Microevolution and Speciation in Thalassiosira weissflogii (Bacillariophyta)

Protist

Volumn 161, Issue 2, 2010, Pages 237-249

  Sorhannus, Ulf ^a   Ortiz, Joseph D ^b   Wolf, Matthias ^c   Fox, Martin G ^a  

^a EDINBORO UNIVERSITY OF PENNSYLVANIA   (United States)

^b KENT STATE UNIVERSITY   (United States)

^c UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

biological species; compensatory base change; diatom; geographic variation; internal transcribed spacers; sexually induced gene 1; Thalassiosira weissflogii

Indexed keywords

ALGAL DNA; ALGAL PROTEIN; RIBOSOMAL SPACER DNA; TUBULIN;

ARTICLE; ATLANTIC OCEAN; CHEMISTRY; CLASSIFICATION; DIATOM; DNA SEQUENCE; GENETICS; GEOGRAPHY; ISOLATION AND PURIFICATION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PACIFIC OCEAN; PHYLOGENY;

ALGAL PROTEINS; ATLANTIC OCEAN; DIATOMS; DNA, ALGAL; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; GEOGRAPHY; MOLECULAR SEQUENCE DATA; PACIFIC OCEAN; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TUBULIN;

BACILLARIOPHYTA; THALASSIOSIRA WEISSFLOGII;

EID: 77249136257     PISSN: 14344610     EISSN: 16180941     Source Type: Journal    
DOI: 10.1016/j.protis.2009.10.003     Document Type: Article

References (70)

