Analytical approaches for DNA barcoding data – how to find a way for plants?

References

• Adams , K and Palmer , J . 2003 . Evolution of mitochondrial gene content: Gene loss and transfer to the nucleus . Mol Phylogenet Evol , 29 : 380 – 395 .
   PubMed Web of Science ®Google Scholar
• Altschul , S , Gish , W , Miller , W , Myers , E and Lipman , D . 1990 . Basic local alignment search tool . J Mol Biol , 215 : 403 – 410 .
   PubMed Web of Science ®Google Scholar
• Attar , F , Riahi , M , Daemi , F and Aghabeigi , F . 2011 . Preliminary molecular phylogeny of Eurasian Scrophularia (Scrophulariaceae), based on DNA sequence data from trnS-trnG and ITS . Plant Biosyst , 145 : 857 – 865 .
   Web of Science ®Google Scholar
• Austerlitz , F , David , O , Schaeffer , B , Bleakley , K , Olteanu , M Leblois , R . 2009 . DNA barcode analysis: A comparison of phylogenetic and statistical classification methods . BMC Bioinformatics , 10 : S10
   Web of Science ®Google Scholar
• Bergsten , J , Bilton , D , Fujisawa , T , Elliott , M , Monaghan , M Balke , M . 2012 . The effect of geographical scale of sampling on DNA barcoding . Syst Biol , 61: 851–869
   PubMed Web of Science ®Google Scholar
• Bertolazzi , P , Felici , G and Weitschek , E . 2009 . Learning to classify species with barcodes . BMC Bioinformatics , 10 : S7
   PubMed Web of Science ®Google Scholar
• Bidartondo , M . 2008 . Preserving accuracy in Genbank . Science , 319 : 1616
   PubMed Web of Science ®Google Scholar
• Brown , S DJ , Collins , R A , Boyer , S , Lefort , M C , Malumbres-Olarte , J Vink , C J . 2012 . Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding . Mol Ecol Resour , 12: 562–565
   Web of Science ®Google Scholar
• Bruni , I , De Mattia , F , Galimberti , A , Galasso , G , Banfi , E Casiraghi , M . 2010 . Identification of poisonous plants by DNA barcoding approach . Int J Legal Med , 124 : 595 – 603 .
   PubMed Web of Science ®Google Scholar
• Bruni , I , De Mattia , F , Martellos , S , Galimberti , A , Savadori , P Casiraghi , M . 2012 . DNA barcoding as an effective tool in improving a digital plant identification system: A case study for the area of Mt. Valerio, Trieste (NE Italy) . PLoS ONE , 7 ( 9 ) : e43256
   PubMed Web of Science ®Google Scholar
• Burgess , K , Fazekas , A J , Kesanakurti , P R , Graham , S W , Husband , B C Newmaster , S G . 2011 . Discriminating plant species in a local temperate flora using the rbcL+matK DNA barcode . Meth Ecol Evol , 2: 333–340
   Web of Science ®Google Scholar
• Casiraghi , M , Labra , M , Ferri , E , Galimberti , A and De Mattia , F . 2010 . DNA barcoding: A six-question tour to improve users' awareness about the method . Brief Bioinform , 11 : 440 – 453 .
   PubMed Web of Science ®Google Scholar
• Cennamo , P , Del Guacchio , E , Jury , S L and Caputo , P . 2011 . Molecular markers in Viola L. subsect. Viola: Application and taxonomic implications for the identification of dubious herbarium specimens . Plant Biosyst , 145 ( 2 ) : 306 – 323 .
   Web of Science ®Google Scholar
• Chase , M , Salamin , N , Wilkinson , M , Dunwell , J , Kesanakurthi , R Haidar , N . 2005 . Land plants and DNA barcodes: Short-term and long-term goals . Philos T R Soc B , 360 : 1889 – 1895 .
