DNA barcoding gap: Reliable species identification over morphological and geographical scales

Molecular Ecology Resources

Volumn 15, Issue 2, 2015, Pages 268-277

  Čandek, Klemen ^a   Kuntner, Matjaž ^a,b,c  

^a ANTON MELIK GEOGRAPHICAL INSTITUTE   (Slovenia)

^b HUBEI UNIVERSITY   (China)

^c DEPARTMENT OF PALEOBIOLOGY   (United States)

Author keywords

Barcoding gap; Biogeography; CO1; DNA barcodes; Morphology; Spiders

Indexed keywords

ARANEAE; DIPTERA; GASTROPODA; PAPILIONOIDEA;

ANATOMY AND HISTOLOGY; ANIMAL; CLASSIFICATION; COMPARATIVE ANATOMY; DNA BARCODING; GENETICS; PHYLOGEOGRAPHY; PROCEDURES; SPIDER; STATISTICS;

ANATOMY, COMPARATIVE; ANIMALS; DNA BARCODING, TAXONOMIC; PHYLOGEOGRAPHY; SPIDERS; STATISTICS AS TOPIC;

EID: 84922660807     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12304     Document Type: Article

References (77)

1. Agnarsson I, Coddington JA, Kuntner M (2013) Systematics: progress in the study of spider diversity and evolution. In: Spider Research in the 21st Century: Trends and Perspectives (ed. Penney D), pp. 58-111. Siri Scientific Press, Manchester, UK.
2. Aliabadian M, Kaboli M, Nijman V, Vences M (2009) Molecular identification of birds: performance of distance-based DNA barcoding in three genes to delimit parapatric species. PLoS ONE, 4, e4119.
3. Arnedo MA, Ferrández MA (2007) Mitochondrial markers reveal deep population subdivision in the European protected spider Macrothele calpeiana (Walckenaer, 1805) (Araneae, Hexathelidae). Conservation Genetics, 8, 1147-1162.
4. Ashfaq M, Hebert PDN, Mirza JH, Khan AM, Zafar Y, Mirza MS (2014) Analyzing mosquito (Diptera: Culicidae) diversity in Pakistan by DNA barcoding. PLoS ONE, 9, e97268.
5. Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, Massachusetts, 447 pp.
6. Barrett RDH, Hebert PDN (2005) Identifying spiders through DNA barcodes. Canadian Journal of Zoology-Revue Canadienne De Zoologie, 83, 481-491.
7. Bell JR, Bohan DA, Shaw EM, Weyman GS (2005) Ballooning dispersal using silk: World fauna, phylogenies, genetics and models. Bulletin of Entomological Research, 95, 69-114.
8. Bergsten J, Bilton DT, Fujisawa T et al. (2012) The effect of geographical scale of sampling on DNA barcoding. Systematic Biology, 61, 851-869.
9. Bertolazzi P, Felici G, Weitschek E (2009) Learning to classify species with barcodes. BMC Bioinformatics, 10, S7.
10. BioEssays (2009) DNA barcoding for ecologists. Trends in Ecology & Evolution, 24, 110-117.
11. Blagoev G, Hebert P, Adamowicz S, Robinson E (2009) Prospects for using DNA barcoding to identify spiders in species-rich genera. Zookeys, 16, 27-46.
12. Boykin LM, Armstrong KF, Kubatko L, Barro PD (2012) Species delimitation and global biosecurity. Evolutionary Bioinformatics, 8, 1-37.
13. Bridge PD, Roberts PJ, Spooner BM, Panchal G (2003) On the unreliability of published DNA sequences. New Phytologist, 160, 43-48.
14. Bromham L, Woolfit M, Lee MSY, Rambaut A (2002) Testing the relationship between morphological and molecular rates of change along phylogenies. Evolution, 56, 1921-1930.
15. Burns JM, Janzen DH, Hajibabaei M, Hallwachs W, Hebert PDN (2007) DNA barcodes of closely related (but morphologically and ecologically distinct) species of skipper butterflies (Hesperiidae) can differ by only one to three nucleotides. Journal of the Lepidopterists' Society, 61, 138-153.
16. Carr CM, Hardy SM, Brown TM, Macdonald TA, Hebert PDN (2011) A tri-oceanic perspective: DNA barcoding reveals geographic structure and cryptic diversity in Canadian polychaetes. PLoS ONE, 6, e22232.