1. Alverson A.J. Molecular systematics and the diatom species. Protist 159 (2008) 339-353
2. Alverson A.J., Jansen R.K., and Theriot E.C. Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms. Mol Phylogenet Evol 45 (2007) 193-210
3. Amato A., WHCF K., Levialdi Ghiron J.H., Mann D.G., Pröschold T., and Montresor M. Reproductive isolation among sympatric cryptic species in marine diatoms. Protist 158 (2007) 193-207
4. Antoine D., Andre J.M., and Morel A. Oceanic primary production 2. Estimation at global scale from satellite (coastal zone color scanner) chlorophyll. Global Biogeochem Cycles 10 (1996) 57-69
5. Armbrust E.V., and Galindo H.M. Rapid evolution of a sexual reproduction gene in centric diatoms of the genus Thalassiosira. Appl Environ Microbiol 67 (2001) 3501-3513
6. Bartoli G., Sarnthein M., Weinelt M., Erlenkeuser H., Garbe-Schonberg D., and Lea D.W. Final closure of Panama and the onset of northern hemisphere glaciation. Earth Planet Sci Lett 237 (2005) 33-44
7. Behnke A., Friedl T., Chepurnov V.A., and Mann D.G. Reproductive compatibility and rDNA sequence analyses in the Sellaphora pupula species complex (Bacillariophyta). J Phycol 40 (2004) 193-208
8. Beszteri B., Acs E., and Medlin L.K. Ribosomal DNA sequence variation among sympatricstrains of the Cyclotella meneghiniana complex (Bacillariophyceae) reveals cryptic diversity. Protist 156 (2005) 317-333
9. Carr M.E., Friedrichs M., Schmeltzm M., Aita M., Antoine D., Arrigo K., Asanuma I., Aumont O., Barber R., Behrenfeld M., Bidigare R., Buitenhuis E., Campbell J., Ciotti A., Dierssen H., Dowell M., Dunne J., Esaias W., Gentili B., Gregg W., Groom S., Hoepffner N., Ishizaka J., Kameda T.L., Quere C., Lohrenz S., Marra J., Melin F., Moore K., Morel A., Reddy T., Ryan J., Scardi M., Smyth T., Turpie K., Tilstone G., Waters K., and Yamanaka Y. A comparison of global estimates of marine primary productivity from ocean color. Deep-Sea Res II 53 (2006) 741-770
10. Cermeno P., and Falkowski P.G. Controls on diatom biogeography in the ocean. Science 325 (2009) 1539-1541
11. Coleman A.W., and Vacquier V.D. Exploring the phylogenetic utility of ITS sequences for animals: a test case for abalone (Haliotis). J Mol Evol 54 (2002) 246-257
12. Coleman A.W. The significance of a coincidence between evolutionary landmarks found in mating affinity and a DNA sequence. Protist 151 (2000) 1-9
13. Coleman A.W. ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends Genet 19 (2003) 370-375
14. Coleman A.W. Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Res 35 (2007) 3322-3329
15. Coleman A.W. Is there a molecular key to the level of "biological species" in eukaryotes? A DNA guide. Mol Phylogenet Evol 50 (2009) 197-203
16. D'Alelio D., Amato A., WHCF K., Procaccini G., Casotti R., and Montresor M. Internal transcribed spacer polymorphism in Pseudo-nitzschia multistriata (Bacillariophyceae) in the Gulf of Naples: recent divergence or intraspecific hybridization?. Protist 160 (2009) 9-20
17. Darling K.F., Kucera M., and Wade C.M. Global molecular phylogeography reveals persistent Arctic circumpolar isolation in a marine planktonic protist. Proc Natl Acad Sci USA 104 (2007) 5002-5007
18. Darling K.F., Kucera M., Pudsey C.J., and Wade C.M. Molecular evidence links cryptic diversification in polar planktonic protests to Quaternary climate dynamics. Proc Natl Acad Sci USA 101 (2004) 7657-7662
19. Darling K.F., Wade C.M., Stewart I.A., Kroon D., Dingle R., and Brown A. Molecular evidence for genetic mixing of Arctic and Antarctic subpolar population of planktonic forminifers. Nature 405 (2000) 43-47
20. von Dassow P., Petersen T.W., Chepurnov V.A., and Armbrust E.V. Inter- and intraspecific relations between nuclear DNA content and cell size in selected members of Thalassiosira (Bacillariophyceae). J Phycol 44 (2008) 335-349
21. Daugbjerg N., and Andersen R.A. A molecular phylogeny of the heterokont algae based on analyses of chloroplast-encoded rbcL sequence data. J Phycol 33 (1997) 1031-1041
22. De Boer A.M., and Nof D. The Bering Strait's grip on the northern hemisphere climate. Deep-Sea Res I 51 (2004) 1347-1366
23. de Vargas C., Norris R., Zaninetti L., Gibb S.W., and Pawlowski J. Molecular evidence of cryptic speciation in planktonic foraminifers and their relation to oceanic provinces. Proc Natl Acad Sci USA 96 (1999) 2864-2868
24. Ellegaard M., Godhe A., Härnström K., and McQuoid M.R. The species concept in a marine diatom: LSU rDNA-based phylogenetic differentiation in Skeletonema marinoi/dohrnii (Bacillariophyceae) is not reflected in morphology. Phycologia 47 (2008) 156-167
25. Engelmann J.C., Rahmann S., Wolf M., Schultz J., Fritzilas E., Kneitz S., Dandekar T., and Müller T. Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Mol Ecol Res 9 (2009) 83-93
26. Evans K.M., Bates S.S., Medlin L.K., and Hayes P.K. Microsatellite marker development and genetic variation in the toxic marine diatom Pseudo-nitzschia multiseries (Bacillariophyceae). J Phycol 40 (2004) 911-920
27. Finlay B.J., and Fenchel T. Cosmopolitan metapopulations of free-living microbial eukaryotes. Protist 155 (2004) 237-244
28. Finlay B.J. Global dispersal of free-living microbial eukaryote species. Science 296 (2002) 1061-1063
29. Flament P., Carande R., Holt B., and Bernstein R. Multi-frequency and interferometric SAR mapping of wind-driven mesoscale oceanic processes off Northern California and in the lee of the island of Hawaii. In Geoscience and Remote Sensing Symposium. Quantitative Remote Sensing for Science and Applications, IGARSS '95 2 (1995) 1120-1122
30. Fleminger A (1986) The Pleistocene Equatorial Barrier Between the Indian and Pacific Oceans and a Likely Cause for Wallace's Line. In Pierrot-Bults AC, van der Spoel S, Zahuranec BJ, Johnson RK (eds) Pelagic Marine Science. UNESCO Tech Pap Mar Sci, Vol 49, pp 84-97
31. Godhe A., McQuoid M.R., Karunasagar I., Karunasagar I., and Rehnstam-Holm N.S. Comparison of three common molecular tools for distinguishing among geographically separated clones of the diatom Skeletonema marinoi Sarno et Zingone (Bacillariophyceae). J Phycol 42 (2006) 280-291
