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Tukhbatullin A, Ermakov O, Kapustina S, Starikov V, Tambovtseva V, Titov S, Brandler O. Surrounded by Kindred: Spermophilus major Hybridization with Other Spermophilus Species in Space and Time. BIOLOGY 2023; 12:880. [PMID: 37372163 DOI: 10.3390/biology12060880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Among the numerous described cases of hybridization in mammals, the most intriguing are (a) cases of introgressive hybridization deeply affecting the evolutionary history of species, and (b) models involving not a pair of species but a multi-species complex. Therefore, the hybridization history of the russet ground squirrel Spermophilus major, whose range has repeatedly changed due to climatic fluctuations and now borders the ranges of four related species, is of great interest. The main aims of this study were to determine the direction and intensity of gene introgression, the spatial depth of the infiltration of extraneous genes into the S. major range, and to refine the hypothesis of the hybridogenic replacement of mitochondrial genomes in the studied group. Using phylogenetic analysis of the variability of mitochondrial (CR, cytb) and nuclear (SmcY, BGN, PRKCI, c-myc, i6p53) markers, we determined the contribution of neighboring species to the S. major genome. We showed that 36% of S. major individuals had extraneous alleles. All peripheral species that were in contact with S. major contributed towards its genetic variability. We also proposed a hypothesis for the sequence and localization of serial hybridization events. Our assessment of the S. major genome implications of introgression highlights the importance of implementing conservation measures to protect this species.
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Affiliation(s)
- Andrey Tukhbatullin
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Oleg Ermakov
- Faculty of Physics, Mathematics and Natural Sciences, Belinsky Institute of Teacher Education, Penza State University, Lermontov Str. 37, Penza 440026, Russia
| | - Svetlana Kapustina
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Vladimir Starikov
- Department of Biology and Biotechnology, Institute of Natural and Technical Sciences, Surgut State University, Lenin Avenue 1, Surgut 628412, Russia
| | - Valentina Tambovtseva
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Sergey Titov
- Faculty of Physics, Mathematics and Natural Sciences, Belinsky Institute of Teacher Education, Penza State University, Lermontov Str. 37, Penza 440026, Russia
| | - Oleg Brandler
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
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2
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Mills KK, Everson KM, Hildebrandt KPB, Brandler OV, Steppan SJ, Olson LE. Ultraconserved elements improve resolution of marmot phylogeny and offer insights into biogeographic history. Mol Phylogenet Evol 2023; 184:107785. [PMID: 37085130 DOI: 10.1016/j.ympev.2023.107785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/01/2023] [Accepted: 04/13/2023] [Indexed: 04/23/2023]
Abstract
Marmots (Marmota spp.) comprise a lineage of large-bodied ground squirrels that diversified rapidly in the Pleistocene, when the planet quickly transitioned to a drier, colder, and highly seasonal climate-particularly at high latitudes. Fossil evidence indicates the genus spread from North America, across Beringia, and into the European Alps over the course of only a few million years, beginning in the late Pliocene. Marmots are highly adapted to survive long and severely cold winters, and this likely favored their expansion and diversification over this time period. Previous phylogenetic studies have identified two major subgenera of marmots, but the timing of important speciation events and some species relationships have been difficult to resolve. Here we use ultraconserved elements and mitogenomes, with samples from all 15 extant species, to more precisely retrace how and when marmots came to inhabit a vast Holarctic range. Our results indicate marmots arose in North America in the mid Miocene (∼16.3 Mya) and dispersed across the Bering Land Bridge in the late Pliocene (∼3-4 Mya); in addition, our fossil-calibrated timeline is suggestive of the rise and spread of open grasslands as being particularly important to marmot diversification. The woodchuck (M. monax) and the Alaska marmot (M. broweri) are found to be more closely related to the Eurasian species than to the other North American species. Paraphyly is evident in the bobak marmot (M. bobak) and the hoary marmot (M. caligata), and in the case of the latter the data are highly suggestive of a second, cryptic species in the Cascade Mountains of Washington.
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Affiliation(s)
- Kendall K Mills
- Department of Biology and Wildlife, University of Alaska Fairbanks, 982 North Koyukuk Drive, Fairbanks, AK 99775, USA; Department of Mammalogy, University of Alaska Museum, 1962 Yukon Drive, Fairbanks, AK 99775, USA.
| | - Kathryn M Everson
- Department of Mammalogy, University of Alaska Museum, 1962 Yukon Drive, Fairbanks, AK 99775, USA; Department of Integrative Biology, Oregon State University, 2701 SW Campus Way, Corvallis, OR 97331, USA
| | - Kyndall P B Hildebrandt
- Department of Mammalogy, University of Alaska Museum, 1962 Yukon Drive, Fairbanks, AK 99775, USA
| | - Oleg V Brandler
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Vavilova 26, Moscow, Russia
| | - Scott J Steppan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Link E Olson
- Department of Mammalogy, University of Alaska Museum, 1962 Yukon Drive, Fairbanks, AK 99775, USA
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Trejo-Salazar RE, Castellanos-Morales G, Hernández-Rosales D, Gámez N, Gasca-Pineda J, Morales Garza MR, Medellin R, Eguiarte LE. Discordance in maternal and paternal genetic markers in lesser long-nosed bat Leptonycteris yerbabuenae, a migratory bat: recent expansion to the North and male phylopatry. PeerJ 2021; 9:e12168. [PMID: 34703665 PMCID: PMC8487242 DOI: 10.7717/peerj.12168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/26/2021] [Indexed: 11/20/2022] Open
Abstract
Leptonycteris yerbabuenae, the lesser long-nosed bat is an abundant migratory nectar-feeding bat found in most of Mexico, and in some areas of northern Central America and small sections of southwestern USA. We analyzed the distribution of the maternal and paternal lineages of this species with phylogeographic methods based on two mitochondrial markers, Cyt-b and D-loop, and a marker located in the Y chromosome, DBY. We obtained tissue samples from 220 individuals from 23 localities. Levels of genetic diversity (haplotype diversity, Hd ) were high (Cyt-b = 0.757; D-loop = 0.8082; DBY = 0.9137). No clear patterns of population genetic structure were found for mitochondrial markers, while male genetic differentiation suggested the presence of two lineages: one from Mexican Pacific coast states and another from central-southern Mexico; in accordance to strong male philopatry and higher female migration. We used genealogical reconstructions based on Bayesian tools to calculate divergence times, and to test coalescent models to explain changes in L. yerbabuenae historical demography. Our results show that recent demographic changes were consistent with global climatic changes (∼130,000 kyr ago for Cyt-b and ∼160,000 kyr for D-loop) and divergence times dated from molecular genealogies exhibited older divergence times, Cyt-b (4.03 mya), D-loop (10.26 mya) and DBY (12.23 mya). Accordingly, the female lineage underwent demographic expansion associated to Pleistocene climate change, whereas the male lineage remained constant.
