The best-fitting model of nucleotide substitution calculated for each partition was: GTR+ I+Γ (CytB 1st and 2nd position, Myh6 1st and 2nd position, Rag1 1st position), TVM+I+F (Myh6 3rd position, Rag1 2nd position, Rag2 1st position), K81uf+I+ Γ (Rag2 2nd position, Rag2 3rd position), TIM+I+ Γ (CytB 3rd position), TrN+I+ Γ (Rag1 3rd position).
The GC contents for the total and three individual codon positions were similar for the same gene but those at the 3rd position (GC3) is higher in TFIIAγ1 than in TFIIAγ5 (75.9% vs. 70.1%, P < 0.001) [Additional file 3].
Perl scripts were also used to calculate GC content at 3rd position 4-fold degenerate sites (3GCS) and codon bias, measured as effective number of codons (ENC; [ 64]), for each sequence for each gene family.
Frequencies of substitutions were 1st position (61%), 2nd position (32%), and 3rd position (7%).
About 3.1% (691/22193) of the 1st + 2nd position sites and 15.2% (1687/11096) of the 3rd position sites do not fit the Gnepine tree.
To do this, we correlated the GC content of introns and with the GC content at the 3rd position of 2-and 4-fold degenerate amino acids in the exons of the same gene.
In this regard, it is also worth mentioning that some reports [ 41, 42] suggested that the 3rd position of codons can also potentially bias the construction of phylogenetic trees.
DPB1∗39 01v also has a synonymous C > T substitution at the 3rd position of codon 3 in exon 1 (Data not shown).
This hit was ranked in the 14th position by Glide, in the 265th position by Surflex, the 3rd position by FlexX and the 368th position by Gold (see Table 1).
It emphasizes again on the heightened stability of theses complexes than for target DNA sequences rich in A at 2nd and 3rd position of the repeating triplet5' GN(2nd)N 3rd) 3' followed by A at 2nd and T at 3rdposition, then by T at 2nd and 3rd position which form lesser number of H-bond.
Independent contrast plots of recombination rate vs GC content at 3rd position synonymous sites (3GCS) and codon bias (ENC).