32. Haug G.H., and Tiedemann R. Effect of the formation of the Isthmus of Panama on Atlantic Ocean thermohaline circulation. Nature 393 (1998) 673-676
33. Keller A., Schleicher T., Schultz J., Müller T., Dandekar T., and Wolf M. 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene 430 (2009) 50-57
34. Kooistra WHCF S.D., Balzano S., Gu H., Andersen R.A., and Zingone A. Global diversity and biogeography of Skeletonema species (Bacillariophyta). Protist 159 (2008) 177-193
35. Lundholm N., Moestrup Ø., Kotaki Y., Hoef-Emden K., Scholin C., and Miller P. Inter- and intraspecific variation of the Pseudo-nitzschia delicatissima complex (Bacillariophyceae) illustrated by rRNA probes, morphological data and phylogenetic analyses. J Phycol 42 (2006) 464-481
36. Mathews D.H., Disney M.D., Childs J.L., Schroeder S.J., Zuker M., and Turner D.H. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA 101 (2004) 7287-7292
37. Moniz M.B.J., and Kaczmarska I. Barcoding diatoms: is there a good marker?. Mol Ecol Res 9 Suppl 1 (2009) 65-74
38. Moniz MBJ, Kaczmarska I (2009b) Barcoding of diatoms: Nuclear encoded ITS revisited. Protist, in press.
39. Montresor M., Sgrosso S., Procaccini G., and Kooistra W.H.C.F. Intraspecific diversity in Scrippsiella trochoidea (Dinophyceae): evidence for cryptic species. Phycologia 42 (2003) 56-70
40. Müller T., Philippi N., Dandekar T., Schultz J., and Wolf M. Distinguishing species. RNA 13 (2007) 1469-1472
41. Müller T., Rahmann S., Dandekar T., and Wolf M. Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evol Biol 4 (2004) 20
42. Norris R.D. Pelagic Species Diversity, Biogeography and Evolution. In: Erwin D.H., and Wing S.L. (Eds). Deep Time: Paleobiology's Perspective (2000), Allen Press, Lawrence 236-258
43. Nylander J.A., Wilgenbusch J.C., Warren D.L., and Swofford D.L. AWTY (Are We There Yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24 (2008) 581-583
44. Pagel M., and Meade A. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst Biol 53 (2004) 571-581
45. Reid J.L. On the total geostrophic circulation of the Pacific Ocean: flow patterns, tracers, and transports. Progr Oceanogr 39 (1997) 263-352
46. Rynearson T., Lin E.O., and Armbrust E.V. Metapopulation structure in the planktonic diatom Ditylum brightwellii (Bacillariophyceae). Protist 160 (2009) 111-121
47. Rynearson T.A., and Armbrust E.V. Genetic differentiation among populations of the planktonic marine diatom Ditylum brightwellii (Bacillariophyceae). J Phycol 40 (2004) 34-43
48. Sáez A.G., Probert I., Geisen M., Quinn P., Young J.R., and Medlin L.K. Pseudo-cryptic speciation in coccolithophores. Proc Natl Acad Sci USA 100 (2003) 7163-7168
49. Sandal C., and Nof D. The collapse of the Bering Strait ice-dam and the abrupt temperature rise in the beginning of the Holocene. J Phys Oceanogr 38 (2008) 1979-1991
50. Sarno D., WHCF K., Medlin L.K., Percopo I., and Zingone A. Diversity in the genus Skeletonema (Bacillariophyceae). II. An assessment of the taxonomy of S. costatum-like species with the description of four new species. J Phycol 41 (2005) 151-176
51. Schultz J., Müller T., Achtziger M., Seibel P.N., Dandekar T., and Wolf M. The internal transcribed spacer 2 database-a web server for (not only) low level phylogenetic analyses. Nucleic Acids Res 34 (2006) W704-W707
52. Schultz J., and Wolf M. ITS2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematics. Mol Phylogenet Evol 52 (2009) 520-523
53. Seibel P.N., Müller T., Dandekar T., Schultz J., and Wolf M. 4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics 7 (2006) 498
54. Seibel P.N., Müller T., Dandekar T., and Wolf M. Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC Research Notes 1 (2008) 91
55. Selig C., Wolf M., Müller T., Dandekar T., and Schultz J. The ITS2 Database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Res 36 (2008) D377-D380
56. Slapeta J., Lopez-Garcia P., and Moreira D. Global dispersal and ancient cryptic species in the smallest marine eukaryotes. Mol Biol Evol 23 (2006) 23-29
57. Sorhannus U., and Kosakovsky Pond S.L. Evidence for positive selection on a sexual reproduction gene in the diatom Genus Thalassiosira (Bacillariophyta). J Mol Evol 63 (2006) 231-239
58. Sorhannus U. A nuclear-encoded small-subunit ribosomal RNA timescale for diatom evolution. Mar Micropaleontol 65 (2007) 1-12
59. *and Other Methods). Version 4.0b10 (2002), Sinauer Associates, Sunderland
60. Theriot E.C., Cannone J.J., Gutell R.R., and Alverson A.J. The limits of nuclear-encoded SSU rDNA for resolving the diatom phylogeny. Eur J Phycol 44 (2009) 277-290
61. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22 (1994) 4673-4680
62. Vanormelingen P., Chepurnov V.A., Mann D.G., Cousin S., and Vyverman W. Congruence of morphological, reproductive and ITS rDNA sequence data in some Australasian Eunotia bilunaris (Bacillariophyta). Eur J Phycol 42 (2007) 61-79
63. Vanormelingen P., Chepurnov V.A., Mann D.G., Sabbe K., and Vyverman W. Genetic divergence and reproductive barriers between morphologically heterogeneous sympatric clones of Eunotia bilunaris sensu lato (Bacillariophyta). Protist 159 (2008) 73-90
64. Venditti C., Meade A., and Pagel M. Phylogenetic mixture models can reduce node-density artifacts. Syst Biol 57 (2008) 286-293
65. Wilgenbusch JC, Warren DL, Swofford DL (2004) AWTY: A system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. http://ceb.csit.fsu.edu/awty.
66. Wolf M., Friedrich J., Dandekar T., and Müller T. CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. Silico Bio 5 (2005) 291-294
67. Wolf M., Ruderisch B., Dandekar T., and Müller T. ProfdistS: (Profile-) Distance based phylogeny on sequence-structure alignments. Bioinformatics 24 (2008) 2401-2402
68. Wolf M., Achtziger M., Schultz J., Dandekar T., and Müller T. Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA 11 (2005) 1616-1623
69. Xia X. Data Analysis in Molecular Biology and Evolution (2001), Kluwer Academic Publishers, Boston
70. Zuccon A, Zuccon D (2008) MrEnt v.2. Program distributed by the authors. http://www.mrent.org