title: An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa.
abstract: Phylogenetic reconstructions of relations within the phylum Nematoda are inherently difficult but have been advanced with the introduction of large-scale molecular-based techniques. However, the most recent revisions were heavily biased towards terrestrial and parasitic species and greater representation of clades containing marine species (e.g. Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, Enoplida, and Monhysterida) is needed for accurate coverage of known taxonomic diversity. We now add small subunit ribosomal DNA (SSU rDNA) sequences for 100 previously un-sequenced species of nematodes, including 46 marine taxa. SSU rDNA sequences for >200 taxa have been analysed based on Bayesian inference and LogDet-transformed distances. The resulting phylogenies provide support for (i) the re-classification of the Secernentea as the order Rhabditida that derived from a common ancestor of chromadorean orders Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, and Monhysterida and (ii) the position of Bunonema close to the Diplogasteroidea in the Rhabditina. Other, previously controversial relationships can now be resolved more clearly: (a) Alaimus, Campydora, and Trischistoma belong in the Enoplida, (b) Isolaimium is placed basally to a big clade containing the Axonolaimidae, Plectidae, and Rhabditida, (c) Xyzzors belongs in the Desmodoridae, (d) Comesomatidae and Cyartonema belongs in the Monhysterida, (e) Globodera belongs in the Hoplolaimidae and (f) Paratylenchus dianeae belongs in the Criconematoidea. However, the SSU gene did not provide significant support for the class Chromadoria or clear evidence for the relationship between the three classes, Enoplia, Dorylaimia, and Chromadoria. Furthermore, across the whole phylum, the phylogenetically informative characters of the SSU gene are not informative in a parsimony analysis, highlighting the short-comings of the parsimony method for large-scale phylogenetic modelling.
authors.affiliation: School of Ocean and Earth Science, Southampton Oceanography Centre, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK. bhmm2@hutchison-mrc.cam.ac.uk
authors.forename: Birgit H M
authors.initials: BH
authors.lastname: Meldal
authors.forename: Nicola J
authors.initials: NJ
authors.lastname: Debenham
authors.forename: Paul
authors.initials: P
authors.lastname: De Ley
authors.forename: Irma Tandingan
authors.initials: IT
authors.lastname: De Ley
authors.forename: Jacques R
authors.initials: JR
authors.lastname: Vanfleteren
authors.forename: Andy R
authors.initials: AR
authors.lastname: Vierstraete
authors.forename: Wim
authors.initials: W
authors.lastname: Bert
authors.forename: Gaetan
authors.initials: G
authors.lastname: Borgonie
authors.forename: Tom
authors.initials: T
authors.lastname: Moens
authors.forename: Paul A
authors.initials: PA
authors.lastname: Tyler
authors.forename: Melanie C
authors.initials: MC
authors.lastname: Austen
authors.forename: Mark L
authors.initials: ML
authors.lastname: Blaxter
authors.forename: Alex D
authors.initials: AD
authors.lastname: Rogers
authors.forename: P J D
authors.initials: PJ
authors.lastname: Lambshead
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D029422:Campanulaceae / Q000235:genetics*; D017753:Ecosystem; D019143:Evolution, Molecular; D008954:Models, Biological; D009348:Nematoda / Q000145:classification / Q000235:genetics*; D010802:Phylogeny