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Utility of DNA Barcoding for Tellinoidea: A Comparison of Distance, Coalescent and Character-based Methods on Multiple Genes

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Abstract

DNA barcoding has become a promising tool for rapid species identification using a short fragment of mitochondrial gene. Currently, an increasing number of analytical methods are available to assign DNA barcodes to taxa. The methods can be broadly divided into three main categories: (i) distance-based methods (the classical approach and the automatic barcode gap discovery (ABGD) approach), (ii) coalescent-based methods (the monophyly-based method and the general mixed Yule coalescent (GMYC) model) and (iii) the character-based method (CAOS). This study is set out to evaluate the availability of each method in barcoding Tellinoidea on the cytomchrome c oxidase subunit I (COI) and the 16 small-subunit ribosomal DNA (16S rDNA) genes. As a result, the character-based method was found to be the best in all cases, especially on a genus level. For distance-based methods, the elaborate one gained a success equal or greater than the basic one. The traditional coalescent-based method nicely delimited all of the tellinoideans on a species level. The GMYC model, which is the most radical, clearly inflated the number of species units by 34.6 % for COI gene and by 58.8 % for 16S gene. Thus, we conclude that CAOS better approximates a real barcode, and suggest the use of the ABGD method and the monophyly-based method for primary partitions. Additionally, COI gene may be more suitable as a standard barcode marker than 16S gene, particularly for tree-based methods.

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Acknowledgments

We are extremely grateful to Dr. Jun Chen from Ocean University of China, who collected all the samples used here. The study was supported by research grants from National Natural Science Foundation of China (41276138, 31372524) and Fundamental Research Funds for the Central Universities.

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  1. The Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, 266003, China

    Zhenzhen Yu, Qi Li, Lingfeng Kong & Hong Yu

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  1. Zhenzhen Yu
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Correspondence to Qi Li.

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Table S1

Information of specimens sequenced in this study. The individuals which were marked with * were amplified by universal COI primers. (DOC 112 kb)

Table S2

Primers used in this study. (DOC 30 kb)

Table S3

Information of sequences downloaded from GenBank. (DOC 49 kb)

Table S4

Character-based DNA barcodes for 17 tellinoidean species; character states (nucleotides) at 32 selected positions of the 16S gene region (ranging from 20–420); Taxa = abbreviations according to Table S1 and S3; numbers of individuals analyzed per species were given in brackets. (DOC 38 kb)

Table S5

Character-based DNA barcodes at the genus level: Character states (nucleotides) at 26 selected positions of the 16S rDNA gene region (ranging from 21–419); dashed cells indicate the occurrence of three or all four bases at this particular nucleotide position within a genus; numbers of analysed species and individuals were shown in brackets. (DOC 34 kb)

Fig. S1

Relative frequency distributions of intraspecific and interspecific distances according to different taxonomic levels for the 16S rDNA gene. (GIF 53 kb)

High-resolution image (TIFF 322 kb)

Fig. S2

Automatic partition of tellinoideans based on the16S rDNA gene. The number of groups inside the partition (initial and recursive) of each given prior intraspecific divergence value was reported. (GIF 15 kb)

High-resolution image (TIFF 201 kb)

Fig. S3

Bayesian tree of 16S gene of tellinoideans with Cardioidea as outgroups using CTR + G model. The posterior probabilities were shown when ≥0.80. (GIF 69 kb)

High-resolution image (TIFF 916 kb)

Fig. S4

Ultrametric NJ tree of tellinoideans species on based on the 16S rDNA gene, generated from 42 unique haplotypes. The red vertical line in the tree was the threshold point obtained from the GMYC model. (GIF 23 kb)

High-resolution image (TIFF 260 kb)

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Yu, Z., Li, Q., Kong, L. et al. Utility of DNA Barcoding for Tellinoidea: A Comparison of Distance, Coalescent and Character-based Methods on Multiple Genes. Mar Biotechnol 17, 55–65 (2015). https://doi.org/10.1007/s10126-014-9596-6

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