2,399
Views
72
CrossRef citations to date
0
Altmetric
Original Articles

The use of partial cox1, rbcL and LSU rDNA sequences for phylogenetics and species identification within the Nitzschia palea species complex (Bacillariophyceae)

, , , , &
Pages 413-425 | Received 15 Feb 2010, Accepted 25 May 2010, Published online: 13 Dec 2010

References

  • Alverson , AJ and Kolnick , L . 2005 . Intragenomic nucleotide polymorphism among small subunit (18S) rDNA paralogs in the diatom genus Skeletonema (Bacillariophyta) . J. Phycol. , 41 : 1248 – 1257 .
  • Amato , A , Kooistra , WHCF , Levialdi Ghiron , JH , Mann , DG , Pröschold , T and Montresor , M . 2007 . Reproductive isolation among sympatric cryptic species in marine diatoms . Protist , 158 : 193 – 207 .
  • Archibald , REM . 1983 . The diatoms of the Sundays and Great Fish Rivers in the Easter Cape Province of South Africa . Biblioth. Diatomol. , 1 : 1 – 362 .
  • Behnke , A , Friedl , T , Chepurnov , VA and Mann , DG . 2004 . Reproductive compatibility and rDNA sequence analyses in the Sellaphora pupula species complex (Bacillariophyta) . J. Phycol. , 40 : 193 – 208 .
  • Beszteri , B , Acs , E and Medlin , LK . 2005 . Ribosomal DNA sequence variation among sympatric strains of the Cyclotella meneghiniana complex (Bacillariophyceae) reveals cryptic diversity . Protist , 156 : 317 – 333 .
  • Cerino , F , Orsini , L , Sarno , D , Dell’Aversano , C , Tartaglione , L and Zingone , A . 2005 . The alternation of different morphotypes in the seasonal cycle of the toxic diatom Pseudo-nitzschia galaxiae . Harmful Algae , 4 : 33 – 48 .
  • D’Alelio , D , Amato , A , Kooistra , WHCF , Procaccini , G , Casotti , R and Montresor , M . 2009 . Internal transcribed spacer polymorphism in Pseudo-nitzschia multistriata (Bacillariophyceae) in the Gulf of Naples: recent divergence or intraspecific hybridization? . Protist , 160 : 9 – 20 .
  • Ehara , M , Inagaki , Y , Watanabe , KI and Ohama , T . 2000 . Phylogenetic analysis of diatom cox1 genes and implications of a fluctuating GC content on mitochondrial genetic code evolution . Curr. Genet. , 37 : 29 – 33 .
  • Ellegaard , M , Godhe , A , Härnström , K and McQuoid , M . 2008 . The species concept in a marine diatom: LSU rDNA-based phylogenetic differentiation in Skeletonema marinoi/dohrnii (Bacillariophyceae) is not reflected in morphology . Phycologia , 47 : 156 – 167 .
  • Evans , KM , Wortley , AH and Mann , DG . 2007 . An assessment of potential diatom “barcode” genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta) . Protist , 158 : 349 – 364 .
  • Evans , KM , Wortley , AH , Simpson , GE , Chepurnov , VA and Mann , DG . 2008 . A molecular systematic approach to explore diversity within the Sellaphora pupula species complex (Bacillariophyta) . J. Phycol. , 44 : 215 – 231 .
  • Farris , JS , Källersjö , M , Kluge , AG and Bult , C . 1995 . Constructing a significance test for incongruence . Syst. Biol. , 44 : 570 – 572 .
  • Felsenstein , J . 1985 . Confidence limits on phylogenies: an approach using the bootstrap . Evolution , 39 : 783 – 791 .
  • Finlay , BJ , Monaghan , EB and Maberly , SC . 2002 . Hypothesis: the rate and scale of dispersal of freshwater diatom species is a function of their global abundance . Protist , 153 : 261 – 273 .
  • Hall , TA . 1999 . BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT . Nucl. Acids Symp. Ser. , 41 : 95 – 98 .
  • Hillis , DM , Mable , BK and Moritz , C . 1996 . “ Applications of molecular systematics ” . In Molecular Systematics , Edited by: Hillis , DM , Moritz , C and Mable , BK . 515 – 544 . Sunderland, MA : Sinauer Associates .
  • JAHN, R., ZETZSCHE, H., REINHARDT, R. & GEMEINHOLZER, B. (2007). Diatoms and DNA barcoding: a pilot study on an environmental sample. In Proceedings of the 1st Central European Diatom Meeting (Kusber, H.-W. & Jahn, R., editors), 63–68. Botanic Garden and Botanical Museum Berlin-Dahlem (FU-Berlin), Germany [doi: 10.3372/cediatom.113]
  • Jones , HM , Simpson , GE , Stickle , AJ and Mann , DG . 2005 . Life history and systematics of Petroneis (Bacillariophyta), with special reference to British waters . Eur. J. Phycol. , 40 : 43 – 71 .
  • Khan , I . 1990 . Assessment of water-pollution using diatom community structure and species distribution – a case-study in a tropical river basin . Int. Rev. Gesamten Hydrobiol. , 75 : 317 – 338 .
  • KRAMMER, K. & LANGE-BERTALOT, H. (1988). Bacillariophyceae. 2. Teil: Bacillariaceae, Epithemiaceae, Surirellaceae. In Süsswasserflora von Mitteleuropa (Ettl, H., Gerloff, J., Heynig, H. & Mollenhauer, D., editors), Vol. 2/2. G. Fischer, Stuttgart, Germany
