Genome composition (such as GC- and AT-content) and subsequent balance of codon usage and eukaryotic translation machinery play an important role in the evolution of the nucleotides at the wobble position.
First, we ignore the effects of neighboring nucleotides while, in principle, co-evolution of the nucleotide immediately after the stop codon may be effecting TAG frequency more than that of TGA and TAA frequencies through either contextually-dependent mutational effects [ 18, 19] or by affecting the efficiency of stop-codon recognition [ 9- 12].
Competence has important implications for the ecology and evolution of bacteria: the nucleotides salvaged from the degradation of incoming DNA provide nutrients, and the alleles introduced by transformation can provide genetic novelty and templates for DNA repair.
MrModelTest [ 87] and ProtTest 1.3 [ 88] were used to select the appropriate model of sequences evolution for the nucleotides and amino acid data, respectively.
Used a methodology could be transferred to other computationally intensive routines in the PHYLIP Package, such as the routines in the package that are relevant to the study of evolution at the nucleotide level.
Additionally, our results were inferred through analysis of haplotypes in a phylogenetic framework, thus allowing a more accurate representation of the evolution of particular nucleotides within the lineage of an allele.
Although among site-rate heterogeneity can be efficiently modelled by fitting a gamma-distribution [ 24] or by assuming a proportion of invariable sites [ 25], these standard models make several assumptions, such as the independent evolution of nucleotide sites, and the spatial homogeneity of the substitution process across sites.
The neutral theory of molecular evolution accentuates that most of the nucleotide substitutions in a gene are due to the random fixation of neutral mutations (Kimura 1983), which is in accordance with the proposal that functionally important genes should evolve slower than less important genes (Kimura and Ohta 1974).
To study the origin and evolution of the UCRs, we concatenated the nucleotide sequences of 32 UCRs which were shared by 22 mammalian Hox sequences (see Additional file 2) for the seven eutherian species.
ModelTest 3.7 [46] and ProtTest 2.4 [47] were used to find the most appropriate models of evolution respectively for the nucleotide datasets and the amino-acid dataset.