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Affiliation(s)
- Roberto-Emiliano Trejo-Salazar
- Pograma de Doctorado en Ciencias Biomédicas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de Mexico, México
- Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | | | - DulceCarolina Hernández-Rosales
- Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Niza Gámez
- Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Ciudad de Mexico, Ciudad de Mexico, Mexico
| | - Jaime Gasca-Pineda
- Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Miguel Rene Morales Garza
- Facultad de Ciencia y Tecnología, Universidad Simón Bolívar, Ciudad de Mexico, Ciudad de Mexico, Mexico
| | - Rodrigo Medellin
- Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de Mexico, Ciudad de Mexico, Mexico
| | - Luis E. Eguiarte
- Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
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Phylogeographic pattern and Pleistocene range reconstruction in the long-tailed hamster Cricetulus longicaudatus (Rodentia, Cricetidae) support its Tibetan origin. MAMMAL RES 2021. [DOI: 10.1007/s13364-021-00585-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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Cardini A. Modern morphometrics and the study of population differences: Good data behind clever analyses and cool pictures? Anat Rec (Hoboken) 2020; 303:2747-2765. [PMID: 32220106 DOI: 10.1002/ar.24397] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/03/2020] [Accepted: 02/08/2020] [Indexed: 12/16/2022]
Abstract
The study of phenotypic variation in time and space is central to evolutionary biology. Modern geometric morphometrics is the leading family of methods for the quantitative analysis of biological forms. This set of techniques relies heavily on technological innovation for data acquisition, often in the form of 2D or 3D digital images, and on powerful multivariate statistical tools for their analysis. However, neither the most sophisticated device for computerized imaging nor the best statistical test can produce accurate, robust and reproducible results, if it is not based on really good samples and an appropriate use of the 'measurements' extracted from the data. Using examples mostly from my own work on mammal craniofacial variation and museum specimens, I will show how easy it is to forget these most basic assumptions, while focusing heavily on analytical and visualization methods, and much less on the data that generate potentially powerful analyses and visually appealing diagrams.
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Affiliation(s)
- Andrea Cardini
- Dipartimento di Scienze Chimiche e Geologiche, Università di Modena e Reggio Emilia, Modena, Italy.,School of Anatomy, Physiology and Human Biology, The University of Western Australia, Crawley, Western Australia, Australia
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Boundenga L, Moukodoum DN, Ngoubangoye B. Data on Gabonese rodents and their Plasmodium. Data Brief 2019; 27:104646. [PMID: 31687447 PMCID: PMC6820074 DOI: 10.1016/j.dib.2019.104646] [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: 07/29/2019] [Revised: 09/20/2019] [Accepted: 10/03/2019] [Indexed: 12/01/2022] Open
Abstract
In this paper present data on the description of rodent species living around human dwelling in some villages of Gabon and their malaria parasites. Rodents are known to colonize various environments, such as forest; domestic or peridomestic environment. They are known to be the hosts of many parasites. Data presented here the circulation of malaria parasites in Gabonese rodents was shown; the estimation of pairwise genetic distances (p-distance) between rodents malaria parasites. We also provide data on rodent species diversity in Gabon. Three hundred and forty-five samples from rodents conserved in biobank of International Center of Medical Researches of Franceville (CIRMF) were used for the study. These samples were collected in six villages of southeastern of Gabon between 2009 and 2016 for routine monitoring of infectious disease. Such data can be used to describe and understanding the evolution and systematics of malaria parasite. This data set support the main findings presented in the research article [1].
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Affiliation(s)
- Larson Boundenga
- Centre International de Recherches Médicales de Franceville (CIRMF), BP: 769 Franceville, Gabon
| | | | - Barthélémy Ngoubangoye
- Centre International de Recherches Médicales de Franceville (CIRMF), BP: 769 Franceville, Gabon
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7
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Rodent malaria in Gabon: Diversity and host range. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2019; 10:117-124. [PMID: 31453086 PMCID: PMC6702409 DOI: 10.1016/j.ijppaw.2019.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 12/26/2022]
Abstract
Malaria parasites infect a wide range of vertebrate hosts, such as reptiles, birds and mammals (i.e., primates, ungulates, bats, and rodents). Four Plasmodium species and their subspecies infect African Muridae. Since their discoveries in the 1940s, these rodent Plasmodium species have served as biological models to explore many aspects of the biology of malaria agents and their interactions with their hosts. Despite that, surprisingly, little is known about their ecology, natural history and evolution. Most field studies on these parasites, performed from the 1940s to the early 1980s, showed that all rodent Plasmodium species infect only one main host species, the thicket rat. In the present study, we re-explored the diversity of Plasmodium parasites infecting rodent species living in peridomestic habitats in Gabon, Central Africa. Using molecular approaches, we found that at least two Plasmodium species (Plasmodium vinckei and Plasmodium yoelii) circulated among five rodent species (including the invasive species Mus musculus). This suggests that the host range of these parasites might be larger than previously considered. Our results also showed that the diversity of these parasites could be higher than currently recognized, with the discovery of a new phylogenetic lineage that could represent a new species of rodent Plasmodium. Circulation of at least two Plasmodium species in multiple rodent species in Gabon. African rodent Plasmodium host range is higher than previously recognized. Existence of a potentially new Plasmodium species (Plasmodium sp GAB), closely related to Plasmodium yoelii.
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Liu S, Feng J, Pu J, Xu X, Lu S, Yang J, Wang Y, Jin D, Du X, Meng X, Luo X, Sun H, Xiong Y, Ye C, Lan R, Xu J. Genomic and molecular characterisation of Escherichia marmotae from wild rodents in Qinghai-Tibet plateau as a potential pathogen. Sci Rep 2019; 9:10619. [PMID: 31337784 PMCID: PMC6650469 DOI: 10.1038/s41598-019-46831-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/03/2019] [Indexed: 12/25/2022] Open
Abstract
Wildlife is a reservoir of emerging infectious diseases of humans and domestic animals. Marmota himalayana mainly resides 2800-4000 m above sea level in the Qinghai-Tibetan Plateau, and is the primary animal reservoir of plague pathogen Yersinia pestis. Recently we isolated a new species, Escherichia marmotae from the faeces of M. himalayana. In this study we characterised E. marmotae by genomic analysis and in vitro virulence testing to determine its potential as a human pathogen. We sequenced the genomes of the seven E. marmotae strains and found that they contained a plasmid that carried a Shigella-like type III secretion system (T3SS) and their effectors, and shared the same O antigen gene cluster as Shigella dysenterae 8 and E. coli O38. We also showed that E. marmotae was invasive to HEp-2 cells although it was much less invasive than Shigella. Thus E. marmotae is likely to be an invasive pathogen. However, E. marmotae has a truncated IpaA invasin, and lacks the environmental response regulator VirF and the IcsA-actin based intracellular motility, rendering it far less invasive in comparison to Shigella. E. marmotae also carried a diverse set of virulence factors in addition to the T3SS, including an IS1414 encoded enterotoxin gene astA with 37 copies, E. coli virulence genes lifA/efa, cif, and epeA, and the sfp gene cluster, Yersinia T3SS effector yopJ, one Type II secretion system and two Type VI secretion systems. Therefore, E. marmotae is a potential invasive pathogen.
