Systematics and DNA barcoding of free-living marine nematodes with emphasis on tropical desmodorids using nuclear SSU rDNA and mitochondrial COI sequences

in Nematology
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The diversity and phylogenetic relationships of the Desmodoridae, a widespread tropical family of free-living marine nematodes, is hitherto poorly known both from molecular and taxonomic points of view. We performed a molecular phylogenetic analysis of marine nematodes to: i) disentangle relationships among tropical desmodorid species; and ii) compare the performance of the nuclear SSU rDNA and mitochondrial COI nucleotide sequences in 42 and 45 nominal species, respectively, to identify species. We generated 27 new sequences of SSU rDNA belonging to five genera not previously sequenced, and 34 new sequences of COI belonging to six genera and four families not previously sequenced. The SSU rDNA tree confirmed the Enoplida to be a monophyletic sister group to the Chromadorida. The family Comesomatidae is a sister group of the Xyalidae within the Monhysterida. Both DNA markers confirmed the congruence between the morphology- and molecular-based phylogenetic inferences for most of the families. Desmodoridae was a monophyletic group, but the relationships within the family could not be recovered; the subfamilies Desmodorinae and Spiriniinae were not monophyletic meanwhile the monophyly of Stilbonematinae was not fully supported due to a few specimens of questionable identity. COI performed better than SSU rDNA to disentangle relationships among closely related species and suggested the presence of cryptic diversity within Desmodoridae. COI is effective to explore cryptic diversity and barcode species within Nematoda, with a possible threshold of genetic distance of 5% between conspecific and interspecific sequences, but DNA barcoding is limited by the poor knowledge of the diversity and taxonomy of the group and the lack of a good reference database of vouchered COI sequences.

Systematics and DNA barcoding of free-living marine nematodes with emphasis on tropical desmodorids using nuclear SSU rDNA and mitochondrial COI sequences

in Nematology

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Figures

  • View in gallery

    Maximum likelihood tree of marine nematode species based on 51 DNA sequences of SSU rDNA. The root of the tree is placed based on midpoint rooting technique. Numbers above/below the branches indicate branch support based on 100 bootstrap replicates (values < 75% are not shown). Taxa above the family level are indicated by capital letters on the nodes (A: Chromadorida, B: Enoplida, C: Monhysterida). Families are indicated by square brackets. Sequences obtained in this study are coded as NN. This figure is published in colour in the online edition of this journal, which can be accessed via http://booksandjournals.brillonline.com/content/journals/15685411.

  • View in gallery

    A section of the maximum likelihood tree (SSU rDNA) in Figure 1 showing only the family Desmodoridae. Numbers above/below the branches indicate branch support based on 100 bootstrap replicates (values < 75% are not shown). Subfamily membership is indicated by colour: Stilbonematinae (red), Desmodorinae (blue) and Spiriniinae (green). Sequences obtained in this study are coded as ND. This figure is published in colour in the online edition of this journal, which can be accessed via http://booksandjournals.brillonline.com/content/journals/15685411.

  • View in gallery

    Relative frequencies of pairwise p-distances for SSU rDNA (top) and COI (bottom) genetic markers.

  • View in gallery

    Maximum likelihood tree of marine nematode species based on 61 DNA sequences of COI. The root of the tree is placed based on midpoint rooting technique. Numbers above/below the branches indicate branch support based on 100 bootstrap replicates (values < 75% are not shown). Families are indicated by square brackets. Sequences obtained in this study are coded as NN. This figure is published in colour in the online edition of this journal, which can be accessed via http://booksandjournals.brillonline.com/content/journals/15685411.

  • View in gallery

    A section of the maximum likelihood tree (COI) in Figure 4 showing only the family Desmodoridae. Numbers above/below the branches indicate branch support based on 100 bootstrap replicates (values < 75% are not shown). Subfamily membership is indicated by colour: Stilbonematinae (red), Desmodorinae (blue) and Spiriniinae (green). Sequences obtained in this study are coded as ND. This figure is published in colour in the online edition of this journal, which can be accessed via http://booksandjournals.brillonline.com/content/journals/15685411.

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