Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward crown Clades.

@article{Holterman2006PhylumwideAO,
  title={Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward crown Clades.},
  author={Martijn H.M. Holterman and Andr{\'e} W. G. van der Wurff and Sven J.J. van den Elsen and Hanny van Megen and Tom Bongers and Oleksandr Holovachov and Jaap A. Bakker and Johannes Helder},
  journal={Molecular biology and evolution},
  year={2006},
  volume={23 9},
  pages={
          1792-800
        }
}
Inference of evolutionary relationships between nematodes is severely hampered by their conserved morphology, the high frequency of homoplasy, and the scarcity of phylum-wide molecular data. To study the origin of nematode radiation and to unravel the phylogenetic relationships between distantly related species, 339 nearly full-length small-subunit rDNA sequences were analyzed from a diverse range of nematodes. Bayesian inference revealed a backbone comprising 12 consecutive dichotomies that… 

Figures and Tables from this paper

Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny
TLDR
Expanded transcriptome sequencing of free-living nematodes has contributed to better resolution among deep nematode lineages, though the dataset is still strongly biased toward parasites.
Small subunit rDNA-based phylogeny of the Tylenchida sheds light on relationships among some high-impact plant-parasitic nematodes and the evolution of plant feeding.
TLDR
The data suggest that root knot nematodes have evolved from an ancestral member of the genus Pratylenchus, but it remains unclear which species is closest to this branching point, and resolution till species was observed, suggesting that SSU rDNA sequences have a potential for DNA barcode-based species identification with.
Reconstructing the phylogenetic relationships of nematodes using draft genomes and transcriptomes
TLDR
The analysis of the supermatrix with maximum likelihood and Bayesian inference methods sheds light into the early splitting clades of the phylogenetic tree of nematodes and the derived clades III, IV and V, unveiling the evolutionary history of these important taxa.
Molecular characterization and phylogeny of whipworm nematodes inferred from DNA sequences of cox1 mtDNA and 18S rDNA
TLDR
It is demonstrated that the 18S rDNA and cox1 mtDNA genes provide resolution at different levels, but together resolve relationships among geographic populations and species in the genus Trichuris.
Monophyly of clade III nematodes is not supported by phylogenetic analysis of complete mitochondrial genome sequences
BackgroundThe orders Ascaridida, Oxyurida, and Spirurida represent major components of zooparasitic nematode diversity, including many species of veterinary and medical importance. Phylum-wide
Systematics and DNA barcoding of free-living marine nematodes with emphasis on tropical desmodorids using nuclear SSU rDNA and mitochondrial COI sequences
TLDR
COI performed better than SSU rDNA to disentangle relationships among closely related species and suggested the presence of cryptic diversity within Desmodoridae, which is effective to explore cryptic diversity and barcode species within Nematoda.
Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes
TLDR
The topology of the Nematoda backbone was consistent with previous studies, including polyphyletic placement of sampled representatives of Monhysterida and Araeolaimida, and all suborders within Strongylida.
Moving towards a complete molecular framework of the Nematoda: a focus on the Enoplida and early-branching clades
TLDR
The authors' analysis could not unequivocally confirm the earliest splits in the nematode tree, and outgroup choice significantly affected the observed branching order of the Dorylaimia and Enoplia, so it appears unlikely that single-gene phylogenies using the conserved 18S gene will be useful for confirming the branching order at the base of the nem atode tree-future efforts will require multi-gree analyses or phylogenomic methods.
...
...

References

SHOWING 1-10 OF 71 REFERENCES
A molecular evolutionary framework for the phylum Nematoda
TLDR
It is suggested that animal parasitism arose independently at least four times, and plant parasitism three times, which indicates that convergent morphological evolution may be extensive and that present higher-level classification of the Nematoda will need revision.
Phylogeny of Nematoda and Cephalorhyncha Derived from 18S rDNA
TLDR
Nematodes, nematomorphs, tardigrades, arthropods, and cephalorhynchs are a paraphyletic association of closely related taxa that is the closest to the coelomate animals.
Patterns and processes in the evolution of animal parasitic nematodes
TLDR
With this dataset, the Strongylida is placed as a monophyletic clade nested within the Rhabditina, and the Ascaridida, Oxyurida and Spirurida are closely related, but currently have no clear closest free-living sister taxon.
Evolution of plant parasitism among nematodes.
TLDR
Although Tylenchida rRNA phylogenies are not fully resolved, they strongly support convergent evolution of sedentary endoparasitism and plant nurse cells in cyst and root-knot nematodes and the possible use of genes obtained by horizontal transfer from prokaryotes.
The new phylogeny of eukaryotes.
Evidence for a clade of nematodes, arthropods and other moulting animals
TLDR
The results suggest that ecdysis (moulting) arose once and support the idea of a new clade, Ecdysozoa, containing moulting animals: arthropods, tardigrades, onychophorans, nematodes, Nematomorphs, kinor-hynchs and priapulids.
Molecular phylogeny: pitfalls and progress.
  • D. Moreira, H. Philippe
  • Biology
    International microbiology : the official journal of the Spanish Society for Microbiology
  • 2000
TLDR
The discovery of several pitfalls affecting molecular phylogenetic reconstruction challenged the general validity of this approach and strategies proposed to overcome their effects are discussed.
Nematode phylogeny and embryology
TLDR
It is pointed out that three distinct patterns of early embryonic development reported for nematodes are in good agreement with this new classification, which could be more consistent with the natural nematode system than with the usual morphological criteria.
Molecular barcodes for soil nematode identification
TLDR
A molecular barcode derived from single‐specimen polymerase chain reaction (PCR) and sequencing of the 5′ segment of the small subunit ribosomal RNA (SSU) gene is developed, which allows a rapid assessment of nematode taxon diversity in soils.
Unusual cleavage and gastrulation in a freshwater nematode: developmental and phylogenetic implications
TLDR
It is shown by using Nomarski optics that development of the freshwater nematode Tobrilus diversipapillatus differs from this pattern in two prominent aspects and is allowed to reject a number of conceivable correlations between the type of gastrulation and other developmental parameters.
...
...