A three-gene dinoflagellate phylogeny suggests monophyly of Prorocentrales and a basal position for Amphidinium and Heterocapsa

Journal of Molecular Evolution

Volumn 65, Issue 4, 2007, Pages 463-474

  Zhang, Huan ^a   Bhattacharya, Debashish ^b   Lin, Senjie ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

^b UNIVERSITY OF IOWA   (United States)

Author keywords

cob; cox1; Cytochrome b; Cytochrome c oxidase I; Dinoflagellates; Phylogeny; rDNA

Indexed keywords

CONCATENATED DNA; CYTOCHROME B; CYTOCHROME C OXIDASE; RIBOSOME DNA;

AMPHIDINIUM; ARTICLE; BAYES THEOREM; DINOFLAGELLATE; GENETIC ANALYSIS; HETEROCAPSA; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PARSIMONY ANALYSIS; PHYLOGENY; UNINDEXED SEQUENCE;

ANIMALS; BASE SEQUENCE; CLONING, MOLECULAR; CYTOCHROMES B; DINOFLAGELLIDA; DNA PRIMERS; DNA, COMPLEMENTARY; ELECTRON TRANSPORT COMPLEX IV; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA;

AMPHIDINIUM; DINOPHYCEAE; HETEROCAPSA; PROROCENTRALES; PROROCENTRUM;

EID: 35748983183     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-007-9038-4     Document Type: Article

References (62)

