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Pay Attention to the Overlooked Cryptic Diversity in Existing Barcoding Data: the Case of Mollusca with Character-Based DNA Barcoding

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Abstract

With the global biodiversity crisis, DNA barcoding aims for fast species identification and cryptic species diversity revelation. For more than 10 years, large amounts of DNA barcode data have been accumulating in publicly available databases, most of which were conducted by distance or tree-building methods that have often been argued, especially for cryptic species revelation. In this context, overlooked cryptic diversity may exist in the available barcoding data. The character-based DNA barcoding, however, has a good chance for detecting the overlooked cryptic diversity. In this study, marine mollusk was as the ideal case for detecting the overlooked potential cryptic species from existing cytochrome c oxidase I (COI) sequences with character-based DNA barcode. A total of 1081 COI sequences of mollusks, belonging to 176 species of 25 families of Gastropoda, Cephalopoda, and Lamellibranchia, were conducted by character analysis. As a whole, the character-based barcoding results were consistent with previous distance and tree-building analysis for species discrimination. More importantly, quite a number of species analyzed were divided into distinct clades with unique diagnostical characters. Based on the concept of cryptic species revelation of character-based barcoding, these species divided into separate taxonomic groups might be potential cryptic species. The detection of the overlooked potential cryptic diversity proves that the character-based barcoding mode possesses more advantages of revealing cryptic biodiversity. With the development of DNA barcoding, making the best use of barcoding data is worthy of our attention for species conservation.

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References

  • Bellwood DR, Hughes TP, Folke C, Nystrom M (2004) Confronting the coral reef crisis. Nature 429:827–833

    Article  CAS  PubMed  Google Scholar 

  • Bergmann T, Hadrys H, Breves G, Schierwater B (2009) Character-based DNA barcoding: a superior tool for species classification. Berl Munch Tierarztl Wochenschr 122:446–450

    CAS  PubMed  Google Scholar 

  • Bertolazzi P, Felici G, Weitschek E (2009) Learning to classify species with barcodes. BMC Bioinformatics 10(Suppl14):S7

    Article  PubMed  PubMed Central  Google Scholar 

  • Blaxter M, Mann J, Chapman T, Thomas F, Whitton C et al (2005) Defining operational taxonomy units using DNA barcode data. Philos Trans R Soc B 360:1935–1943

    Article  CAS  Google Scholar 

  • 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(6):e21326

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Coissac E, Riaz T, Puillandre N (2012) Bioinformatic challenges for DNA metabarcoding of plants and animals. Mol Ecol 21:1834–1847

    Article  CAS  PubMed  Google Scholar 

  • Dai L, Zheng X, Kong L, Li Q (2012) DNA barcoding analysis of Coleoidea (Mollusca: Cephalopoda) from Chinese waters. Mol Ecol Resour 12:437–447

    Article  CAS  PubMed  Google Scholar 

  • Damm S, Schierwater B, Hadrys H (2010) An integrative approach to species discovery in odonates: from character-based DNA barcoding to ecology. Mol Ecol 19:3881–3893

    Article  PubMed  Google Scholar 

  • Desalle R (2006) Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff. Conserv Biol 20:1545–1547

    Article  PubMed  Google Scholar 

  • DeSalle R, Egan MG, Siddall M (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc B 360:1905–1916

    Article  CAS  Google Scholar 

  • Dong W, Cheng T, Li C (2014) Discriminating plants using the DNA barcode rbcLb: an appraisal based on a large data set. Mol Ecol Resour 14(2):336–343

    Article  CAS  PubMed  Google Scholar 

  • Feng Y, Li Q, Kong LF, Zheng X (2011) COI-based DNA barcoding of Arcoida species (Bivalvia: Pteriomorphia) along the coast of China. Mol Ecol Resour 11:435–441

    Article  PubMed  Google Scholar 

  • FitzJohn RG (2010) Quantitative traits and diversification. Syst Biol 59:619–633

    Article  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • Goldstein PZ, DeSalle R (2010) Integrating DNA barcode data and taxonomic practice: determination, discovery, and description. BioEssays 33:135–147

    Article  Google Scholar 

  • Hamilton CA, Hendrixson BE, Brewer MS et al (2014) An evaluation of sampling effects on multiple DNA barcoding methods leads to an integrative approach for delimiting species: a case study of the North American tarantula genus Aphonopelma (Araneae, Mygalomorphae, Theraphosidae). Mol Phylogenet Evol 71:79–93

    Article  CAS  PubMed  Google Scholar 

  • Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003a) Biological identifications through DNA barcodes. Proc R Soc Lond Ser B 270:313–321

    Article  CAS  Google Scholar 

  • Hebert PDN, Ratnasingham S, DeWaard JR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond Ser B 270:S96–S99