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Affiliation(s)
- Sha Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China.,Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Jie Feng
- Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing, 100101, China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Xuefang Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Yiting Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Xiaochen Du
- Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Beijing, 100101, China
| | - Xiangli Meng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Xia Luo
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Hui Sun
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Yanwen Xiong
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Changyun Ye
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center of Diagnosis and Treatment of Infectious Diseases, National Institute of Communicable Disease Control and Prevention, Chinese Center of Disease Control and Prevention, Beijing, 102206, China. .,Shanghai Institute of Emerging and Re-emerging infectious diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, China.
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Rankin AM, Schwartz RS, Floyd CH, Galbreath KE. Contrasting consequences of historical climate change for marmots at northern and temperate latitudes. J Mammal 2019. [DOI: 10.1093/jmammal/gyz025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Andrew M Rankin
- Department of Biological Sciences Program in Bioinformatics and Computational Biology, University of Idaho, Moscow, ID USA
| | - Rachel S Schwartz
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Chris H Floyd
- Department of Natural Resources Science, University of Rhode Island, Kingston, RI USA
| | - Kurt E Galbreath
- Department of Biology, Northern Michigan University, Marquette, MI USA (KEG)
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10
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Bai L, Liu B, Ji C, Zhao S, Liu S, Wang R, Wang W, Yao P, Li X, Fu X, Yu H, Liu M, Han F, Guan N, Liu H, Liu D, Tao Y, Wang Z, Yan S, Florant G, Butcher MT, Zhang J, Zheng H, Fan J, Enqi Liu. Hypoxic and Cold Adaptation Insights from the Himalayan Marmot Genome. iScience 2018; 11:519-530. [PMID: 30581096 PMCID: PMC6354217 DOI: 10.1016/j.isci.2018.11.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 12/21/2022] Open
Abstract
The Himalayan marmot (Marmota himalayana) is a hibernating mammal that inhabits the high-elevation regions of the Himalayan mountains. Here we present a draft genome of the Himalayan marmot, with a total assembly length of 2.47 Gb. Phylogenetic analyses showed that the Himalayan marmot diverged from the Mongolian marmot approximately 1.98 million years ago. Transcriptional changes during hibernation included genes responsible for fatty acid metabolism in liver and genes involved in complement and coagulation cascades and stem cell pluripotency pathways in brain. Two selective sweep genes, Slc25a14 and ψAamp, showed apparent genotyping differences between low- and high-altitude populations. As a processed pseudogene, ψAamp may be biologically active to influence the stability of Aamp through competitive microRNA binding. These findings shed light on the molecular and genetic basis underlying adaptation to extreme environments in the Himalayan marmot.
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Affiliation(s)
- Liang Bai
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, Shaanxi 710061, China; Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, Shaanxi 710061, China
| | - Baoning Liu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, Shaanxi 710061, China; Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, Shaanxi 710061, China
| | - Changmian Ji
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Sihai Zhao
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, Shaanxi 710061, China; Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, Shaanxi 710061, China
| | - Siyu Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rong Wang
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, Shaanxi 710061, China; Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, Shaanxi 710061, China
| | - Weirong Wang
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, Shaanxi 710061, China; Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, Shaanxi 710061, China
| | - Pu Yao
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Xiaojun Fu
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Haiyan Yu
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Fengming Han
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Ning Guan
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Hui Liu
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Dongyuan Liu
- Biomarker Technologies Corporation, Beijing 101200, China
| | - Yuanqing Tao
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai 811602, China
| | - Zhongdong Wang
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai 811602, China
| | - Shunsheng Yan
- Centers for Disease Control and Prevention, Urumqi, Xinjiang 830054, China
| | - Greg Florant
- Department of Biology, Colorado State University, Ft. Collins, CO 80523, USA
| | - Michael T Butcher
- Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
| | - Jifeng Zhang
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing 101200, China.
| | - Jianglin Fan
- Department of Molecular Pathology, Faculty of Medicine, Interdisciplinary Graduate School of Medicine, University of Yamanashi, 1110, Shimokato, Chuo, Yamanashi 409-3898, Japan.
| | - Enqi Liu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, Shaanxi 710061, China; Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, Shaanxi 710061, China.
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11
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Mclean BS, Bell KC, Allen JM, Helgen KM, Cook JA. Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini). Syst Biol 2018; 68:298-316. [DOI: 10.1093/sysbio/syy064] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/12/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Bryan S Mclean
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Kayce C Bell
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
- Department of Invertebrate Zoology, Smithsonian Institution National Museum of Natural History, P.O. Box 37012, MRC 163, Washington, DC 20013-7012, USA
| | - Julie M Allen
- Department of Biology, University of Nevada, 1664 N. Virginia Street, Reno, NV 89557, USA
| | - Kristofer M Helgen
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
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Genetic diversity distribution among seasonal colonies of a nectar-feeding bat (Leptonycteris yerbabuenae) in the Baja California Peninsula. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Yan J, Chen H, Lin G, Li Q, Chen J, Qin W, Su J, Zhang T. Genetic evidence for subspecies differentiation of the Himalayan marmot, Marmota himalayana, in the Qinghai-Tibet Plateau. PLoS One 2017; 12:e0183375. [PMID: 28809943 PMCID: PMC5557547 DOI: 10.1371/journal.pone.0183375] [Citation(s) in RCA: 3] [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: 06/05/2017] [Accepted: 08/02/2017] [Indexed: 01/14/2023] Open
Abstract
The primary host of plague in the Qinghai-Tibet Plateau (QTP), China, is Marmota himalayana, which plays an essential role in the maintenance, transmission, and prevalence of plague. To achieve a more clear insight into the differentiation of M. himalayana, complete cytochrome b (cyt b) gene and 11 microsatellite loci were analyzed for a total of 423 individuals from 43 localities in the northeast of the QTP. Phylogenetic analyses with maximum likelihood and Bayesian inference methods showed that all derived haplotypes diverged into two primary well-supported monophyletic lineages, I and II, which corresponded to the referential sequences of two recognized subspecies, M. h. himalayana and M. h. robusta, respectively. The divergence between the two lineages was estimated to be at about 1.03 million years ago, nearly synchronously with the divergence between M. baibacina and M. kastschenkoi and much earlier than that between M. vancouverensis and M. caligata. Genetic structure analyses based on the microsatellite dataset detected significant admixture between the two lineages in the mixed region, which verified the intraspecies level of the differentiation between the two lineages. Our results for the first time demonstrated the coexistence of M. h. himalayana and M. h. robusta, and also, determined the distribution range of the two subspecies in the northeast of QTP. We provided fundamental information for more effective plague control in the QTP.
