General Patterns of Diversity in Major Marine Microeukaryote Lineages

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Pernice, Massimo C ^a   Logares, Ramiro ^a   Guillou, Laure ^b,c   Massana, Ramon ^a  

^a INSTITUT DE CIÈNCIES DEL MAR   (Spain)

^b STATION BIOLOGIQUE   (France)

^c STATION BIOLOGIQUE DE ROSCOFF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA 18S;

ALVEOLATA; ARTICLE; BOLIDOPHYCEAE; CENTROHELIOZOA; CHOANOFLAGELLATE; CLADOGENESIS; CRYPTOPHYTA; DINOFLAGELLATE; DNA SEQUENCE; EUKARYOTE; EUKARYOTE EVOLUTION; GENETIC DISTANCE; GENETIC PARAMETERS; GENETIC VARIABILITY; HAPTOPHYTA; HIGH THROUGHPUT SEQUENCING; LABYRINTHULIDA; LINEAGE THROUGH TIME PLOT; MARINE MICROEUKARYOTE; MARINE SPECIES; MAST 4; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERATIONAL TAXONOMIC UNIT; PELAGOPHYCEAE; PHYLOGENETIC TREE; PRASINOPHYCEAE; RHIZARIA; SANGER SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STRAMENOPILE; TAXONOMIC IDENTIFICATION; TELONEMIA;

ALVEOLATA; AQUATIC ORGANISMS; EUKARYOTA; GENETIC SPECIATION; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PHYLOGENY; RHIZARIA; RNA, RIBOSOMAL, 18S; SEQUENCE ANALYSIS, DNA; STRAMENOPILES;

EID: 84874311437     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0057170     Document Type: Article

References (48)

