Bioinformatic challenges for DNA metabarcoding of plants and animals

Molecular Ecology

Volumn 21, Issue 8, 2012, Pages 1834-1847

  Coissac, Eric ^a   Riaz, Tiayyba ^a   Puillandre, Nicolas ^b,c  

^a UNIVERSITÉ JOSEPH FOURIER   (France)

^b ATHERIS LABORATORIES   (Switzerland)

^c MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

Author keywords

bioinformatics; data analysis; DNA metabarcoding; primer design

Indexed keywords

DNA; PLANT DNA; PRIMER DNA;

ANIMAL; BIODIVERSITY; BIOLOGY; DNA BARCODING; GENETICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; PLANT; REVIEW; SPECIES DIFFERENCE;

ANIMALS; BASE SEQUENCE; BIODIVERSITY; COMPUTATIONAL BIOLOGY; DNA; DNA BARCODING, TAXONOMIC; DNA PRIMERS; DNA, PLANT; PLANTS; SPECIES SPECIFICITY;

ANIMALIA;

EID: 84859574767     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05550.x     Document Type: Review

References (137)

1. Abarenkov K, Henrik Nilsson R, Larsson KH, et al. (2010) The unite database for molecular identification of fungi-recent updates and future perspectives. New Phytologist, 186, 281-285.
2. Abdo Z, Golding BG, (2007) A step toward barcoding life: a model-based, decision-theoretic method to assign genes to preexisting species groups. Systematic Biology, 56, 44-56.
3. Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz MF, (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Applied and Environmental Microbiology, 71, 8966-8969.
4. Agogue H, Lamy D, Neal PR, Sogin ML, Herndl GJ, (2011) Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing. Molecular Ecology, 20, 258-274.
5. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. Journal of Molecular Biology, 215, 403-410.
6. Andersen K, Bird KL, Rasmussen M, et al. (2012) Meta-barcoding of 'dirt' DNA from soil reflects vertebrate biodiversity. Molecular Ecology, 21, 1966-1979.
7. Anderson MP, (2009) Bayesian classification of DNA barcodes. PhD thesis, Kansas State University, Manhattan, Kansas.
8. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ, (2005) At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Applied and Environmental Microbiology, 71, 7724-7736.
9. Austerlitz F, David O, Schaeffer B, et al. (2009) DNA barcode analysis: a comparison of phylogenetic and statistical classification methods. BMC Bioinformatics, 10, S10.
10. Bai Z, Kremer SC, (2011) Deep belief network: a step towards better DNA barcoding classification. Proceedings of the 6th Canadian Student Conference on Biomedical Computing and Engineering, 9, 94.
11. Bekaert M, Teeling EC, (2008) UniPrime: a workflow-based platform for improved universal primer design. Nucleic Acids Research, 36, e56.
12. Bellemain E, Carlsen T, Brochmann C, et al. (2010) ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiology, 10, 189.
13. Berger SA, Krompass D, Stamatakis A, (2011) Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Systematic Biology, 60, 291-302.
14. Bergmann T, Hadrys H, Breves G, Schierwater B, (2009) Character-based DNA barcoding: a superior tool for species classification. Berliner und Münchener Tierärztliche Wochenschrift, 122, 446-450.
15. Bertolazzi P, Felici G, Weitschek E, (2009) Learning to classify species with barcodes. BMC Bioinformatics, 10, S7.
16. Bienert R, de Danieli S, Miquel C, et al. (2012) Tracking earthworm communities from soil DNA. Molecular Ecology, 21, 2017-2030.
17. Binladen J, Gilbert M, Thomas P, et al. (2007) The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One, 2, e197.
18. Birky JCW, Adams J, Gemmel M, Perry J, (2010) Using population genetic theory and DNA sequences for species detection and identification in asexual organisms. PLoS One, 5, e10609.
19. Blaxter M, Mann J, Chapman T, et al. (2005) Defining operational taxonomy units using DNA barcode data. Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 1935-1943.
20. Bonferroni CE, (1935) Il calcolo delle assicurazioni sui gruppi di teste. In: Studi in Onore del Professore Salvatore Ortu Carboni (ed, Carboni SO,), pp. 13-60. Tipografia del Senato, Rome.
21. Bouveyron C, Girard S, Olteanu M, (2009) Supervised classification of categorical data with uncertain labels for DNA barcoding. 17th European Symposium on Artificial Neural Networks, (ESANN 2009), 29-34.
