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Lophotrochozoa Internal Phylogeny: New Insights from an Up-to-Date Analysis of Nuclear Ribosomal Genes

Jordi Paps, Jaume Baguñà and Marta Riutort
Proceedings: Biological Sciences
Vol. 276, No. 1660 (Apr. 7, 2009), pp. 1245-1254
Published by: Royal Society
Stable URL: http://www.jstor.org/stable/30243985
Page Count: 10
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Since scans are not currently available to screen readers, please contact JSTOR User Support for access. We'll provide a PDF copy for your screen reader.
Lophotrochozoa Internal Phylogeny: New Insights from an Up-to-Date Analysis of Nuclear Ribosomal Genes
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Abstract

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.

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