17. Collins RA, Boykin LM, Cruickshank RH, Armstrong KF (2012) Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification. Methods in Ecology and Evolution, 3, 457-465.
18. Conn PB, McClintock BT, Cameron MF, Johnson DS, Moreland EE, Boveng PL (2013) Accommodating species identification errors in transect surveys. Ecology, 94, 2607-2618.
19. Cummings MP, Neel MC, Shaw KL (2008) A genealogical approach to quantifying lineage divergence. Evolution, 62, 2411-2422.
20. Davies TJ, Savolainen V (2006) Neutral theory, phylogenies, and the relationship between phenotypic change and evolutionary rates. Evolution, 60, 476-483.
21. Delsinne T, Sonet G, Nagy ZT et al. (2012) High species turnover of the ant genus Solenopsis (Hymenoptera: Formicidae) along an altitudinal gradient in the Ecuadorian Andes, indicated by a combined DNA sequencing and morphological approach. Invertebrate Systematics, 26, 457-469.
22. Dexter KG, Pennington TD, Cunningham CW (2010) Using DNA to assess errors in tropical tree identifications: how often are ecologists wrong and when does it matter? Ecological Monographs, 80, 267-286.
23. Foelix R (2010) Biology of Spiders, 3rd edn. Oxford University Press, NY, New York.
24. Fujita MK, Leache AD, Burbrink FT, McGuire JA, Moritz C (2012) Coalescent-based species delimitation in an integrative taxonomy. Trends in Ecology and Evolution, 27, 480-488.
25. Goldie X, Lanfear R, Bromham L (2011) Diversification and the rate of molecular evolution: no evidence of a link in mammals. Bmc Evolutionary Biology, 11, 286.
26. Haase P, Murray-Bligh J, Lohse S et al. (2006) Assessing the impact of errors in sorting and identifying macroinvertebrate samples. In: The Ecological Status of European Rivers: Evaluation and Intercalibration of Assessment Methods (eds Furse MT, Hering D, Brabec K, Buffagni A, Sandin L, Verdonschot PM). Developments in Hydrobiology 188, pp. 505-521. Springer, Dordrecht, the Netherlands.
27. Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN (2006) DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences, USA, 103, 968-971.
28. Hebert PDN, Barrett RDH (2005) Reply to the comment by L. Prendini on "Identifying spiders through DNA barcodes". Canadian Journal of Zoology-Revue Canadienne De Zoologie, 83, 505-506.
29. Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society B-Biological Sciences, 270, 313-321.
30. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004a) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences, USA, 101, 14812-14817.
31. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004b) Identification of birds through DNA barcodes. Plos Biology, 2, 1657-1663.
32. Hebert PDN, deWaard JR, Landry J-F (2010) DNA barcodes for 1/1000 of the animal kingdom. Biology Letters, 6, 359-362.
33. Hendrixson BE, DeRussy BM, Hamilton CA, Bond JE (2013) An exploration of species boundaries in turret-building tarantulas of the Mojave Desert (Araneae, Mygalomorphae, Theraphosidae, Aphonopelma). Molecular Phylogenetics and Evolution, 66, 327-340.
34. Hull JM, Fish AM, Keane JJ, Mori SR, Sacks BJ, Hull AC (2010) Estimation of species identification error: Implications for raptor migration counts and trend estimation. Journal of Wildlife Management, 74, 1326-1334.
35. Janecka J, Chowdhary B, Murphy W (2012) Exploring the correlations between sequence evolution rate and phenotypic divergence across the Mammalian tree provides insights into adaptive evolution. Journal of Biosciences, 37, 897-909.
