1
|
Zheng JX, Sun XH, Wei X, Wang G, Yuan CQ, Weng XD, Zuo QQ, Liu JY, Mu ZQ, Mao TC, Ding YZ, Wang XM, Wang X, Wang ZH. Species Composition of a Small Mammal Community and Prevalence of Echinococcus spp. in the Alpine Pastoral Area of the Eastern Tibetan Plateau. Pathogens 2024; 13:558. [PMID: 39057785 PMCID: PMC11280319 DOI: 10.3390/pathogens13070558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 06/23/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
We aimed to investigate the species composition of a small mammal community and the prevalence of Echinococcus spp. in a typical endemic area of the Tibetan Plateau. One pika and five rodent species were identified based on the morphological characteristics of 1278 small mammal specimens collected during 2014-2019. Detection of Echinococcus DNA in tissue samples from small mammal specimens revealed that Ochotona curzoniae (pika, total prevalence: 6.02%, 26/432), Neodon fuscus (5.91%, 38/643), N. leucurus (2.50%, 3/120), and Alexandromys limnophilus (21.74%, 10/46) were infected by both E. multilocularis and E. shiquicus; Cricetulus longicaudatus (16.67%, 1/6) was infected by E. shiquicus; and no infection was detected in N. irene (0/15). Neodon fuscus and O. curzoniae were the two most abundant small mammal species. There was no significant difference in the prevalence of pika and the overall rodent species assemblage (6.26%, 53/846); however, the larger rodent populations suggested that more attention should be paid to their role in the transmission of echinococcosis in the wildlife reservoir, which has long been underestimated. Moreover, although DNA barcoding provides a more efficient method than traditional morphological methods for identifying large numbers of small mammal samples, commonly used barcodes failed to distinguish the three Neodon species in this study. The close genetic relationships between these species suggest the need to develop more powerful molecular taxonomic tools.
Collapse
Affiliation(s)
- Jia-Xin Zheng
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xiao-Hui Sun
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xu Wei
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Gang Wang
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Chang-Qing Yuan
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xiao-Dong Weng
- School of Life Sciences, East China Normal University, Shanghai 200241, China
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China
| | - Qing-Qiu Zuo
- School of Life Sciences, East China Normal University, Shanghai 200241, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai 200025, China
- Key Laboratory of Parasite and Vector Biology, National Health Commission of the People’s Republic of China, Shanghai 200025, China
- World Health Organization Collaborating Center for Tropical Diseases, Shanghai 200025, China
| | - Jia-Yu Liu
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Zhi-Qiang Mu
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Tian-Ci Mao
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - You-Zhong Ding
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xiao-Ming Wang
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xu Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai 200025, China
- Key Laboratory of Parasite and Vector Biology, National Health Commission of the People’s Republic of China, Shanghai 200025, China
- World Health Organization Collaborating Center for Tropical Diseases, Shanghai 200025, China
| | - Zheng-Huan Wang
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| |
Collapse
|
2
|
Withnell CB, Scarpetta SG. A new perspective on the taxonomy and systematics of Arvicolinae (Gray, 1821) and a new time-calibrated phylogeny for the clade. PeerJ 2024; 12:e16693. [PMID: 38223757 PMCID: PMC10785794 DOI: 10.7717/peerj.16693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 11/28/2023] [Indexed: 01/16/2024] Open
Abstract
Background Arvicoline rodents are one of the most speciose and rapidly evolving mammalian lineages. Fossil arvicolines are also among the most common vertebrate fossils found in sites of Pliocene and Pleistocene age in Eurasia and North America. However, there is no taxonomically robust, well-supported, time-calibrated phylogeny for the group. Methods Here we present well-supported hypotheses of arvicoline rodent systematics using maximum likelihood and Bayesian inference of DNA sequences of two mitochondrial genes and three nuclear genes representing 146 (82% coverage) species and 100% of currently recognized arvicoline genera. We elucidate well-supported major clades, reviewed the relationships and taxonomy of many species and genera, and critically compared our resulting molecular phylogenetic hypotheses to previously published hypotheses. We also used five fossil calibrations to generate a time-calibrated phylogeny of Arvicolinae that permitted some reconciliation between paleontological and neontological data. Results Our results are largely congruent with previous molecular phylogenies, but we increased the support in many regions of the arvicoline tree that were previously poorly-sampled. Our sampling resulted in a better understanding of relationships within Clethrionomyini, the early-diverging position and close relationship of true lemmings (Lemmus and Myopus) and bog lemmings (Synaptomys), and provided support for recent taxonomic changes within Microtini. Our results indicate an origin of ∼6.4 Ma for crown arvicoline rodents. These results have major implications (e.g., diversification rates, paleobiogeography) for our confidence in the fossil record of arvicolines and their utility as biochronological tools in Eurasia and North America during the Quaternary.
