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Pictures used on the evolutionary trees were obtained from previous studies (Baum et al. 2005; Gregory 2008) and from the internet, and some of these were modified to be silhouettes.
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We amplified 14 autosomal loci (Table 1) previously shown to be noncoding and selectively neutral and used in studies on the evolutionary histories of great apes [ 57- 60, 71].
Finally, the ratios of K3u/ Ks were used to estimate the evolutionary constraints on the 3'UTRs for individual genes.
Besides an impact on the methodology used to infer the evolutionary relationship of organisms, there has been a movement towards looking at the evolutionary history at different levels of biological complexity besides organisms.
The program PAUP* 4 [ 54] was used to reconstruct the evolutionary relationships based on cox 1 and intron sequences, and to obtain the corresponding matrices of patristic distances.
Codon substitution rate data was loaded into the MySQL relational database and used to assess the evolutionary pressure exerted on specific groups of genes.
Then, the alignment containing 24 diverse orthologous sequences (mentioned above) was used to calculate the conservation on individual positions using the evolutionary trace algorithm (Lichtarge et al, 2003) and the level of residue conservation was mapped to its corresponding position in the model and visualized with YASARA (Krieger et al, 2004).
The divergence times were estimated based on Bayesian inference using the evolutionary rates of Cytb obtained in the previous section.
Their comparative analysis has been used to shed light on the evolutionary history of given taxa and on the molecular processes that regulate the evolution of the mitochondrial genome.
This method relies on our ability to use the evolutionary history of a group to predict the characteristics of an extinct member, given what we know of its living relatives.
Tests for heterogeneous selective pressures were carried out on the resolved phylogeny using the evolutionary models implemented in PAML 3.15 [ 39] and the complete MSA.
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