Integrating a DNA barcoding project with an ecological survey: a case study on temperate intertidal polychaete communities in Qingdao, China

Hong Zhou; Zhinan Zhang; Haiyan Chen; Renhua Sun; Hui Wang; Lei Guo; Haijian Pan

doi:10.1007/s00343-010-9131-1

Your Location：

Home >

Browse articles >

Integrating a DNA barcoding project with an ecological survey: a case study on temperate intertidal polychaete communities in Qingdao, China

Updated：2023-05-16

- Integrating a DNA barcoding project with an ecological survey: a case study on temperate intertidal polychaete communities in Qingdao, China
- Journal of Oceanology and Limnology Vol. 28, Issue 4, Pages: 899-910(2010)
- Affiliations：
  
  College of Marine Life Sciences Ocean University of China
- Author bio：
- Funds：
- DOI：10.1007/s00343-010-9131-1
  CLC：
- Online First：29 June 2010，
  
  Published：2010
- Accepted：
Scan QR Code
Zhou, H., Zhang, Z., Chen, H. et al. Integrating a DNA barcoding project with an ecological survey: a case study on temperate intertidal polychaete communities in Qingdao, China., Chin. J. Ocean. Limnol. 28, 899–910 (2010). https://doi.org/10.1007/s00343-010-9131-1
DOI：

Zhou, H., Zhang, Z., Chen, H. et al. Integrating a DNA barcoding project with an ecological survey: a case study on temperate intertidal polychaete communities in Qingdao, China., Chin. J. Ocean. Limnol. 28, 899–910 (2010). https://doi.org/10.1007/s00343-010-9131-1 DOI：

摘要

Abstract

In this study

we integrated a DNA barcoding project with an ecological survey on intertidal polychaete communities and investigated the utility of CO1 gene sequence as a DNA barcode for the classification of the intertidal polychaetes. Using 16S rDNA as a complementary marker and combining morphological and ecological characterization

some of dominant and common polychaete species from Chinese coasts were assessed for their taxonomic status. We obtained 22 haplotype gene sequences of 13 taxa

including 10 CO1 sequences and 12 16S rDNA sequences. Based on intra- and inter-specific distances

we built phylogenetic trees using the neighbor-joining method. Our study suggested that the mitochondrial CO1 gene was a valid DNA barcoding marker for species identification in polychaetes

but other genes

such as 16S rDNA

could be used as a complementary genetic marker. For more accurate species identification and effective testing of species hypothesis

DNA barcoding should be incorporated with morphological

ecological

biogeographical

and phylogenetic information. The application of DNA barcoding and molecular identification in the ecological survey on the intertidal polychaete communities demonstrated the feasibility of integrating DNA taxonomy and ecology.

关键词

Keywords

references

Antoniadou C, Chintiroglou C. 2006. Trophic relationships of polychaetes associated with different algal growth forms. Helgol. Mar. Res., 60: 39–49.

Clarke K R, Warwick R M. 2001. Change in Marine Communities: An Approach to Statistical Analysis and Interpretation, 2nd edition. PRIMER-E, Plymouth.

Dasmahapatra K K, Mallet J. 2006. DNA barcodes: recent successes and future prospects. Heredity, 2006: 1–2.

DeSalle R, Egan M G, Siddall M. 2005. The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philosophical Transactions of the Royal Society B-Biological Sciences, 360: 1 905–1 916.

Ekrem T, Willassen E, Stur E. 2007. A comprehensive DNA sequence library is essential for identification with DNA barcodes. Molecular Phylogenetics and Evolution, 43: 530–542.

Fauchald K. 1977. The polychaete worms. Definitions and keys to the orders, families and genera. Nat. Hist. Mus. LA County Sci. Ser., 28: 1–188.

Fauchald K. 2009. World Register of Polychaeta, available online at http://www.marinespecies.org.

Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol., 3: 294–299.

Hajibabaei M, Singer G A C, Hebert P D N, Hickey D A. 2007. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends in Genetics, 23: 167–172.

Hebert P D N, Penton E H, Burns J M, Janzen D H, Hallwachs 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 of the United States of America, 101: 14 812–14 817.

Hebert P D N, Cywinska A, Ball S L, deWaard J R. 2003a. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B. Biol. Sci., 270: 313–321.

Hebert P D N, Ratnasingham S, deWaard J R. 2003b. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. Lond. B. Biol. Sci., 270(Suppl.1): S96–S99.

Kim J, Chae C. 2001. Optimized protocols for the detection of porcine circovirus DNA from formalin-fixed paraffin-embedded tissues using nested polymerase chain reaction and comparison of nested PCR with in situ hybridization. Journal of Virological Methods, 92: 105–111.