   PubMed Web of Science ®Google Scholar
• Cho , Y , Mower , J , Qiu , Y and Palmer , J . 2004 . Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants . PNAS , 101 : 17741 – 17746 .
   PubMed Web of Science ®Google Scholar
• Cho , Y , Qiu , Y , Kuhlman , P and Palmer , J . 1998 . Explosive invasion of plant mitochondria by a group I intron . PNAS , 95 : 14244 – 14249 .
   PubMed Web of Science ®Google Scholar
• Chu , K H , Li , C P and Qi , L . 2006 . Ribosomal RNA as molecular barcodes: A simple correlation analysis without sequence alignment . Bioinformatics , 22 : 1690 – 1701 .
   PubMed Web of Science ®Google Scholar
• Cowan , R S and Fay , M F . 2012 . Challenges in the DNA barcoding of plant material . Mol Biol , 862 : 23 – 33 .
   Google Scholar
• DasGupta , B , Konwar , K , Mandoiu , I and Shvartsman , A . 2005 . DNA-BAR: Distinguisher selection for DNA barcoding . Bioinformatics , 21 : 3424 – 3426 .
   PubMed Web of Science ®Google Scholar
• De Mattia , F , Gentili , R , Bruni , I , Galimberti , A , Sgorbati , S Casiraghi , M . 2012 . A multi-marker DNA barcoding approach to save time and resources in vegetation surveys . Bot J Linn Soc , 169 : 518 – 529 .
   Web of Science ®Google Scholar
• DeSalle , R . 2006 . Species discovery versus species identification in DNA barcoding efforts: Response to Rubinoff . Conserv Biol , 20 : 1545 – 1547 .
   PubMed Web of Science ®Google Scholar
• DeSalle , R , Egan , M and Siddall , M . 2005 . The unholy trinity: Taxonomy, species delimitation and DNA barcoding . Philos T R Soc B , 360 : 1905 – 1916 .
   PubMed Web of Science ®Google Scholar
• Edgar , R . 2004a . MUSCLE: A multiple sequence alignment method with reduced time and space complexity . BMC Bioinformat , 5 : 113
   PubMed Web of Science ®Google Scholar
• Edgar , R . 2004b . MUSCLE: Multiple sequence alignment with high accuracy and high throughput . Nucleic Acid Res , 32 : 1792 – 1797 .
   PubMed Web of Science ®Google Scholar
• Edwards , A and Cavalli-Sforza , L . 1963 . The reconstruction of evolution . Ann Hum Genet , 27 : 105 – 106 .
   Web of Science ®Google Scholar
• Elias , M , Hill , R , Willmott , K , Dasmahapatra , K , Brower , A Mallet , J . 2007 . Limited performance of DNA barcoding in a diverse community of tropical butterflies . P Roy Soc B-Biol Sci , 274 : 2881 – 2889 .
   PubMed Web of Science ®Google Scholar
• Fazekas , A , Burgess , K , Kesanakurti , P , Graham , S , Newmaster , S Husband , B . 2008 . Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well . PLoS One , 3 : e2802
   PubMed Web of Science ®Google Scholar
• Felici , G and Truemper , K . 2002 . A MINISAT approach for learning in logic domains . INFORMS J Comput , 14 : 20 – 36 .
   Web of Science ®Google Scholar
• Felsenstein , J . 1993 . {PHYLIP}: Phylogenetic inference package, version 3.5c
   Google Scholar
• Ferguson , J . 2002 . On the use of genetic divergence for identifying species . Biol J Linn Soc , 75 : 509 – 516 .
   Web of Science ®Google Scholar
• Ferri , G , Al[ugrave] , M , Corradini , B and Beduschi , G . 2009 . Forensic botany: Species identification of botanical trace evidence using a multigene barcoding approach . Int J Legal Med , 123 : 395 – 401 .
   PubMed Web of Science ®Google Scholar
• Ghazoul , J . 2005 . Pollen and seed dispersal among dispersed plants . Biol Rev , 80 : 413 – 443 .
