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Animal EvolutionGenomes, Fossils, and Trees$
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Maximilian J. Telford and D.T.J. Littlewood

Print publication date: 2009

Print ISBN-13: 9780199549429

Published to Oxford Scholarship Online: September 2009

DOI: 10.1093/acprof:oso/9780199549429.001.0001

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Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

Chapter:
(p.127) CHAPTER 12 Improvement of molecular phylogenetic inference and the phylogeny of Bilateria
Source:
Animal Evolution
Author(s):

Nicolas Lartillot

Hervé Philippe

Publisher:
Oxford University Press
DOI:10.1093/acprof:oso/9780199549429.003.0012

Inferring the relationships among Bilateria has been an active and controversial research area since Haeckel. The lack of a sufficient number of phylogenetically reliable characters was the main limitation of traditional phylogenies based on morphology. With the advent of molecular data, this problem has been replaced by another, statistical inconsistency, which stems from an erroneous interpretation of convergences induced by multiple changes. The analysis of alignments rich in both genes and species, combined with a probabilistic method (Maximum Likelihood or Bayesian) using sophisticated models of sequence evolution, should alleviate these two major limitations. This chapter applies this approach to a dataset of 94 genes from 79 species using the CAT model, which accounts for site-specific amino-acid replacement patterns. The resulting tree is in good agreement with current knowledge: the monophyly of most major groups (e.g. Chordata, Arthropoda, Lophotrochozoa, Ecdysozoa, Protostomia) was recovered with high support. Two results are surprising and are discussed in an evo-devo framework: the sister-group relationship of Platyhelminthes and Annelida to the exclusion of Mollusca, contradicting the Neotrochozoa hypothesis, and, with a lower statistical support, the paraphyly of Deuterostomia. These results, in particular the status of deuterostomes, need further confirmation, both through increased taxonomic sampling, and future improvements of probabilistic models.

Keywords:   phylogenomics, deuterostomes, systematic error, taxon sampling

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