusion with an autosome. Chromosome Res 2012; 20:111-25. [PMID: 22198613 DOI: 10.1007/s10577-011-9268-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
The genus Tokudaia comprises three species, two of which have lost their Y chromosome and have an XO/XO sex chromosome constitution. Although Tokudaia muenninki (Okinawa spiny rat) retains the Y chromosome, both sex chromosomes are unusually large. We conducted a molecular cytogenetic analysis to characterize the sex chromosomes of T. muenninki. Using cross-species fluorescence in situ hybridization (Zoo-FISH), we found that both short arms of the T. muenninki sex chromosomes were painted by probes from mouse chromosomes 11 and 16. Comparative genomic hybridization analysis was unable to detect sex-specific regions in the sex chromosomes because both sex probes highlighted the large heterochromatic blocks on the Y chromosome as well as five autosomal pairs. We then performed comparative FISH mapping using 29 mouse complementary DNA (cDNA) clones of the 22 X-linked genes and the seven genes linked to mouse chromosome 11 (whose homologue had fused to the sex chromosomes), and FISH mapping using two T. muenninki cDNA clones of the Y-linked genes. This analysis revealed that the ancestral gene order on the long arm of the X chromosome and the centromeric region of the short arm of the Y chromosome were conserved. Whereas six of the mouse chromosome 11 genes were also mapped to Xp and Yp, in addition, one gene, CBX2, was also mapped to Xp, Yp, and chromosome 14 in T. muenninki. CBX2 is the candidate gene for the novel sex determination system in the two other species of Tokudaia, which lack a Y chromosome and SRY gene. Overall, these results indicated that the Y chromosome of T. muenninki avoided a loss event, which occurred in an ancestral lineage of T. osimensis and T. tokunoshimensis, through fusion with an autosome. Despite retaining the Y chromosome, sex determination in T. muenninki might not follow the usual mammalian pattern and deserves further investigation.
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Chen WC, Hao HB, Sun ZY, Liu Y, Liu SY, Yue BS. Phylogenetic position of the genus Proedromys (Arvicolinae, Rodentia): Evidence from nuclear and mitochondrial DNA. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Jojić V, Nenadović J, Blagojević J, Paunović M, Cvetković D, Vujošević M. Phenetic relationships among four Apodemus species (Rodentia, Muridae) inferred from skull variation. ZOOL ANZ 2012. [DOI: 10.1016/j.jcz.2011.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pagès M, Chevret P, Gros-Balthazard M, Hughes S, Alcover JA, Hutterer R, Rando JC, Michaux J, Hänni C. Paleogenetic analyses reveal unsuspected phylogenetic affinities between mice and the extinct Malpaisomys insularis, an endemic rodent of the Canaries. PLoS One 2012; 7:e31123. [PMID: 22363563 PMCID: PMC3283599 DOI: 10.1371/journal.pone.0031123] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 01/03/2012] [Indexed: 12/22/2022] Open
Abstract
Background The lava mouse, Malpaisomys insularis, was endemic to the Eastern Canary islands and became extinct at the beginning of the 14th century when the Europeans reached the archipelago. Studies to determine Malpaisomys' phylogenetic affinities, based on morphological characters, remained inconclusive because morphological changes experienced by this insular rodent make phylogenetic investigations a real challenge. Over 20 years since its first description, Malpaisomys' phylogenetic position remains enigmatic. Methodology/Principal Findings In this study, we resolved this issue using molecular characters. Mitochondrial and nuclear markers were successfully amplified from subfossils of three lava mouse samples. Molecular phylogenetic reconstructions revealed, without any ambiguity, unsuspected relationships between Malpaisomys and extant mice (genus Mus, Murinae). Moreover, through molecular dating we estimated the origin of the Malpaisomys/mouse clade at 6.9 Ma, corresponding to the maximal age at which the archipelago was colonised by the Malpaisomys ancestor via natural rafting. Conclusion/Significance This study reconsiders the derived morphological characters of Malpaisomys in light of this unexpected molecular finding. To reconcile molecular and morphological data, we propose to consider Malpaisomys insularis as an insular lineage of mouse.
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Affiliation(s)
- Marie Pagès
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Pascale Chevret
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail:
| | - Muriel Gros-Balthazard
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Josep Antoni Alcover
- Institut Mediterrani d'Estudis Avançats, Esporles, Mallorca, Spain
- Department of Mammalogy, American Museum of Natural History, New York, New York, United States of America
| | - Rainer Hutterer
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Juan Carlos Rando
- Departamento de Biología Animal (UDI Zoología), Universidad de La Laguna La Laguna, Tenerife, Canary Islands, Spain
- Island Ecology and Evolution Research Group (IPNA-CSIC), La Laguna, Tenerife, Canary Islands, Spain
| | - Jacques Michaux
- EPHE–ISEM, UMR 5554 CNRS Université Montpellier II, Université de Montpellier, Montpellier, France
| | - Catherine Hänni
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Lyon, France
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Bogdanov AS, Stakheev VV, Zykov AE, Yakimenko VV, Mal’kova MG. Genetic variation and differentiation of wood mice from the genus Sylvaemus inferred from sequencing of the cytochrome oxidase subunit 1 gene fragment. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412020044] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Amrein I, Isler K, Lipp HP. Comparing adult hippocampal neurogenesis in mammalian species and orders: influence of chronological age and life history stage. Eur J Neurosci 2012; 34:978-87. [PMID: 21929629 DOI: 10.1111/j.1460-9568.2011.07804.x] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adult hippocampal neurogenesis is a prominent event in rodents. In species with longer life expectancies, newly born cells in the adult dentate gyrus of the hippocampal formation are less abundant or can be completely absent. Several lines of evidence indicate that the regulatory mechanisms of adult neurogenesis differ between short- and long-lived mammals. After a critical appraisal of the factors and problems associated with comparing different species, we provide a quantitative comparison derived from seven laboratory strains of mice (BALB, C57BL/6, CD1, outbred) and rats (F344, Sprague-Dawley, Wistar), six other rodent species of which four are wild-derived (wood mouse, vole, spiny mouse and guinea pig), three non-human primate species (marmoset and two macaque species) and one carnivore (red fox). Normalizing the number of proliferating cells to total granule cell number, we observe an overall exponential decline in proliferation that is chronologically equal between species and orders and independent of early developmental processes and life span. Long- and short-lived mammals differ with regard to major life history stages; at the time points of weaning, age at first reproduction and average life expectancy, long-lived primates and foxes have significantly fewer proliferating cells than rodents. Although the database for neuronal differentiation is limited, we find indications that the extent of neuronal differentiation is subject to species-specific selective adaptations. We conclude that absolute age is the critical factor regulating cell genesis in the adult hippocampus of mammals. Ontogenetic and ecological factors primarily influence the regulation of neuronal differentiation rather than the rate of cell proliferation.
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Affiliation(s)
- Irmgard Amrein
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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