Are nuclear loci ideal for barcoding plants? A case study of genetic delimitation of two sister species using multiple loci and multiple intraspecific individuals

Journal of Systematics and Evolution

Volumn 49, Issue 3, 2011, Pages 182-188

  Wang, Qian ^a   Yu, Qiu Shi ^a,b   Liu, Jian Quan ^a  

^a LANZHOU UNIVERSITY   (China)

^b Gansu Desert Control Research Institute   (China)

Author keywords

Chloroplast DNA; DNA barcoding; Internal transcribed spacer (ITS); Low copy nuclear loci; Pugionium

Indexed keywords

BRASSICACEAE;

EID: 84860389904     PISSN: 16744918     EISSN: 17596831     Source Type: Journal    
DOI: 10.1111/j.1759-6831.2011.00135.x     Document Type: Article

References (44)

1. Alvarez I, Wendle JF. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434. (Pubitemid 37491888)
2. Caicedo AL, Schaal BA, Kunkel BN. 1999. Diversity and molecular evolution of the RPS2 resistance gene in Arabidopsis thaliana. Proceedings of the National Academy of Sciences USA 96: 302-306. (Pubitemid 29036094)
3. CBOL Plant Working Group. 2009. A DNA barcode for land plants. Proceedings of the National Academy of Sciences USA 106: 12794-12797.
4. Chase MW, Salamin N, Winkinson M, Dunwell JM, Kesanakurthi RP, Haidar N, Savolainen V. 2005. Land plants and DNA barcodes: short-term and long-term goals. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1889-1895. (Pubitemid 44365049)
5. Chen S, Yao H, Han J, Liu C, Song J, Shi L, Zhu Y, Ma X, Gao T, Pang X, Luo K, Li Y, Li X, Jia X, Lin Y, Leon C. 2010. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PloS one 5: e8613.
6. Dasmahapatra KK, Mallet J. 2006. DNA barcodes: recent successes and future prospects. Heredity 97: 254-255. (Pubitemid 44454239)
7. Devey DS, Chase MW, Clarkson JJ. 2009. A stuttering start to plant DNA barcoding: microsatellites present a previously overlooked problem in non-coding plastid regions. Taxon 58: 7-15.
8. Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf material. Phytochemical Bulletin 19: 11-15.
9. Edwards D, Horn A, Taylor D, Savolainen V, Hawkins JA. 2008. DNA barcoding of a large genus, Aspalathus L. (Fabaceae). Taxon 57: 1317-1327.
10. Elias M, Hill RI, Willmott KR, Dasmahapatra KK, Brower AVZ, Mallet J, Jiggins CD. 2007. Limited performance of DNA barcoding in a diverse community of tropical butterflies. Proceedings of the Royal Society B: Biological Sciences 274: 2881-2889. (Pubitemid 350057943)
11. Fazekas AJ, Kesanakurti PR, Burgess KS, Percy DM, Graham SW, Barrett SCH, Newmaster SG, Hajibabaei M, Husband BC. 2009. Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? Molecular Ecology Resources 9: 130-139.
12. Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
13. 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. (Pubitemid 36228536)
14. 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. (Pubitemid 39410757)
15. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. 2004b. Identification of birds through DNA barcodes. PLoS Biology 2: e312.
16. Huang XM, Hao LZ, Hu NB, Zhao QY, Zhang JW. 2009. Studies on the breeding system and pollination biology of China species: Pugionium cornutum. Acta Botanica Boreali-Occidentalia Sinica 29: 2232-2237.
17. Illarionova ID. 1999. Synopsis of the genus Pugionium Gaertn. (Brassicaceae). Komarovia 1: 35-37.
18. Kerr KCR, Stoeckle MY, Dove CJ, Weigt LA, Francis CM, Hebert PDN. 2007. Comprehensive DNA barcode coverage of North American birds. Molecular Ecology Notes 7: 535-543. (Pubitemid 47035498)
19. Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16:111-134.
20. Koch MA, Karl R, Kiefer C, Al-Shehbaz I. 2010. Colonizing the American continent: systematics of the genus Arabis in North America (Brassicaceae). American Journal of Botany 97: 1040-1057.
21. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH. 2005. Use of DNA barcodes to identify flowering plants. Proceedings of theNationalAcademy of Sciences USA 102:8369-8374. (Pubitemid 40803501)
22. Kuittinen H, Aguade M, Charlesworth D, Haan ADE, Lauga B, Mitchell-Olds T, Oikarinen S, Ramos-Onsins S, Stranger B, Tienderen PV, Savolanien O. 2002. Primers for 22 candidate genes for ecological adaptations in Brassicaceae. Molecular Ecology Notes 2: 258-262.
23. Lane N. 2009. On the origin of barcodes. Nature 462: 272-274.
24. Liu J, Müller M, Gao LM, Zhang DQ, Li DZ. 2011. DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae), and the discovery of cryptic species. Molecular Ecology Resources 11: 89-100.
25. Mogensen HL. 1996. The hows and whys of cytoplasmic inheritance in seed plants. American Journal of Botany 83: 383-404.
26. Newmaster SG, Fazekas AJ, Ragupathy S. 2006. DNA barcoding in the land plants: evaluation of rbcL in a multigene tiered approach. Canadian Journal of Botany 84: 335-341. (Pubitemid 44426667)
27. Pennisi E. 2007. Taxonomy. Wanted: a barcode for plants. Science 318: 190-191.
28. Ran JH, Wang PP, Zhao HJ, Wang XQ. 2010. A test of seven candidate barcode regions from the plastome in Picea (Pinaceae). Journal of Integrative Plant Biology 52: 1109-1126.
29. Ren BQ, Xiang XG, Chen ZD. 2010. Species identification of Alnus (Betulaceae) using nr DNA and cp DNA genetic markers. Molecular Ecology Resources 10: 594-605.
30. Sang T, Crawford DJ, Sruessy TF. 1997. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany 84: 1120-1136. (Pubitemid 28106981)
31. Saunders GW. 2005. Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1879-1888. (Pubitemid 44365048)
32. Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R. 2005. Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1805-1811. (Pubitemid 44365041)
33. Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, Vermat T, Corthier G, Brochmann C, Willerslev E. 2007. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research 35: 1-8.
34. Tamura K, Dudley J, NeiM, Kumar S. 2007. MEGA4:Molecular Evolutionary Genetics Analysis (MEGA) software version 4. 0. Molecular Biology and Evolution 24: 1596-1599. (Pubitemid 47236692)
35. Tavares ES, Baker AJ. 2008. Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds. BMC Evolutionary Biology 8: 81.
36. Tian B, Liu TL, Liu JQ. 2010. Ostryopsis intermedia, a new species of Betulaceae from Yunnan, China. Botanical Studies 51: 257-262.
37. Thompson JD, Gibson TJ, Plewinak F, Jeanmougin F, Higgins DG. 1997. The Clustal-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876-4882. (Pubitemid 28022245)
38. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1847-1857. (Pubitemid 44365045)
39. White TJ, Bruns TD, Lee SB, Taylor JW. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: InnisMA, Gelfand DH, Sninsky JJ, White TJ eds. PCR protocols: a guide to methods and applications. London: Academic Press. 315-322.
40. Wu CI, Ting CT. 2004. Genes and speciation. Nature Review Genetics 5: 114-122.
41. Yoo HS, Eah JY, Kim JS, Kim YJ, Min MS, Paek WK, Lee H, Kim CB. 2006. DNA barcoding Korean birds. Molecules and Cells 22: 323-327. (Pubitemid 46062297)
42. Yu QS, Wang Q, Wang AL, Wu GL, Liu JQ. 2010. Interspecific delimitation and phylogenetic origin of Pugionium (Brassicaceae). Journal of Systematics and Evolution 48: 195-206.
43. Zhao YZ. 1999. A taxonomic revision and floristic analysis of the genus Pugionium. Acta Scientiarum Naturalium Universitatis Neimongol 30: 197-199.
44. Zhou YF, Abbott RJ, Jiang ZY, Du FK, Milne RI, Liu JQ. 2010. Genetic variation, gene flow and species delimitation: a case study of Pinus massoniana and P. hwangshanensis (Pinaceae) with overlapping distributions. Evolution 64: 2342-2352.