Collapse
Affiliation(s)
- Charles B. Withnell
- Department of Medical Education/ Anne Burnett Marion School of Medicine, Texas Christian University, Fort Worth, TX, United States of America
- Department of Earth and Planetary Sciences/ Jackson School of Geosciences, The University of Texas at Austin, Austin, TX, United States of America
| | - Simon G. Scarpetta
- Department of Earth and Planetary Sciences/ Jackson School of Geosciences, The University of Texas at Austin, Austin, TX, United States of America
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, United States of America
- Department of Environmental Science, University of San Francisco, San Francisco, CA, United States of America
| |
Collapse
|
3
|
Zhao S, Wang X, Li BV, Dou L, Liu Y, Yang S, Fan R, Jiang Y, Li Q, Liao R, Hu M, Jiang X, Liu S, Chen S. Molecular phylogeny and taxonomy of the genus Vernaya (Mammalia: Rodentia: Muridae) with the description of two new species. Ecol Evol 2023; 13:e10628. [PMID: 37953988 PMCID: PMC10636494 DOI: 10.1002/ece3.10628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/14/2023] [Accepted: 10/04/2023] [Indexed: 11/14/2023] Open
Abstract
The climbing mouse is a rare, small mammal listed as an endangered species on the China species red list. Molecular phylogenetic analyses and the evolutionary history of the genus remain unexplored because of the extreme difficulty in capturing individuals and their narrow distribution. Here, we collected 44 specimens, sequenced one mitochondrial and eight nuclear genes, and integrated morphological approaches to estimate phylogenetic relationships, delimit species boundaries, and explore evolutionary history. Molecular analyses and morphological results supported the validity of these four species. Here, we describe two new species, Vernaya meiguites sp. nov. and Vernaya nushanensis sp. nov., and recognize Vernaya foramena, previously considered a subspecies of Vernaya fulva, as a valid species. The estimated divergence time suggests that the climbing mouse began to diversify during the Pliocene (3.36 Ma).
Collapse
Affiliation(s)
- Songping Zhao
- Ministry of EducationKey Laboratory of Land Resources Evaluation and Monitoring in Southwest (Sichuan Normal University)ChengduChina
- Sichuan Normal UniversityChengduChina
| | | | - Binbin V. Li
- Environment Research CenterDuke Kunshan UniversityKunshanChina
- Nicholas School of the EnvironmentDuke UniversityDurhamNorth CarolinaUSA
| | | | | | - Siyu Yang
- Sichuan Normal UniversityChengduChina
| | | | - Yong Jiang
- Gongga Mountain National Nature Reserve Administration of Sichuan ProvinceKangdingChina
| | - Quan Li
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of ZoologyThe Chinese Academy of ScienceKunmingChina
| | - Rui Liao
- Sichuan Academy of ForestryChengduChina
| | - Miao Hu
- Environment Research CenterDuke Kunshan UniversityKunshanChina
- Nicholas School of the EnvironmentDuke UniversityDurhamNorth CarolinaUSA
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of ZoologyThe Chinese Academy of ScienceKunmingChina
| | | | - Shunde Chen
- Ministry of EducationKey Laboratory of Land Resources Evaluation and Monitoring in Southwest (Sichuan Normal University)ChengduChina
- Sichuan Normal UniversityChengduChina
| |
Collapse
|
4
|
Ren Y, Jia T, Cai Y, Zhang L, Zhang H, Wang Z, Zhu W. Molecular genetics and quantitative traits divergence among populations of Eothenomys miletus from Hengduan Mountain region. Ecol Evol 2023; 13:e10370. [PMID: 37546571 PMCID: PMC10400278 DOI: 10.1002/ece3.10370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 08/08/2023] Open
Abstract