22. Brinkman BM, Hildebrand F, Kubica M, et al. (2011) Caspase deficiency alters the murine gut microbiome. Cell Death and Disease, 2, e220.
23. Caporaso JG, Kuczynski J, Stombaugh J, et al. (2010) Qiime allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335-336.
24. Carstens BC, Dewey TA, (2010) Species delimitation using a combined coalescent and information-theoretic approach: an example from North American Myotis bats. Systematic Biology, 59, 400-414.
25. Carstens BC, Knowles LL, (2007) Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Systematic Biology, 56, 400-411.
26. CBOL Plant Working Group (2009) A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America, 106, 12794-12797.
27. Chu KH, Xu M, Li CP, (2009) Rapid DNA barcoding analysis of large datasets using the composition vector method. BMC Bioinformatics, 10, S8.
28. Coissac E, (2012) OligoTag a program for designing set of tags for next generation sequencing of multiplexed samples. In: Data Production and Analysis in Population Genomics (eds, Bonin A, and, Pompanon F,). Methods in Molecular Biology Series, Humana Press, New York.
29. Cole JR, Wang Q, Cardenas E, et al. (2009) The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Research, 37, D141-D145.
30. DasGupta B, Konwar M, Mandoiu II, Shvartsman AA, (2005) DNA-BAR: distinguisher selection for DNA barcoding. Bioinformatics, 21, 3424-3426.
31. DeSalle R, (2006) Species discovery versus species identification in DNA Barcoding efforts: response to Rubinoff. Conservation Biology, 20, 1545-1547.
32. DeSalle R, Egan MG, Sidall M, (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 1905-1916.
33. Duitama J, Kumar DM, Hemphill E, et al. (2009) PrimerHunter: a primer design tool for PCR-based virus subtype identification. Nucleic Acids Research, 37, 2483-2492.
34. Edgar RC, (2004) Muscle: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
35. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R, (2011) Uchime improves sensitivity and speed of chimera detection. Bioinformatics, 27, 2194-2200.
36. Ence DD, Carstens BC, (2011) SpedeSTEM: a rapid and accurate method for species delimitation. Molecular Ecology Resources, 11, 473-480.
37. Epp L, Boessenkool S, Bellemain E, et al. (2012) New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Molecular Ecology, 21, 1821-1833.
38. Ficetola GF, Coissac E, Zundel S, et al. (2010) An in silico approach for the evaluation of DNA barcodes. BMC Genomics, 11, 434.
39. Flores GE, Bates ST, Knights D, et al. (2011) Microbial biogeography of public restroom surfaces. PLoS One, 6, e28132.
40. Frank DN, (2009) BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinformatics, 10, 362.
41. Frezal L, Leblois R, (2008) Four years of DNA barcoding: current advances and prospects. Infection, Genetics and Evolution, 8, 727-736.
42. Gadberry MD, Malcomber ST, Doust AN, Kellogg EA, (2005) Primaclade-a flexible tool to find conserved PCR primers across multiple species. Bioinformatics, 21, 1263-1264.
43. Gilbert JA, Field D, Swift P, et al. (2009) The seasonal structure of microbial communities in the Western English Channel. Environmental Microbiolgy, 11, 3132-3139.
44. Goldstein PZ, Desalle R, (2003) Calibrating phylogenetic species formation in a threatened insect using DNA from historical specimens. Molecular Ecology, 12, 1993-1998.
45. Goldstein PZ, DeSalle R, (2011) Integrating DNA barcode data and taxonomic practice: determination, discovery, and description. BioEssays, 33, 135-147.
46. Haas BJ, Gevers D, Earl AM, et al. (2011) Chimeric 16S rRNA sequence formation and detection in sanger and 454-pyrosequenced PCR amplicons. Genome Research, 21, 494-504.
47. Hajibabaei M, Singer GAC, (2009) Googling DNA sequences on the World Wide Web. BMC Bioinformatics, 10, S4.
48. Hajibabaei M, Smith AM, Janzen DH, et al. (2006) A minimalist barcode can identify a specimen whose DNA is degraded. Molecular Ecology Notes, 6, 959-964.
49. Hajibabaei M, Shokralla S, Zhou X, Singer GAC, Baird DJ, (2011) Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One, 6, e17497.
50. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R, (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nature Methods, 5, 235-237.
51. Hausdorf B, Hennig C, (2010) Species delimitation using dominant and codominant multilocus markers. Systematic Biology, 59, 491-503.
52. Hebert PDN, Cywinska A, Ball SL, deWaard JR, (2003a) Biological identifications through DNA barcodes. Proceedings. Biological Sciences, 270, 313-321.
53. Hebert PDN, Ratnasingham S, deWaard JR, (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings. Biological Sciences, 270, 96-99.
54. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM, (2004) Identification of birds through DNA barcodes. PLoS Biology, 2, 1657-1663.
55. Hoffmann C, Minkah N, Leipzig J, et al. (2007) DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Research, 35, e91.
56. Huber T, Faulkner G, Hugenholtz P, (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics, 20, 2317-2319.
57. Huse SM, Welch DMM, Morrison HG, Sogin ML, (2010) Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environmental microbiology, 12, 1889-1898.
58. Jabado OJ, Palacios G, Kapoor V, et al. (2006) Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments. Nucleic Acids Research, 34, 6605-6611.
59. Jarman SN, (2004) Amplicon: software for designing PCR primers on aligned DNA sequences. Bioinformatics, 20, 1644-1645.
60. Jones M, Ghoorah A, Blaxter M, (2011) jMOTU and Taxonerator: turning DNA barcode sequences into annotated operational taxonomic units. PLoS One, 6, e19259.
61. Kim N, Lee C, (2007) QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments. Bioinformatics, 23, 2331-2333.
62. Knowles LL, (2009) Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. Systematic Biology, 58, 463-467.
63. Knowles LL, Carstens BC, (2007) Delimiting species without monophyletic gene trees. Systematic Biology, 56, 887-895.
64. Kobayashi N, Tamura K, Aotsuka T, (1999) PCR error and molecular population genetics. Biochemical Genetics, 37, 317-321.
65. Komatsoulis GA, Waterman MS, (1997) A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations. Applied and Environmental Microbiology, 63, 2338-2346.
66. Koressaar T, Remm M, (2007) Enhancements and modifications of primer design program primer3. Bioinformatics, 23, 1289-1291.
67. Kostka JE, Prakash O, Overholt WA, et al. (2011) Hydrocarbon-degrading bacteria and the bacterial community response in gulf of mexico beach sands impacted by the deepwater horizon oil spill. Applied and Environmental Microbiology, 77, 7962-7974.
68. Kristina MS, Robert BP, Michael D, (2006) Sorenson single base errors in PCR products from avian museum specimens and their effect on estimates of historical genetic diversity. Conservation Genetics, 8, 879-884.
69. Kubatko LS, Carstens BC, Knowles LL, (2009) STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics, 25, 971-973.
70. Kuksa P, Pavlovic V, (2009) Efficient alignment-free DNA barcode analytics. BMC Bioinformatics, 10, S9.
71. Kunin V, Hugenholtz P, (2010) Pyrotagger: a fast, accurate pipeline for analysis of rRNA amplicon pyrosequence data. The Open Journal, 1, 1.
72. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P, (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environmental Microbiology, 12, 118-123.
73. Lahaye R, van der Bank M, Bogarin D, et al. (2008) DNA barcoding the floras of biodiversity hotspots. Proceedings of the National Academy of Sciences of the United States of America, 105, 2923-2928.
74. Leaché AD, Fujita MK, (2010) Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proceedings of the Royal Society B: Biological Sciences, 277, 3071-3077.
75. Little DP, (2011) DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability. PLoS One, 6, e20552.
76. Little DP, Stevenson DW, (2007) A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms. Cladistics, 23, 1-21.
77. Lou M, Golding BG, (2010) Assigning sequences to species in the absence of large interspecific differences. Molecular Phylogenetics and Evolution, 56, 187-194.
78. Luo A, Zhang A, Ho SY, et al. (2011) Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals. BMC Genomics, 12, 84.
79. Margulies M, Egholm M, Altman WE, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
