title: Multigene phylogenies of clonal Spumella-like strains, a cryptic heterotrophic nanoflagellate, isolated from different geographical regions.
abstract: Many nanoflagellate morphospecies comprise an enormous variation of genotypes, probably indicating cryptic species. One of the best-investigated morphospecies with respect to molecular and ecophysiological variation are flagellates of the Spumella morphotype. Here, we have phylogenetically analysed three protein-coding genes (actin, alpha-tubulin, beta-tubulin), internal transcribed spacers (ITS1, ITS2) and the 5.8S rDNA of 17 Spumella-like strains isolated from soil, freshwater and marine samples in order to (i) test the validity of the current Spumella-like phylogenetic classification system based exclusively on small subunit (SSU) rDNA, (ii) elucidate the phylogenetic associations of SSU rDNA-unresolved strains and (iii) evaluate the validity of the assignment of ecophysiological adaptations to previously identified SSU rDNA sequence clades. All single-gene analyses show different patterns of support, are incongruent and identify a number of conflicting nodes. Likewise, a concatenation of all protein genes fails to recover specific SSU rDNA clades. However, a combined analysis of all genes confidently resolved the conflicts of the single genes and the protein-gene concatenations and resulted in a tree topology that is identical to the SSU rDNA analysis, but with enhanced phylogenetic resolution and decisively greater support. We conclude that, depending on the genes concatenated, a 'supergene' analysis minimizes artefactual effects of single genes and may be superior in its performance in phylogenetically analysing cryptic species. We confirm the validity of the SSU rDNA Spumella-like phyloclades and support the suggestion that these clades indeed seem to reflect certain ecophysiological adaptations.
authors.affiliation: School of Biology, University Kaiserslautern, Erwin-Schrödinger Str. 14, D-67663 Kaiserslautern, Germany. stoeck@rhrk.uni-kl.de
authors.forename: Thorsten
authors.initials: T
authors.lastname: Stoeck
authors.forename: Steffen
authors.initials: S
authors.lastname: Jost
authors.forename: Jens
authors.initials: J
authors.lastname: Boenigk
mesh_terms: D000199:Actins / Q000235:genetics; D000818:Animals; D016054:DNA, Protozoan / Q000032:analysis; D021903:DNA, Ribosomal Spacer / Q000032:analysis; D056890:Eukaryota / Q000145:classification / Q000235:genetics* / Q000254:growth & development / Q000302:isolation & purification; D005618:Fresh Water / Q000469:parasitology*; D005843:Geography; D052836:Heterotrophic Processes; D008969:Molecular Sequence Data; D010802:Phylogeny; D015800:Protozoan Proteins / Q000235:genetics*; D012340:RNA, Ribosomal, 5.8S / Q000235:genetics; D012623:Seawater / Q000469:parasitology*; D017422:Sequence Analysis, DNA; D012987:Soil / Q000469:parasitology*; D014404:Tubulin / Q000235:genetics
chemical_list: D000199:Actins; D016054:DNA, Protozoan; D021903:DNA, Ribosomal Spacer; D015800:Protozoan Proteins; D012340:RNA, Ribosomal, 5.8S; D012987:Soil; D014404:Tubulin