An important objective of evolutionary biology has always been to grasp the evolutionary and genetic processes that contribute to speciation. The present work provides the first detailed account of the genetic and physiological adaptation to changing environmental temperatures as well as the reasons causing intraspecific divergence in the Eothenomys miletus from the Hengduan Mountain (HM) region, one of the biodiversity hotspots. One hundred sixty-one E. miletus individuals from five populations in the HM region had their reduced-representation genome sequenced, and one additional individual from each community had their genomes resequenced. We then characterized the genetic diversity and population structure of each population and compared the phenotypic divergence in traits using neutral molecular markers. We detected significant phenotypic and genetic alterations in E. miletus from the HM region that were related to naturally occurring diverse habitats by combining morphometrics and genomic techniques. There was asymmetric gene flow among the E. miletus populations, indicating that five E. miletus populations exhibit an isolation-by-island model, and this was supported by the correlation between F ST and geographic distance. Finally, P ST estimated by phenotypic measures of most wild traits were higher than differentiation at neutral molecular markers, indicating directional natural selection favoring different phenotypes in different populations must have been involved to achieve this much differentiation. Our findings give information on the demographic history of E. miletus, new insights into their evolution and adaptability, and literature for studies of a similar nature on other wild small mammals from the HM region.
Collapse
Affiliation(s)
- Yue Ren
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals‐Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life SciencesYunnan Normal UniversityKunmingChina
- College of Plant ProtectionShanxi Agricultural UniversityTaiyuanChina
| | - Ting Jia
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals‐Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life SciencesYunnan Normal UniversityKunmingChina
| | - Yanfei Cai
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals‐Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life SciencesYunnan Normal UniversityKunmingChina
| | - Lin Zhang
- Hubei University of Chinese MedicineWuhanChina
| | - Hao Zhang
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals‐Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life SciencesYunnan Normal UniversityKunmingChina
| | - Zhengkun Wang
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals‐Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life SciencesYunnan Normal UniversityKunmingChina
| | - Wanlong Zhu
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals‐Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life SciencesYunnan Normal UniversityKunmingChina
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy Ministry of EducationKunmingChina
- Key Laboratory of Yunnan Province for Biomass Energy and Environment BiotechnologyKunmingChina
| |
Collapse
|
5
|
Wang X, Liang D, Wang X, Tang M, Liu Y, Liu S, Zhang P. Phylogenomics reveals the evolution, biogeography, and diversification history of voles in the Hengduan Mountains. Commun Biol 2022; 5:1124. [PMID: 36284161 DOI: 10.1038/s42003-022-04108-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022] Open
Abstract
The Hengduan Mountains (HDM) of China are a biodiversity hotspot whose temperate flora and fauna are among the world's richest. However, the origin and evolution of biodiversity in the HDM remain poorly understood, especially in mammals. Given that the HDM shows the highest richness of vole species in the world, we used whole-exome capture sequencing data from the currently most comprehensive sampling of HDM voles to investigate their evolutionary history and diversification patterns. We reconstructed a robust phylogeny and re-estimated divergence times of the HDM voles. We found that all HDM voles could be divided into a western lineage (Volemys, Proedromys, and Neodon) and an eastern lineage (Caryomys and Eothenomys), and the two lineages originated from two migration events from North Eurasia to the HDM approximately 9 Mya. Both vole lineages underwent a significant acceleration of net diversification from 8-5 Mya, which was temporally congruent with the orogeny of the HDM region. We also identified strong intertribal gene flow among the HDM voles and hypothesized that frequent gene flow might have facilitated the speciation burst of the HDM voles. Our study highlights the importance of both environmental and biotic factors in shaping the biodiversity of mammals in mountain ecosystems.
