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Phylogeography of the Plateau Pika (Ochotona curzoniae) in Response to the Uplift of the Qinghai-Tibet Plateau. DIVERSITY 2023. [DOI: 10.3390/d15020307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The evolution and current distribution of species on the Qinghai-Tibet Plateau have been significantly impacted by historical occurrences, including the uplift of the plateau and the Quaternary climate upheaval. As a remnant species, the plateau pika (Ochotona curzoniae) is a great model for researching historical events. In this study, 302 samples from 42 sample sites were utilized to analyze the impact of historical events on the evolution and distribution pattern of plateau pikas. The genetic diversity, patterns of differentiation, and historical dynamics of the plateau pika were investigated using molecular markers that included four mitochondrial genes (COI, D-loop, Cytb, and 12S rRNA) and three nuclear genes (GHR, IRBP, and RAG1). The results showed that: (1) The genetic diversity of the plateau pika was high in the Tibetan Plateau (Hd = 0.9997, π = 0.01205), and the plateau pika evolved into five lineages that occupied different geographical areas, with lineage 1 (Group 1) in the south of the Yarlung Zangbo River, lineage 2 (Group 2) in the hinterland of the plateau, lineage 3 (Group 3) in the northeastern part of the plateau, lineage 4 (Group 4) in the Hengduan Mountains, and lineage 5 (Group 5) in the eastern part of the plateau. (2) The gene flow among the five lineages was low, and the differentiation level was high (Nm < 0.25; Fst > 0.25), indicating that the geographical barriers between the five lineages, such as the Yarlung Zangbo River, the Qaidam-Ghuong-Guide Basin, and the Lancang River, effectively promoted the population differentiation of the plateau pika. (3) The plateau pika first spread from the Hengduan Mountains to the entire Qinghai-Tibet Plateau and then conducted small-scale migration and dispersal in several refuges across the plateau in response to climate changes during the glacial and interglacial periods. (4) Except for Group 1 and Group 4, all the other populations exhibited a rapid expansion between 0.06 and 0.01 Mya, but the expansion was considerably delayed or halted by the effects of climate change during the last glacial maximum (0.02 Mya). Overall, the plateau pika on the Qinghai-Tibet Plateau exhibits high genetic diversity, and topographic obstacles, including mountains, valleys, and basins, created by the uplift of the plateau and climatic changes since the Quaternary period have played an important role in the differentiation and historical dynamics of the plateau pika population.
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Mohammadi Z, Ghorbani F, Aliabadian M, Lissovsky AA, Yazdani Moghaddam F, Olsson U. Multilocus phylogeny reveals habitat driven cryptic diversity in
Ochotona rufescens
(Ochotonidae). ZOOL SCR 2022. [DOI: 10.1111/zsc.12564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Fatemeh Ghorbani
- Department of Biology, Faculty of Sciences Ferdowsi University of Mashhad Mashhad Iran
| | - Mansour Aliabadian
- Department of Biology, Faculty of Sciences Ferdowsi University of Mashhad Mashhad Iran
- Zoological Innovations Research Department, Institute of Applied Zoology, Faculty of Sciences Ferdowsi University of Mashhad Mashhad Iran
| | | | - Faezeh Yazdani Moghaddam
- Department of Biology, Faculty of Sciences Ferdowsi University of Mashhad Mashhad Iran
- Zoological Innovations Research Department, Institute of Applied Zoology, Faculty of Sciences Ferdowsi University of Mashhad Mashhad Iran
| | - Urban Olsson
- University of Gothenburg Department of Biology and Environmental Sciences, Systematics and Biodiversity Göteborg Sweden
- Gothenburg Global Biodiversity Centre Gothenburg Sweden
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Liu N, Tian H, Yu Z, Zhao H, Li W, Sang D, Lin K, Cui Y, Liao M, Xu Z, Chen C, Guo Y, Wang Y, Huang HW, Wang J, Zhang H, Wu W, Huang H, Lv S, Guo Z, Wang W, Zheng S, Wang F, Zhang Y, Cai T, Zhang EE. A highland-adaptation mutation of the Epas1 protein increases its stability and disrupts the circadian clock in the plateau pika. Cell Rep 2022; 39:110816. [PMID: 35584682 DOI: 10.1016/j.celrep.2022.110816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/07/2022] [Accepted: 04/20/2022] [Indexed: 11/30/2022] Open
Abstract
The Qinghai-Tibet Plateau (QTP) harbors hundreds of species well adapted to its extreme conditions, including its low-oxygen (hypoxic) atmosphere. Here, we show that the plateau pika-a keystone mammal of the QTP-lacks robust circadian rhythms. The major form of the plateau pika Epas1 protein includes a 24-residue insert caused by a point mutation at the 5' juncture site of Intron14 and is more stable than other mammalian orthologs. Biochemical studies reveal that an Epas1-Bmal1 complex with lower trans-activation activity occupies the E1/E2 motifs at the promoter of the core-clock gene Per2, thus explaining how an Epas1 mutation-selected in the hypoxic conditions of the QTP-disrupts the molecular clockwork. Importantly, experiments with hypoxic chambers show that mice expressing the plateau pika Epas1 ortholog in their suprachiasmatic nucleus have dysregulated central clocks, and pika Epas1 knockin mice reared in hypoxic conditions exhibit dramatically reduced heart damage compared with wild-type animals.
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Affiliation(s)
- Na Liu
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China; Hubei Engineering Research Center of Special Wild Vegetables Breeding and Comprehensive Utilization Technology, Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, School of Life Sciences, Hubei Normal University, Huangshi, Hubei Province 435002, China
| | - Hongni Tian
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China; Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China; Department of Neurosurgery, Xinqiao Hospital, Chongqing 400038, China
| | - Ziqing Yu
- National Institute of Biological Sciences, Beijing 102206, China; Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100006, China
| | - Haijiao Zhao
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Wenjing Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province 810008, China
| | - Di Sang
- National Institute of Biological Sciences, Beijing 102206, China; Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100006, China
| | - Keteng Lin
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yilin Cui
- National Institute of Biological Sciences, Beijing 102206, China; Neuroscience Program, Smith College, Northampton, MA 01063, USA
| | - Meimei Liao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhancong Xu
- National Institute of Biological Sciences, Beijing 102206, China; Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100006, China
| | - Chen Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Ying Guo
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yibing Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Huan-Wei Huang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jiawen Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - He Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province 810008, China; Department of Pathology, Henan Cancer Hospital, Zhengzhou, Henan Province 450008, China
| | - Wei Wu
- Department of Neurology, The Second Affiliated Hospital of Nanchang University Medical School, Nanchang, Jiangxi Province 330006, China
| | - He Huang
- Department of Anesthesiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Shengqing Lv
- Department of Neurosurgery, Xinqiao Hospital, Chongqing 400038, China
| | | | - Wei Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Sanduo Zheng
- National Institute of Biological Sciences, Beijing 102206, China
| | - Fengchao Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai Province 810008, China; Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining, Qinghai Province 810008, China.
| | - Tao Cai
- National Institute of Biological Sciences, Beijing 102206, China.
| | - Eric Erquan Zhang
- National Institute of Biological Sciences, Beijing 102206, China; Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100006, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China.