    Article  CAS  Google Scholar 

  • Hickerson MJ, Meyer CP, Moritz C (2006) DNA barcoding will often fail to discover new animal species over broad parameter space. Syst Biol 55:729–739

    Article  PubMed  Google Scholar 

  • Hopkins GW, Freckleton RP (2002) Declines in the numbers of amateur and professional taxonomists: implications for conservation. Anim Conserv 5:245–249

    Article  Google Scholar 

  • Hudson RR, Coyne JA (2002) Mathematical consequences of the genealogical species concept. Evolution 56:1557–1565

    Article  PubMed  Google Scholar 

  • Hyde JR, Underkoffler KE, Sundberg MA (2014) DNA barcoding provides support for a cryptic species complex within the globally distributed and fishery important opah (Lampris guttatus). Mol Ecol Resour 14:1239–1247

    Article  CAS  PubMed  Google Scholar 

  • Joly S, Davies TJ, Archambault A, Bruneau A, Derry A et al (2014) Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead. Mol Ecol Resour 14:221–232

    Article  CAS  PubMed  Google Scholar 

  • Jones M, Ghoorah A, Blaxter M (2011) jMOTU and Taxonerator: turning DNA barcode sequences into annotated operational taxonomic units. PLoS One 6:e19259

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Katoh K, Asimenos G, Toh H (2009) Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol 537:39–64

    Article  CAS  PubMed  Google Scholar 

  • Kizirian D, Donnelly MA (2004) The criterion of reciprocal monophyly and classification of nested diversity at the species level. Mol Phylogenet Evol 32:1072–1076

    Article  PubMed  Google Scholar 

  • Knowles LL, Carstens BC (2007) Delimiting species without monophyletic gene trees. Syst Biol 56:887–895

    Article  PubMed  Google Scholar 

  • Kulsantiwong J, Prasopdee S, Ruangsittichai J, Ruangjirachuporn W, Boonmars T et al (2014) DNA barcode identification of freshwater snails in the family Bithyniidae from Thailand. PLoS One 8(11):e79144

    Article  Google Scholar 

  • Liu J, 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. Mol Ecol 20:4332–4345

    Article  PubMed  Google Scholar 

  • Maddison WP, Maddison DR (2005) MACCLADE: analysis of phylogeny and character evolution. Version 3.0. Sinauer Associates, Sunderland

    Google Scholar 

  • Nevill PG, Wallace MJ, Miller JT, Krauss SL (2013) DNA barcoding for conservation, seed banking and ecological restoration of Acacia in the Midwest of Western Australia. Mol Ecol Resour 13:1033–1042

    CAS  PubMed  Google Scholar 

  • Novacek MJ, Cleland EE (2001) The current biodiversity extinction event: scenarios for mitigation and recovery. Proc Natl Acad Sci U S A 98:5466–5470

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rach J, DeSalle R, Sarkar IN, Schierwater B, Hadrys H (2008) Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Proc R Soc Lond Ser B 275:237–247

    Article  CAS  Google Scholar 

  • Ratnasingham S, Hebert PDN (2007) BOLD: The Barcode of Life Data System (www.barcodinglife.org). Mol Ecol Notes 7:355–364

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Raupach MJ, Hendrich L, Küchler SM, Deister F, Morinière J (2014) Building-up of a DNA barcode library for true bugs (Insecta: Hemiptera: Heteroptera) of Germany reveals taxonomic uncertainties and surprises. PLoS One 9(9):e106940

    Article  PubMed  PubMed Central  Google Scholar 

  • Reid BN, Le M, McCord WP et al (2011) Comparing and combining distance-based and character-based approaches for barcoding turtles. Mol Ecol Resour 11:956–967

    Article  CAS  PubMed  Google Scholar 

  • Ristau K, Steinfartz S, Traunspurger W (2013) First evidence of cryptic species diversity and significant population structure in a widespread freshwater nematode morphospecies (Tobrilus gracilis). Mol Ecol 22:4562–4575

    Article  CAS  PubMed  Google Scholar 

  • Rougerie R, Kitching IJ, Haxaire J, Miller SE, Hausmann A (2014) Australian Sphingidae—DNA barcodes challenge current species boundaries and distributions. PLoS One 9(7):e101108

    Article  PubMed  PubMed Central  Google Scholar 

  • Rubinoff D (2006) Utility of mitochondrial DNA barcodes in species conservation. Conserv Biol 20:1026–1033

    Article  PubMed  Google Scholar 

  • Rubinoff D, Cameron S, Will K (2006) A genomic perspective on the shortcomings of mitochondrial DNA for “barcoding” identification. J Hered 97:581–594

    Article  CAS  PubMed  Google Scholar 

  • Sarkar IN, Thornton JW, Planet PJ et al (2002) An automated phylogenetic key for classifying homeoboxes. Mol Phylogenet Evol 24:388–399

