A clustering optimization strategy for molecular taxonomy applied to planktonic foraminifera SSU rDNA

Evolutionary Bioinformatics

Volumn 2010, Issue 6, 2010, Pages 97-112

  Göker, Markus ^a   Grimm, Guido W ^b   Auch, Alexander F ^c   Aurahs, Ralf ^c   Kučera, Michal ^c  

^a LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^b SWEDISH MUSEUM OF NATURAL HISTORY   (Sweden)

^c UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

Automated taxonomy; Linkage clustering; Parameter optimization; Planktonic foraminifera; SSU rDNA

Indexed keywords

SMALL SUBUNIT RIBOSOMAL RNA;

ARTICLE; AUTOMATION; GENE CLUSTER; GENE SEQUENCE; GENETIC LINKAGE; GENETIC VARIABILITY; GLOBIGERINELLA SIPHONIFERA; GLOBIGERINITA UVULA; GLOBIGERINOIDES RUBER; GLOBOROTALIA INFLATA; HASTIGERINA PELAGICA; MOLECULAR DYNAMICS; MORPHOLOGY; NEOGLOBOQUADRINA DUTERTREI; NEOGLOBOQUADRINA PACHYDERMA; NONHUMAN; NUCLEOTIDE SEQUENCE; ORBULINA UNIVERSA; PLANKTONIC FORAMINIFERA; PROCESS OPTIMIZATION; PULLENIATINA OBLIQUILOCULATA; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; TAXONOMY; TURBOROTALITA QUINQUELOBA;

FORAMINIFERA;

EID: 77957245259     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: None     Document Type: Article

References (82)

