title: Utility of DNA barcoding for Tellinoidea: a comparison of distance, coalescent and character-based methods on multiple genes.
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.
authors.affiliation: The Key Laboratory of Mariculture Ministry of Education, Ocean University of China, Qingdao, 266003, China.
authors.forename: Zhenzhen
authors.initials: Z
authors.lastname: Yu
authors.forename: Qi
authors.initials: Q
authors.lastname: Li
authors.forename: Lingfeng
authors.initials: L
authors.lastname: Kong
authors.forename: Hong
authors.initials: H
authors.lastname: Yu
mesh_terms: D000818:Animals; D049872:Bivalvia / Q000235:genetics*; D058893:DNA Barcoding, Taxonomic / Q000379:methods* / Q000592:standards*; D003576:Electron Transport Complex IV / Q000235:genetics; D008957:Models, Genetic; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013045:Species Specificity
chemical_list: D012336:RNA, Ribosomal, 16S; D003576:Electron Transport Complex IV
references.citation: Syst Biol. 2004 Oct;53(5):793-808
references.pmid: 15545256
references.citation: Mol Ecol. 2012 Apr;21(8):1864-77
references.pmid: 21883587
references.citation: Syst Biol. 2009 Aug;58(4):439-42; discussion 442-4
references.pmid: 20525596
references.citation: Philos Trans R Soc Lond B Biol Sci. 2005 Oct 29;360(1462):1905-16
references.pmid: 16214748
references.citation: Mol Phylogenet Evol. 2004 Sep;32(3):1072-6
references.pmid: 15288076
references.citation: Mol Ecol Resour. 2008 Nov;8(6):1256-9
references.pmid: 21586014
references.citation: Mol Ecol Resour. 2011 Nov;11(6):956-67
references.pmid: 21635698
references.citation: Syst Biol. 2006 Oct;55(5):729-39
references.pmid: 17060195
references.citation: Bioinformatics. 2003 Aug 12;19(12):1572-4
references.pmid: 12912839
references.citation: Syst Biol. 2007 Dec;56(6):887-95
references.pmid: 18027282
references.citation: Syst Biol. 2010 May;59(3):307-21
references.pmid: 20525638
references.citation: Bioinformatics. 2003 Jan 22;19(2):301-2
references.pmid: 12538260
references.citation: Front Zool. 2009 Dec 09;6:29
references.pmid: 20003213
references.citation: BMC Evol Biol. 2012 Dec 18;12:245
references.pmid: 23244441
references.citation: Proc Biol Sci. 2003 Aug 7;270 Suppl 1:S96-9
references.pmid: 12952648
references.citation: Mol Ecol Resour. 2009 Sep;9(5):1302-10
references.pmid: 21564901
references.citation: Bioinformatics. 2003 Dec 12;19(18):2496-7
references.pmid: 14668244
references.citation: PLoS Biol. 2005 Dec;3(12):e422
references.pmid: 16336051
references.citation: Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3997-4002
references.pmid: 18852104
references.citation: Proc Biol Sci. 2003 Feb 7;270(1512):313-21
references.pmid: 12614582
references.citation: Philos Trans R Soc Lond B Biol Sci. 2008 Sep 27;363(1506):2987-96
references.pmid: 18522916
references.citation: PLoS One. 2009 Oct 16;4(10):e7483
references.pmid: 19834612
references.citation: Syst Biol. 2006 Aug;55(4):595-609
references.pmid: 16967577
references.citation: Syst Biol. 2006 Feb;55(1):162-9
references.pmid: 16507534
references.citation: Mol Ecol Resour. 2012 May;12(3):437-47
references.pmid: 22348331
references.citation: J Hered. 2006 Nov-Dec;97(6):581-94
references.pmid: 17135463
references.citation: Evolution. 2007 Feb;61(2):317-23
references.pmid: 17348942
references.citation: Front Zool. 2005 Mar 16;2(1):5
references.pmid: 15771783
references.citation: PLoS One. 2011;6(10):e26619
references.pmid: 22039517
references.citation: PLoS One. 2012;7(8):e43479
references.pmid: 22952689
references.citation: Mol Biol Evol. 2007 Aug;24(8):1596-9
references.pmid: 17488738
references.citation: Mol Ecol Resour. 2012 Mar;12(2):209-18
references.pmid: 22035191
references.citation: Infect Genet Evol. 2008 Sep;8(5):727-36
references.pmid: 18573351
references.citation: Proc Biol Sci. 2008 Feb 7;275(1632):237-47
references.pmid: 17999953
references.citation: Mol Phylogenet Evol. 2010 Nov;57(2):509-17
references.pmid: 20800099
references.citation: J Biosci. 2012 Nov;37(5):887-96
references.pmid: 23107924
references.citation: Proc Natl Acad Sci U S A. 2004 Oct 12;101(41):14812-7
references.pmid: 15465915
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references.pmid: 7984417
references.citation: Bioessays. 2007 Feb;29(2):188-97
references.pmid: 17226815
references.citation: PLoS One. 2009 Nov 18;4(11):e7866
references.pmid: 19924239
references.citation: Syst Biol. 2009 Jun;58(3):298-311
references.pmid: 20525585
references.citation: Syst Biol. 2008 Oct;57(5):809-13
references.pmid: 18853366