80. Matsen FA, Kodner RB, Armbrust EV, (2010) Pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics, 11, 538.
81. 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.
82. Meusnier I, Singer GAC, Landry JF, et al. (2008) A universal DNA mini-barcode for biodiversity analysis. BMC Genomics, 9, 214.
83. Monaghan MT, Wild R, Elliot M, et al. (2009) Accelerated species inventory on Madagascar using coalescent-based models of species delineation. Systematic Biology, 58, 298-311.
84. Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R, (2008) Statistical assignment of DNA sequences using Bayesian phylogenetics. Systematic Biology, 57, 750-757.
85. Murray DC, Bunce M, Cannell BL, et al. (2011) DNA-based faecal dietary analysis: a comparison of qPCR and high throughput sequencing approaches. PLoS One, 6, e25776.
86. Needleman SB, Wunsch CD, (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48, 443-453.
87. Nielsen R, Matz M, (2006) Statistical approaches for DNA barcoding. Systematic Biology, 55, 162-169.
88. Nijman V, Aliabadian M, (2010) Performance of distance-based DNA barcoding in the molecular identification of primates. Comptes Rendus Biologies, 333, 11-16.
89. Notredame C, Higgins DG, Heringa J, (2000) T-coffee: a novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology, 302, 205-217.
90. O'Meara BC, (2010) New heuristic methods for joint species delimitation and species tree inference. Systematic Biology, 59, 59-73.
91. Padial JM, Miralles A, De la Riva I, Vences M, (2010) The integrative future of taxonomy. Frontiers in Zoology, 7, 16.
92. Parameswaran P, Jalili R, Tao L, et al. (2007) A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Research, 35, e130.
93. Pegard A, Miquel C, Valentini A, et al. (2009) Universal DNA-based methods for assessing the diet of grazing livestock and wildlife from feces. Journal of Agricultural and Food Chemistry, 57, 5700-5706.
94. Pettengill JB, Neel MC, (2010) An evaluation of candidate plant DNA barcodes and assigment methods in diagnosing 29 species in the gens Agalinis (Orobanchaceae). American Journal of Botany, 97, 1391-1406.
95. Pommier T, Neal PR, Gasol JM, et al. (2010) Spatial patterns of bacterial richness and evenness in the NW Mediterranean Sea explored by pyrosequencing of the 16S rRNA. Aquatic Microbial Ecology, 61, 212-224.
96. Pompanon F, Deagle BE, Symondson WOC, et al. (2012) Who is eating what: diet assessment using next generation sequencing. Molecular Ecology, 21, 1931-1950.
97. Pons J, Barraclough TG, Gomez-Zurita J, et al. (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology, 55, 595-609.
98. Pruesse E, Quast C, Knittel K, et al. (2007) Silva: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research, 35, 7188-7196.
99. Puillandre N, Lambert A, Brouillet S, Achaz G, (2012) ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology, 21, 1864-1877.
100. Quince C, Lanzén A, Curtis TP, et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods, 6, 639-641.
101. Quince C, Lanzen A, Davenport R, Turnbaugh P, (2011) Removing noise from pyrosequenced amplicons. BMC Bioinformatics, 12, 38.
102. R Development Core Team (2008) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna. ISBN 3-900051-07-0. Available from.
103. Rach J, DeSalle R, Sarkar IN, Schierwater B, Hadrys H, (2008) Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Proceedings of the Royal Society B: Biological Sciences, 275, 237-247.
104. Ratnasingham S, Hebert PDN, (2007) BOLD: the barcode of life data system (). Molecular Ecology Notes, 7, 355-364.
105. Reeder J, Knight R, (2010) Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution. Nature Methods, 7, 668-669.
106. Riaz T, Shehzad W, Viari A, et al. (2011) ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Research, 39, e145.
107. Rice P, Longden I, Bleasby A, (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends in Genetics, 16, 276-277.
108. Ross HA, Murugan S, Li WLS, (2008) Testing the reliability of genetic methods of species identification via simulation. Systematic Biology, 57, 216-230.
109. Ross KG, Gotzek D, Ascunce MS, Shoemaker DD, (2010) Species delimitation: a case study in a problematic ant taxon. Systematic Biology, 59, 162-184.