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Lissovsky AA, Yatsentyuk SP, Obolenskaya EV, Koju NP, Ge D. Diversification in highlands: phylogeny and taxonomy of pikas of the subgenus
Conothoa
(Lagomorpha, Ochotonidae). ZOOL SCR 2022. [DOI: 10.1111/zsc.12538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrey A. Lissovsky
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences Moscow Russia
| | - Svetlana P. Yatsentyuk
- The All‐Russian State Center for Quality and Standardization of Veterinary Drugs and Feed Moscow Russia
| | | | - Narayan P. Koju
- Center for Postgraduate Studies Nepal Engineering College Pokhara University Pokhara Nepal
| | - Deyan Ge
- Institute of Zoology Chinese Academy of Sciences Beijing China
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Metagenomic Comparisons between Soft and Hard Feces of Plateau Pikas ( Ochotona curzoniae). Animals (Basel) 2022; 12:ani12020149. [PMID: 35049773 PMCID: PMC8772556 DOI: 10.3390/ani12020149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Plateau pika produces hard and soft feces with different morphology, component and microbial structure. Hard feces had more abundant Firmicutes, while soft feces had more abundant Akkermansia. The differences of microbial communities between hard and soft feces were mainly driven by core microbomes. Soft feces had a comprehensive advances in predict functional pathways compared to hard feces, these strengthened functional pathways were closely associated with metabolism of energy, vitamins, and amino acid. Our study preliminarily explored the differences in microbial structure and function between hard and soft feces, provided a foundation for future systematic explorations of the cecotrophy. Abstract The division of hard and soft feces is an effective digestion strategy in the order Lagomorpha. Although previous studies have reported that hard and soft feces differ in morphology and component, the discrepancy in the microbiome remains unclear. This study explored the microbiomes of hard and soft feces in plateau pikas by sequencing the V3 and V4 regions of 16S rDNA. We found that hard feces harbored higher Firmicutes, while soft feces harbored higher Akkermansia. Increased rare bacterial taxa were observed in hard feces compared with soft feces. Moreover, hard and soft feces displayed a greater difference in terms of core operational taxonomy units (OTUs) compared to the total OTUs. The soft feces showed enhancements in all predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functions, indicating an advancing microbial metabolism compared to hard feces. The significantly upregulated pathways in soft feces were mainly enriched in metabolism of energy and carbohydrate, glycan biosynthesis, cofactors and vitamins, and amino acids—all of which are associated with increased contents of microbial proteins, vitamins, and short-chain fatty acids. Our study reports, for the first time, the differential microbiomes between hard and soft feces of pikas and provides direction for the future studies on cecotrophy.
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Fu H, Zhang L, Fan C, Li W, Liu C, Zhang H, Cheng Q, Zhang Y. Sympatric Yaks and Plateau Pikas Promote Microbial Diversity and Similarity by the Mutual Utilization of Gut Microbiota. Microorganisms 2021; 9:microorganisms9091890. [PMID: 34576785 PMCID: PMC8467723 DOI: 10.3390/microorganisms9091890] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 01/17/2023] Open
Abstract
Interactions between species provide the basis for understanding coexisting mechanisms. The plateau pika (Ochotona curzoniae) and the yak (Bos grunniens) are considered competitors because they have shared habitats and consumed similar food on the Qinghai–Tibetan Plateau for more than 1 million years. Interestingly, the population density of plateau pikas increases with yak population expansion and subsequent overgrazing. To reveal the underlying mechanism, we sequenced the fecal microbial 16S rDNA from both sympatric and allopatric pikas and yaks. Our results indicated that sympatry increased both gut microbial diversity and similarity between pikas and yaks. The abundance of Firmicutes, Proteobacteria, Cyanobacteria, and Tenericutes decreased, while that of Verrucomicrobia increased in sympatric pikas. As for sympatric yaks, Firmicutes, Bacteroidetes, and Spirochaetes significantly increased, while Cyanobacteria, Euryarchaeota, and Verrucomicrobia significantly decreased. In sympatry, plateau pikas acquired 2692 OTUs from yaks, and yaks obtained 453 OTUs from pikas. The predominant horizontally transmitted bacteria were Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria. These bacteria enhanced the enrichment of pathways related to prebiotics and immunity for pikas, such as heparin sulfate, heparin, chitin disaccharide, chondroitin-sulfate-ABC, and chondroitin-AC degradation pathways. In yaks, the horizontally transmitted bacteria enhanced pathways related to hepatoprotection, xenobiotic biodegradation, and detoxification. Our results suggest that horizontal transmission is a process of selection, and pikas and yaks tend to develop reciprocity through the horizontal transmission of gut microbiota.
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Affiliation(s)
- Haibo Fu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Chao Fan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjing Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Chuanfa Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - He Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Qi Cheng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China; (H.F.); (L.Z.); (C.F.); (W.L.); (C.L.); (H.Z.); (Q.C.)
- Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Correspondence:
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Kraatz B, Belabbas R, Fostowicz-Frelik Ł, Ge DY, Kuznetsov AN, Lang MM, López-Torres S, Mohammadi Z, Racicot RA, Ravosa MJ, Sharp AC, Sherratt E, Silcox MT, Słowiak J, Winkler AJ, Ruf I. Lagomorpha as a Model Morphological System. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.636402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Due to their global distribution, invasive history, and unique characteristics, European rabbits are recognizable almost anywhere on our planet. Although they are members of a much larger group of living and extinct mammals [Mammalia, Lagomorpha (rabbits, hares, and pikas)], the group is often characterized by several well-known genera (e.g., Oryctolagus, Sylvilagus, Lepus, and Ochotona). This representation does not capture the extraordinary diversity of behavior and form found throughout the order. Model organisms are commonly used as exemplars for biological research, but there are a limited number of model clades or lineages that have been used to study evolutionary morphology in a more explicitly comparative way. We present this review paper to show that lagomorphs are a strong system in which to study macro- and micro-scale patterns of morphological change within a clade that offers underappreciated levels of diversity. To this end, we offer a summary of the status of relevant aspects of lagomorph biology.
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Fu H, Zhang L, Fan C, Liu C, Li W, Cheng Q, Zhao X, Jia S, Zhang Y. Environment and host species identity shape gut microbiota diversity in sympatric herbivorous mammals. Microb Biotechnol 2021; 14:1300-1315. [PMID: 33369229 PMCID: PMC8313255 DOI: 10.1111/1751-7915.13687] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 10/07/2020] [Indexed: 02/01/2023] Open
Abstract
The previous studies have reported that the mammalian gut microbiota is a physiological consequence; nonetheless, the factors influencing its composition and function remain unclear. In this study, to evaluate the contributions of the host and environment to the gut microbiota, we conducted a sequencing analysis of 16S rDNA and shotgun metagenomic DNA from plateau pikas and yaks, two sympatric herbivorous mammals, and further compared the sequences in summer and winter. The results revealed that both pikas and yaks harboured considerably more distinct communities between summer and winter. We detected the over-representation of Verrucomicrobia and Proteobacteria in pikas, and Archaea and Bacteroidetes in yaks. Firmicutes and Actinobacteria, associated with energy-efficient acquisition, significantly enriched in winter. The diversity of the microbial community was determined by the interactive effects between the host and season. Metagenomic analysis revealed that methane-metabolism-related pathway of yaks was significantly enriched in summer, while some pathogenic pathways were more abundant in pikas. Both pikas and yaks had a higher capacity for lipid degradation in winter. Pika and yak shared more OTUs when food shortage occurred in winter, and this caused a convergence in gut microbial composition and function. From winter to summer, the network module number increased from one to five in pikas, which was different in yaks. Our study demonstrates that the host is a dominant factor in shaping the microbial communities and that seasonality promotes divergence or convergence based on dietary quality across host species identity.