Collapse
Affiliation(s)
- XiaoYun Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | | | | | - Yang Liu
- Sichuan Academy of Forestry, Chengdu, China
| | | | - Peng Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China. .,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong Province, China.
| |
Collapse
|
6
|
Pereverzeva VV, Dokuchaev NE, Primak AA, Dubinin EA. Variability of the Cytochrome b Polypeptide in the Gray Red-Backed Vole (Craseomys rufocanus). BIOL BULL+ 2022. [DOI: 10.1134/s1062359022020145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
7
|
Shi L, Liu L, Li X, Wu Y, Tian X, Shi Y, Wang Z. Phylogeny and evolution of Lasiopodomys in subfamily Arvivolinae based on mitochondrial genomics. PeerJ 2021; 9:e10850. [PMID: 33777513 PMCID: PMC7977381 DOI: 10.7717/peerj.10850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/06/2021] [Indexed: 01/02/2023] Open
Abstract
The species of Lasiopodomys Lataste 1887 with their related genera remains undetermined owing to inconsistent morphological characteristics and molecular phylogeny. To investigate the phylogenetic relationship and speciation among species of the genus Lasiopodomys, we sequenced and annotated the whole mitochondrial genomes of three individual species, namely Lasiopodomys brandtii Radde 1861, L. mandarinus Milne-Edwards 1871, and Neodon (Lasiopodomys) fuscus Büchner 1889. The nucleotide sequences of the circular mitogenomes were identical for each individual species of L. brandtii, L. mandarinus, and N. fuscus. Each species contained 13 protein-coding genes (PCGs), 22 transfer RNAs, and 2 ribosomal RNAs, with mitochondrial genome lengths of 16,557 bp, 16,562 bp, and 16,324 bp, respectively. The mitogenomes and PCGs showed positive AT skew and negative GC skew. Mitogenomic phylogenetic analyses suggested that L. brandtii, L. mandarinus, and L. gregalis Pallas 1779 belong to the genus Lasiopodomys, whereas N. fuscus belongs to the genus Neodon grouped with N. irene. Lasiopodomys showed the closest relationship with Microtus fortis Büchner 1889 and M. kikuchii Kuroda 1920, which are considered as the paraphyletic species of genera Microtus. TMRCA and niche model analysis revealed that Lasiopodomys may have first appeared during the early Pleistocene epoch. Further, L. gregalis separated from others over 1.53 million years ago (Ma) and then diverged into L. brandtii and L. mandarinus 0.76 Ma. The relative contribution of climatic fluctuations to speciation and selection in this group requires further research.
Collapse
Affiliation(s)
- Luye Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Likuan Liu
- School of Life Sciences, Qinghai Normal University, Xining, Qinghai, China
| | - Xiujuan Li
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yue Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiangyu Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuhua Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| |
Collapse
|
8
|
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]
|
9
|
Mu Y, Duan Y, Di Z, Wang Z, Wanlong Z. The complete mitochondrial genome of the Yunnan red-backed vole Eothenomys miletus (Rodentia: Cricetidae) and its phylogeny. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1598801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Yuan Mu
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life Science of Yunnan Normal University, Kunming, China
| | - Yanqiong Duan
- College of Biological Resources and Food Engineering of Qujing Normal University, Qujing, China
| | - Zhang Di
- Medical college of Yunnan College of Business Management, Kunming, 650106, China
| | - Zhengkun Wang
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life Science of Yunnan Normal University, Kunming, China
| | - Zhu Wanlong
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life Science of Yunnan Normal University, Kunming, China
| |
Collapse
|
10
|