36. Johnsen A, Rindal E, Ericson PGP et al. (2010) DNA barcoding of Scandinavian birds reveals divergent lineages in trans-Atlantic species. Journal of Ornithology, 151, 565-578.
37. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide-sequences. Journal of Molecular Evolution, 16, 111-120.
38. Knowles LL, Carstens BC (2007) Delimiting species without monophyletic gene trees. Systematic Biology, 56, 887-895.
39. Kuntner M, Agnarsson I (2011a) Biogeography and diversification of hermit spiders on Indian Ocean islands (Nephilidae: Nephilengys). Molecular Phylogenetics and Evolution, 59, 477-488.
40. Kuntner M, Agnarsson I (2011b) Phylogeography of a successful aerial disperser: the golden orb spider Nephila on Indian Ocean islands. Bmc Evolutionary Biology, 11, 119.
41. Links MG, Dumonceaux TJ, Hemmingsen SM, Hill JE (2012) The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data. PLoS ONE, 7, e49755.
42. Longhorn SJ, Nicholas M, Chuter J, Vogler AP (2007) The utility of molecular markers from non-lethal DNA samples of the cites II protected "tarantula" Brachypelma vagans (Araneae, Theraphosidae). Journal of Arachnology, 35, 278-292.
43. Masters BC, Fan V, Ross HA (2011) Species delimitation-a Geneious plugin for the exploration of species boundaries. Molecular Ecology Resources, 11, 154-157.
44. Meier R, Shiyang K, Vaidya G, Ng PKL (2006) DNA barcoding and taxonomy in diptera: a tale of high intraspecific variability and low identification success. Systematic Biology, 55, 715-728.
45. Meier R, Zhang G, Ali F (2008) The use of mean instead of smallest interspecific distances exaggerates the size of the "barcoding gap" and leads to misidentification. Systematic Biology, 57, 809-813.
46. Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. Plos Biology, 3, 1-10.
47. Negri M, Pileggi LG, Mantelatto FL (2012) Molecular barcode and morphological analyses reveal the taxonomic and biogeographical status of the striped-legged hermit crab species Clibanarius sclopetarius (Herbst, 1796) and Clibanarius vittatus (Bosc, 1802) (Decapoda: Diogenidae). Invertebrate Systematics, 26, 561-571.
48. Nekola JC, White PS (1999) The distance decay of similarity in biogeography and ecology. Journal of Biogeography, 26, 867-878.
49. Nijman V, Aliabadian M (2013) DNA barcoding as a tool for elucidating species delineation in wide-ranging species as Illustrated by owls (Tytonidae and Strigidae). Zoological Science, 30, 1005-1009.
50. Nuñez JJ, Vejar-Pardo A, Guzmán BE, Barriga EH, Gallardo CS (2012) Phylogenetic and mixed Yule-coalescent analyses reveal cryptic lineages within two South American marine snails of the genus Crepipatella (Gastropoda: Calyptraeidae). Invertebrate Biology, 131, 301-311.
51. Nwani CD, Becker S, Braid HE, Ude EF, Okogwu OI, Hanner R (2011) DNA barcoding discriminates freshwater fishes from southeastern Nigeria and provides river system-level phylogeographic resolution within some species. Mitochondrial DNA, 22, 43-51.
52. Oliver I, Beattie AJ (1996) Invertebrate morphospecies as surrogates for species: a case study. Conservation Biology, 10, 99-109.
53. O'Meara BC (2010) New heuristic methods for joint species delimitation and species tree inference. Systematic Biology, 59, 59-73.
54. Platnick NI (2014) The World Spider Catalog. American Museum of Natural History, NY, New York.
55. Prendini L (2005) Comment on "Identifying spiders through DNA barcodes". Canadian Journal of Zoology-Revue Canadienne De Zoologie, 83, 498-504.
56. Ratnasingham S, Hebert PDN (2007) bold: the barcode of life data system: barcoding. Molecular Ecology Notes, 7, 355-364.