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Affiliation(s)
- Haibo Fu
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
- University of Chinese Academy of SciencesBeijing100049China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
| | - Chao Fan
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
- University of Chinese Academy of SciencesBeijing100049China
| | - Chuanfa Liu
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
- University of Chinese Academy of SciencesBeijing100049China
| | - Wenjing Li
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
| | - Qi Cheng
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
- University of Chinese Academy of SciencesBeijing100049China
| | - Xinquan Zhao
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
| | - Shangang Jia
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijing100193China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai810008China
- Qinghai Provincial Key Laboratory of Animal Ecological GenomicsXiningQinghai ProvinceChina
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Wang X, Liang D, Jin W, Tang M, Liu S, Zhang P. Out of Tibet: Genomic Perspectives on the Evolutionary History of Extant Pikas. Mol Biol Evol 2021; 37:1577-1592. [PMID: 32027372 DOI: 10.1093/molbev/msaa026] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Pikas are widely distributed in the Northern Hemisphere and are highly adapted to cold and alpine environments. They are one of the most complex and problematic groups in mammalian systematics, and the origin and evolutionary history of extant pikas remain controversial. In this study, we sequenced the whole coding sequences of 105 pika samples (29 named species and 1 putative new species) and obtained DNA data for more than 10,000 genes. Our phylogenomic analyses recognized four subgenera of extant pikas: Alienauroa, Conothoa, Ochotona, and Pika. The interrelationships between the four subgenera were strongly resolved as (Conothoa, (Alienauroa, (Ochotona, Pika))), with the mountain group Conothoa being the sister group of all other pikas. Our divergence time and phylogeographic analyses indicated that the last common ancestor of extant pikas first occurred on in the middle Miocene, ∼14 Ma. The emergence of opportunities related to the climate, food supply, and spreading paths in concert promoted the dispersal of pikas from the Qinghai-Tibetan Plateau (QTP) to other parts of Eurasia and North America. We found that the genes that were positively selected in the early evolution of pikas were most concentrated in functional categories related to cold tolerance. These results suggest that the QTP may have served as a training ground for cold tolerance in early pikas, which gives pikas a great advantage when the climate continued to cool after the middle Miocene. Our study highlights the importance of the QTP as a center of origin for many cold-adapted animals.
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Affiliation(s)
- XiaoYun Wang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wei Jin
- Sichuan Academy of Forestry, Chengdu, China
| | | | | | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Ding L, Liao J. Phylogeography of the Tibetan hamster Cricetulus kamensis in response to uplift and environmental change in the Qinghai-Tibet Plateau. Ecol Evol 2019; 9:7291-7306. [PMID: 31380051 PMCID: PMC6662396 DOI: 10.1002/ece3.5301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/28/2019] [Accepted: 05/08/2019] [Indexed: 11/16/2022] Open
Abstract
AIM The evolutionary process of an organism provides valuable data toward an understanding of the Earth evolution history. To investigate the relationship between the uplift of the Qinghai-Tibet Plateau (QTP) and mammalian evolution since the late Cenozoic, the geographic distribution of genetic variations in the Tibetan hamster Cricetulus kamensis was investigated using phylogeographical methods. In particular, population divergence, demographic history, genetic variation, and the prediction of species distribution area were investigated. LOCATION The Qinghai-Tibet Plateau. METHODS A total of 53 specimens, representing 13 geographic populations, were collected from the QTP. The phylogeographical pattern and demographic history of C. kamensis were analyzed, and the probable factors in the QTP uplift and the Quaternary glacial periods were inferred from one nuclear and four mitochondrial genes. Furthermore, the species distribution model (SDM) was used to predict changes in potentially suitable habitats since the last Interglacial. RESULTS Phylogenetic analysis demonstrated that two major genetic differentiations of the C. kamensis population occurred during the Early Pleistocene that were influenced by the Qing-Zang tectonic movement from the Middle Pliocene to the Early Pleistocene. Genetic distance between two major clades indicated low genetic divergence. Demographic history analysis showed that the C. kamensis population was affected by the Quaternary glacial period. SDM analysis indicated that C. kamensis was endemic to the QTP and the suitable habitat was affected by climate change, especially during the Last Glacial Maximum (LGM). MAIN CONCLUSION Our results indicated that the QTP uplift led to the population divergence of C. kamensis, and vicariance well accounted for the geographic distribution of genetic variation in C. kamensis as a result of genetic divergence and lack of gene flow. The genetic distance shows that C. alticola may be a subspecies of C. kamensis. Demographic history analysis suggests that the QTP was affected by the last glacial period. SDM analysis supports that almost the entire QTP is covered by a huge ice sheet during the LGM.
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Affiliation(s)
- Li Ding
- School of Life SciencesLanzhou UniversityLanzhouChina
| | - Jicheng Liao
- School of Life SciencesLanzhou UniversityLanzhouChina
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11
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Sheftel BI, Bannikova AA, Fang Y, Demidova TB, Alexandrov DY, Lebedev VS, Sun YH. Notes on the Fauna, Systematics, and Ecology of Small Mammals in Southern Gansu, China. BIOL BULL+ 2019. [DOI: 10.1134/s1062359018080150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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The structure of morphological variation in the shape of occlusal surface of permanent teeth in pikas Ochotona (Lagomorpha: Ochotonidae). RUSSIAN JOURNAL OF THERIOLOGY 2018. [DOI: 10.15298/rusjtheriol.17.2.05] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Lissovsky AA, Yatsentyuk SP, Koju NP. Multilocus phylogeny and taxonomy of pikas of the subgenus
Ochotona
(Lagomorpha, Ochotonidae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12325] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Svetlana P. Yatsentyuk
- The All‐Russian State Center for Quality and Standardization of Veterinary Drugs and Feed Moscow Russia
| | - Narayan P. Koju
- Nepal Engineering College Pokhara University Kathmandu Nepal
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14
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Qu J, Fletcher QE, Réale D, Li W, Zhang Y. Independence between coping style and stress reactivity in plateau pika. Physiol Behav 2018; 197:1-8. [PMID: 30236525 DOI: 10.1016/j.physbeh.2018.09.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/07/2018] [Accepted: 09/16/2018] [Indexed: 10/28/2022]
Abstract
The concept of coping style represents the way individual animals react to a stressful situation, both behaviourally and neurophysiologically. Over the last decades coping style has been linked to the development of research on animal personality. Based on this concept, we should find a proactive-reactive continuum in animal populations, with proactive individuals being fast explorer, bold, aggressive, and show high sympathetic reactivity (higher heart rate), as well as low hypothalamus-pituitary-adrenocortical (PHA) axis reactivity to external stressor (higher plasma glucocorticoid level). At the other extreme, shy, lowly aggressive, reactive individuals should be slow in their exploration, and show a low sympathetic reactivity and a high HPA axis reactivity. However, a recent two-tier model proposed that coping style and stress reactivity should be independent of each other. In this study, we tested the two-tier model in a wild plateau pika (Ochotona curzoniae) population on the Tibetan Plateau, by quantifying the associations between several behavioural and physiological traits at the among- and within-individual levels. We repeatedly measured exploration, docility, boldness, heart rate and plasma cortisol concentration in individuals between April and September of 2013. All traits tested were repeatable. At the among-individual level, all behavioural traits were correlated with each other and with heart rate, but were independent of both basal level and variation of plasma cortisol concentration. Most correlations were negligible at the within-individual level. In support of the two-tier model, these results suggest that coping style (i.e. behaviour and heart rate associations) is independent of stress reactivity (i.e. glucocorticoid reactivity) in that species.
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Affiliation(s)
- Jiapeng Qu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai 810008, China; Qinghai Provincial Key Laboratory of Restoration Ecology in Cold Region, Qinghai 810008, China.
| | - Quinn E Fletcher
- Department of Biology, The University of Winnipeg, Winnipeg, MB, Canada
| | - Denis Réale
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Wenjing Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai 810008, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Qinghai 810008, China.