1. Blaxter M, Floyd R. Molecular taxonomics for biodiversity surveys: already a reality. Trends Ecol Evol. 2003;18:268-9.
2. Blaxter M, Mann J, Chapman T, et al. Defining operational taxonomic units using DNA barcode data. Phil Trans Roy Soc London B. 2005; 360:1935-43.
3. Daniell TJ, Husband R, Fitter AH, Young JPW. Molecular diversity of arbuscular mycorrhizal fungi colonising arable crops. FEMS Microbiol Ecol. 2001;36:203-9.
4. Floyd R, Abebe E, Papert A, Blaxter M. Molecular barcodes for soil nematode identification. Mol Ecol. 2002;11:839-50.
5. Helgason T, Watson IJ, Young JPW. Phylogeny of the Glomerales and Diversisporales (Fungi: Glomeromycota) from actin and elongation factor 1-alpha sequences. FEMS Microbiol Ecol. 2003;229:127-32.
6. Husband R, Herre EA, Turner SL, Gallery R, Young JPW. Molecular diversity of arbuscular mycorrhizal fungi and pattern of host association over time and space in a tropical forest. Mol Ecol. 2002;11: 2669-78.
7. Schloss P, Handelsman J. Status of the microbial census. Microbiol Mol Biol Rev. 2004;68:686-91.
8. Schloss PD, Handelsman J. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 2005;71:1501-6.
9. Wubet T, Weiß M, Kottke I, Teketay D, Oberwinkler F. Phylogenetic analysis of nuclear small subunit rDNA sequences suggests that the endangered African Pencil Cedar, Juniperus procera, is associated with distinct members of Glomeraceae. Mycol Res. 2006;110: 1059-69.
10. Knowlton N. Sibling species in the sea. Annual Review of Ecology and Systematics. 1993;24:189-216.
11. Rusch DB, Halpern AL, Sutton G, et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 2007;5:e77
12. Tringe SG, Rubin EM. Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet. 2005;6:805-14.
13. Hebert P, Gregory T. The promise of DNA barcoding for taxonomy. Syst Biol. 2005;54:852-9.
14. Kress WJ, Erickson DL. DNA barcoding-a windfall for tropical biology? Biotropica. 2008;40:405-8.
15. Ferguson JWH. On the use of genetic divergence for identifying species. Biol J Linn Soc. 2002;75:509-16.
16. Will K, Mishler B, Wheeler Q. The perils of DNA barcoding and the need for integrative taxonomy. Syst Biol. 2005;54:844-51.
17. DeSalle R, Egan MG, Siddall M. The unholy trinity: Taxonomy, species delimitation and DNA barcoding. Phil Trans Roy Soc London B. 2005;360: 1905-16.
18. Will KW, Rubinoff D. Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics. 2004;20:47-55.
19. Göker M, García-Blázquez G, Voglmayr H, Tellería MT, Martín MP. Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora. PLoS ONE. 2009;4:e6319.
20. Sokal RR, Sneath PHA. Principles of Numerical Taxonomy. San Francisco: Freeman WH and Company; 1963
21. Meier R, Shiyang K, Vaidya G, Ng PKL. DNA barcoding and taxonomy in Diptera: A tale of high intraspecific variability and low identification success. Syst Biol. 2006;55:715-28.
22. Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson K-H. Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinf. 2008;4:193-201.
23. Abdo Z, Golding B. A step toward barcoding life: A model-based, decisiontheoretic method to assign genes to preexisting species groups. Syst Biol. 2007;56:44-56.
24. Nielsen R, Matz M. Statistical approaches for DNA barcoding. Syst Biol. 2006;55:162-9.
25. Bidartondo MI, et al. (256 authors). Preserving accuracy in Genbank. Science. 2008;319:1616
26. Lake JA. The order of sequence alignment can bias the selection of tree topology. Mol Biol Evol. 1991;8:378-85.
27. Morrison DA, Ellis JT. Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of Apicomplexa. Mol Biol Evol. 1997;14:428-41.
28. Aurahs R, Göker M, Grimm GW, et al. Using the multiple analysis approach to reconstruct phylogenetic relationships among planktonic Foraminifera from highly divergent and length-polymorphic SSU rDNA sequences. Bioinf Biol Insights. 2009;3:155-77.
29. Höhl M, Ragan MA. Is multiple-sequence alignment required for accurate inference of phylogeny? Syst Biol. 2007;56:206-21.
30. Otu HH, Sayood K. A new sequence distance measure for phylogenetic tree construction. Bioinformatics. 2003;19:2122-30.
31. Vinga S, Almeida J. Alignment-free seqeunce comparison-a review. Bioinformatics. 2003;19:513-23.
32. Hall N. Advanced sequencing technologies and their wider impact in microbiology. J Exp Biol. 2007;209:1518-25.
33. Hemleben C, Spindler M, Anderson OR. Modern Planktonic Foraminifera. New York: Springer-Verlag; 1989
34. Kučera M. Planktonic foraminifera as tracers of past oceanic environments. In: Hillaire-Marcel C, de Vernal A, editors. Proxies in Late Cenozoic Paleoceanography. Vol. 1. Amsterdam: Elsevier; 2007:213-62.
35. Ravelo AC, Hillaire-Marcel C. The use of oxygen and carbon isotopes of foraminifera in paleoceanography. In: Hillaire-Marcel C, de Vernal A, editors. Proxies in Late Cenozoic Paleoceanography. Vol. 1. Amsterdam: Elsevier; 2007:735-6.
36. Grimm GW, Stögerer K, Ertan KT, Kitazato H, Hemleben V, Hemleben C. Diversity of rDNA in Chilostomella: molecular differentiation patterns and putative hermit types. Mar Micropaleontol. 2007;62:75-90.
37. Darling KF, Wade CM. The genetic diversity of planktic foraminifera and the global distribution of ribosomal RNA genotypes. Mar Micropaleontol. 2008;67:216-38.
38. de Vargas C, Norris R, Zaninetti L, Gibb SW, Pawlowski J. Molecular evidence of cryptic speciation in planktonic foraminifers and their relation to oceanic provinces. Proc Nat Acad Sci U S A. 1999;96:2864-8.
39. Kučera M, Darling KF. Cryptic species of planktonic foraminifera: their effect on palaeoceanographic reconstructions. Phil Trans Roy Soc London A. 2002;360:695-718.
40. Darling KF, Wade CM, Kroon D, Leigh Brown AJ, Bijma J. The diversity and distribution of modern planktic foraminiferal small subunit ribosomal RNA genotypes and their potential as tracers of present and past ocean circulations. Paleoceanogr. 1999;14:3-12.
