Lophotrochozoa internal phylogeny: New insights from an up-to-date analysis of nuclear ribosomal genes

Jordi Paps, Jaume Baguñà, Marta Riutort*

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

99 Citations (Scopus)


Resolving the relationships among animal phyla is a key biological problem that remains to be solved. Morphology is unable to determine the relationships among most phyla and although molecular data have unveiled a new evolutionary scenario, they have their own limitations. Nuclear ribosomal genes (18S and 28S rDNA) have been used effectively for many years. However, they are considered of limited use for resolving deep divergences such as the origin of the bilaterians, due to certain drawbacks such as the long-branch attraction (LBA) problem. Here, we attempt to overcome these pitfalls by combining several methods suggested in previous studies and routinely used in contemporary standard phylogenetic analyses but that have not yet been applied to any bilaterian phylogeny based on these genes. The methods used include maximum likelihood and Bayesian inference, the application of models with rate heterogeneity across sites, wide taxon sampling and compartmentalized analyses for each problematic clade. The results obtained show that the combination of the above-mentioned methodologies minimizes the LBA effect, and a new Lophotrochozoa phylogeny emerges. Also, the Acoela and Nemertodermatida are confirmed with maximum support as the first branching bilaterians. Ribosomal RNA genes are thus a reliable source for the study of deep divergences in the metazoan tree, provided that the data are treated carefully.

Original languageEnglish
Pages (from-to)1245-1254
Number of pages10
JournalProceedings of the Royal Society B: Biological Sciences
Issue number1660
Publication statusPublished - 7 Apr 2009


  • Bayesian inference
  • Deuterostomia
  • Ecdysozoa
  • Long-branch attraction
  • Maximum likelihood
  • Ribosomal genes


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