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Affiliation(s)
- Jingyan Yan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongjian Chen
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Gonghua Lin
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, China
| | - Qian Li
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Jiarui Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, China
| | - Wen Qin
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, China
| | - Jianping Su
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, China
- * E-mail: (JS); (TZ)
| | - Tongzuo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
- Qinghai Key Laboratory of Animal Ecological Genomics, Xining, Qinghai, China
- * E-mail: (JS); (TZ)
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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: 178] [Impact Index Per Article: 25.4] [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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Liu Y, Wang B, Wang L, Vikash V, Wang Q, Roggendorf M, Lu M, Yang D, Liu J. Transcriptome Analysis and Comparison of Marmota monax and Marmota himalayana. PLoS One 2016; 11:e0165875. [PMID: 27806133 PMCID: PMC5091844 DOI: 10.1371/journal.pone.0165875] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/19/2016] [Indexed: 12/12/2022] Open
Abstract
The Eastern woodchuck (Marmota monax) is a classical animal model for studying hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC) in humans. Recently, we found that Marmota himalayana, an Asian animal species closely related to Marmota monax, is susceptible to woodchuck hepatitis virus (WHV) infection and can be used as a new mammalian model for HBV infection. However, the lack of genomic sequence information of both Marmota models strongly limited their application breadth and depth. To address this major obstacle of the Marmota models, we utilized Illumina RNA-Seq technology to sequence the cDNA libraries of liver and spleen samples of two Marmota monax and four Marmota himalayana. In total, over 13 billion nucleotide bases were sequenced and approximately 1.5 billion clean reads were obtained. Following assembly, 106,496 consensus sequences of Marmota monax and 78,483 consensus sequences of Marmota himalayana were detected. For functional annotation, in total 73,603 Unigenes of Marmota monax and 78,483 Unigenes of Marmota himalayana were identified using different databases (NR, NT, Swiss-Prot, KEGG, COG, GO). The Unigenes were aligned by blastx to protein databases to decide the coding DNA sequences (CDS) and in total 41,247 CDS of Marmota monax and 34,033 CDS of Marmota himalayana were predicted. The single nucleotide polymorphisms (SNPs) and the simple sequence repeats (SSRs) were also analyzed for all Unigenes obtained. Moreover, a large-scale transcriptome comparison was performed and revealed a high similarity in transcriptome sequences between the two marmota species. Our study provides an extensive amount of novel sequence information for Marmota monax and Marmota himalayana. This information may serve as a valuable genomics resource for further molecular, developmental and comparative evolutionary studies, as well as for the identification and characterization of functional genes that are involved in WHV infection and HCC development in the woodchuck model.
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Affiliation(s)
- Yanan Liu
- Department of Infectious Diseases, Institute of Infection and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Baoju Wang
- Department of Infectious Diseases, Institute of Infection and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lu Wang
- Department of Infectious Diseases, Institute of Infection and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Vikash Vikash
- Department of Infectious Diseases, Institute of Infection and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qin Wang
- Department of Infectious Diseases, Institute of Infection and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Michael Roggendorf
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Mengji Lu
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Dongliang Yang
- Department of Infectious Diseases, Institute of Infection and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- * E-mail: (DY); (JL)
| | - Jia Liu
- Department of Infectious Diseases, Institute of Infection and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- * E-mail: (DY); (JL)
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Kerhoulas NJ, Gunderson AM, Olson LE. Complex history of isolation and gene flow in hoary, Olympic, and endangered Vancouver Island marmots. J Mammal 2015. [DOI: 10.1093/jmammal/gyv089] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Climate change resulting in a reduction of alpine habitat is believed to pose a considerable risk to alpine-dependent species, including many marmots. Hoary marmots (Marmota caligata) range throughout much of the mountainous Pacific Northwest (PNW) and Rocky Mountains while the closely related Olympic and Vancouver Island marmots (M. olympus and M. vancouverensis, respectively) are restricted to small isolated regions of the PNW. The endemic Vancouver Island marmot is currently classified as Critically Endangered and the Olympic marmot has recently experienced dramatic population declines. Previous phylogenetic studies of PNW marmot species have had limited power as they focused on resolving interspecific relationships, implicitly assumed an absence of gene flow among currently recognized species, included relatively few individuals, and relied heavily or entirely on mitochondrial DNA. We sequenced 2 mitochondrial and 4 nuclear markers from 167 hoary, 4 Vancouver Island, and 5 Olympic marmots in order to investigate phylogenetic relationships and historic gene flow among these species. We recovered 2 monophyletic (and predominantly allopatric) mitochondrial clades of hoary marmots that are not sister groups. Instead, Vancouver Island marmots formed a monophyletic mitochondrial sister clade to 1 of the hoary marmot clades. Nuclear loci did not recover the 2 mitochondrial clades of hoary marmots and suggest that Vancouver Island marmots may have experienced mitochondrial introgression from coastal mainland hoary marmots. Additionally, our nuclear results suggest possible gene flow between hoary and Olympic marmots despite different chromosomal formulas. Rather than resolving what has previously been considered a straightforward 3-taxon phylogenetic question, our findings suggest a complicated history of rapid divergence of the 3 species followed by intermittent and possibly ongoing gene flow between hoary marmots and both Olympic and Vancouver Island marmots. These results therefore have significant implications for the conservation of the latter 2 species, both of which are conservation concerns.
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Kapustina SY, Brandler OV, Adiya Y. Phylogeny of genus Spermophilus and position of Alashan ground squirrel (Spermophilus alashanicus, Büchner, 1888) on phylogenetic tree of Paleartic short-tailed ground squirrels. Mol Biol 2015. [DOI: 10.1134/s0026893315030085] [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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Lanier HC, Gunderson AM, Weksler M, Fedorov VB, Olson LE. Comparative phylogeography highlights the double-edged sword of climate change faced by arctic- and alpine-adapted mammals. PLoS One 2015; 10:e0118396. [PMID: 25734275 PMCID: PMC4348485 DOI: 10.1371/journal.pone.0118396] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 01/15/2015] [Indexed: 11/23/2022] Open
Abstract
Recent studies suggest that alpine and arctic organisms may have distinctly different phylogeographic histories from temperate or tropical taxa, with recent range contraction into interglacial refugia as opposed to post-glacial expansion out of refugia. We use a combination of phylogeographic inference, demographic reconstructions, and hierarchical Approximate Bayesian Computation to test for phylodemographic concordance among five species of alpine-adapted small mammals in eastern Beringia. These species (Collared Pikas, Hoary Marmots, Brown Lemmings, Arctic Ground Squirrels, and Singing Voles) vary in specificity to alpine and boreal-tundra habitat but share commonalities (e.g., cold tolerance and nunatak survival) that might result in concordant responses to Pleistocene glaciations. All five species contain a similar phylogeographic disjunction separating eastern and Beringian lineages, which we show to be the result of simultaneous divergence. Genetic diversity is similar within each haplogroup for each species, and there is no support for a post-Pleistocene population expansion in eastern lineages relative to those from Beringia. Bayesian skyline plots for four of the five species do not support Pleistocene population contraction. Brown Lemmings show evidence of late Quaternary demographic expansion without subsequent population decline. The Wrangell-St. Elias region of eastern Alaska appears to be an important zone of recent secondary contact for nearctic alpine mammals. Despite differences in natural history and ecology, similar phylogeographic histories are supported for all species, suggesting that these, and likely other, alpine- and arctic-adapted taxa are already experiencing population and/or range declines that are likely to synergistically accelerate in the face of rapid climate change. Climate change may therefore be acting as a double-edged sword that erodes genetic diversity within populations but promotes divergence and the generation of biodiversity.