57. Rodrigo A, Bertels F, Heled J, Noder R, Shearman H, Tsai P (2008) The perils of plenty: what are we going to do with all these genes? Philosophical Transactions of the Royal Society of London Series B: Biological Sciences, 363, 3893-3902.
58. Rosenberg NA (2007) Statistical tests for taxonomic distinctiveness from observations of monophyly. Evolution, 61, 317-323.
59. Scott WA, Hallam CJ (2002) Assessing species misidentification rates through quality assurance of vegetation monitoring. Plant Ecology, 165, 101-115.
60. Shea CP, Peterson JT, Wisniewski JM, Johnson NA (2011) Misidentification of freshwater mussel species (Bivalvia:Unionidae): contributing factors, management implications, and potential solutions. Journal of the North American Benthological Society, 30, 446-458.
61. Smith FA (2008) Body size, energetics and evolution. In: Encyclopedia of Ecology (eds Jørgensen SE, Fath BD), pp. 477-482. Elsevier, Oxford.
62. Srivathsan A, Meier R (2012) On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature. Cladistics, 28, 190-194.
63. Tamura K, Peterson D, Peterson N et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731-2739.
64. Tavares ES, Goncalves P, Miyaki CY, Baker AJ (2011) DNA barcode detects high genetic structure within neotropical bird species. PLoS ONE, 6, e28543.
65. Taylor HR, Harris WE (2012) An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Molecular Ecology Resources, 12, 377-388.
66. Van Der Bank H, Herbert D, Greenfield R, Yessoufou K (2013) Revisiting species delimitation within the genus Oxystele using DNA barcoding approach. Zookeys, 365, 337-354.
67. Vuataz L, Sartori M, Gattolliat JL, Monaghan MT (2012) Endemism and diversification in freshwater insects of Madagascar revealed by coalescent and phylogenetic analysis of museum and field collections. Molecular Phylogenetics and Evolution, 66, 979-991.
68. Webster BL, Emery AM, Webster JP et al. (2012) Genetic diversity within Schistosoma haematobium: DNA barcoding reveals two distinct groups. PLOS Neglected Tropical Diseases, 6, e1882.
69. Weitschek E, Velzen R, Felici G, Bertolazzi P (2013) blog 2.0: a software system for character-based species classification with DNA Barcode sequences. What it does, how to use it. Molecular Ecology Resources, 13, 1043-1046.
70. White BP, Pilgrim EM, Boykin LM, Stein ED, Mazor RD (2014) Comparison of four species-delimitation methods applied to a DNA barcode data set of insect larvae for use in routine bioassessment. Freshwater Science, 33, 338-348.
71. Wiemers M, Fiedler K (2007) Does the DNA barcoding gap exist? - A case study in blue butterflies (Lepidoptera: Lycaenidae). Frontiers in Zoology, 4, 8.
72. Wright S (1943) Isolation by distance. Genetics, 28, 114-138.
73. Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences, USA, 107, 9264-9269.
74. Yassin A, Markow TA, Narechania A, O'Grady PM, DeSalle R (2010) The genus Drosophila as a model for testing tree- and character-based methods of species identification using DNA barcoding. Molecular Phylogenetics and Evolution, 57, 509-517.
75. Zaldívar-Riverón A, Martínez JJ, Ceccarelli FS et al. (2010) DNA barcoding a highly diverse group of parasitoid wasps (Braconidae: Doryctinae) from a Mexican nature reserve. Mitochondrial DNA, 21, 18-23.
76. Zhang C, Zhang DX, Zhu T, Yang Z (2011) Evaluation of a Bayesian coalescent method of species delimitation. Systematic Biology, 60, 747-761.
77. Zuckerkandl E, Pauling L (1965) Molecules as documents of evolutionary history. Journal of Theoretical Biology, 8, 357-366.