DNA条形码技术在海洋贝类鉴定中的实践: 以大亚湾生态监控区为例

doi:10.17520/biods.2014261

摘要/Abstract

摘要：

为提高物种鉴定的准确性, 本研究采用DNA条形码技术对大亚湾生态监控区冬季采集的贝类样品进行了种类鉴定。结果表明, 26个形态种中, 有15个可以通过线粒体COI和16S rRNA基因的系统发育分析鉴定到种的水平。部分形态上难以鉴定的种类, 如线缝摺塔螺(Ptychobela suturalis)和区系螺(Funa sp.)可以通过条形码实现有效鉴定。锯齿巴非蛤(Paphia gallus)、西格织纹螺(Nassarius siquijorensis)、爪哇拟塔螺(Turricula javana)等种类存在相当大的种内遗传距离, 有存在隐存种的可能性。尽管基于线粒体COI和16S rRNA基因的种内遗传距离和属内种间的遗传距离发生重合, 无明显的条形码间隙, 但通过系统树的方法仍能有效鉴定物种。可见, DNA条形码技术能有效提高海洋贝类物种鉴定的准确性并发现隐存种。

关键词: DNA条形码, 生物多样性, 监测, COI基因, 16S rRNA基因, 海洋贝类

Abstract

To improve the accuracy of seashell species identification in the ecological monitoring zone of Daya Bay, Guangdong, we used DNA barcoding based on mitochondrial COI and 16S rRNA genes from specimens sampled in the winter of 2013. Among the 26 morphospecies, 15 can be identified to the species level using phylogenetic analyses. Some species, Ptychobela suturalis and Funa sp., were difficult to identify by shell morphology but were successfully identified using DNA barcoding. A high level of intraspecific sequence variation was observed in Paphia gallus, Nassarius siquijorensis and Turricula javana, suggesting that cryptic species may occur in these three morphospecies. Although the barcoding gap does not exist between intra- and interspecific variations based on COI and 16S rRNA genes, a phylogenetic approach can provide effective identification. DNA barcoding is an effective tool for accurate species identification and discovery of cryptic species in seashells.

Key words: DNA barcoding, biodiversity, monitoring, COI, 16S rRNA, seashells

李海涛, 张保学, 高阳, 时小军, 周鹏 (2015) DNA条形码技术在海洋贝类鉴定中的实践: 以大亚湾生态监控区为例. 生物多样性, 23, 299-305. DOI: 10.17520/biods.2014261.

Haitao Li, Baoxue Zhang, Yang Gao, Xiaojun Shi, Peng Zhou (2015) DNA barcoding in species identification of seashells: a case study in the ecological monitoring zone of Daya Bay, Guangdong. Biodiversity Science, 23, 299-305. DOI: 10.17520/biods.2014261.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2014261

https://www.biodiversity-science.net/CN/Y2015/V23/I3/299

图/表 2

图1 基于COI基因序列通过邻接法构建的系统发育树(黑体显示的种名表示含有本研究测得的序列, 节点处数值表示自展支持率和贝叶斯树后验概率)

Fig. 1 Phylogenetic tree based on COI gene sequences using neighbor-joining (NJ) method. Species names in bold contain sequences obtained from this study. NJ bootstrap values (>50%) and Bayesian inference posterior probabilities (in percentage) are shown at nodes.

图2 基于16S rRNA基因序列通过邻接法构建的系统发育树(黑体显示的种名表示含有本研究测得的序列, 节点处数值表示自展支持率和贝叶斯树后验概率)

Fig. 2 Phylogenetic tree based on 16S rRNA gene sequences using neighbor-joining (NJ) method. Species names in bold contain sequences obtained from this study. NJ bootstrap values (>50%) and Bayesian inference posterior probabilities (in percentage) are shown at nodes.

