Biodiv Sci ›› 2012, Vol. 20 ›› Issue (2): 193-198. DOI: 10.3724/SP.J.1003.2012.06188
Special Issue: 青藏高原生物多样性与生态安全
• Original Papers • Previous Articles Next Articles
Ying Ma1, Hailong Li1, Liang Lu2,*(), Qiyong Liu2
Received:
2011-10-20
Accepted:
2012-03-10
Online:
2012-03-20
Published:
2012-04-09
Contact:
Liang Lu
Ying Ma, Hailong Li, Liang Lu, Qiyong Liu. Application for identification of small mammals by DNA barcoding in Haidong area, Qinghai Province, China[J]. Biodiv Sci, 2012, 20(2): 193-198.
物种 Species | 样本来源 Source of samples | 样本数量 Number of samples | 序列数目 Number of sequence |
---|---|---|---|
啮齿目 Rodentia 仓鼠科 Circetidae 长尾仓鼠 Cricetulus longicaudatus | 互助县、平安县、循化县、民和县 Huzhu, Ping’an, Xunhua and Minhe counties | 14 | 14 |
高原松田鼠 Pitymys irene | 互助县、平安县 Huzhu and Ping’an counties | 6 | 6 |
柴达木根田鼠 Microtus limnophilus | 互助县、平安县 Huzhu and Ping’an counties | 9 | 9 |
洮州绒鼠 Caryomys eva | 循化县 Xunhua County | 5 | 5 |
甘肃鼢鼠 Myospalax cansus | 互助县、民和县 Huzhu and Minhe counties | 6 | 6 |
子午沙鼠 Meriones meridianus | 民和县 Minhe County | 5 | 5 |
鼠科 Muridae 黄胸鼠 Rattus tanezumi | 循化县 Xunhua County | 4 | 4 |
褐家鼠 R. norvegicus | 互助县、循化县 Huzhu and Xunhua counties | 4 | 4 |
社鼠 Niviventer confucianus | 循化县 Xunhua County | 4 | 4 |
小家鼠 Mus musculus | 平安县、循化县 Ping’an and Xunhua counties | 9 | 9 |
朝鲜姬鼠 Apodemus peninsulae | 互助县、平安县、循化县、民和县 Huzhu, Ping’an, Xunhua and Minhe counties | 13 | 13 |
黑线姬鼠 A. agrarius | 民和县 Minhe County | 2 | 2 |
松鼠科 Sciuridae | |||
小飞鼠 Pteromys volans | 互助县 Huzhu County | 3 | 3 |
花鼠 Tamias sibiricus | 循化县 Xunhua County | 2 | 2 |
林跳鼠科 Zapodidae 中国蹶鼠 Sicista concolor | 平安县 Ping’an County | 2 | 2 |
兔形目 Lagomorpha | |||
鼠兔科 Ochotonidae | |||
甘肃鼠兔 Ochotona cansus | 互助县、平安县、循化县 Huzhu, Ping’an and Xunhua counties | 10 | 10 |
食虫目 Insectivora | |||
鼩鼱科 Soricidae | |||
山地背纹鼩鼱 Sorex bedfordiae | 互助县、循化县 Huzhu and Xunhua counties | 13 | 13 |
鼩鼱(待定种) Sorex sp. | 循化县 Xunhua County | 1 | 1 |
Table 1 Sources of samples in this research
物种 Species | 样本来源 Source of samples | 样本数量 Number of samples | 序列数目 Number of sequence |
---|---|---|---|
啮齿目 Rodentia 仓鼠科 Circetidae 长尾仓鼠 Cricetulus longicaudatus | 互助县、平安县、循化县、民和县 Huzhu, Ping’an, Xunhua and Minhe counties | 14 | 14 |
高原松田鼠 Pitymys irene | 互助县、平安县 Huzhu and Ping’an counties | 6 | 6 |
柴达木根田鼠 Microtus limnophilus | 互助县、平安县 Huzhu and Ping’an counties | 9 | 9 |
洮州绒鼠 Caryomys eva | 循化县 Xunhua County | 5 | 5 |
甘肃鼢鼠 Myospalax cansus | 互助县、民和县 Huzhu and Minhe counties | 6 | 6 |