1. Abascal F, Zardoya R, Posada D, et al. (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105
2. Avise JC (1994) Molecular markers, natural history and evolution. Chapman & Hall, New York
3. Barker FK, Lutzoni FM (2001) The utility of the incongruence length difference test. Syst Biol 51:625-637
4. Bergholtz T, Daugbjerg N, Moestrup Ø, Fernández-Tejedor M (2005) On the identity of Karlodinium veneficum and description of Karlodinium armiger sp. nov. (Dinophyceae), based on light and electron microscopy, nuclear-encoded LSU rDNA, and pigment composition. J Phycol 42:170-193
5. Bujak JP, Williams GL (1981) The evolution of dinoflagellates. Can J Bot 59:2077-2087
6. Cavalier-Smith T (1998) A revised six-kingdom system of life. Biol Rev Cambr Philos Soc 73:203-266
7. Chaput H, Wang Y, Morse D (2002) Dinoflagellate mitochondrial transcripts are polyadenylated at random sites and contain numerous gene fragments. Protist 153:111-122
8. Cienkowski L (1881) Bericht über eine exkursion ins weisse meer im Jahre 1880. Trav Soc Imperiale Nat St. Petersbourg 12:130-171
9. Conway DJ, Fanello C, Lloyd JM, et al. (2000) Origin of Plasmodium falciparum malaria is traced by mitochondrial DNA. Mol Biochem Parasitol 111:163-171
10. Dodge JD (1975) The Prorocentrales (Dinophyceae) II. Revision of the taxonomy within the genus Prorocentrum. Bot J Linn Soc 71:103-125
11. Dodge JD (1985) Atlas of dinoflagellates. A scanning electron microscope survey. Farrand Press, London
12. Ehrenberg C (1834) Dritter beitrag zur erkenntnis grosser organisation in der richtung des kleinsten raumes. Abhandlungen der Königliche Akademie Wissenschaften zu Berlin (Phys Kl) 1833:145-336
13. Faust MA (1991) Morphology of ciguatera-causing Prorocentrum lima (Pyrrophyta) from widely differing sites. J Phycol 27:642-648
14. Fensome RA, Taylor FJR, Norris G, Sarjeant WAS, Wharton DI, Williams GL (1993) A classification of fossil and living dinoflagellates. Micropaleontol Press Spec Publ 7
15. Flø-Jorgensen MF, Murray S, Daugbjerg N (2004) Amphidnium revisited. I. Redefinition of Amphidinium (Dinophyceae) based on cladistic and molecular phylogenetic analysis. J Phycol 40:351-365
16. Garesse R, Vallejo CG (2001) Animal mitochondrial biogenesis and function: a regulatory cross-talk between two genomes. Gene 263:1-16
17. Gómez F (2005) A list of free-living dinoflagellate species in the world's oceans. Acta Bot Croat 64:129-212
18. Gray MW, Burger G, Lang BF (1999) Mitochondrial evolution. Science 283:1476-1481
19. Grzebyk D, Sako Y, Berland B (1998) Phylogenetic analysis of nine species of Prorocentrum (Dinophyceae) inferred from 18S ribosomal DNA sequences, morphological comparisons, and description of Prorocentrum panamensis, sp. nov. J Phycol 34:1055-1068
20. Hackett JD, Anderson DM, Erdner DL, Bhattacharya D (2004) Dinoflagellates: a remarkable evolutionary experiment. Am J Bot 91:1523-1534
21. Hansen G (1995) Analysis of the thecal plate pattern in the dinoflagellate Heterocapsa rotundata (Lohmann) comb. nov. (=Katodinium rotundatum (Lohmann) Loeblich). Phycologia 34:166-170
22. Harper JT, Keeling PJ (2003) nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol Biol Evol 20:1730-1735
23. Hebert PDN, Penton E. H, Burns JM, Janzen DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA 101:14812-14817
24. Hipp AL, Hall JC, Sytsma KJ (2004) Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test. Syst Biol 53:81-89
25. Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755
26. Inagaki Y, Simpson AG, Dacks JB, Roger AJ (2004) Phylogenetic artifacts can be caused by leucine, serine and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study. Syst Biol 53:582-593
27. Lin S, Zhang H, Spencer D, Norman J, Gray M (2002) Widespread and extensive editing of mitochondrial mRNAs in dinoflagellates. J Mol Biol 320:727-739
28. Lin S, Zhang H, Jiao N (2006) Potential utility of mitochondrial cytochrome b and its mRNA editing in resolving closely related dinoflagellates: a case study of Prorocentrum (Dinophyceae). J Phycol 42:646-654
29. Litaker RW, Steidinger KA, Mason PL, Landsberg JH, Shields JD, Reece KS, Haas LW, Vogelbein WK, Vandersea MW, Kibler SR, Tester PA (2005) The reclassification of Pfiesteria shumwayae (dinophyceae): Pseudopfiesteria, gen. nov. J Phycol 41:643-651
30. Loeblich AR, Sherley JL, Schmidt RJ (1979) The correct position of flagellar insertion in Prorocentrum and description of Prorocentrum rhathymum sp. nov. (Pyrrhophyta). J Plankton Res 1:113-120
31. López-García P, Rodriguez-Valera F, Pedros-Allo C, Moreira D (2001) Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409:603-607
32. Maddison DR, Maddison WP (2002) MacClade V4.05. Sinauer, Sunderland, MA
33. Marshall HG, Hargraves PE, Burkholder JM, Parrow MW, Elbrächter M, Allen EH, Knowlton VM, Rublee PA, Hynes WL, Egerton TA, Remington DL, Wyatt KB, Lewitus AJ, Henrich VC (2006) Taxonomy of Pfiesteria (Dinophyceae). Harmful Algae 5:481-496