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Affiliation(s)
- Hayley C. Lanier
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
- * E-mail:
| | - Aren M. Gunderson
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
| | - Marcelo Weksler
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
| | - Vadim B. Fedorov
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
| | - Link E. Olson
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, Alaska 99775, United States of America
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Riddle BR, Jezkova T, Hornsby AD, Matocq MD. Assembling the modern Great Basin mammal biota: insights from molecular biogeography and the fossil record. J Mammal 2014. [DOI: 10.1644/14-mamm-s-064] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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20
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Wang B, Zhu Z, Zhu B, Wang J, Song Z, Huang S, Fan W, Tao Y, Wang Z, Wang H, Lu M, Yang D. Nucleoside analogues alone or combined with vaccination prevent hepadnavirus viremia and induce protective immunity: alternative strategy for hepatitis B virus post-exposure prophylaxis. Antiviral Res 2014; 105:118-25. [PMID: 24583157 DOI: 10.1016/j.antiviral.2014.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 01/08/2023]
Abstract
OBJECTIVES The current strategies for hepatitis B virus (HBV) post-exposure prophylaxis (PEP) are not generally available in remote and rural areas of developing countries and/or carry potential risks for infection with blood-borne transmitted pathogens. Nucleotide analogues (NAs) are successfully used for human immunodeficiency virus PEP, and maybe effective for HBV PEP. In this study, we tested the NA-based strategies for HBV PEP using the Chinese woodchuck model. METHODS Chinese woodchucks were inoculated intravenously with different doses of woodchuck hepatitis virus (WHV). A deoxyguanosine analogue entacavir (ETV), a DNA vaccine pWHcIm, or ETV plus pWHcIm were applied to the infected animals 24h later. Twenty weeks later, the animals were re-challenged with WHV to test for the presence of immunity against WHV. RESULTS Inoculation with different WHV doses had a strong influence on the course of WHV infection; NA alone or in combination with a DNA vaccine completely prevented viremia after a high dose of WHV inoculation in Chinese woodchucks and induced partial or complete protective immunity, respectively. CONCLUSIONS NA-based PEP strategies (NA alone or in combination with vaccine) may be an alternative of HBV PEP, especially in those living in the remote and rural areas of the developing countries and the non-responders to the current vaccine, and may be valuable in the PEP of HBV and HIV co-infection after occupational and non-occupational exposure. Further clinical studies are warranted to confirm the valuable of NA-based strategies in HBV PEP.
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Affiliation(s)
- Baoju Wang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zhenni Zhu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Bin Zhu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Junzhong Wang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zhitao Song
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shunmei Huang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Wei Fan
- Qinghai Institute for Endemic Disease Prevention and Control, Xining 811602, China
| | - Yuanqing Tao
- Qinghai Institute for Endemic Disease Prevention and Control, Xining 811602, China
| | - Zhongdong Wang
- Qinghai Institute for Endemic Disease Prevention and Control, Xining 811602, China
| | - Hu Wang
- Qinghai Institute for Endemic Disease Prevention and Control, Xining 811602, China
| | - Mengji Lu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institut für Virologie, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen 45122, Germany.
| | - Dongliang Yang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
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Rupert JE, Rose JA, Organ JM, Butcher MT. Forelimb muscle architecture and myosin isoform composition in the groundhog (Marmota monax). J Exp Biol 2014; 218:194-205. [DOI: 10.1242/jeb.107128] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Scratch-digging mammals are commonly described as having large, powerful forelimb muscles for applying high force to excavate earth, yet studies quantifying the architectural properties of the musculature are largely unavailable. To further test hypotheses about traits that represent specializations for scratch-digging, we quantified muscle architectural properties and fiber type in the forelimb of the groundhog (Marmota monax), a digger that constructs semi-complex burrows. Architectural properties measured were muscle moment arm, muscle mass (MM), belly length (ML), fascicle length (lF), pennation angle, and physiological cross-sectional area (PCSA), and these metrics were used to estimate maximum isometric force, joint torque, and power. Myosin heavy chain (MHC) isoform composition was determined in selected forelimb muscles by SDS-PAGE and densitometry analysis. Groundhogs have large limb retractors and elbow extensors that are capable of applying moderately high torque at the shoulder and elbow joints, respectively. Most of these muscles (e.g., latissimus dorsi and pectoralis superficialis) have high lF/ML ratios, indicating substantial shortening ability and moderate power. The unipennate triceps brachii long head has the largest PCSA and is capable of the highest joint torque at both the shoulder and elbow joints. The carpal and digital flexors show greater pennation and shorter fascicle lengths than the limb retractors and elbow extensors, resulting in higher PCSA:MM ratios and force production capacity. Moreover, the digital flexors have the capacity for both appreciable fascicle shortening and force production indicating high muscle work potential. Overall, the forelimb musculature of the groundhog is capable of relatively low sustained force and power, and these properties are consistent with the findings of a predominant expression of the MHC-2A isoform. Aside from the apparent modifications to the digital flexors, the collective muscle properties observed are consistent with its behavioral classification as a less specialized burrower and these may be more representative of traits common to numerous rodents with burrowing habits or mammals with some fossorial ability.