Liu SY, Chen SD, He K, Tang M, Liu Y, Jin W, Li S, Li Q, Zeng T, Sun ZY, Fu JR, Liao R, Meng Y, Wang X, Jiang XL, Murphy RW. Molecular phylogeny and taxonomy of subgenus Eothenomys (Cricetidae: Arvicolinae: Eothenomys) with the description of four new species from Sichuan, China. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | - Kai He
- Kunming Institute of Zoology, the Chinese Academy of Science, Kunming, China
| | | | - Yang Liu
- Sichuan Academy of Forestry, Chengdu, China
| | - Wei Jin
- Sichuan Academy of Forestry, Chengdu, China
| | - Song Li
- Kunming Institute of Zoology, the Chinese Academy of Science, Kunming, China
| | - Quan Li
- Kunming Institute of Zoology, the Chinese Academy of Science, Kunming, China
| | - Tao Zeng
- Sichuan University, Chengdu, China
| | - Zhi-Yu Sun
- Sichuan Academy of Forestry, Chengdu, China
| | | | - Rui Liao
- Sichuan Academy of Forestry, Chengdu, China
| | | | - Xin Wang
- Sichuan Academy of Forestry, Chengdu, China
| | - Xue-Long Jiang
- Kunming Institute of Zoology, the Chinese Academy of Science, Kunming, China
| | - Robert W Murphy
- Kunming Institute of Zoology, the Chinese Academy of Science, Kunming, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
| |
Collapse
|
11
|
Yu P, Kong L, Li Y, Cong H, Li Y. Analysis of complete mitochondrial genome and its application to phylogeny of Caryomys inez (Rodentia: Cricetidae: Arvicolinae). MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:343-344. [PMID: 33644377 PMCID: PMC7871860 DOI: 10.1080/23802359.2016.1172275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In this study, the complete mitochondrial genome of Inez’s red-backed vole Caryomys inez was sequenced and analyzed as the first species in genus Caryomys. The complete mitochondrial genome of C. inez is 16,354 bp in length and shows a typical vertebrate pattern with 13 PCGs, 22 tRNAs, 2 rRNAs and 2 non-coding regions. To gain a clear phylogenetic position of C. inez, a ML phylogenetic tree was constructed based on 12 PCGs on H-strand from 23 rodent species except for ND6 gene which is on L-strand. As a result, C. inez is clustered with genera Eothenomys and Myodes, showing their close phylogenetic relationships. The present study may facilitate further investigation of the taxonomic studies and phylogenetic analyses of the genus Caryomys.
Collapse
Affiliation(s)
- Pei Yu
- Marine College, Shandong University, Weihai, China
| | | | - Yiqiao Li
- Marine College, Shandong University, Weihai, China
| | - Haiyan Cong
- Marine College, Shandong University, Weihai, China
| | - Yuchun Li
- Marine College, Shandong University, Weihai, China.,Institute of Ecology and Biodiversity, Shandong University, Jinan, China
| |
Collapse
|
12
|
Zhang Z, Sun T, Kang C, Liu Y, Liu S, Yue B, Zeng T. The complete mitochondrial genome of lesser long-tailed Hamster Cricetulus longicaudatus (Milne-Edwards, 1867) and phylogenetic implications. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1303-4. [PMID: 25090399 DOI: 10.3109/19401736.2014.945567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome sequence of Cricetulus longicaudatus (Rodentia Cricetidae: Cricetinae) was determined and was deposited in GenBank (GenBank accession no. KM067270). The mitochondrial genome of C. longicaudatus was 16,302 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region, with an identical order to that of other rodents' mitochondrial genomes. The phylogenetic analysis was performed with Bayesian inference based on the concatenated nucleotide sequence of 12 protein-coding genes on the heavy strand. The result showed that these species from Cricetidae and its two subfamilies (Cricetinae and Arvicolines) formed solid monophyletic group, respectively. The Cricetulus had close phylogenetic relationship with Tscherskia among three genera (Cricetulus, Cricetulus and Mesocricetus). Neodon irene and Myodes regulus were embedded in Microtus and Eothenomys, respectively. The unusual phylogenetic positions of Neodon irene and Myodes regulus remain further study in the future.