参考文献 26

1	Chen J, Li Q, Kong L, Yu H (2011) How DNA barcodes complement taxonomy and explore species diversity: the case study of a poorly understood marine fauna.PLoS ONE, 6, e21326.
2	Du FY (杜飞雁), Zhang HH (张汉华), Li CH (李纯厚), Wang XH (王雪辉), Jia XP (贾晓平) (2008a) Species composition and diversity of macrobenthic fauna in Daya Bay.Journal of Fishery Sciences of China(中国水产科学), 15, 252-259. (in Chinese with English abstract)
3	Du FY (杜飞雁), Zhang HH (张汉华), Li CH (李纯厚), Wang XH (王雪辉), Jia XP (贾晓平) (2008b) Study on species diversity of macrobenthos in Daya Bay, South China Sea.South China Fisheries Science(南方水产科学), 4(6), 33-41. (in Chinese with English abstract)
4	Du FY (杜飞雁), Wang XH (王雪辉), Li CH (李纯厚), Zhang HH (张汉华), Jia XP (贾晓平) (2009) Macrobenthic community structure in Daya Bay, South China Sea.Acta Ecologica Sinica(生态学报), 29, 1091-1098. (in Chinese with English abstract)
5	Du FY (杜飞雁), Wang XH (王雪辉), Jia XP (贾晓平), Yang SY (杨圣云), Ma SW (马胜伟), Chen HG (陈海刚), Li CH (李纯厚) (2011) Species composition and characteristics of macrobenthic fauna in Daya Bay, South China Sea.Journal of Fishery Sciences of China(中国水产科学), 18, 877-892. (in Chinese with English abstract)
6	Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit 1 from diverse metazoan invertebrates.Molecular Marine Biology and Biotechnology, 3, 294-299.
7	Hajibabaei M, Singer GA, Clare EL, Hebert PD (2007) Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring.BMC Biology, 5, 24.
8	Hebert PD, Cywinska A, Ball SL, deWaard JR (2003a) Biological identifications through DNA barcodes.Proceedings of the Royal Society of London B: Biological Sciences, 270, 313-321.
9	Hebert PD, 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 B: Biological Sciences, 270(Suppl. 1), S96-99.
10	Hishida Y (菱田嘉一) (2000) The Great Pictorial Book of Seashells. Kumi Corporation, Tokyo. (in Japanese)
11	Johnson SB, Warén A, Vrijenhoek RC (2008) DNA barcoding of Lepetodrilus limpets reveals cryptic species.Journal of Shellfish Research, 27, 43-51.
12	Knowlton N (1993) Sibling species in the sea.Annual Review of Ecology and Systematics, 24, 189-216.
13	Liu J, Li Q, Kong L, Zheng X (2011) Cryptic diversity in the pen shell Atrina pectinata (Bivalvia: Pinnidae): high divergence and hybridization revealed by molecular and morphological data.Molecular Ecology, 20, 4332-4345.
14	Liu RY (刘瑞玉) (2011) Progress of marine biodiversity studies in China seas.Biodiversity Science(生物多样性), 19, 614-626. (in Chinese with English abstract)
15	Liu SF (柳淑芳), Chen LL (陈亮亮), Dai FQ (戴芳群), Zhuang ZM (庄志猛) (2010) Application of DNA barcoding gene COI for classification family Sciaenidae.Oceanologia et Limnologia Sinica(海洋与湖沼), 41, 223-232. (in Chinese with English abstract)
16	Posada D (2008) jModelTest: phylogenetic model averaging.Molecular Biology and Evolution, 25, 1253-1256.
17	Puillandre N, Strong EE, Bouchet P, Boisselier MC, Couloux A, Samadi S (2009) Identifying gastropod spawn from DNA barcodes: possible but not yet practicable.Molecular Ecology Resources, 9, 1311-1321.
18	Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models.Bioinformatics, 19, 1572-1574.
19	Shen Y, Chen X, Murphy RW (2013) Assessing DNA barcoding as a tool for species identification and data quality control.PLoS ONE, 8, e57125.
20	Simon C, Frati F, Beckenbach A, Crespi B, Liu H, Flook P (1994) Evolution, weighting and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers.Annals of the Entomological Society of America, 87, 651-701.
21	Terranova MS, Brutto SL, Arculeo M, Mitton JB (2007) A mitochondrial phylogeography of Brachidontes variabilis (Bivalvia: Mytilidea) reveals three cryptic species.Journal of Zoological Systematics and Evolutionary Research, 45, 289-298.
22	Wang MX (王敏晓), Cheng FP (程方平), Li CL (李超伦), Sun S (孙松) (2011) DNA barcoding of zooplankton in the Jiaozhou Bay for species identification.Oceanologia et Limnologia Sinica(海洋与湖沼), 42, 702-710. (in Chinese with English abstract)
23	Wilke T, Falniowski A (2001) The genus Adriohydrobia (Hydrobiidae: Gastropoda): polytypic species or polymorphic populations?Journal of Zoological Systematics and Evolutionary Research, 39, 227-234.
24	Williams ST, Reid DG, Littlewood DT (2003) A molecular phylogeny of the Littorininae (Gastropoda: Littorinidae): unequal evolutionary rates, morphological parallelism, and biogeography of the Southern Ocean.Molecular Phylogenetics and Evolution, 28, 60-86.
25	Xu GZ (徐恭昭) (1989) Environments and Resources of Daya Bay (大亚湾环境与资源). Anhui Science and Technology Press, Hefei. (in Chinese)
26	Zhang SP (张素萍) (2007) On nine new record species of Ergalataxinae (Gastropoda, Muricidae) from China coast.Oceanologia et Limnologia Sinica(海洋与湖沼), 38, 542-548. (in Chinese with English abstract)

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