Liao X Z. 2006. Molecular Phylogenetic Analysis of Marine Sedentary Polychaeta. Master Thesis. Xiamen University, China. (in Chinese)

Liao X Z, Lin C R. 2006. Phylogenetic analysis of polychaetes based on sequences of 18S rDNA and CO1 segments. Journal of Oceanography in Taiwan Strait, 25(4): 490–497. (in Chinese)

Mikkelsen N T, Schander C, Willassen E. 2007. Local scale DNA barcoding of bivalves (Mollusca): a case study. Zoologica Scripta, 36: 455–463.

Moritz C, Cicero C. 2004. DNA barcoding: promise and pitfalls. PLoS Biology, 2(10): e279–e354.

Palumbi S R. 1996. Nucleic acids II: the polymerase chain reaction. In: Hillis D M, Moritz C, Mable B K eds. Molecular Systematics, 2nd edition. Sinauer Associates, Sunderland, Massachusetts. p. 205–247.

Purschke G, Ding Z, Mfiller M C. 2005. Ultrastructural differences as a taxonomic marker: the segmental ocelli of Polyophthalmus pictus and Polyophthalmus qingdaoensis sp. n. (Polychaeta, Opheliidae). Zoomorphology, 115: 229–241.

Ratnasingham S, Hebert P D N. 2007. BOLD: The Barcode of Life Data System (www.barcodinglife.org). Molecular Ecology Notes, 7: 355–364.

Schander C, Willassen E. 2005. What can biological barcoding do for marine biology? Marine Biology Research, 1: 79–83.

Sun R P, Yang D J. 2004. Fauna Sinica: Invertebrata Vol. 33, Annelida, Polyhaeta II. Nereidida (= Nereimorpha). Science Press, Beijing, China. 520p. (in Chinese)

Tamura K, Kumar S. 2002. Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Molecular Biology and Evolution, 19: 1 727–1 736.

Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA 4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24: 1 596–1 599.

Thompson J D, Higgins D G, Gibson T J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22: 4 673–4 680.

Will K W, Rubinoff D. 2004. Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics, 20: 47–55.

Wu B L, Wu Q Q, Qiu J W, Lu H. 1997. Fauna Sinica: Phylum Annelida, Class Polychaeta, Order Phyllodocimorpha. Science Press, Beijing, China. 329p. (in Chinese)

Wu B L, Sun R P, Yang D J. 1981. Study on the Nereidae from China. Ocean Press, Beijing, China. 228p. (in Chinese)

Yang D J, Sun R P. 1988. Polychaeta Annelids from China. Agriculture Press, Beijing, China. 351p. (in Chinese)

Zhou J. 2008. Study on the Taxonomy and Faunistic Characters of Families Paraonidae and Spionidae (Annelida: Polychaeta) from China Seas. PhD Thesis. Institute of Oceanology, Chinese Academy of Sciences, Qingdao and Graduate University of Chinese Academy of Sciences, Beijing. (in Chinese)

Views

Downloads

CSCD

Alert me when the article has been cited

Submit

Tools

Publicity Resources

First record of abnormal body coloration in a rockfish Sebastes koreanus (Scorpaenoidei: Sebastidae) from coastal water of China based on morphological characteristics and DNA barcoding

DNA barcoding of fishes from Zhoushan coastal waters using mitochondrial COI and 12S rRNA genes

Relationship between morphospecies and microcystinproducing genotypes of Microcystis species in Chinese freshwaters

Spatial distribution and structure of benthic polychaete communities of Essaouira intertidal rocky shores (Atlantic coast of Morocco)

DNA barcoding of the family Sparidae along the coast of China and revelation of potential cryptic diversity in the IndoWest Pacific oceans based on COI and 16S rRNA genes

Related Author

Shufang LIU

Changting AN

Huan WANG

Ang LI

Tianxiang GAO

Anle XU

Zhi CHEN

Shude LIU

Related Institution

Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory

Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences

School of Fishery, Zhejiang Ocean University

College of Fisheries and Life Science, Hainan Tropical Ocean University

Shandong Fisheries Development and Resources Conservation Center

Address：Editorial Office of JOL, 88 Haijun Rd. Qingdao, 266000, China
Tel：+86-532-82898754 Email：jol@qdio.ac.cn
Technical support is provided by Beijing Founder electronics co., LTD 京ICP备09064830号-19 京公网安备11010802024621
It is recommended to read the content of this site in Chrome&IE9+. Please switch to extreme mode in browser 360.
Cookies We use cookies to help provide and enhance our service and tailor content. By continuing, you agree to the use of cookies.

⁰