The Hedgehog Signaling Cascade System: Evolution and Functional Dynamics

10.1007/s10541-008-2014-9

“…Molecular evolution of genes encoding proteins of Hh and Dpp/BMP cascade signals. Gene evolution modes were analyzed in two steps [41,42]. The first step includ ed search of protein sites for which there was positive selection at the codon level in corresponding gene regions.…”

“…We used standard programs of molecular evolution analysis [41,42]. Positive selection was considered as valid when it was confirmed by most programs.…”

“…Although nematodes are not an ancestral group for Bilateria, they diverged from the common trunk a long time ago and therefore the presence of some fea tures typical for the nematode Hh/Ptc cascade could not be ruled out in common Bilateria ancestors. Several methods were used, and positive selection was considered as valid when most methods indicated statistically signifi cant presence of the positive selection [42]. Statistical sig nificance under conditions of large evolutionary distances was additionally evaluated by the computer test based on modeling of protein evolution [42].…”

“…Several methods were used, and positive selection was considered as valid when most methods indicated statistically signifi cant presence of the positive selection [42]. Statistical sig nificance under conditions of large evolutionary distances was additionally evaluated by the computer test based on modeling of protein evolution [42]. Simulated genes were built up by means of random reverse translation from amino acids into codons of the modeled proteins.…”

“…The resulting limits of intervals were compared with degree of positive selection [42] calculated for real genes. If degree of posi tive selection calculated for real genes exceeded upper limits of statistical intervals, positive selection was identi fied for the tree branch.…”