   PubMed Web of Science ®Google Scholar
• Goloboff , P , Farris , J and Nixon , K . 2008 . TNT, a free program for phylogenetic analysis . Cladistics , 24 : 774 – 786 .
   Web of Science ®Google Scholar
• Hall , J , Fucikova , K , Lo , C , Lewis , L and Karol , K . 2010 . An assessment of proposed DNA barcodes in freshwater green algae. Cryptogamie . Algologie , 31 : 529 – 555 .
   Web of Science ®Google Scholar
• Hebert , P , Cywinska , A , Ball , S and deWaard , J R . 2003 . Biological identifications through DNA barcodes . P Roy Soc B-Biol Sci , 270 : 313 – 321 .
   PubMed Web of Science ®Google Scholar
• Hollingsworth , M , Clark , A , Forrest , L , Richardson , J , Pennington , R Long , D . 2009 . Selecting barcoding loci for plants: Evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants . Mol Ecol Resour , 9 : 439 – 457 .
   PubMed Web of Science ®Google Scholar
• Hollingsworth , P , Graham , S and Little , D . 2011 . Choosing and using a plant DNA barcode . PloS one , 6 : e19254
   PubMed Web of Science ®Google Scholar
• Howe , K , Bateman , A and Durbin , R . 2002 . Quicktree: Building huge neighbour-joining trees of protein sequences . Bioinformatics , 18 : 1546 – 1547 .
   PubMed Web of Science ®Google Scholar
• Huelsenbeck , J and Ronquist , F . 2001 . Mrbayes: Bayesian inference of phylogenetic trees . Bioinformatics , 17 : 754 – 755 .
   PubMed Web of Science ®Google Scholar
• Janzen , D . 2009 . A DNA barcode for land plants . PNAS , 106 : 12794 – 12797 .
   PubMed Web of Science ®Google Scholar
• Jones , M , Ghoorah , A and Blaxter , M . 2011 . jMOTU and Taxonerator: Turning DNA barcode sequences into annotated operational taxonomic units . PLoS One , 6 : e19259
   PubMed Web of Science ®Google Scholar
• Katoh , K , Kuma , K , Toh , H and Miyata , T . 2005 . MAFFT version 5: Improvement in accuracy of multiple sequence alignment . Nucleic Acids Res , 33 : 511 – 518 .
   PubMed Web of Science ®Google Scholar
• Katoh , K , Misawa , K , Kuma , K and Miyata , T . 2002 . MAFFT: A novel method for rapid multiple sequence alignment based on fast fourier transform . Nucleic Acids Res , 30 : 3059 – 3066 .
   PubMed Web of Science ®Google Scholar
• Kress , W , Wurdack , K , Zimmer , E , Weigt , L and Janzen , D . 2005 . Use of DNA barcodes to identify flowering plants . PNAS , 102 : 8369
   PubMed Web of Science ®Google Scholar
• Li , D Z , Gao , L M , Li , H T , Wang , H , Ge , X J Liu , J Q . 2011 . Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants . PNAS , 108 : 19641 – 19646 .
   PubMed Web of Science ®Google Scholar
• Little , D and Stevenson , D . 2007 . A comparison of algorithms for the identification of specimens using DNA barcodes: Examples from gymnosperms . Cladistics , 23 : 1 – 21 .
   PubMed Web of Science ®Google Scholar
• Little , D . 2011 . DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability . PloS one , 6 : e20552
   PubMed Web of Science ®Google Scholar
• Meier , R , Shiyang , K , Vaidya , G and Ng , P . 2006 . DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success . Syst Biol , 55 : 715 – 728 .
   PubMed Web of Science ®Google Scholar
• Meier , R , Zhang , G and Ali , F . 2008 . The use of mean instead of smallest inter-specific distances exaggerates the size of the “barcoding gap” and leads to misidentification . Syst Biol , 57 : 809 – 813 .