    Article  PubMed  Google Scholar 

  • Sarkar IN, Planet PJ, Desalle R (2008) CAOS software for use in character-based DNA barcoding. Mol Ecol Resour 8:1256–1259

    Article  CAS  PubMed  Google Scholar 

  • Schoch CL, Seifertb KA, Huhndorfc S, Robertd V, Spougea JL et al (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc R Soc Lond Ser B 109(16):6241–6246

    CAS  Google Scholar 

  • Shneer VS (2009) DNA barcoding of animal and plant species as an approach for their molecular identification and describing of diversity. Zh Obshch Biol 70:296–315

    CAS  PubMed  Google Scholar 

  • Sosa V, Mejía-Saules T, Cuéllar MA, Vovides AP (2013) DNA barcoding in endangered Mesoamerican groups of plants. Bot Rev 79:469–482

    Article  Google Scholar 

  • Stern RF, Horak A, Andrew RL (2010) Environmental barcoding reveals massive dinoflagellate diversity in marine environments. PLoS One 5(11):e13991

    Article  PubMed  PubMed Central  Google Scholar 

  • Sun Y, Li Q, Kong L, Zheng X (2012) DNA barcoding of Caenogastropoda along coast of China based on the COI gene. Mol Ecol Resour 12:209–218

    Article  CAS  PubMed  Google Scholar 

  • Waugh J (2007) DNA barcoding in animal species: progress, potential and pitfalls. BioEssays 29(2):188–197

    Article  CAS  PubMed  Google Scholar 

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

    Article  Google Scholar 

  • Wong LL, Peatman E, Lu J et al (2011) DNA barcoding of catfish: species authentication and phylogenetic assessment. PLoS One 6(3):e17812

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yassin A, Markow TA, Narechania A, OGrad PM, DeSalle R (2010) The genus Drosophila as a model for testing tree- and character-based methods of species identification using DNA barcoding. Mol Phylogenet Evol 57:509–517

    Article  CAS  PubMed  Google Scholar 

  • Yu Z, Li Q, Kong L, Yu H (2015) Utility of DNA barcoding for Tellinoidea: a comparison of distance, coalescent and character-based methods on multiple genes. Mar Biotechnol 17(1):55–65

    Article  PubMed  Google Scholar 

  • Zou S, Li Q, Kong L, Yu H, Zheng X (2011) Comparing the usefulness of distance, monophyly and character-based DNA barcoding methods in species identification: a case study of Neogastropoda. PLoS One 6:e26619

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zou S, Li Q, Kong L (2012a) Multigene barcoding and phylogeny of geographically widespread muricids (Gastropoda: Neogastropoda) along the coast of China. Mar Biotechnol 14(1):21–34

    Article  CAS  PubMed  Google Scholar 

  • Zou S, Li Q, Kong L (2012b) Monophyly, distance and character-based multigene barcoding reveal extraordinary cryptic diversity in Nassarius: a complex and dangerous community. PLoS One 7(10):e47276

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

The study was supported by research grants from Fundamental Research Funds for the Central Universities and the Natural Science Fund project of Jiangsu Province (BK20150680).

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Correspondence to Qi Li.

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Figure S1

COI Neighbour joining tree of Caenogastropoda. Taxonomic groups in red might be potential cryptic species and would be analyzed by character-based barcoding. (GIF 92 kb)

High Resolution Image (TIF 1616 kb)

Figure S2

COI Neighbour joining tree of venerid species. Taxonomic groups in red might be potential cryptic species and would be analyzed by character-based barcoding. (GIF 112 kb)

High Resolution Image (TIF 3028 kb)

Figure S3

Neighbour joining tree of Arcoida species based on COI sequences. Taxonomic groups in red might be potential cryptic species and would be analyzed by character-based barcoding. (GIF 94 kb)

High Resolution Image (TIF 2341 kb)

Figure S4

Neighbour joining tree of Atrina pectinata based on COI sequences. Taxonomic groups in red were potential cryptic species revealed by Liu et al. (2011) and would be analyzed by character-based barcoding. (GIF 37 kb)

High Resolution Image (TIF 1156 kb)

Table S1

Character-based COI barcodes for 49 defined clades of Caenogastropoda (DOC 151 kb)

Table S2

Character-based COI barcodes for 69 defined clades of marine venerids. (DOC 208 kb)

Table S3

Character-based COI barcodes for 48 defined clades of Arcoida species. (DOC 163 kb)

Table S4

Character-based COI barcodes for 6 defined clades of Atrina pectinata (Bivalvia: Pinnidae). (DOC 38 kb)

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Zou, S., Li, Q. Pay Attention to the Overlooked Cryptic Diversity in Existing Barcoding Data: the Case of Mollusca with Character-Based DNA Barcoding. Mar Biotechnol 18, 327–335 (2016). https://doi.org/10.1007/s10126-016-9692-x

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