Maximum likelihood phylogenies reconstructed from alignments of orthologues to the human CHondroitin sulfate GlucUronylTransferase (CHGUT_HUMAN) exon 4 [left], and to the human Nuclear receptor CO-Activator 1 gene (NCOA1) exon 11 [right]. Values on nodes are ML bootstrap support. Taxa for which the CHGUT_HUMAN and NCOA1 exons were obtained in vivo are indicated in bold + asterisk. Sequences from other taxa were recovered in silico from traces, pre-assembled, and assembled EnsEMBL genomes. The name of major clades is provided on the right, and blue rectangles correspond to Euarchontoglires mammals. The outgroup Monodelphis is drawn with midpoint rooting. Horizontal branch lengths are proportional to the DNA divergence (same scale for both exons = 0.1 nucleotide substitutions per site). Maximum likelihood details about CHGUT_HUMAN|NCOA1 phylograms are respectively as follows: log-likelihoods are lnL = -8,868.8|8,899.4, and estimates of model parameters are: %A = 15.6|29.2, %C = 32.6|27.5, %G = 33.0|21.2, and %T = 18.8|22.1 for base frequencies ; A-C = 1.11|0.63, A-G = 4.61|4.04, A-T = 1.38|0.68, C-G = 0.44|0.54, C-T = 4.17|3.31, and G-T = 1.00 for GTR relative substitution rates ; and α = 0.30|0.51 for rate heterogeneity among sites.
Ranwez et al. BMC Evolutionary Biology 2007 7:241 doi:10.1186/1471-2148-7-241