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Ge DY, Liu X, Lv XF, Zhang ZQ, Xia L, Yang QS. Historical Biogeography and Body Form Evolution of Ground Squirrels (Sciuridae: Xerinae). Evol Biol 2013. [DOI: 10.1007/s11692-013-9250-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Kryštufek B, Abi-Said M, Hladnik M. The Iranian voleMicrotus iranioccurs in Lebanon (Mammalia: Rodentia). ZOOLOGY IN THE MIDDLE EAST 2013. [DOI: 10.1080/09397140.2013.810863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Fernández JA. Phylogenetics and biogeography of the microendemic rodentXerospermophilus perotensis(Perote ground squirrel) in the Oriental Basin of Mexico. J Mammal 2012. [DOI: 10.1644/11-mamm-a-409.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Junker K, Medger K, Lutermann H, Bain O. Monanema joopi n. sp. (Nematoda, Onchocercidae) from Acomys (Acomys) spinosissimus Peters, 1852 (Muridae) in South Africa, with comments on the filarial genus. Parasite 2012; 19:331-40. [PMID: 23193517 PMCID: PMC3671456 DOI: 10.1051/parasite/2012194331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Accepted: 06/16/2012] [Indexed: 11/14/2022] Open
Abstract
Monanema joopi n. sp. is described from blood drawn from the heart of the murid Acomys (Acomys) spinosissimus in South Africa. It is characterised by a non-bulbous cephalic extremity, shared with only one of its five congeners, and a cylindrical tail with caudal alae and a spicular ratio of 2.7 in the male. As is typical for the genus, microfilariae are skin-dwelling. They are 185 to 215 micrometres long and have no refractory granules beneath their sheath. A key to the species of Monanema is presented and an amended generic description, based on the six currently known species, is proposed. Species of Monanema are primarily lymphatic and the low intensity of infection with M. joopi n. sp. in blood from the heart, might suggest that not all adults settle in the heart cavities. One might also consider that other, more susceptible rodents serve as hosts for this parasite as well. To date, the geographic range of Monanema includes North America, Africa and Australia, each with representatives of a different lineage. Given the present hypotheses on the evolutionary origin and subsequent migrations of rodents, we expect the origin of Monanema to be in the Palearctic-Oriental region.
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Affiliation(s)
- K Junker
- ARC-Onderstepoort Veterinary Institute, Private Bag X05, Onderstepoort, South Africa.
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Molecular characterization of the type I IFN receptor in two woodchuck species and detection of its expression in liver samples from woodchucks infected with woodchuck hepatitis virus (WHV). Cytokine 2012; 60:179-85. [PMID: 22705153 DOI: 10.1016/j.cyto.2012.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 05/15/2012] [Accepted: 05/17/2012] [Indexed: 02/06/2023]
Abstract
Type I interferons (IFN-α/β) serve as the first line of defense against viral infection and share the same type I IFN receptor (IFNAR) complex, which is composed of IFNAR1 and -2. The Eastern woodchuck (Marmota monax) and Chinese woodchuck (Marmota himalayana) are suitable for studying hepatitis B virus (HBV) infection. Here, the complete or partial sequences of the IFNARs of both species were obtained and analyzed. Small interference RNAs targeting wIFNAR1 and -2 specifically down-regulated the expression of wIFNAR1 and -2 and the IFN-stimulated gene MxA in a woodchuck cell line, respectively. IFNAR2 was significantly up-regulated in primary woodchuck hepatocytes stimulated with IFN-α or -γ. The expression of woodchuck IFNAR1 and -2 was decreased in woodchucks chronically infected with woodchuck hepatitis virus (WHV). These results are essential for studying type I IFN-related innate immunity and therapy in hepadnaviral infection in the woodchuck model.
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Fabre PH, Hautier L, Dimitrov D, Douzery EJP. A glimpse on the pattern of rodent diversification: a phylogenetic approach. BMC Evol Biol 2012; 12:88. [PMID: 22697210 PMCID: PMC3532383 DOI: 10.1186/1471-2148-12-88] [Citation(s) in RCA: 300] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 05/14/2012] [Indexed: 11/17/2022] Open
Abstract
Background Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia. Results Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56% and 81% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation. Conclusions The present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes.
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Affiliation(s)
- Pierre-Henri Fabre
- Center for Macroecology, Evolution and Climate (CMEC, Department of Biology), Zoological Museum, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
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Platt II RN, Ray DA. A non-LTR retroelement extinction in Spermophilus tridecemlineatus. Gene 2012; 500:47-53. [DOI: 10.1016/j.gene.2012.03.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 10/28/2022]
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Gunderson AM, Lanier HC, Olson LE. Limited phylogeographic structure and genetic variation in Alaska's arctic and alpine endemic, the Alaska marmot. J Mammal 2012. [DOI: 10.1644/10-mamm-a-380.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Hoberg EP, Galbreath KE, Cook JA, Kutz SJ, Polley L. Northern host-parasite assemblages: history and biogeography on the borderlands of episodic climate and environmental transition. ADVANCES IN PARASITOLOGY 2012; 79:1-97. [PMID: 22726642 DOI: 10.1016/b978-0-12-398457-9.00001-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Diversity among assemblages of mammalian hosts and parasites in northern terrestrial ecosystems was structured by a deep history of biotic and abiotic change that overlies a complex geographic arena. Since the Pliocene, Holarctic ecosystems assembled in response to shifting climates (glacial and interglacial stages). Cycles of episodic dispersal/isolation and diversification defined northern diversity on landscape to regional scales. Episodes of geographic expansion and colonisation linked Eurasia and North America across Beringia and drove macroevolutionary structure of host and parasite associations. Asynchronous dispersal from centres of origin in Eurasia into the Nearctic resulted in gradients in parasite diversity in the carnivoran, lagomorph, rodent and artiodactyl assemblages we reviewed. Recurrent faunal interchange and isolation in conjunction with episodes of host colonisation have produced a mosaic structure for parasite faunas and considerable cryptic diversity among nematodes and cestodes. Mechanisms of invasion and geographic colonisation leading to the establishment of complex faunal assemblages are equivalent in evolutionary and ecological time, as demonstrated by various explorations of diversity in these high-latitude systems. Our ability to determine historical responses to episodic shifts in global climate may provide a framework for predicting the cascading effects of contemporary environmental change.
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Steppan SJ, Kenagy GJ, Zawadzki C, Robles R, Lyapunova EA, Hoffmann RS. Molecular data resolve placement of the Olympic marmot and estimate dates of trans-Beringian interchange. J Mammal 2011. [DOI: 10.1644/10-mamm-a-272.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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GeMBiD, a Geometric Morphometric Approach to the Study of Biological Diversity: An Example Study of the Red Colobus (Procolobus [Piliocolobus]) Species Complex. INT J PRIMATOL 2010. [DOI: 10.1007/s10764-010-9475-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Wang BJ, Tian YJ, Meng ZJ, Jiang M, Wei BQ, Tao YQ, Fan W, Li AY, Bao JJ, Li XY, Zhang ZM, Wang ZD, Wang H, Roggendorf M, Lu MJ, Yang DL. Establishing a new animal model for hepadnaviral infection: susceptibility of Chinese Marmota-species to woodchuck hepatitis virus infection. J Gen Virol 2010; 92:681-91. [PMID: 21084496 DOI: 10.1099/vir.0.025023-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Hepatitis B virus infection (HBV) is a major medical problem in China. The lack of a suitable infection model in China is recognized as an obstacle for research on HBV in China. Chinese Marmota-species is phylogenetically closely related to Marmota monax, thus, it might be suitable to serve as an animal model for HBV infection. Therefore, we attempted to prove the claim about the existence of woodchuck hepatitis virus (WHV)-like viruses in Chinese Marmota-species and to determine the susceptibility of these species to experimental WHV infection. In the present study, 653 sera from three Chinese Marmota-species, Marmota himalayana, Marmota baibacina and Marmota bobak, were screened for WHV-like viruses by serological and molecular assays. The susceptibility to WHV of three species was investigated by experimental infection and monitored by testing of anti-WHc and WHsAg by ELISA, detection of WHV DNA by PCR, and detection of WHV replication intermediates and antigens in liver samples. No evidence for the existence of a genetically closely related virus to WHV in three Chinese Marmota-species was found by serological assays and PCR. M. himalayana was susceptible to WHV infection as inoculated animals became positive for anti-WHc, WHsAg and WHV DNA. Further, WHV replication intermediates and proteins were detected in liver samples. In contrast, M. baibacina remained negative for tested virological parameters. M. bobak species showed a limited susceptibility to WHV. Our data do not support early reports about WHV-like viruses in China. M. himalayana is suitable for the establishment of a model for hepadnaviral infection.