Collapse
Affiliation(s)
- Ziqi Zhang
- a West China School of Medicine, Sichuan University , Chengdu , P.R. China
| | - Tong Sun
- a West China School of Medicine, Sichuan University , Chengdu , P.R. China
| | - Chunlan Kang
- b Key Laboratory of Bio-resources and Eco-environment (Ministry of Education) , College of Life Sciences, Sichuan University , Chengdu , P.R. China , and
| | - Yang Liu
- c Sichuan Academy of Forestry , Chengdu , P.R. China
| | - Shaoying Liu
- c Sichuan Academy of Forestry , Chengdu , P.R. China
| | - Bisong Yue
- b Key Laboratory of Bio-resources and Eco-environment (Ministry of Education) , College of Life Sciences, Sichuan University , Chengdu , P.R. China , and
| | - Tao Zeng
- b Key Laboratory of Bio-resources and Eco-environment (Ministry of Education) , College of Life Sciences, Sichuan University , Chengdu , P.R. China , and
| |
Collapse
|
13
|
Li J, Zheng X, Cai Y, Zhang X, Yang M, Yue B, Li J. DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China. Mol Ecol Resour 2014; 15:153-67. [PMID: 24838015 DOI: 10.1111/1755-0998.12279] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/24/2014] [Accepted: 05/07/2014] [Indexed: 12/25/2022]
Abstract
Identification of rodents is very difficult mainly due to high similarities in morphology and controversial taxonomy. In this study, mitochondrial cytochrome oxidase subunit I (COI) was used as DNA barcode to identify the Murinae and Arvicolinae species distributed in China and to facilitate the systematics studies of Rodentia. In total, 242 sequences (31 species, 11 genera) from Murinae and 130 sequences (23 species, 6 genera) from Arvicolinae were investigated, of which 90 individuals were novel. Genetic distance, threshold method, tree-based method, online BLAST and BLOG were employed to analyse the data sets. There was no obvious barcode gap. The average K2P distance within species and genera was 2.10% and 12.61% in Murinae, and 2.86% and 11.80% in Arvicolinae, respectively. The optimal threshold was 5.62% for Murinae and 3.34% for Arvicolinae. All phylogenetic trees exhibited similar topology and could distinguish 90.32% of surveyed species in Murinae and 82.60% in Arvicolinae with high support values. BLAST analyses yielded similar results with identification success rates of 92.15% and 93.85% for Murinae and Arvicolinae, respectively. BLOG successfully authenticated 100% of detected species except Leopoldamys edwardsi based on the latest taxonomic revision. Our results support the species status of recently recognized Micromys erythrotis, Eothenomys tarquinius and E. hintoni and confirm the important roles of comprehensive taxonomy and accurate morphological identification in DNA barcoding studies. We believe that, when proper analytic methods are applied or combined, DNA barcoding could serve as an accurate and effective species identification approach for Murinae and Arvicolinae based on a proper taxonomic framework.
Collapse
Affiliation(s)
- Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | | | | | | | | | | | | |
Collapse
|
14
|
Kohli BA, Speer KA, Kilpatrick CW, Batsaikhan N, Damdinbazar D, Cook JA. Multilocus systematics and non-punctuated evolution of Holarctic Myodini (Rodentia: Arvicolinae). Mol Phylogenet Evol 2014; 76:18-29. [PMID: 24594062 DOI: 10.1016/j.ympev.2014.02.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 02/06/2014] [Accepted: 02/18/2014] [Indexed: 11/17/2022]
Abstract
The tribe Myodini consists of five genera of forest and alpine voles (Alticola, Caryomys, Eothenomys, Hyperacrius and Myodes) distributed throughout the Holarctic. Because mitochondrial evidence has revealed paraphyly and polyphyly among genera, we apply the first multilocus tests to clarify taxonomy and phylogenetic relationships. Our analyses of 28 of 36 species within Myodini, including three not previously sequenced (A. montosa, A. albicaudus, and H. fertilis), identify four distinct clades and provide the first molecular evidence that Hyperacrius may not belong in Myodini. Myodes is paraphyletic, while polyphyly of Alticola reflects apparent ancient mitochondrial introgression. Diversification in this tribe was hypothesized to be tightly linked to Late Cenozoic climatic events, however, lineage through time analysis indicates diversification over the last 4 My was gradual and not strongly punctuated.
Collapse
Affiliation(s)
- Brooks A Kohli
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131-1051, USA.
| | - Kelly A Speer
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131-1051, USA
| | | | - Nyamsuren Batsaikhan
- Department of Zoology, Faculty of Biology, National University of Mongolia, Ulaan Bataar, Mongolia
| | - Darmaa Damdinbazar
- Department of Zoology, Faculty of Biology, National University of Mongolia, Ulaan Bataar, Mongolia
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131-1051, USA
| |
Collapse
|