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Int J Biol Sci
2006 Jan 01;22:32-7. doi: 10.7150/ijbs.2.32.
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Metaphylogeny of 82 gene families sheds a new light on chordate evolution.
Vienne A
,
Pontarotti P
.
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Achieving a better comprehension of the evolution of species has always been an important matter for evolutionary biologists. The deuterostome phylogeny has been described for many years, and three phyla are distinguishable: Echinodermata (including sea stars, sea urchins, etc...), Hemichordata (including acorn worms and pterobranchs), and Chordata (including urochordates, cephalochordates and extant vertebrates). Inside the Chordata phylum, the position of vertebrate species is quite unanimously accepted. Nonetheless, the position of urochordates in regard with vertebrates is still the subject of debate, and has even been suggested by some authors to be a separate phylum from cephalochordates and vertebrates. It was also the case for agnathans species -myxines and hagfish- for which phylogenetic evidence was recently given for a controversial monophyly. This raises the following question: which one of the cephalochordata or urochordata is the sister group of vertebrates and what are their relationships? In the present work, we analyzed 82 protein families presenting homologs between urochordata and other deuterostomes and focused on two points: 1) testing accurately the position of urochordata and cephalochordata phyla in regard with vertebrates as well as chordates monophyly, 2) performing an estimation of the rate of gene loss in the Ciona intestinalis genome. We showed that the urochordate phyla is the vertebrate sister group and that gene loss played a major role in structuring the urochordate genome.
Figure 1. Schematic representation of the relationships among tripoblasts.
Figure 2. Hypotheses of the phylogenetic relationship among the deuterostome phylum.
Figure 3. Example of phylogenetic reconstruction performed for 4 gene families yielding amphioxus as the sister group of vertebrates, which is the most commonly observed topology. Values at nodes are Bootstrap Proportions (BP) values for the Neighbour-Joining reconstruction.
Figure 4. The concatenated phylogenetic tree obtained using 56 gene families. Values at nodes are Bootstrap Proportion – used to assess the topologies (Felsenstein 1985) – for the Neighbor-Joining, the Maximum Parcimony and the Maximum Likelihood method.
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