子午沙鼠 Meriones meridianus | 民和县 Minhe County | 5 | 5 |
鼠科 Muridae 黄胸鼠 Rattus tanezumi | 循化县 Xunhua County | 4 | 4 |
褐家鼠 R. norvegicus | 互助县、循化县 Huzhu and Xunhua counties | 4 | 4 |
社鼠 Niviventer confucianus | 循化县 Xunhua County | 4 | 4 |
小家鼠 Mus musculus | 平安县、循化县 Ping’an and Xunhua counties | 9 | 9 |
朝鲜姬鼠 Apodemus peninsulae | 互助县、平安县、循化县、民和县 Huzhu, Ping’an, Xunhua and Minhe counties | 13 | 13 |
黑线姬鼠 A. agrarius | 民和县 Minhe County | 2 | 2 |
松鼠科 Sciuridae | |||
小飞鼠 Pteromys volans | 互助县 Huzhu County | 3 | 3 |
花鼠 Tamias sibiricus | 循化县 Xunhua County | 2 | 2 |
林跳鼠科 Zapodidae 中国蹶鼠 Sicista concolor | 平安县 Ping’an County | 2 | 2 |
兔形目 Lagomorpha | |||
鼠兔科 Ochotonidae | |||
甘肃鼠兔 Ochotona cansus | 互助县、平安县、循化县 Huzhu, Ping’an and Xunhua counties | 10 | 10 |
食虫目 Insectivora | |||
鼩鼱科 Soricidae | |||
山地背纹鼩鼱 Sorex bedfordiae | 互助县、循化县 Huzhu and Xunhua counties | 13 | 13 |
鼩鼱(待定种) Sorex sp. | 循化县 Xunhua County | 1 | 1 |
引物名称 Primer name | 引物序列(5′-3′) Primer sequence 5′-3′ | 引物间比例 Ratio |
---|---|---|
BatL5310 | CCTACTCRGCCATTTTACCTATG | 1 |
R6036R | ACTTCTGGGTGTCCAAAGAATCA | 1 |
VF1LFt1 | ||
LepF1_t1 | TGTAAAACGACGGCCAGTATTCAACCAATCATAAAGATATTGG | 1 |
VF1_t1 | TGTAAAACGACGGCCAGTTCTCAACCAACCACAAAGACATTGG | 1 |
VF1d_t | TGTAAAACGACGGCCAGTTCTCAACCAACCACAARGAYATYGG | 1 |
VF1i_t1 | TGTAAAACGACGGCCAGTTCTCAACCAACCAIAAIGAIATIGG | 3 |
VR1LRt1 | ||
LepRI_t1 | CAGGAAACAGCTATGACTAAACTTCTGGATGTCCAAAAAATCA | 1 |
VR1d_t1 | CAGGAAACAGCTATGACTAGACTTCTGGGTGGCCRAARAAYCA | 1 |
VR1_t1 | CAGGAAACAGCTATGACTAGACTTCTGGGTGGCCAAAGAATCA | 1 |
VR1i_t1 | CAGGAAACAGCTATGACTAGACTTCTGGGTGICCIAAIAAICA | 3 |
Table 2 PCR primer sequences used to amplify COI gene
引物名称 Primer name | 引物序列(5′-3′) Primer sequence 5′-3′ | 引物间比例 Ratio |
---|---|---|
BatL5310 | CCTACTCRGCCATTTTACCTATG | 1 |
R6036R | ACTTCTGGGTGTCCAAAGAATCA | 1 |
VF1LFt1 | ||
LepF1_t1 | TGTAAAACGACGGCCAGTATTCAACCAATCATAAAGATATTGG | 1 |
VF1_t1 | TGTAAAACGACGGCCAGTTCTCAACCAACCACAAAGACATTGG | 1 |
VF1d_t | TGTAAAACGACGGCCAGTTCTCAACCAACCACAARGAYATYGG | 1 |
VF1i_t1 | TGTAAAACGACGGCCAGTTCTCAACCAACCAIAAIGAIATIGG | 3 |
VR1LRt1 | ||
LepRI_t1 | CAGGAAACAGCTATGACTAAACTTCTGGATGTCCAAAAAATCA | 1 |
VR1d_t1 | CAGGAAACAGCTATGACTAGACTTCTGGGTGGCCRAARAAYCA | 1 |
VR1_t1 | CAGGAAACAGCTATGACTAGACTTCTGGGTGGCCAAAGAATCA | 1 |
VR1i_t1 | CAGGAAACAGCTATGACTAGACTTCTGGGTGICCIAAIAAICA | 3 |
[1] |
Baker RJ, Bradley RD (2006) Speciation in mammals and the genetic species concept. Journal of Mammalogy, 87, 643-662.