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15
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Pleistocene diversification of Afghan pikas Ochotona rufescens (Gray, 1842) (Lagomorpha; Ochotonidae) in Western Asia. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Zheng F, Liu H, Jiang M, Xu Z, Wang Z, Wang C, Du F, Shen Z, Wang B. The complete mitochondrial genome of the Caulerpa lentillifera (Ulvophyceae, Chlorophyta): Sequence, genome content, organization structure and phylogenetic consideration. Gene 2018; 673:225-238. [PMID: 29933020 DOI: 10.1016/j.gene.2018.06.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 04/21/2018] [Accepted: 06/15/2018] [Indexed: 11/19/2022]
Abstract
The complete mitochondrial genome is greatly important for studies on genetic structure and phylogenetic relationship at various taxonomic levels. To obtain information about the evolutionary trends of mtDNA in the Ulvophyceae and also to gain insights into the phylogenetic relationships between ulvophytes and other chlorophytes, we determined the mtDNA sequence of Caulerpa lentillifera (sea grape) using de novo mitochondrial genome sequencing. The complete genomic DNA of C. lentillifera was circular and 209,034 bp in length, and it was the largest green-algal mitochondrial genome sequenced to date, with a low gene density of 65.2%, which is reminiscent of the "expanded" pattern of evolution exhibited by embryophyte mtDNAs. The C. lentillifera mtDNA consisted of a typical set of 17 protein-coding genes (PCGs), 20 transfer RNA (tRNA) genes, three ribosomal RNA (rRNA) genes, 42 putative open reading frames (ORFs) and 29 introns, which had homologs in green-algal mtDNAs displaying an "ancestral" or a "reduced-derived" pattern of evolution. The overall base composition of its mitochondrial genome was 24.19% for A, 24.94% for T, 25.80% for G, 25.07% for C and 50.87% for GC. The mitochondrial genome of C. lentillifera was characterized by numerous small intergenic regions and introns, which was clearly different from other green algae. With the exception of the NADH dehydrogenase subunit 6 (ND6), ND1, ATP and three tRNA genes (tRNA-His, tRNA-Thr and tRNA-Ala), all other mitochondrial genes were encoded on the heavy strand. All of the PCGs had ATG as their start codon and employed TAA, TGA or TAG as their termination codon. To gain insights into the evolutionary trends of mtDNA in the Ulvophyceae, we inferred the complete mtDNA sequence of C. lentillifera, an ulvophyte belonging to a distinct, early-diverging lineage. Taken together, our data offered useful information for the studies on phylogenetic hypotheses and phylogenetic relationships of C. lentillifera within the Chlorophyta.
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Affiliation(s)
- Fengrong Zheng
- First Institute of Oceanography SOA, Qingdao 266061, China; Key laboratory of Marine Bioactive substance SOA, Qingdao 266061, China
| | - Hongzhan Liu
- Marine College of Shandong University, Weihai 264209, China.
| | - Meijing Jiang
- First Institute of Oceanography SOA, Qingdao 266061, China
| | - Zongjun Xu
- First Institute of Oceanography SOA, Qingdao 266061, China
| | - Zongxing Wang
- First Institute of Oceanography SOA, Qingdao 266061, China
| | - Claire Wang
- Qingdao Haiputao Organic Green Algae Research and Development Breed CO., LTD, Qingdao 266000, China
| | - Fei Du
- Qingdao Haiputao Organic Green Algae Research and Development Breed CO., LTD, Qingdao 266000, China
| | - Zhen Shen
- First Institute of Oceanography SOA, Qingdao 266061, China; Key laboratory of Marine Bioactive substance SOA, Qingdao 266061, China
| | - Bo Wang
- First Institute of Oceanography SOA, Qingdao 266061, China.
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17
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A new subspecies of large-eared pika, Ochotona macrotis (Lagomorpha: Ochotonidae), from the Eastern Himalaya. RUSSIAN JOURNAL OF THERIOLOGY 2017. [DOI: 10.15298/rusjtheriol.16.1.03] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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The geography and timing of genetic divergence in the lizard Phrynocephalus theobaldi on the Qinghai-Tibetan plateau. Sci Rep 2017; 7:2281. [PMID: 28536444 PMCID: PMC5442162 DOI: 10.1038/s41598-017-02674-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 04/18/2017] [Indexed: 11/27/2022] Open
Abstract
The Qinghai-Tibetan Plateau (QTP) represents one of the earth’s most significant physical features and there is increasing interest in the historical generation of biodiversity within this region. We hypothesized that there should be clear geographically coherent genetic structuring within one of the world’s highest altitude lizards, Phrynocephalus theobaldi, due to considerable historical population fragmentation in this environment. This was tested using a major mitochondrial DNA (mtDNA) survey and sequencing of two nuclear markers (AME and RAG-1) from P. theobaldi, from across the southern QTP. A Bayesian method (BPEC) was used to detect four geographically structured mtDNA clusters. A Bayesian phylogenetic tree, together with associated dating analyses, supported four corresponding evolutionary lineages with a timing of 3.74–7.03 Ma for the most basal P. theobaldi split and Pliocene splits of 2.97–5.79 Ma and 2.40–5.39 Ma in the two daughter lineages. Himalayan uplift and changes in the Jilong basin may have contributed to these divergences, but uplift of the Gangdese mountains is rejected due to its timing. The nuclear markers appeared to be sorted between the four mtDNA groups, and species delimitation analyses supported the four phylogeographical groups as candidate species. The study contributes to our understanding of biodiversity on the QTP.
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19
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Koju NP, He K, Chalise MK, Ray C, Chen Z, Zhang B, Wan T, Chen S, Jiang X. Multilocus approaches reveal underestimated species diversity and inter-specific gene flow in pikas (Ochotona) from southwestern China. Mol Phylogenet Evol 2016; 107:239-245. [PMID: 27838310 DOI: 10.1016/j.ympev.2016.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 11/05/2016] [Accepted: 11/08/2016] [Indexed: 11/30/2022]
Abstract
The phylogeny of living pikas (Ochotonidae, Ochotona) remains obscure, and pika species diversity in southwestern China has never been well explored. In this study, 96 tissue samples from 11 valid species in three classified subgenera (Pika, Ochotona and Conothoa) from 23 locations were characterized using multilocus sequences of 7031bp. Two mitochondrial (CYT B and COI) and five nuclear gene segments (RAG1, RAG2, TTN, OXAIL and IL1RAPL1) were sequenced. We analysed evolutionary histories using maximum likelihood (RAxML) and Bayesian analyses (BEAST), and we also used molecular species delimitation analyses (BPP) to explore species diversity. Our study supported O. syrinx (O. huangensis) as a distinct clade from all named subgenera. Relationships among subgenera were not fully resolved, which may be due to a rapid diversification in the middle Miocene (∼13.90Ma). Conflicting gene trees implied mitochondrial introgression from O. cansus to O. curzoniae. We uncovered three cryptic species from Shaanxi, Sichuan and Yunnan with strong support, suggesting an underestimation of species diversity in the "sky-island" mountains of southwest China.