110. Rozen S, Skaletsky H, (2000) Primer3 on the www for general users and for biologist programmers. Methods in Molecular Biology, 132, 365-386.
111. Sakalidis ML, St. J. Hardy GE, Burgess TI, (2011) Use of the Genealogical Sorting Index (GSI) to delineate species boundaries in the Neofusicoccum parvum-Neofusicoccum ribis species complex. Molecular Phylogenetics and Evolution, 60, 333-334.
112. Schmieder R, Edwards R, (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics, 27, 863-864.
113. Shehzad W, McCarthy TM, Pompanon F, et al. (2012) Prey preference of snow leopard (Panthera uncia) in South Gobi, Mongolia. PLoS One, 7, e32104.
114. Sirovich L, Stoeckle M, Zhang Y, (2009) A scalable method for analysis and display of DNA sequences. PLoS One, 4, e7051.
115. Sirovich L, Stoeckle M, Zhang Y, (2010) Structural analysis of biodiversity. PLoS One, 5, e9266.
116. Sites JW, Marshall JC, (2003) Delimiting species: a renaissance issue in systematic biology. Trends in Ecology and Evolution, 19, 462-470.
117. Sogin ML, Morrison HG, Huber JA, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences of the United States of America, 103, 12115-12120.
118. Soininen EM, Valentini A, Coissac E, et al. (2009) Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Frontiers in Zoology, 6, 16.
119. Sønstebø JH, Gielly L, Brysting AK, et al. (2010) Using next-generation sequencing for molecular reconstruction of past arctic vegetation and climate. Molecular Ecology Resources, 10, 1009-1018.
120. Steinke D, Vences M, Salzburger W, Meyer A, (2005) TaxI: a software tool for DNA barcoding using distance methods. Proceedings of the Royal Society B: Biological Sciences, 360, 1975-1980.
121. Steinley D, Brusco MJ, (2007) Initializing K-means batch clustering: a critical evaluation of several techniques. Journal of Classification, 24, 99-121.
122. Stoeck T, Bass D, Nebel M, et al. (2010) Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular Ecology, 19, 21-31.
123. Taberlet P, Coissac E, Pompanon F, et al. (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research, 35, e14.
124. Taberlet P, Prud'Homme S, Campione E, et al. (2012a) Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies. Molecular Ecology, 21, 1816-1820.
125. Taberlet P, Coissac E, Pompanon F, et al. (2012b) Towards next-generation biodiversity assessment using DNA metabarcoding. Molecular Ecology, 21, 2045-2050.
126. Thompson JD, Higgins DG, Gibson TJ, (1994) ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673-4680.
127. Valentini A, Miquel C, Ali Nawaz M, et al. (2009a) New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach. Molecular Ecology Resources, 9, 51-60.
128. Valentini A, Pompanon F, Taberlet P, (2009b) DNA barcoding for ecologists. Trends in Ecology and Evolution, 24, 110-117.
129. Vences M, Thomas M, van der Meijden A, Chiari Y, Vieites DR, (2005) Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Frontiers in Zoology, 2, 5.
130. Wandeler P, Hoeck PEA, Keller LF, (2007) Back to the future: museum specimens in population genetics. Trends in Ecology and Evolution, 22, 634-642.
131. Willerslev E, Hansen AJ, Binladen J, et al. (2003) Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science, 300, 791-795.
132. Willerslev E, Cappellini E, Boomsma W, et al. (2007) Ancient biomolecules from deep ice cores reveal a forested Southern Greenland. Science, 317, 111-114.
133. Yeates D, Seago A, Nelson L, et al. (2010) Integrative taxonomy, or iterative taxonomy? Systematic Entomology, 36, 209-217.
134. Zhang AB, Sikes DS, Muster C, Li SQ, (2008) Inferring species membership using DNA sequences with back-propagation neural networks. Systematic Biology, 57, 202-215.
135. Zhang AB, Muster C, Liang HB, et al. (2011) A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding. Molecular Ecology, 21, 1848-1863.
136. Zinger L, Coissac E, Choler P, Geremia RA, (2009) Assessment of microbial communities by graph partitioning in a study of soil fungi in two Alpine meadows. Applied and Environmental Microbiology, 75, 5863-5870.
137. Zinger L, Gobet A, Pmmier T, (2012) Two decades of describing aquatic microbial diversity. Molecular Ecology, 21, 1878-1896.