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Affiliation(s)
- Bao-Ju Wang
- Division of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
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SHAFER AARONBA, CULLINGHAM CATHERINEI, CÔTÉ STEEVED, COLTMAN DAVIDW. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol Ecol 2010; 19:4589-621. [PMID: 20849561 DOI: 10.1111/j.1365-294x.2010.04828.x] [Citation(s) in RCA: 254] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- AARON B. A. SHAFER
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - CATHERINE I. CULLINGHAM
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - STEEVE D. CÔTÉ
- Département de Biologie and Centre for Northern Studies, Université Laval, Québec, Québec G1V 0A6, Canada
| | - DAVID W. COLTMAN
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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The woodchuck: a model for therapeutic vaccination against hepadnaviral infection. ACTA ACUST UNITED AC 2010; 58:308-14. [PMID: 20646874 DOI: 10.1016/j.patbio.2010.04.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 04/16/2010] [Indexed: 12/27/2022]
Abstract
Interferon-alpha and nucleoside analogues are available for the treatment of chronic hepatitis B virus (HBV) infection but do not lead to a satisfactory result. New findings about the immunological control of HBV during acute infection suggest the pivotal role of T-cell mediated immune responses. Several preclinical and clinical trials were undertaken to explore the possibility of stimulating specific immune responses in chronically infected animals and patients by vaccination. However, vaccination with commercially available HBV vaccines in patients and immunization in woodchucks with core or surface proteins of woodchuck hepatitis virus (WHV) did not result in effective control of HBV and WHV infection, suggesting that new formulations of therapeutic vaccines are needed. Some new approaches combining antiviral treatments with nucleoside analogues, DNA vaccines and protein vaccines were tested in the woodchuck model. It could be shown that therapeutic vaccinations are able to stimulate specific B- and T-cell responses and to achieve transient suppression of viral replication. These results suggest the great potential of therapeutic vaccination in combination with antivirals to reach an effective and sustained control of HBV infection.
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Brandler OV, Lyapunova EA, Bannikova AA, Kramerov DA. Phylogeny and systematics of marmots (Marmota, Sciuridae, Rodentia) inferred from inter-SINE PCR data. RUSS J GENET+ 2010. [DOI: 10.1134/s102279541003004x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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37
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38
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Nagorsen DW, Cardini A. Tempo and mode of evolutionary divergence in modern and Holocene Vancouver Island marmots (Marmota vancouverensis) (Mammalia, Rodentia). J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.2008.00503.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Helgen KM, Cole FR, Helgen LE, Wilson DE. Generic Revision in the Holarctic Ground Squirrel GenusSpermophilus. J Mammal 2009. [DOI: 10.1644/07-mamm-a-309.1] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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40
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Genetic relatedness and space use in a behaviorally flexible species of marmot, the woodchuck (Marmota monax). Behav Ecol Sociobiol 2009. [DOI: 10.1007/s00265-009-0726-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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41
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Kruckenhauser L, Bryant AA, Griffin SC, Amish SJ, Pinsker W. Patterns of within and between-colony microsatellite variation in the endangered Vancouver Island marmot (Marmota vancouverensis): implications for conservation. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9779-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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42
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Shiao MS, Liao BY, Long M, Yu HT. Adaptive evolution of the insulin two-gene system in mouse. Genetics 2008; 178:1683-91. [PMID: 18245324 PMCID: PMC2278064 DOI: 10.1534/genetics.108.087023] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2008] [Accepted: 01/14/2008] [Indexed: 02/05/2023] Open
Abstract
Insulin genes in mouse and rat compose a two-gene system in which Ins1 was retroposed from the partially processed mRNA of Ins2. When Ins1 originated and how it was retained in genomes still remain interesting problems. In this study, we used genomic approaches to detect insulin gene copy number variation in rodent species and investigated evolutionary forces acting on both Ins1 and Ins2. We characterized the phylogenetic distribution of the new insulin gene (Ins1) by Southern analyses and confirmed by sequencing insulin genes in the rodent genomes. The results demonstrate that Ins1 originated right before the mouse-rat split ( approximately 20 MYA), and both Ins1 and Ins2 are under strong functional constraints in these murine species. Interestingly, by examining a range of nucleotide polymorphisms, we detected positive selection acting on both Ins2 and Ins1 gene regions in the Mus musculus domesticus populations. Furthermore, three amino acid sites were also identified as having evolved under positive selection in two insulin peptides: two are in the signal peptide and one is in the C-peptide. Our data suggest an adaptive divergence in the mouse insulin two-gene system, which may result from the response to environmental change caused by the rise of agricultural civilization, as proposed by the thrifty-genotype hypothesis.
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Affiliation(s)
- Meng-Shin Shiao
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
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43
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Brandler OV, Lyapunova EA, Boeskorov GG. Comparative karyology of Palearctic marmots (Marmota, Sciuridae, Rodentia). MAMMALIA 2008. [DOI: 10.1515/mamm.2008.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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44
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Lu Y, Wang B, Huang H, Tian Y, Bao J, Dong J, Roggendorf M, Lu M, Yang D. The interferon-alpha gene family of Marmota himalayana, a Chinese marmot species with susceptibility to woodchuck hepatitis virus infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2007; 32:445-457. [PMID: 17936902 DOI: 10.1016/j.dci.2007.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Revised: 08/12/2007] [Accepted: 08/12/2007] [Indexed: 05/25/2023]
Abstract
The interferon-alpha (IFN-alpha) gene family is an important part of the immune system. Recombinant interferon-alpha is widely used to treat viral hepatitis and malignant diseases. Marmota himalayana has been found to be susceptible to woodchuck hepatitis virus, a virus genetically related to hepatitis B virus (HBV), and is suitable as an animal model for studies on HBV infection. Here, the IFN-alpha gene family of M. himalayana (cwIFN-alpha) was characterized. Sequence data indicate that the cwIFN-alpha family consists of at least 8 functional sequences and 6 pseudogenes with high homology within the family and to IFN-alpha of Marmota monax, a related species and well-established animal model. The recombinant cwIFN-alpha subtypes were expressed and tested to be active in viral protection assay and to induce expression of MxA in a species-specific manner. This work provides essential information for future work on testing new therapeutic approaches of HBV infection based on IFN-alpha in M. himalayana.
