Supplementary information
From the following article:
Tunicates and not cephalochordates are the closest living relatives of vertebrates
Frédéric Delsuc, Henner Brinkmann, Daniel Chourrout and Hervé Philippe
Nature 439, 965-968 (23 February 2006)
doi:10.1038/nature04336
Supplementary methods
This file describes the protocol used to assemble the genomic data. More details on the phylogenetic analyses are also provided with investigations of the effects of taxon sampling, compositional bias and heterotachy on tree reconstruction.
Supplementary Table 1
This table provides the list of all 146 gene names and the number of amino acid positions conserved for each gene alignment.
Supplementary Table 2
This table summarizes the amount and occurrence of missing data per taxa in the complete dataset.
Supplementary Figure 1
This figure presents the most parsimonious tree obtained with Oikopleura dioica used as the single representative of tunicates.
Supplementary Figure 2
This figure shows the maximum likelihood tree obtained with a reduced dataset using Oikopleura as the single representative of tunicates.
Supplementary Figure 3
This figure presents a principal component analysis (PCA) of amino acid frequencies on the complete dataset.
Supplementary Figure 4
This figure shows the maximum likelihood tree obtained with a reduced dataset where the sea-urchin (Strongylocentrotus) is removed from the complete dataset.
Supplementary Figure 5
This figure shows the most parsimonious tree obtained from the complete dataset recoded into six Dayhoff categories.
Supplementary Figure 6
This figure presents the maximum likelihood topology identified by the partitioned-likelihood analysis on the complete dataset.
Supplementary Figure 7
This figure shows the majority rule consensus tree obtained from Bayesian analysis of the complete dataset under a covarion model.
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