DOI URL PMID |
[2] |
Borsenko AV, Lim BK, Ivanova NV, Hanner RH, Hebert PDN (2008) DNA barcoding in surveys of small mammal communities, a field study in Suriname. Molecular Ecology Resources, 8, 471-479.
DOI URL PMID |
[3] | Clare EL, Lim BK, Engstrom MD, Eger JL, Hebert PDN (2007) DNA barcoding of Neotropical bats, species identification and discovery within Guyana. Molecular Eco- logy Notes, 7, 184-190. |
[4] |
Ebach MC, Holdrege C (2005) DNA barcoding is no substitute for taxonomy. Nature, 434, 697.
DOI URL PMID |
[5] | Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences, USA, 103, 968-971. |
[6] |
Hajibabaei M, Singer GAC, Clare EL, Hebert PDN (2007) Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biology, 5, 24.
DOI URL PMID |
[7] | Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003a) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, Series B, Biological Sciences, 270, 313-321. |
[8] | Hebert PDN, Ratnasingham S, deWaard JR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London, Series B, Biological Sciences, 270, 96-99. |
[9] |
Hebert PDN, Penton EH, Burns JM, Janzen DH, Halleachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences, USA, 101, 14812-14817.
DOI URL |
[10] |
Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN (2007) Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes, 7, 544-548.
DOI URL |
[11] | Janzen DH, Hajibabaei M, Burns JM, Hallwachs W, Remigio E, Hebert PDN (2005) Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences, 360, 1835-1845. |
[12] |
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111-120.
DOI URL PMID |
[13] |
Marshall E (2005) Will DNA barcodes breathe life into classification. Science, 307, 1037.
DOI URL PMID |
[14] | Northwest Institute of Plateau Biology, Chinese Academy of Sciences (中国科学院西北高原生物研究所) (1989) Qinghai Economic Fauna (青海经济动物志). Qinghai People’s Publishing House, Xining. (in Chinese) |
[15] |
Robins JH, Hingston M, Matisoo-Smith E, Ross HA (2007) Identifying Rattus species using mitochondrial DNA. Molecular Ecology Notes, 7 , 717-729.
DOI URL |
[16] | Simmons NB (2005) Order Chiroptera. In: Mammal Species of the World: A Taxonomic and Geographic Reference, 3rd edn. Johns Hopkins University Press, Baltimore. |
[17] | Smith MA, Fisher BL, Hebert PDN (2005) DNA barcoding for effective biodiversity assessment of a hyperdiverse arthr- opod group, the ants of Madagascar. Philosophical Transac- tions of the Royal Society of London, Series B, Biological Sciences, 360, 1825-1834. |
[18] |
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Molecular Biology and Evolution, 24, 1596-1599.