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Affiliation(s)
- Narayan Prasad Koju
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China; Central Department of Zoology, Tribhuvan University, Kathmandu, Nepal
| | - Kai He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Smithsonian Institution, National Museum of Natural History, Washington, DC 20004, USA; The Kyoto University Museum, Kyoto University, Kyoto 606-8501, Japan.
| | | | - Chris Ray
- Department of Ecology and Evolutionary Biology and Institute of Arctic and Alpine Research, University of Colorado-Boulder, 450 UCB, Boulder, CO 80309-0450, USA
| | - Zhongzheng Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Bin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China
| | - Tao Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Shunde Chen
- College of Life Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
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20
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Diversification of Sisorid catfishes (Teleostei: Siluriformes) in relation to the orogeny of the Himalayan Plateau. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-016-1104-0] [Citation(s) in RCA: 3] [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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21
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Lissovsky AA, Yatsentyuk SP, Ge D. Phylogeny and taxonomic reassessment of pikasOchotona pallasiiandO. argentata(Mammalia, Lagomorpha). ZOOL SCR 2016. [DOI: 10.1111/zsc.12180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrey A. Lissovsky
- Zoological Museum; Moscow State University; B. Nikitskaya, 6 Moscow 125009 Russia
| | - Svetlana P. Yatsentyuk
- The All-Russian State Center for Quality and Standardization of Veterinary Drugs and Feed; Zvenigorodskoe Avenue, 5 Moscow 123022 Russia
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution; Institute of Zoology; Chinese Academy of Sciences; Beichen West Road, Chaoyang District Beijing 100101 China
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22
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Zhang H, Li W, Hu Y, Zhang Y. Opposite companion effect on flight initiation distance in sympatric species: plateau pika ( Ochotona curzoniae) and White-rumped Snowfinch ( Onychostruthus taczanowskii). CAN J ZOOL 2016. [DOI: 10.1139/cjz-2015-0126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
There are many factors influencing prey’s risk perception and escape decision during predator–prey encounters. The distance at which animals move away from perceived danger (often quantified as flight initiation distance or FID) has been used by behavioral ecologists to understand the economics of antipredator behavior. Using general linear models, we investigated escape decision-making processes in plateau pika (Ochotona curzoniae (Hodgson, 1858)) and White-rumped Snowfinch (Onychostruthus taczanowskii (Prjevalsky, 1876), formerly known as Montifringilla taczanowskii Przewalski, 1876) together and we found that (i) there are significant positive correlations between starting distance and FID in both species; (ii) pika escapes at a longer distance from an approaching intruder when it is far from its burrow; (iii) foraging animals tolerate closer distances than watching ones, both in pikas and in Snowfinches; (iv) conspecifics seem to have no effect on pikas’ escaping behavior, while the appearance of Snowfinches dramatically decreases the FID of pikas. On the contrary, conspecifics significantly decrease the FID of Snowfinches, while the presence of pikas has no effects. These findings provide new evidence, which are consistent with optimal escape theory. These novel results in multispecies interactions prompt us to pay attention to the potential relationship between pikas and Snowfinches, as well as the “bird–pika in one hole” phenomenon.
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Affiliation(s)
- He Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Wenjing Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, People’s Republic of China
- University of the Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Yanping Hu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, People’s Republic of China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, People’s Republic of China
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23
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Comprehensive Transcriptome Analysis of Six Catfish Species from an Altitude Gradient Reveals Adaptive Evolution in Tibetan Fishes. G3-GENES GENOMES GENETICS 2015; 6:141-8. [PMID: 26564948 PMCID: PMC4704712 DOI: 10.1534/g3.115.024448] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Glyptosternoid fishes (Siluriformes), one of the three broad fish lineages (the two other are schizothoracines and Triplophysa), have a limited distribution in the rivers in the Tibetan Plateau and peripheral regions. To investigate the genetic mechanisms underlying adaptation to the Tibetan Plateau in several fish species from gradient altitudes, a total of 20,659,183–37,166,756 sequence reads from six species of catfish were generated by Illumina sequencing, resulting in six assemblies. Analysis of the 1,656 orthologs among the six assembled catfish unigene sets provided consistent evidence for genome-wide accelerated evolution in the three glyptosternoid lineages living at high altitudes. A large number of genes refer to functional categories related to hypoxia and energy metabolism exhibited rapid evolution in the glyptosternoid lineages relative to yellowhead catfish living in plains areas. Genes showing signatures of rapid evolution and positive selection in the glyptosternoid lineages were also enriched in functions associated with energy metabolism and hypoxia. Our analyses provide novel insights into highland adaptation in fishes and can serve as a foundation for future studies aiming to identify candidate genes underlying the genetic basis of adaptation in Tibetan fishes.
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24
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Ma X, Kang J, Chen W, Zhou C, He S. Biogeographic history and high-elevation adaptations inferred from the mitochondrial genome of Glyptosternoid fishes (Sisoridae, Siluriformes) from the southeastern Tibetan Plateau. BMC Evol Biol 2015; 15:233. [PMID: 26511921 PMCID: PMC4625616 DOI: 10.1186/s12862-015-0516-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 10/20/2015] [Indexed: 01/19/2023] Open
Abstract
Background The distribution of the Chinese Glyptosternoid catfish is limited to the rivers of the Tibetan Plateau and peripheral regions, especially the drainage areas of southeastern Tibet. Therefore, Glyptosternoid fishes are ideal for reconstructing the geological history of the southeastern Tibet drainage patterns and mitochondrial genetic adaptions to high elevations. Results Our phylogenetic results support the monophyly of the Sisoridae and the Glyptosternoid fishes. The reconstructed ancestral geographical distribution suggests that the ancestral Glyptosternoids was widely distributed throughout the Brahmaputra drainage in the eastern Himalayas and Tibetan area during the Late Miocene (c. 5.5 Ma). We found that the Glyptosternoid fishes lineage had a higher ratio of nonsynonymous to synonymous substitutions than those found in non-Glyptosternoids. In addition, ωpss was estimated to be 10.73, which is significantly higher than 1 (p-value 0.0002), in COX1, which indicates positive selection in the common ancestral branch of Glyptosternoid fishes in China. We also found other signatures of positive selection in the branch of specialized species. These results imply mitochondrial genetic adaptation to high elevations in the Glyptosternoids. Conclusions We reconstructed a possible scenario for the southeastern Tibetan drainage patterns based on the adaptive geographical distribution of the Chinese Glyptosternoids in this drainage. The Glyptosternoids may have experienced accelerated evolutionary rates in mitochondrial genes that were driven by positive selection to better adapt to the high-elevation environment of the Tibetan Plateau. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0516-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiuhui Ma
- School of Life Science, Southwest University, Beibei, Chongqing, 400715, China. .,The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
| | - Jingliang Kang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 10001, China.
| | - Weitao Chen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 10001, China.
| | - Chuanjiang Zhou
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China.
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25
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Melo-Ferreira J, Lemos de Matos A, Areal H, Lissovsky AA, Carneiro M, Esteves PJ. The phylogeny of pikas (Ochotona) inferred from a multilocus coalescent approach. Mol Phylogenet Evol 2015; 84:240-4. [PMID: 25637497 DOI: 10.1016/j.ympev.2015.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 12/18/2014] [Accepted: 01/19/2015] [Indexed: 11/18/2022]
Abstract
The clarification of the systematics of pikas (genus Ochotona) has been hindered by largely overlapping morphological characters among species and the lack of a comprehensive molecular phylogeny. Here we estimate the first multilocus phylogeny of the genus to date, by analysing 12 nuclear DNA markers (total of 7.5Kb) in 11 species of pikas from the four classified subgenera (Pika, Ochotona, Lagotona and Conothoa) using a multispecies coalescent-based framework. The species-tree confirmed the subgeneric classification by retrieving as monophyletic the subgenera represented here by more than one species. Contrary to previous phylogenies based on mtDNA alone, Lagotona was found to be sister to Pika. Also, support for the monophyly of the alpina group was not strong, thus caution should be used in future analyses of this group. A relaxed molecular clock calibrated using the Ochotonidae-Leporidae divergence resulted in more recent estimates of divergence times relative to previous studies. Strong concordance with inferences based on fossil records was found, suggesting that the initial diversification of the genus took place by the end of late Miocene. Finally, this work sets up methodologies and gathers molecular markers that can be used to extend the understanding of the evolutionary history of the genus.