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Affiliation(s)
- Yinping Lu
- Division of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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Cardini A, Thorington RW, Polly PD. Evolutionary acceleration in the most endangered mammal of Canada: speciation and divergence in the Vancouver Island marmot (Rodentia, Sciuridae). J Evol Biol 2007; 20:1833-46. [PMID: 17714301 DOI: 10.1111/j.1420-9101.2007.01398.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The Vancouver Island marmot is the most endangered mammal of Canada. Factors which have brought this population to the verge of extinction have not yet been fully elucidated, but the effects of deforestation and habitat fragmentation on survival rates, as well as those of variation in rainfall, temperature, snowpack depth and snowmelt strongly suggest that marmots on the island are struggling to keep pace with environmental changes. Genetic analyses, however, seem to indicate that the Vancouver Island marmot may merely represent a melanistic population of its parental species on the mainland. Were it not for its black pelage colour, it is unlikely that it would have attracted much attention as a conservation priority. Our study uses three-dimensional coordinates of cranial landmarks to further assess phenotypic differentiation of the Vancouver Island marmot. A pattern of strong interspecific divergence and low intraspecific variation was found which is consistent with aspects of drift-driven models of speciation. However, the magnitude of shape differences relative to the putatively neutral substitutions in synonymous sites of cytochrome b is too large for being compatible with a simple neutral model. A combination of bottlenecks and selective pressures due to natural and human-induced changes in the environment may offer a parsimonious explanation for the large phenotypic differentiation observed in the species. Our study exemplifies the usefulness of a multidisciplinary approach to the study of biological diversity for a better understanding of evolutionary models and to discover aspects of diversity that may be undetected by using only a few genetic markers to characterize population divergence and uniqueness.
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Affiliation(s)
- A Cardini
- Museo di Paleobiologia e dell'Orto Botanico, Universitá di Modena e Reggio Emilia, Modena, Italy.
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46
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Blumstein DT. The Evolution, Function, and Meaning of Marmot Alarm Communication. ADVANCES IN THE STUDY OF BEHAVIOR 2007. [DOI: 10.1016/s0065-3454(07)37008-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
We define a genetic species as a group of genetically compatible interbreeding natural populations that is genetically isolated from other such groups. This focus on genetic isolation rather than reproductive isolation distinguishes the Genetic Species Concept from the Biological Species Concept. Recognition of species that are genetically isolated (but not reproductively isolated) results in an enhanced understanding of biodiversity and the nature of speciation as well as speciation-based issues and evolution of mammals. We review criteria and methods for recognizing species of mammals and explore a theoretical scenario, the Bateson-Dobzhansky-Muller (BDM) model, for understanding and predicting genetic diversity and speciation in mammals. If the BDM model is operating in mammals, then genetically defined phylogroups would be predicted to occur within species defined by morphology, and phylogroups experiencing stabilizing selection will evolve genetic isolation without concomitant morphological diversification. Such species will be undetectable using classical skin and skull morphology (Morphological Species Concept). Using cytochrome-b data from sister species of mammals recognized by classical morphological studies, we estimated the number of phylogroups that exist within mammalian species and hypothesize that there will be >2,000 currently unrecognized species of mammals. Such an underestimation significantly affects conclusions on the nature of speciation in mammals, barriers associated with evolution of genetic isolation, estimates of biodiversity, design of conservation initiatives, zoonoses, and so on. A paradigm shift relative to this and other speciation-based issues will be needed. Data that will be effective in detecting these "morphologically cryptic genetic species" are genetic, especially DNA-sequence data. Application of the Genetic Species Concept uses genetic data from mitochondrial and nuclear genomes to identify species and species boundaries, the extent to which the integrity of the gene pool is protected, nature of hybridization (if present), and introgression. Genetic data are unique in understanding species because the use of genetic data 1) can quantify genetic divergence from different aspects of the genome (mitochondrial and nuclear genes, protein coding genes, regulatory genes, mobile DNA, microsatellites, chromosomal rearrangements, heterochromatin, etc.); 2) can provide divergence values that increase with time, providing an estimate of time since divergence; 3) can provide a population genetics perspective; 4) is less subject to convergence and parallelism relative to other sets of characters; 5) can identify monophyly, sister taxa, and presence or absence of introgression; and 6) can accurately identify hybrid individuals (kinship and source of hybrid individuals, F(1)s, backcrosses, direction of hybridization, and in concert with other data identify which hybrids are sterile or fertile). The proposed definition of the Genetic Species Concept is more compatible with a description of biodiversity of mammals than is "reproductively isolated species." Genetic profiles of mammalian species will result in a genetic description of species and mammalian diversity, and such studies are being accelerated by technological advances that reduce cost and increase speed and efficiency of generating genetic data. We propose that this genetic revolution remain museum- and voucher specimen-based and that new names are based on a holotype (including associated tissues) deposited in an accredited museum.
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Affiliation(s)
- Robert J. Baker
- Department of Biological Sciences and the Museum, Texas Tech University, Lubbock, TX 79409-3131, USA
| | - Robert D. Bradley
- Department of Biological Sciences and the Museum, Texas Tech University, Lubbock, TX 79409-3131, USA
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Cardini A, Thorington RW. POSTNATAL ONTOGENY OF MARMOT (RODENTIA, SCIURIDAE) CRANIA: ALLOMETRIC TRAJECTORIES AND SPECIES DIVERGENCE. J Mammal 2006. [DOI: 10.1644/05-mamm-a-242r1.1] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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49
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Cook JA, Hoberg EP, Koehler A, Henttonen H, Wickström L, Haukisalmi V, Galbreath K, Chernyavski F, Dokuchaev N, Lahzuhtkin A, MacDonald SO, Hope A, Waltari E, Runck A, Veitch A, Popko R, Jenkins E, Kutz S, Eckerlin R. Beringia: Intercontinental exchange and diversification of high latitude mammals and their parasites during the Pliocene and Quaternary. MAMMAL STUDY 2005. [DOI: 10.3106/1348-6160(2005)30[33:bieado]2.0.co;2] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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50
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Caumul R, Polly PD. PHYLOGENETIC AND ENVIRONMENTAL COMPONENTS OF MORPHOLOGICAL VARIATION: SKULL, MANDIBLE, AND MOLAR SHAPE IN MARMOTS (MARMOTA, RODENTIA). Evolution 2005. [DOI: 10.1111/j.0014-3820.2005.tb00955.x] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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