   PubMed Web of Science ®Google Scholar
• Meyer , C and Paulay , G . 2005 . DNA barcoding: Error rates based on comprehensive sampling . PLoS Biol , 3 : e422
   PubMed Web of Science ®Google Scholar
• Moritz , C and Cicero , C . 2004 . DNA barcoding: Promise and pitfalls . PLoS Biol , 2 : e354
   PubMed Web of Science ®Google Scholar
• Munch , K , Boomsma , W , Huelsenbeck , J , Willerslev , E and Nielsen , R . 2008a . Statistical assignment of DNA sequences using bayesian phylogenetics . Syst Biol , 57 : 750 – 757 .
   PubMed Web of Science ®Google Scholar
• Munch , K , Boomsma , W , Willerslev , E and Nielsen , R . 2008b . Fast phylogenetic DNA barcoding . Philos T R Soc B , 363 : 3997 – 4002 .
   PubMed Web of Science ®Google Scholar
• Naciri , Y , Caetano , S and Salamin , N . 2012 . Plant DNA barcodes and the influence of gene flow . Mol Ecol Resour , 12: 575–580
   PubMed Web of Science ®Google Scholar
• Needleman , S and Wunsch , C . 1970 . A general method applicable to the search for similarities in the amino acid sequence of two proteins . J Mol Biol , 48 : 443 – 453 .
   PubMed Web of Science ®Google Scholar
• Newmaster , S , Fazekas , A and Ragupathy , S . 2006 . DNA barcoding in land plants: Evaluation of rbcl in a multigene tiered approach . Botany , 84 : 335 – 341 .
   Web of Science ®Google Scholar
• Noé , L and Kucherov , G . 2004 . Improved hit criteria for DNA local alignment . BMC Bioinformat , 5 : 149 – 157 .
   PubMed Web of Science ®Google Scholar
• Notredame , C , Higgins , D and Heringa , J . 2000 . T-coffee: A novel method for fast and accurate multiple sequence alignment . J Mol Biol , 302 : 205 – 218 .
   PubMed Web of Science ®Google Scholar
• Paradis , E , Claude , J and Strimmer , K . 2004 . APE: Analyses of phylogenetics and evolution in R language . Bioinformatics , 20 : 289 – 290 .
   PubMed Web of Science ®Google Scholar
• Petit , R , Duminil , J , Fineschi , S , Hampe , A , Salvini , D and Vendramin , G . 2005 . Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations . Mol Ecol , 14 : 689 – 701 .
   PubMed Web of Science ®Google Scholar
• Petit , R and Excofier , L . 2009 . Gene flow and species delimitation . Trends Ecol Evol , 24 : 386 – 393 .
   PubMed Web of Science ®Google Scholar
• Puillandre , N , Strong , E E , Bouchet , P , Boisselier , M C , Couloux , A and Samadi , S . 2009 . Identifying gastropod spawn from DNA barcodes: Possible but not yet practicable . Mol Ecol Resour , 9 : 1311 – 1321 .
   PubMed Web of Science ®Google Scholar
• Rach , J , DeSalle , R , Sarkar , I , Schierwater , B and Hadrys , H . 2008 . Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata . P Roy Soc B-Biol Sc , 275 : 237 – 247 .
   PubMed Web of Science ®Google Scholar
• Raimondo , F M and Spadaro , V . 2008 . A new species of Centaurea (Asteraceae) from Sicily . Bot J Linn Soc , 157 ( 4 ) : 785 – 788 .
   Web of Science ®Google Scholar
• Ratnasingham , S and Hebert , P . 2007 . Bold: The barcode of life data system (http://www.barcodinglife.org) . Mol Ecol Notes , 7 : 355 – 364 .
   PubMed Web of Science ®Google Scholar
• Reid , B , Le , M , McCord , W , Iverson , J , Georges , A Bergmann , T . 2011 . Comparing and combining distance-based and character-based approaches for barcoding turtles . Mol Ecol Resour , 11 : 956 – 967 .
