Abstract
Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. Ramp sequences were compared from 247 vertebrates (114 Mammalian and 133 non-mammalian), where the presence and absence of ramp sequences was analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life synthetic tree to determine the number of parallelisms and reversals that occurred, and those results were compared to random permutations. Parsimony and maximum likelihood analyses of the presence and absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, 81% of vertebrate mammalian ramps and 81.2% of other vertebrate ramps had less parallelisms and reversals than the mean from 1000 randomly permuted trees. A chi-square analysis of completely orthologous ramp sequences resulted in a p-value < 0.001 as compared to random chance. Ramp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches if many orthologs are taken into account. However, phylogenomic methods utilizing few orthologs should be cautious in incorporating ramp sequences because individual ramp sequences may provide conflicting signals.
Highlights
Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes
The central dogma of biology states that DNA is transcribed into RNA, which is subsequently translated in sets of three consecutive nucleotides, called codons[1]
Given the widespread presence of ramp sequences in most domains of life and their role in regulating translation, here we investigate the hypothesis that the presence or absence of a ramp sequence in a gene may be used as a morphological genomic character that can be used to recover a phylogenetic signal
Summary
Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. If an outlier portion is present at the beginning of the gene, it is considered a ramp sequence Using this algorithm, about 10% of genes in most species across most domains of life were shown to contain ramp sequences[9]. Given the widespread presence of ramp sequences in most domains of life and their role in regulating translation, here we investigate the hypothesis that the presence or absence of a ramp sequence in a gene may be used as a morphological genomic character that can be used to recover a phylogenetic signal. We analyzed the potential of ramp sequences to be used as a novel phylogenetic character state in order to determine the extent to which ramp sequences can be incorporated in phylogenomic analyses. The potential for using ramp sequences in future phylogenomic studies is evaluated
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