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Affiliation(s)
- José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - Ana Lemos de Matos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
| | - Helena Areal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
| | - Andrey A Lissovsky
- Zoological Museum of Moscow State University, B. Nikitskaya, 6, Moscow 125009, Russia
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Pedro J Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, InBIO, Laboratório Associado, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal
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26
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Wan T, He K, Jiang XL. Multilocus phylogeny and cryptic diversity in Asian shrew-like moles (Uropsilus, Talpidae): implications for taxonomy and conservation. BMC Evol Biol 2013; 13:232. [PMID: 24161152 PMCID: PMC3819745 DOI: 10.1186/1471-2148-13-232] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 10/15/2013] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The genus Uropsilus comprises a group of terrestrial, montane mammals endemic to the Hengduan and adjacent mountains. These animals are the most primitive living talpids. The taxonomy has been primarily based on cursory morphological comparisons and the evolutionary affinities are little known. To provide insight into the systematics of this group, we estimated the first multi-locus phylogeny and conducted species delimitation, including taxon sampling throughout their distribution range. RESULTS We obtained two mitochondrial genes (~1, 985 bp) and eight nuclear genes (~4, 345 bp) from 56 specimens. Ten distinct evolutionary lineages were recovered from the three recognized species, eight of which were recognized as species/putative species. Five of these putative species were found to be masquerading as the gracile shrew mole. The divergence time estimation results indicated that climate change since the last Miocene and the uplift of the Himalayas may have resulted in the diversification and speciation of Uropsilus. CONCLUSIONS The cryptic diversity found in this study indicated that the number of species is strongly underestimated under the current taxonomy. Two synonyms of gracilis (atronates and nivatus) should be given full species status, and the taxonomic status of another three potential species should be evaluated using extensive taxon sampling, comprehensive morphological, and morphometric approaches. Consequently, the conservation status of Uropsilus spp. should also be re-evaluated, as most of the species/potential species have very limited distribution.
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Affiliation(s)
- Tao Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- University of Chinese Academy of Sciences, Beijing 100049 China
| | - Kai He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2 Canada
| | - Xue-Long Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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Korrodi-Gregório L, Margarida Lopes A, Esteves SLC, Afonso S, Lemos de Matos A, Lissovsky AA, da Cruz e Silva OAB, da Cruz e Silva EF, Esteves PJ, Fardilha M. An intriguing shift occurs in the novel protein phosphatase 1 binding partner, TCTEX1D4: evidence of positive selection in a pika model. PLoS One 2013; 8:e77236. [PMID: 24130861 PMCID: PMC3795061 DOI: 10.1371/journal.pone.0077236] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 09/01/2013] [Indexed: 12/21/2022] Open
Abstract
T-complex testis expressed protein 1 domain containing 4 (TCTEX1D4) contains the canonical phosphoprotein phosphatase 1 (PPP1) binding motif, composed by the amino acid sequence RVSF. We identified and validated the binding of TCTEX1D4 to PPP1 and demonstrated that indeed this protein is a novel PPP1 interacting protein. Analyses of twenty-one mammalian species available in public databases and seven Lagomorpha sequences obtained in this work showed that the PPP1 binding motif 90RVSF93 is present in all of them and is flanked by a palindromic sequence, PLGS, except in three species of pikas (Ochotona princeps, O. dauurica and O. pusilla). Furthermore, for the Ochotona species an extra glycosylation site, motif 96NLS98, and the loss of the palindromic sequence were observed. Comparison with other lagomorphs suggests that this event happened before the Ochotona radiation. The dN/dS for the sequence region comprising the PPP1 binding motif and the flanking palindrome highly supports the hypothesis that for Ochotona species this region has been evolving under positive selection. In addition, mutational screening shows that the ability of pikas TCTEX1D4 to bind to PPP1 is maintained, although the PPP1 binding motif is disrupted, and the N- and C-terminal surrounding residues are also abrogated. These observations suggest pika as an ideal model to study novel PPP1 complexes regulatory mechanisms.
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Affiliation(s)
- Luís Korrodi-Gregório
- Laboratory of Signal Transduction, Centre for Cell Biology, Health Sciences Department and Biology Department, University of Aveiro, Aveiro, Portugal
| | - Ana Margarida Lopes
- CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos/Universidade do Porto, InBio, Laboratório Associado, Vairão, Portugal
- Departamento de Zoologia e Antropologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- INSERM, Institut National de la Santé et de la Recherche Médicale, Unit 892, Université de Nantes, Nantes, France
| | - Sara L. C. Esteves
- Laboratory of Signal Transduction, Centre for Cell Biology, Health Sciences Department and Biology Department, University of Aveiro, Aveiro, Portugal
| | - Sandra Afonso
- CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos/Universidade do Porto, InBio, Laboratório Associado, Vairão, Portugal
| | - Ana Lemos de Matos
- CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos/Universidade do Porto, InBio, Laboratório Associado, Vairão, Portugal
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
| | | | - Odete A. B. da Cruz e Silva
- Laboratory of Neurosciences, Centre for Cell Biology, Health Sciences Department and Biology Department, University of Aveiro, Aveiro, Portugal
| | - Edgar F. da Cruz e Silva
- Laboratory of Signal Transduction, Centre for Cell Biology, Health Sciences Department and Biology Department, University of Aveiro, Aveiro, Portugal
| | - Pedro José Esteves
- CIBIO/UP, Centro de Investigação em Biodiversidade e Recursos Genéticos/Universidade do Porto, InBio, Laboratório Associado, Vairão, Portugal
- CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra PRD, Portugal
- * E-mail: (MF); (PJE)
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Centre for Cell Biology, Health Sciences Department and Biology Department, University of Aveiro, Aveiro, Portugal
- * E-mail: (MF); (PJE)
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Ge D, Wen Z, Xia L, Zhang Z, Erbajeva M, Huang C, Yang Q. Evolutionary history of lagomorphs in response to global environmental change. PLoS One 2013; 8:e59668. [PMID: 23573205 PMCID: PMC3616043 DOI: 10.1371/journal.pone.0059668] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 02/18/2013] [Indexed: 11/18/2022] Open
Abstract
Although species within Lagomorpha are derived from a common ancestor, the distribution range and body size of its two extant groups, ochotonids and leporids, are quite differentiated. It is unclear what has driven their disparate evolutionary history. In this study, we compile and update all fossil records of Lagomorpha for the first time, to trace the evolutionary processes and infer their evolutionary history using mitochondrial genes, body length and distribution of extant species. We also compare the forage selection of extant species, which offers an insight into their future prospects. The earliest lagomorphs originated in Asia and later diversified in different continents. Within ochotonids, more than 20 genera occupied the period from the early Miocene to middle Miocene, whereas most of them became extinct during the transition from the Miocene to Pliocene. The peak diversity of the leporids occurred during the Miocene to Pliocene transition, while their diversity dramatically decreased in the late Quaternary. Mantel tests identified a positive correlation between body length and phylogenetic distance of lagomorphs. The body length of extant ochotonids shows a normal distribution, while the body length of extant leporids displays a non-normal pattern. We also find that the forage selection of extant pikas features a strong preference for C3 plants, while for the diet of leporids, more than 16% of plant species are identified as C4 (31% species are from Poaceae). The ability of several leporid species to consume C4 plants is likely to result in their size increase and range expansion, most notably in Lepus. Expansion of C4 plants in the late Miocene, the so-called ‘nature’s green revolution’, induced by global environmental change, is suggested to be one of the major ‘ecological opportunities’, which probably drove large-scale extinction and range contraction of ochotonids, but inversely promoted diversification and range expansion of leporids.