  • Kucera , H and Saunders , GW . 2008 . Assigning morphological variants of Fucus (Fucales, Phaeophyceae) in Canadian waters to recognized species using DNA barcoding . Botany (Botanique) , 86 : 1065 – 1079 .
  • Lai , SD , Chen , PC and Hsu , HK . 2003 . Benthic algae as monitors of heavy metals in various polluted rivers by energy dispersive X-ray spectrometer . J. Environ. Sci. Health, Part A: Toxic/Hazard. , 38 : 855 – 866 .
  • Lane , CE , Lindstrom , SC and Saunders , GW . 2007 . A molecular assessment of north east Pacific Alaria species (Laminariales, Phaeophyceae) with reference to the utility of DNA barcoding . Mol. Phylogenet. Evol. , 44 : 634 – 648 .
  • Lange-Bertalot , H . 1979 . Toleranzgrenzen und Populationsdynamik benthischer Diatomeen bei unterschiedlich starker Abwasserbelastung . Arch. Hydrobiol., Suppl. , 56 : 184 – 219 .
  • Lange-Bertalot , H . 1980 . New species, combinations and synonyms in the genus Nitzschia . Bacillaria , 3 : 41 – 77 .
  • Le Gall , L and Saunders , GW . 2010 . DNA barcoding is a powerful tool to uncover algal diversity: a case study of the Phyllophoraceae (Gigartinales, Rhodophyta) in the Canadian flora . J. Phycol. , 46 : 374 – 389 .
  • Mann , DG and Evans , KM . 2007 . “ Molecular genetics and the neglected art of diatomics ” . In Unravelling the Algae – The Past, Present and Future of Algal Systematics , Edited by: Brodie , J and Lewis , J . 231 – 265 . Boca Raton, Florida : CRC Press .
  • Mann , DG , Evans , KM , Chepurnov , VA and Nagai , S . 2009 . Morphology and formal description of Sellaphora bisexualis, sp. nov. (Bacillariophyta) . Fottea , 9 : 199 – 209 .
  • Mann , DG , Thomas , SJ and Evans , KM . 2008 . Revision of the diatom genus Sellaphora: a first account of the larger species in the British Isles . Fottea , 8 : 15 – 78 .
  • Moniz , MBJ and Kaczmarska , I . 2009 . Barcoding diatoms: is there a good marker? . Mol. Ecol. Res. , 9 ( Suppl. 1 ) : 65 – 74 .
  • Moniz , MBJ and Kaczmarska , I . 2010 . Barcoding of diatoms: nuclear encoded ITS revisited . Protist , 161 : 7 – 34 .
  • Posada , D and Buckley , TR . 2004 . Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests . Syst. Biol. , 53 : 793 – 808 .
  • Posada , D and Crandall , KA . 1998 . Modeltest: testing the model of DNA substitution . Bioinformatics , 14 : 817 – 818 .
  • Potapova , M and Charles , DF . 2007 . Diatom metrics for monitoring eutrophication in rivers of the United States . Ecol. Indic. , 7 : 48 – 70 .
  • Riisberg , I and Edvardsen , B . 2008 . Genetic variation in bloom-forming ichthyotoxic Pseudochattonella species (Dictyochophyceae, Heterokonta) using nuclear, mitochondrial and plastid DNA sequence data . Eur. J. Phycol. , 43 : 413 – 422 .
  • Ronquist , F and Huelsenbeck , JP . 2003 . MRBAYES 3: Bayesian phylogenetic inference under mixed models . Bioinformatics , 19 : 1572 – 1574 .
  • Sabater , S . 2000 . Diatom communities as indicators of environmental stress in the Guadiamar River, S-W. Spain, following a major mine tailings spill . J. Appl. Phycol. , 12 : 113 – 124 .
  • Saitou , N and Nei , M . 1987 . The neighbor-joining method: a new method for reconstructing phylogenetic trees . Mol. Biol. Evol. , 4 : 406 – 425 .
  • Saunders , GW . 2005 . Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications . Phil. Trans. R. Soc. , B 360 : 1879 – 1888 .
  • Swofford , DL . 2003 . PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods) , Sunderland, MA : Sinauer Associates .
  • Thompson , JD , Gibson , TJ , Plewniak , F , Jeanmougin , F and Higgins , DG . 1997 . The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools . Nucl. Acids Res. , 24 : 4876 – 4882 .
  • Trobajo , R , Clavero , E , Chepurnov , VA , Sabbe , K , Mann , DG , Ishihara , S and Cox , EJ . 2009 . Morphological, genetic and mating diversity within the widespread bioindicator Nitzschia palea (Bacillariophyceae) . Phycologia , 48 : 443 – 459 .
  • Trobajo , R and Cox , EJ . 2006 . “ Examination of type material of Nitzschia frustulum, N. palea and N. palea var. debilis ” . In Proceedings of the 18th International Diatom Symposium , Edited by: Witkowski , A . 431 – 445 . Bristol, UK : Biopress .
  • Van Dam , H , Mertens , A and Sinkeldam , J . 1994 . A coded checklist and ecological indicator values of freshwater diatoms from the Netherlands . Neth. J. Aquatic. Ecol. , 28 : 117 – 133 .
  • Vanormelingen , P , Chepurnov , VA , Mann , DG , Cousin , S , Sabbe , K and Vyverman , W . 2007 . Congruence of morphological, reproductive and ITS rDNA sequence data in a member of the Eunotia bilunaris (Bacillariophyta) species complex from New Zealand and Tasmania . Eur. J. Phycol. , 42 : 61 – 79 .

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.