   PubMed Web of Science ®Google Scholar
• Rosenberg , N . 2003 . The shapes of neutral gene genealogies in two species: Probabilities of monophyly, paraphyly, and polyphyly in a coalescent model . Evolution , 57 : 1465 – 1477 .
   PubMed Web of Science ®Google Scholar
• Ross , H , Murugan , S and Li , W . 2008 . Testing the reliability of genetic methods of species identification via simulation . Syst Biol , 57 : 216 – 230 .
   PubMed Web of Science ®Google Scholar
• Rubinoff , D , Cameron , S and Will , K . 2006 . Are plant DNA barcodes a search for the Holy Grail . Trends Ecol Evol , 21 : 1 – 2 .
   PubMed Web of Science ®Google Scholar
• Saitou , N and Nei , M . 1987 . The neighbor-joining method: A new method for reconstructing phylogenetic trees . Mol Biol Evol , 4 : 406 – 425 .
   PubMed Web of Science ®Google Scholar
• Sarkar , I , Planet , P and DeSalle , R . 2008 . CAOS software for use in character-based DNA barcoding . Mol Ecol Resour , 8 : 1256 – 1259 .
   PubMed Web of Science ®Google Scholar
• Sarkar , I , Thornton , J , Planet , P , Figurski , D , Schierwater , B and DeSalle , R . 2002 . An automated phylogenetic key for classifying homeoboxes . Mol Phylogenet Evol , 24 : 388 – 399 .
   PubMed Web of Science ®Google Scholar
• Singer , G and Hajibabaei , M . 2009 . ibarcode.org: Web-based molecular biodiversity analysis . BMC Bioinformatics , 10 : S14
   PubMed Web of Science ®Google Scholar
• Smith , T , Waterman , M and Fitch , W . 1981 . Comparative biosequence metrics . J Mol Evol , 18 : 38 – 46 .
   PubMed Web of Science ®Google Scholar
• Stamatakis , A , Aberer , A J , Goll , C , Smith , S A , Berger , S A and Izquierdo-Carrasco , F . 2012 . RAxML-Light: A Tool for computing TeraByte phylogenies . Bioinformatics , 28: 2064--2066
   Web of Science ®Google Scholar
• Swofford , D L . 2003 . PAUP*: Phylogenetic analysis using parsimony, version 4.0b10
   Google Scholar
• Tamura , K , Peterson , D , Peterson , N , Stecher , G , Nei , M and Kumar , S . 2011 . MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods . Mol Biol Evol , 28 : 2731 – 2739 .
   PubMed Web of Science ®Google Scholar
• Taylor , H R and Harris , W E . 2012 . An emergent science on the brink of irrelevance: A review of the past 8 years of DNA barcoding . Mol Ecol Resour , 12: 377–388
   Web of Science ®Google Scholar
• Thompson , J , Higgins , D and Gibson , T . 1994 . CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice . Nucleic Acids Res , 22 : 4673 – 4680 .
   PubMed Web of Science ®Google Scholar
• van Velzen , R , Weitschek , E , Felici , G and Bakker , F . 2012 . DNA barcoding of recently diverged species: Relative performance of matching methods . PloS one , 7 : e30490.
   PubMed Web of Science ®Google Scholar
• Wheeler , T . 2009 . Large-scale neighbor-joining with NINJA . Lect N Bioinformatics , 5724 : 375 – 389 .
   Google Scholar
• Will , K and Rubinoff , D . 2004 . Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification . Cladistics , 20 : 47 – 55 .
   PubMed Web of Science ®Google Scholar
• Zhang , A , He , L , Crozier , R , Muster , C and Zhu , C . 2010 . Estimating sample sizes for DNA barcoding . Mol Phylogenet Evol , 54 : 1035 – 1039 .
   PubMed Web of Science ®Google Scholar
• Zou , S , Li , Q , Kong , L , Yu , H and 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
   PubMed Web of Science ®Google Scholar