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Affiliation(s)
- Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhaoqun Zhang
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Margarita Erbajeva
- Geological Institute, Siberian Branch, Russian Academy of Sciences, Ulan-Ude, Russia
| | - Chengming Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Reese AT, Lanier HC, Sargis EJ. Skeletal indicators of ecological specialization in pika (Mammalia, Ochotonidae). J Morphol 2013; 274:585-602. [DOI: 10.1002/jmor.20127] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 11/16/2012] [Accepted: 12/16/2012] [Indexed: 11/08/2022]
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30
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Qu J, Li W, Yang M, Ji W, Zhang Y. Life history of the plateau pika (Ochotona curzoniae) in alpine meadows of the Tibetan Plateau. Mamm Biol 2013. [DOI: 10.1016/j.mambio.2012.09.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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31
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Vakurin AA, Korablev VP, Xue-Long J, Grigor'eva TV. The chromosomes of Tsing-Ling pika, Ochotona huangensis Matschie, 1908 (Lagomorpha, Ochotonidae). COMPARATIVE CYTOGENETICS 2012; 6:347-58. [PMID: 24260675 PMCID: PMC3834567 DOI: 10.3897/compcytogen.v6i4.3183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 09/18/2012] [Indexed: 06/02/2023]
Abstract
The karyotype of the Tsing-Ling (Huanghe) pika, Ochotona huangensis Matschie, 1908 from the forest habitats of the Qinling Mountains (Shaanxi Province, China) was described for the first time. The chromosome set contains 42 chromosomes (NFa=80). The autosomes are 15 meta-submetacentric pairs and 5 subtelocentric pairs. The X chromosome is a medium sized submetacentric; the Y chromosome is a small sized acrocentric. C-banding revealed a localization of heterochromatin in the pericentromeric regions of all autosomes.
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Affiliation(s)
- Alexey A. Vakurin
- Institute of Biology and Soil Science, Far Eastern Branch of the Russian Academy of Sciences; pr. Stoletiya 159, Vladivostok, 690022, Russia
| | - Vladimir P. Korablev
- Institute of Biology and Soil Science, Far Eastern Branch of the Russian Academy of Sciences; pr. Stoletiya 159, Vladivostok, 690022, Russia
| | - Jiang Xue-Long
- Kunming Institute of Zoology, the Chinese Academy of Sciences; Kunming, Yunnan, 650223, China
| | - Tat'iana V. Grigor'eva
- Faculty of Biology, M. V. Lomonosov Moscow State University; Vorob’evy Gory 1, p. 12, Moscow, 119991, Russia
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Yu F, Li S, Kilpatrick WC, McGuire PM, He K, Wei W. Biogeographical Study of Plateau PikasOchotona curzoniae(Lagomorpha, Ochotonidae). Zoolog Sci 2012; 29:518-26. [DOI: 10.2108/zsj.29.518] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Richard F, Dutrillaux B. Low, complex and probably reticulated chromosome evolution of Sciuromorpha (Rodentia) and Lagomorpha. Cytogenet Genome Res 2012; 137:218-32. [PMID: 22846378 DOI: 10.1159/000341379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Lagomorpha (rabbits and pikas) and Sciuromorpha (squirrels) are grouped in the Glires superorder. Their chromosome diversification, since their separation from the eutherian mammalian common ancestor, was characterized by a low rate of chromosome rearrangements. Consequently, the structure of some chromosomes was either conserved or only slightly modified, making their comparison easy at the genus, family and even order level. Interspecific in situ hybridization (Zoo-FISH) largely corroborates classical cytogenetic data but provides much more reliability in comparisons, especially for distant species. We reconstructed common ancestral karyotypes for Glires, Lagomorpha, Sciuromorpha, and Sciuridae species, and then, determined the chromosome changes separating these ancestors from their common eutherian ancestor. We propose that reticulated evolution occurred during the diversification of Glires, which implies that several pericentric inversions and Robertsonian translocations were conserved in the heterozygous status for an extensive period. Finally, among Lagomorpha and Sciuromorpha, we focused on Leporidae and Sciuridae chromosome evolution. In the various attempts to establish dichotomic evolutionary schemes, it was necessary to admit that multiple homoplasies (convergent and reverse rearrangements) occurred in Sciuridae and in a lesser degree, in Leporidae. In Leporidae, additional rearrangements were sufficient to propose a resolved phylogeny. However, a resolved phylogeny was not possible for Sciuridae because most of the rearrangements occurred in terminal branches. We conclude that a reticulated evolution took place early during the evolution of both families and lasted longer in Sciuridae than in Leporidae. In Sciuridae, most chromosome rearrangements were pericentric inversions involving short fragments. Such rearrangements have only mild meiotic consequences, which may explain the long persistence of the heterozygous status characterizing reticulated evolution.
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Affiliation(s)
- F Richard
- Muséum National d'Histoire Naturelle, Département de Systématique et Evolution, Origine Structure et Evolution de Biodiversité, Paris, France.
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34
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Lu B, Zheng Y, Murphy RW, Zeng X. Coalescence patterns of endemic Tibetan species of stream salamanders (Hynobiidae:Batrachuperus). Mol Ecol 2012; 21:3308-24. [PMID: 22571598 DOI: 10.1111/j.1365-294x.2012.05606.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bin Lu
- Department of Herpetology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, China
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35
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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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Chen W, Hao H, Liu Y, Chen S, Zhang X, Liu S, Yue B. Mitochondrial DNA genetic variation and phylogeography of the recently described vole speciesProedromys liangshanensisLiu, Sun, Zeng and Zhao, 2007 (Rodentia: Arvicolinae). J NAT HIST 2010. [DOI: 10.1080/00222933.2010.501911] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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38
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Henry P, Russello MA. Obtaining high-quality DNA from elusive small mammals using low-tech hair snares. EUR J WILDLIFE RES 2010. [DOI: 10.1007/s10344-010-0449-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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39
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Fostowicz-Frelik Ł, Frelik GJ, Gasparik M. Morphological Phylogeny of Pikas (Lagomorpha:Ochotona), with a Description of a New Species from the Pliocene/Pleistocene Transition of Hungary. PROCEEDINGS OF THE ACADEMY OF NATURAL SCIENCES OF PHILADELPHIA 2010. [DOI: 10.1635/053.159.0107] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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ZHANG DONGRU, CHEN MINGYONG, MURPHY ROBERTW, CHE JING, PANG JUNFENG, HU JIANSHENG, LUO JING, WU SHANJIN, YE HUI, ZHANG YAPING. Genealogy and palaeodrainage basins in Yunnan Province: phylogeography of the Yunnan spiny frog, Nanorana yunnanensis (Dicroglossidae). Mol Ecol 2010; 19:3406-20. [DOI: 10.1111/j.1365-294x.2010.04747.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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SAKKA HÉLA, QUÉRÉ JEANPIERRE, KARTAVTSEVA IRINA, PAVLENKO MARINA, CHELOMINA GALINA, ATOPKIN DMITRY, BOGDANOV ALEKSEY, MICHAUX JOHAN. Comparative phylogeography of four Apodemus species (Mammalia: Rodentia) in the Asian Far East: evidence of Quaternary climatic changes in their genetic structure. Biol J Linn Soc Lond 2010. [DOI: 10.1111/j.1095-8312.2010.01477.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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Durette-Desset MC, Galbreath KE, Hoberg EP. Discovery of New Ohbayashinema spp. (Nematoda: Heligmosomoidea) in Ochotona princeps and Ochotona cansus (Lagomorpha: Ochotonidae) From Western North America and Central Asia, with considerations of Historical Biogeography. J Parasitol 2010; 96:569-79. [DOI: 10.1645/ge-2397.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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43
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Estimated evolutionary tempo of East Asian gobionid fishes (Teleostei: Cyprinidae) from mitochondrial DNA sequence data. CHINESE SCIENCE BULLETIN-CHINESE 2010. [DOI: 10.1007/s11434-010-3159-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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44
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Hafner DJ, Smith AT. Revision of the subspecies of the American pika, Ochotona princeps (Lagomorpha: Ochotonidae). J Mammal 2010. [DOI: 10.1644/09-mamm-a-277.1] [Citation(s) in RCA: 31] [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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45
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Galbreath KE, Hafner DJ, Zamudio KR. When cold is better: climate-driven elevation shifts yield complex patterns of diversification and demography in an alpine specialist (American pika, Ochotona princeps). Evolution 2009; 63:2848-63. [PMID: 19663994 DOI: 10.1111/j.1558-5646.2009.00803.x] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The genetic consequences of climate-driven range fluctuation during the Pleistocene have been well studied for temperate species, but cold-adapted (e.g., alpine, arctic) species that may have responded uniquely to past climatic events have received less attention. In particular, we have no a priori expectation for long-term evolutionary consequences of elevation shifts into and out of sky islands by species adapted to alpine habitats. Here, we examined the influence of elevation shifts on genetic differentiation and historical demography in an alpine specialist, the American pika (Ochotona princeps). Pika populations are divided into five genetic lineages that evolved in association with separate mountain systems, rather than lineages that reflect individual sky islands. This suggests a role for glacial-period elevation shifts in promoting gene flow among high-elevation populations and maintaining regional cohesion of genetic lineages. We detected a signature of recent demographic decline in all lineages, consistent with the expectation that Holocene climate warming has driven range retraction in southern lineages, but unexpected for northern populations that presumably represent postglacial expansion. An ecological niche model of past and future pika distributions highlights the influence of climate on species range and indicates that the distribution of genetic diversity may change dramatically with continued climate warming.