1. Epstein S, López-García P, (2008) "Missing" protists: a molecular prospective. Biodivers Conserv 17: 261-276.
2. Massana R, Pedrós-Alió C, (2008) Unveiling new microbial eukaryotes in the surface ocean. Curr Opin Microbiol 11: 213-218.
3. Vaulot D, Eikrem W, Viprey M, Moreau H, (2008) The diversity of small eukaryotic phytoplankton (≤3 μm) in marine ecosystems. FEMS Microbiol Rev 32: 795-820.
4. Not F, del Campo J, Balagué V, de Vargas C, Massana R, (2009) New Insights into the Diversity of Marine Picoeukaryotes. PLoS ONE 4: e7143.
5. Savin MC, Martin JL, LeGresley M, Giewat M, Rooney-Varga J, (2004) Plankton Diversity in the Bay of Fundy as Measured by Morphological and Molecular Methods. Microb Ecol 48: 51-65.
6. Terrado R, Vincent W, Lovejoy C, (2009) Mesopelagic protists: diversity and succession in a coastal Arctic ecosystem. Aquat Microb Ecol 56: 25-40.
7. Jeon S, Bunge J, Leslin C, Stoeck T, Hong S, et al. (2008) Environmental rRNA inventories miss over half of protistan diversity. BMC Microbiol 8: 222.
8. Massana R, Pernice M, Bunge JA, Campo Jd, (2011) Sequence diversity and novelty of natural assemblages of picoeukaryotes from the Indian Ocean. ISME J 5: 184-195.
9. Not F, Gausling R, Azam F, Heidelberg JF, Worden AZ, (2007) Vertical distribution of picoeukaryotic diversity in the Sargasso Sea. Environ Microbiol 9: 1233-1252.
10. Stoeck T, Kasper J, Bunge J, Leslin C, Ilyin V, et al. (2007) Protistan Diversity in the Arctic: A Case of Paleoclimate Shaping Modern Biodiversity? PLoS ONE 2: e728.
11. Kirkpatrick M, Slatkin M, (1993) Searching for Evolutionary Patterns in the Shape of a Phylogenetic Tree. Evolution 47: 1171-1181.
12. Vamosi SM, Heard SB, Vamosi JC, Webb CO, (2009) Emerging patterns in the comparative analysis of phylogenetic community structure. Mol Ecol 18: 572-592.
13. Purvis A, Nee S, Harvey PH, (1995) Macroevolutionary Inferences from Primate Phylogeny. Proceedings of the Royal Society of London Series B: Biol Sci 260: 329-333.
14. Martin AP, Costello EK, Meyer AF, Nemergut DR, Schmidt SK, et al. (2004) The rate and pattern of cladogenesis in microbes. Evolution 58: 946-955.
15. Caron DA, Countway PD, Savai P, Gast RJ, Schnetzer A, et al. (2009) Defining DNA-based operational taxonomic units for microbial-eukaryote ecology. Appl Environ Microbiol 75: 5797-5808.
16. Nebel M, Pfabel C, Stock A, Dunthorn M, Stoeck T, (2011) Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences. Environ Microbiol Reports 3: 154-158.
17. Guillou L, Viprey M, Chambouvet A, Welsh RM, Kirkham AR, et al. (2008) Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata). Environ Microbiol 10: 397-408.
18. Massana R, Castresana J, Balague V, Guillou L, Romari K, et al. (2004) Phylogenetic and ecological analysis of novel marine stramenopiles. Appl Environ Microbiol 70: 3528-3534.
19. Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, et al. (2010) Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol 19: 21-31.
20. Kunin V, Engelbrektson A, Ochman H, Hugenholtz P, (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12: 118-123.
21. Quince (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Meth 6: 639-641.
22. Burki F, Inagaki Y, Bråte J, Archibald JM, Keeling PJ, et al. (2009) Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates. Gen Biol Evol 1: 231-238.
23. Krabberød AK, Bråte J, Dolven JK, Ose RF, Klaveness D, et al. (2011) Radiolaria Divided into Polycystina and Spasmaria in Combined 18S and 28S rDNA Phylogeny. PLoS ONE 6: e23526.
24. Brate J, Logares R, Berney C, Ree DK, Klaveness D, et al. (2010) Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA. ISME J 4: 1144-1153.
25. Dunthorn M, Klier J, Bunge J, Stoeck T, (2012) Comparing the Hyper-Variable V4 and V9 Regions of the Small Subunit rDNA for Assessment of Ciliate Environmental Diversity. J Eukaryot Microbiol 59: 185-187.
26. Behnke A, Engel M, Christen R, Nebel M, Klein RR, et al. (2011) Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environ Microbiol 13: 340-349.
27. Pawlowski J, Christen R, Lecroq B, Bachar D, Shahbazkia HR, et al. (2011) Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing. PLoS ONE 6: e18169.
28. Brown MV, Philip GK, Bunge JA, Smith MC, Bisset A, et al. (2009) Microbial community structure in the North Pacific Ocean. ISME J 3: 1374-1386.
29. Zhu F, Massana R, Not F, Marie D, Vaulot D, (2005) Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiol Ecol 52: 79-92.
30. Cheung MK, Au CH, Chu KH, Kwan HS, Wong CK, (2010) Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing. ISME J 4: 1053-1059.
31. Moreira D, López-García P, Vickerman K, (2004) An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea. Int J Syst Evol Microbiol 54: 1861-1875.
32. Pybus OG, Harvey PH, (2000) Testing Macro-Evolutionary Models Using Incomplete Molecular Phylogenies. Proceedings: Bio Sci 267: 2267-2272.
33. Nee S, Holmes EC, May RM, Harvey PH, (1994) Extinction Rates can be Estimated from Molecular Phylogenies. Philosophical Transactions of the Royal Society of London Series B: Biol Sci 344: 77-82.
34. McPeek Mark A, (2008) The Ecological Dynamics of Clade Diversification and Community Assembly. Am Nat 172: E270-E284.
35. Barberán A, Fernández-Guerra A, Auguet J-C, Galand PE, Casamayor EO, (2011) Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota. Mol Ecol 20: 1988-1996.
36. Riisberg I, Orr RJS, Kluge R, Shalchian-Tabrizi K, Bowers HA, et al. (2009) Seven Gene Phylogeny of Heterokonts. Protist 160: 191-204.
37. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
38. Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR, et al. (2005) The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists. J Eukaryot Microbiol 52: 399-451.
39. Katoh K, Misawa K, Kuma K, Miyata T, (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30: 3059-3066.
40. Galtier N, Gouy M, Gautier C, (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12: 543-548.
41. Swofford D (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.
42. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Appl Environ Microbiol 75: 7537-7541.
43. Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
44. Letunic I, Bork P, (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23: 127-128.
45. Webb CO, Ackerly DD, Kembel SW, (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24: 2098-2100.
46. Huson D, Richter D, Rausch C, Dezulian T, Franz M, et al. (2007) Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics 8: 460.
47. Paradis E, Claude J, Strimmer K, (2004) APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20: 289-290.
48. Rabosky DL, (2006) LASER: A maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies. Evolutionary bioinformatics online 2: 247-250.