URL PMID |
[19] | Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal X windows interface: flexible strategies for multiple sequences alignment aided by quality analysis tools. Nucleic Acids Research, 24, 4876-4882. |
[20] | Vences M, Thomas M, Bonett RM, Vieites DR (2005) Deciphering amphibian diversity through DNA barcoding: chances and challenges. Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences, 360, 1859-1868. |
[1] | Chao Xing, Yi Lin, Zhiqiang Zhou, Lianjun Zhao, Shiwei Jiang, Zhenzhen Lin, Jiliang Xu, Xiangjiang Zhan. The establishment of terrestrial vertebrate genetic resource bank and species identification based on DNA barcoding in Wanglang National Nature Reserve [J]. Biodiv Sci, 2023, 31(7): 22661-. |
[2] | Jinyu Yang, Wanlong Zhu. Impact of habitat variation and human activities on small mammal community structure and diversity in Diannan Town, Jianchuan County, Yunnan [J]. Biodiv Sci, 2023, 31(11): 23246-. |
[3] | Xiaoxin Pei, Weiying Qu, Xueyang Ren, Jiangxiao Hu, Min Zhang, Lei Fang, Jiangshan Shao, Hailong Wu, Zhongzheng Chen. Diversity and inventory of non-volant small mammals in southern Anhui [J]. Biodiv Sci, 2022, 30(4): 21301-. |
[4] | Shanlin Liu, Na Qiu, Shuyi Zhang, Zhunan Zhao, Xin Zhou. Application of genomics technology in biodiversity conservation research [J]. Biodiv Sci, 2022, 30(10): 22441-. |
[5] | Xiantao Yue, Taxing Zhang, Liang Dou, Jie Liu, Jianghong Ran, Yeming Mao, Xiaolong Ma, Yao Zhang. Species diversity and community composition of non-volant small mammals in Heizhugou region, Sichuan Province [J]. Biodiv Sci, 2020, 28(6): 678-687. |
[6] | Shao Xinning, Song Dazhao, Huang Qiaowen, Li Sheng, Yao Meng. Fast surveys and molecular diet analysis of carnivores based on fecal DNA and metabarcoding [J]. Biodiv Sci, 2019, 27(5): 543-556. |
[7] | Liu Shanlin. DNA barcoding and emerging reference construction and data analysis technologies [J]. Biodiv Sci, 2019, 27(5): 526-533. |
[8] | Hou Qinxi, Ci Xiuqin, Liu Zhifang, Xu Wumei, Li Jie. Assessment of the evolutionary history of Lauraceae in Xishuangbanna National Nature Reserve using DNA barcoding [J]. Biodiv Sci, 2018, 26(3): 217-228. |
[9] | Jinfeng Hao, Xiaohong Zhang, Yusong Wang, Jinlin Liu, Yongchao Zhi, Xinjiang Li. Diversity investigation and application of DNA barcoding of Acridoidea from Baiyangdian Wetland [J]. Biodiv Sci, 2017, 25(4): 409-417. |
[10] | Xiuqin Ci, Jie Li. Phylogenetic diversity and its application in floristics and biodiversity conservation [J]. Biodiv Sci, 2017, 25(2): 175-181. |
[11] | Ya’nan Wei, Xiaomei Wang, Pengcheng Yao, Xiaoyong Chen, Hongqing Li. Comparison of species resolution rates of DNA barcoding for Chinese coastal halo-tolerant plants [J]. Biodiv Sci, 2017, 25(10): 1095-1104. |
[12] | Jing Zhang, Yuan Li, Na Song, Longshan Lin, Tianxiang Gao. Species identification and phylogenetic relationship of Thryssa species in the coastal waters of China [J]. Biodiv Sci, 2016, 24(8): 888-895. |
[13] | Yun Cao, Wenjing Shen, Lian Chen, Feilong Hu, Lei Zhou, Haigen Xu. Application of metabarcoding technology in studies of fungal diversity [J]. Biodiv Sci, 2016, 24(8): 932-939. |
[14] | Qian Jin, Fen Chen, Guijie Luo, Weijia Cai, Xu Liu, Hao Wang, Caiqing Yang, Mengdi Hao, Aibing Zhang. Estimation of species richness of moths (Insecta: Lepidoptera) based on DNA barcoding in Suqian, China [J]. Biodiv Sci, 2016, 24(11): 1296-1305. |
[15] | Haitao Li, Baoxue Zhang, Yang Gao, Xiaojun Shi, Peng Zhou. DNA barcoding in species identification of seashells: a case study in the ecological monitoring zone of Daya Bay, Guangdong [J]. Biodiv Sci, 2015, 23(3): 299-305. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||
Copyright © 2022 Biodiversity Science
Editorial Office of Biodiversity Science, 20 Nanxincun, Xiangshan, Beijing 100093, China
Tel: 010-62836137, 62836665 E-mail: biodiversity@ibcas.ac.cn