34. Mattern MY (2004) Molecular phylogeny of the Gasterosteidae: the importance of using multiple genes. Mol Phylogenet Evol 30:366-377
35. McLachlan JL, Boalch GT, Jahn R (1997) Reinstatement of the genus Exuviaella (Dinophyceae, Prorocentrophycidae) and an assessment of Prorocentrum lima. Phycologia 36:38-46
36. Murray S, Flø-Jorgensen MF, Ho SY, Patterson DJ, Jermiin LS (2005) Improving the analysis of dinoflagellate phylogeny based on rDNA. Protist 156:269-286
37. Pryer KM, Schneider H, Smith AR, Cranfill R, Wolf PG, Hunt JS, Sipes SD (2001) Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 409:618-622
38. Rathore D, Wahl AM, Sullivan M, McCutchan TF (2001) A phylogenetic comparison of gene trees constructed from plastid mitochondrial and genomic DNA of Plasmodium species. Mol Biochem Parasitol 114:89-94
39. Rodriguez F, Oliver JL, Marin A, Medina JR (1990) The general stochastic model of nucleotide substitution. J Theoret Biol 142:485-501
40. Saccone C, Gissi C, Lanave C, Larizza A, Pesole G, Reyes A (2000) Evolution of the mitochondrial genetic system: an overview. Gene 261:153-159
41. Saldarriaga JF, Taylor FJR, Keeling PJ, Cavalier-Smith T (2001) Dinoflagellate nuclear SSU rRNA phylogeny suggests multiple plastid losses and replacements. J Mol Evol 53:204-213
42. Saldarriaga JF, McEwan ML, Fast NM, Taylor FJR, Keeling PJ (2003) Three protein gene phylogenies suggest that Oxyrrhis marina and Perkinsus marinus are early branches of the dinoflagellate lineage. Int J System Evol Microbiol 53:355-365
43. Saldarriaga JF, Taylor FJR, Cavalier-Smith T, Menden-Deuer S, Keeling PJ (2004) Molecular data and the evolutionary history of dinoflagellates. Eur J Protist 40:85-111
44. Saunders GW, Hill DRA, Sexton JP, Andersen RA (1997) Small-subunit ribosomal RNA sequences from selected dinoflagellates: testing classical evolutionary hypotheses with molecular systematic methods. Plant Syst Evol (Suppl) 11:237-259
45. Serizawa K, Suzuki H, Tsuchiya K (2000) A phylogenetic view on species radiation in Apedemus inferred from variation of nuclear and mitochondrial genes. Biochem Genet 38:27-40
46. Shalchian-Tabrizi K, Minge MA, Cavalier-Smith T, Nedreklepp JM, Klaveness D, Jakobsen KS (2006a) Combined heat shock protein 90 and ribosomal RNA sequence phylogeny supports multiple replacements of dinoflagellate plastids. J Euk Microbiol 53:217-224
47. Shalchian-Tabrizi K, Skanseng M, Ronquist F, Klaveness D, Bachvaroff TR, Delwiche CF, Botnen A, Tengs T, Jakobsen KS (2006b) Heterotachy processes in rhodophyte-derived secondhand plastid genes: implications for addressing the origin and evolution of dinoflagellate plastids. Mol Biol Evol 23:1504-1515
48. Shimodaira H, Hasegawa M (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247
49. Sournia A (1986) Atlas du Phytoplancton Marin, Vol. I: Introduction, Cyanophycées, Dictyochophycées, Dinophycées et Raphidophycées. Editions du Centre National de la Recherche Scientifique, Paris
50. Steidinger KA, Tengen K (1997) Dinoflagellates. In: Tomas CR (ed) Identifying marine phytoplankton. Academic Press, New York, pp 387-594
51. Stelter K, El-Sayed NM, Seeber F (2007) The expression of a plant-type ferredoxin redox system provides molecular evidence for a plastid in the early dinoflagellate Perkinsus marinus. Protist 158:119-130
52. Swofford DL (1998) PAUP*: Phylogenetic analysis using parsimony and other methods, v.4.0b10. Sinauer Associates, Sunderland, MA
53. Takabayashi M, Santos SR, Cook CB (2004) Mitochondrial DNA phylogeny of the symbiotic dinoflagellates (Symbiodinium, Dinophyta). J Phycol 40:160-164
54. Taylor MS, Hellberg ME (2003) Genetic evidence for local retention of pelagic larvae in a Caribbean reef fish. Science 299:107-108
55. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-356
56. Yoon HS, Hackett JD, Pinto G, Bhattacharya D (2002) A single, ancient origin of the plastid in the Chromista. Proc Natl Acad Sci USA 99:15507-15512
57. Yoon HS, Hackett J, Ciniglia C, Pinto G, Bhattacharya D (2004) A molecular timeline for the origin of photosynthetic eukaryotes. Mol Biol Evol 21:809-818
58. Zardoya R, Costas E, Lopez-Roda V, Garrido-Pertierra A, Bautista JM (1995) Revised dinoflagellate phylogeny inferred from molecular analysis of large-subunit ribosomal RNA gene sequences. J Mol Evol 41:637-645
59. Zhang H, Lin S (2005) Mitochondrial cytochrome b mRNA editing in dinoflagellates: possible ecological and evolutionary associations? J Euk Microbiol 52:538-545
60. Zhang H, Bhattacharya D, Lin S (2005) Phylogeny of dinoflagellates based on mitochondrial cytochrome b and nuclear small subunit rDNA sequence comparisons. J Phycol 41:411-420
61. Zhang H, Hou Y, Lin S (2006) Isolation and characterization of PCNA from the dinoflagellate Pfiesteria piscicida. J Eukaryot Microbiol 53:142-150
62. Zhang H, Hou Y, Miranda L, Campbell DA, Sturm NR, Gaasterland T, Lin S (2007) Spliced leader RNA trans-splicing in dinoflagellates. Proc Natl Acad Sci USA 104:4618-4623