41. de Vargas C, Bonzon M, Rees NW, Pawlowski J, Zaninetti L. A molecular approach to biodiversity and biogeography in the planktonic foraminifer Globigerinella siphonifera (d'Orbigny). Mar Micropaleontol. 2002;45: 101-16.
42. Stewart IA, Darling KF, Kroon D, Wade CM, Troelstra SR. Genotypic variability in subarctic Atlantic planktic foraminifera. Mar Micropaleontol. 2001;43:143-53.
43. Huber BT, Bijma J, Darling K. Cryptic speciation in the living planktonic foraminifer Globigerinella siphonifera (d'Orbigny). Paleobiology. 1997; 23:33-62.
44. Auch AF, Henz SR, Holland BR, Göker M. Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences. BMC Bioinf. 2006;7:350
45. Auch AF, Klenk H-P, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci. 2010;2:142-8.
46. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci. 2010;2:117-34.
47. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Journal of Molecular Biology. 1990;215:403-10.
48. Hennig W. Phylogenetische Systematik. Vol. 34. Berlin, Hamburg: Verlag Paul Parey; 1982
49. Schuh R. Biological Systematics. Principles and Applications. Ithaca, NY: Comstock Publishing Associates; 2000
50. Wiley EO. The Theory and Practice of Phylogenetic Systematics. New York: John Wiley and Sons Inc.; 1981
51. de Vargas C, Pawlowski J. Molecular versus taxonomic rates of evolution in planktonic foraminifera. Mol Phylogenet Evol. 1998;9:463-9.
52. Fitch WM, Smith TF. Optimal sequence alignments. Proceedings of the National Academy of Sciences, U S A. 1983;80:1382-6.
53. Wheeler WC. The triangle inequality and character analysis. Mol Biol Evol. 1993;20:707-12.
54. Felsenstein J. Inferring phylogenies. Sunderland, MA, USA.: Sinauer Associates Inc.; 2004.
55. Larkin MA, Blackshields G, Brown NP, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23:2947-8.
56. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;24:4876-82.
57. Lassmann T, Sonnhammer ELL. Kalign-an accurate and fast multiple sequence alignment algorithm. BMC Bioinf. 2005;6:298
58. Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005;33:511-8.
59. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792-97.
60. Lu Y, Sze SH. Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. Nucleic Acids Res. 2009;37:463-72.
61. Lee C, Grasso C, Sharlow M. Multiple sequence alignment using partial order graphs. Bioinformatics. 2002;18:452-64.
62. Wilm A, Mainz I, Steger G. An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol Biol. 2006;1:19
63. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta. Sunderland, MA: Sinauer Associates; 2002
64. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM. Phylogenetic Inference. In: Hillis DM, Moritz C, Mable BK, editors. Molecular Systematics. 2nd ed. Sunderland, MA: Sinauer Associates; 1996:407-514.
65. Stamatakis A. RAxML-VI-HPC: Maximum-Likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006; 22:2688-90.
66. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol. 2008;57:758-71.
67. Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406-25.
68. Kemler M, Göker M, Oberwinkler F, Begerow D. Implications of molecular characters for the phylogeny of the Microbotryaceae (Basidiomycota: Urediniomycetes). BMC Evol Biol. 2006;6:35
69. Darling KF, Kucera M, Kroon D, Wade CM. A resolution for the coiling direction paradox in Neogloboquadrina pachyderma. Paleoceanogr. 2006; 21:PA2011, doi:2010.1029/2005PA001189
70. de Vargas C, Zaninetti L, Hilbrecht H, Pawlowski J. Phylogeny and rates of molecular evolution of planktonic Foraminifera: SSU rDNA sequences compared to the fossil record. Journal of Molecular Evolution. 1997;45:285-94.
71. García-Blázquez G, Göker M, Voglmayr H, Martín MP, Tellería MT, Oberwinkler F. Phylogeny of Peronospora parasitic of Fabaceae based on internal transcribed spacer sequences. Mycol Res. 2008;112:502-12.
72. Göker M, Voglmayr H, García Blázquez G, Oberwinkler F. Species delimitation in downy mildews: the case of Hyaloperonospora in the light of nuclear ribosomal ITS and LSU sequences. Mycol Res. 2009;113: 308-25.
73. Darling KF, Wade CM, Stewart IA, Kroon D, Dingle R, Leigh Brown AJ. Molecular evidence for genetic mixing of Arctic and Antarctic subpolar populations of planktonic foraminifers. Nature. 2000;405:43-7.
74. Aurahs R, Grimm GW, Hemleben V, Hemleben C, Kučera M. Geographical distribution of cryptic genetic types in the planktonic foraminifer Globigerinoides ruber. Mol Ecol. 2009;18:1692-706.
75. Darling K, Kucera M, Pudsey CJ, Wade CM. Molecular evidence links cryptic diversification in polar planktonic protists to Quaternary climate dynamics. Proceedings of the National Academy of Sciences of the U S A. 2004;101:7657-62.
76. Stockinger H, Auch AF, Göker M, Meier-Kolthoff J, Stamatakis A. Largescale co-phylogenetic analysis on the grid. Int J Grid High Perform Comput. 2009;1:39-54.
77. Göker M, Grimm GW. General functions to transform associate data to host data, and their use in phylogenetic inference from sequences with intraindividual variability. BMC Evol Biol. 2008;8:86
78. Schlee M, Göker M, Grimm GW, Hemleben V. Relicts within the genus complex Astragalus/Oxytropis (Fabaceae), and the comparison of diversity by objective means. In: Habel JC, Assmann T, editors. Relict Species. Heidelberg, New York: Springer; 2010:105-118.
79. Darling KF, Wade CM, Kroon D, Leigh Brown AJ. Planktic foraminiferal molecular evolution and their polyphyletic origins from benthic taxa. Mar Micropaleontol. 1997;30:251-66.
80. Darling KF, Kroon D, Wade CM, Leigh Brown AJ. Molecular phylogeny of the planktic foraminifera. J Foram Res. 1996;26:324-30.
81. Pawlowski J, Bolivar I, Fahrni J, de Vargas C, Gouy M, Zaninetti L. Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record. Mol Biol Evol. 1997;14:498-505.
82. Darling KF, Kucera M, Wade CM, von Langen P, Pak D. Seasonal distribution of genetic types of planktonic foraminifer morphospecies in the Santa Barbara Channel and its paleoceanographic implications. Paleoceanogr. 2003;18:1032.