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Affiliation(s)
- Kurt E Galbreath
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
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46
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Keckesova Z, Ylinen L, Towers G, Gifford R, Katzourakis A. Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses. Virology 2009; 384:7-11. [PMID: 19070882 PMCID: PMC3556577 DOI: 10.1016/j.virol.2008.10.045] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2008] [Revised: 07/03/2008] [Accepted: 10/30/2008] [Indexed: 02/04/2023]
Abstract
The retroviral genus Lentivirus comprises retroviruses characterised from five mammalian orders. Lentiviruses typically undergo rapid rates of evolution, a feature that has allowed recent evolutionary relationships to be elucidated, but has also obscured their distant evolutionary past. However, the slowdown in the rate of evolution associated with genome invasion, as has occurred in the European rabbit, enables longer-term lentiviral evolutionary history to be inferred. Here we report the identification of orthologous RELIK proviruses in the European hare, demonstrating a minimum age of 12 million years for the lagomorph lentiviruses. This finding indicates an association between lentiviruses and their hosts covering much of the evolutionary history of the lagomorphs, and taking place within species with a worldwide distribution.
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Affiliation(s)
- Z. Keckesova
- Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, 46 Cleveland Street, London W1T4JF, UK
| | - L.M.J. Ylinen
- Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, 46 Cleveland Street, London W1T4JF, UK
| | - G.J. Towers
- Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, 46 Cleveland Street, London W1T4JF, UK
| | - R.J. Gifford
- Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
| | - A. Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK OX1 3PS, UK
- Institute for Emergent Infections, The James Martin 21stCentury School, Oxford University, Oxford, UK
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47
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Taxonomy and distribution of the pikas (Ochotona, Lagomorpha) of alpina-hyperborea group in North-East China and adjacent territories. RUSSIAN JOURNAL OF THERIOLOGY 2008. [DOI: 10.15298/rusjtheriol.07.1.02] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Natural selection and adaptive evolution of leptin in the ochotona family driven by the cold environmental stress. PLoS One 2008; 3:e1472. [PMID: 18213380 PMCID: PMC2194619 DOI: 10.1371/journal.pone.0001472] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Accepted: 12/02/2007] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Environmental stress can accelerate the evolutionary rate of specific stress-response proteins and create new functions specialized for different environments, enhancing an organism's fitness to stressful environments. Pikas (order Lagomorpha), endemic, non-hibernating mammals in the modern Holarctic Region, live in cold regions at either high altitudes or high latitudes and have a maximum distribution of species diversification confined to the Qinghai-Tibet Plateau. Variations in energy metabolism are remarkable for them living in cold environments. Leptin, an adipocyte-derived hormone, plays important roles in energy homeostasis. METHODOLOGY/PRINCIPAL FINDINGS To examine the extent of leptin variations within the Ochotona family, we cloned the entire coding sequence of pika leptin from 6 species in two regions (Qinghai-Tibet Plateau and Inner Mongolia steppe in China) and the leptin sequences of plateau pikas (O. curzonia) from different altitudes on Qinghai-Tibet Plateau. We carried out both DNA and amino acid sequence analyses in molecular evolution and compared modeled spatial structures. Our results show that positive selection (PS) acts on pika leptin, while nine PS sites located within the functionally significant segment 85-119 of leptin and one unique motif appeared only in pika lineages-the ATP synthase alpha and beta subunit signature site. To reveal the environmental factors affecting sequence evolution of pika leptin, relative rate test was performed in pikas from different altitudes. Stepwise multiple regression shows that temperature is significantly and negatively correlated with the rates of non-synonymous substitution (Ka) and amino acid substitution (Aa), whereas altitude does not significantly affect synonymous substitution (Ks), Ka and Aa. CONCLUSIONS/SIGNIFICANCE Our findings support the viewpoint that adaptive evolution may occur in pika leptin, which may play important roles in pikas' ecological adaptation to extreme environmental stress. We speculate that cold, and probably not hypoxia, may be the primary environmental factor for driving adaptive evolution of pika leptin.
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Abrantes J, Esteves PJ, Carmo CR, Müller A, Thompson G, van der Loo W. Genetic characterization of the chemokine receptor CXCR4 gene in lagomorphs: comparison between the families Ochotonidae and Leporidae. Int J Immunogenet 2008; 35:111-7. [PMID: 18205827 DOI: 10.1111/j.1744-313x.2007.00735.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chemokines receptors are transmembrane proteins that bind chemokines. Chemokines and their receptors are known to play a crucial role in the immune system and in pathogen entry. There is evidence that myxoma virus, the causative agent of myxomatosis, can use the chemokine receptor CXCR4 to infect cells. This virus causes a benign disease in its natural host, Sylvilagus, but in the European rabbit (Oryctolagus cuniculus) it causes a highly fatal and infectious disease known as myxomatosis. We have characterized the chemokine receptor CXCR4 gene in five genera of the order Lagomorpha, Ochotona (Ochotonidae), and Oryctolagus, Lepus, Bunolagus and Sylvilagus (Leporidae). In lagomorphs, the CXCR4 is highly conserved, with most of the protein diversity found at surface regions. Five amino acid replacements were observed, two in the intracellular loops, one in the transmembrane domain and two in the extracellular loops. Oryctolagus features unique amino acid changes at the intracellular domains, putting this genus apart of all other lagomorphs. Furthermore, in the 37 European rabbits analysed, which included healthy rabbits and rabbits with clinical symptoms of myxomatosis, 14 nucleotide substitutions were obtained but no amino acid differences were observed.
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Affiliation(s)
- J Abrantes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Vairão, Portugal
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50
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Raoul F, Pleydell D, Quéré JP, Vaniscotte A, Rieffel D, Takahashi K, Bernard N, Wang J, Dobigny T, Galbreath KE, Giraudoux P. Small-mammal assemblage response to deforestation and afforestation in central China. MAMMALIA 2008. [DOI: 10.1515/mamm.2008.045] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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