We therefore tested whether the increase of substitution rate observed in Mecopterida usp could be due, at least in part, to GC-biased gene conversion along branch A. First, the two ancestral sequences for the internal nodes at each extremity of branch A were determined by marginal reconstruction performed with Codeml within PAML software (Yang et al. 1997).
Relative rate test which was used for the estimation of the evolutionary rate among lineages was performed by the pair-wise comparisons of synonymous substitutions (Ks) and non-synonymous substitutions (Ka) for nucleotide and amino acid variations for protein sequences; the node A sequence was used as an outgroup.
For example, if we have an in-degree sequence of {3,2,1}, then we get an in-degree node frequency sequence of {1,1,1,2,2,3} with respect to the given in-degree sequence, for the first node having three in-coming edges in the network.
To generate the degree preserving random network, first the degree sequences for nodes in the regulatory relation network were generated, including both the in-degree sequence and the out-degree sequence.
For each alignment with N sequences, ancestral sequences for the N-1 internal nodes were reconstructed.
Analyzing ancestral sequences is a powerful method to elucidate the evolution of opsin sequences [23], thus we reconstructed ancestral RH1 sequences for internal nodes of the species tree and inferred the changes that occurred on each lineage.
With data from mixed sources, the sequences for each target node can be aligned in a ranked order; on the other hand, the graph representation of reconstructed sequences tolerates inconsistencies between subsequent alignments and the algorithm can resolve conflicting gap patterns among a set of diverged sequences.
The constituent domains of a large fraction of human proteins (13,665, ~ 38.5%) have their origins at a single evolutionary node (number of protein sequences for each node are shown in Figure 9a) out of which, 217 sequences have originated only from the Homo sapiens node.
Briefly, this method reconstructs ancestral sequences for each node in a phylogenetic tree using parsimony and identifies all substitutions that result in nonsynonymous and synonymous changes for each node.
