Abstract
BackgroundPhylogenetic analyses reveal probable patterns of divergence of present day organisms from common ancestors. The points of divergence of lineages can be dated if a corresponding historical or fossil record exists. For many species, in particular viruses, such records are rare. Recently, Bayesian phylogenetic analysis using sequences from closely related organisms isolated at different times have been used to calibrate divergences. Phylogenetic analyses depend on the assumption that the average substitution rates that can be calculated from the data apply throughout the course of evolution. ResultsThe present study tests this crucial assumption by charting the kinds of substitutions observed between pairs of sequences with different levels of total substitutions. Datasets of aligned sequences, both viral and non-viral, were assembled. For each pair of sequences in an aligned set, the distribution of nucleotide interchanges and the total number of changes were calculated. Data were binned according to total numbers of changes and plotted. The accumulation of the six possible interchange types in retroelements as a function of distance followed closely the expected hyperbolic relationship. For other datasets, however, significant deviations from this relationship were noted. A rapid initial accumulation of transition interchanges was frequent among the datasets and anomalous changes occurred at specific divergence levels. ConclusionsThe accumulation profiles suggested that substantial changes in frequencies of types of substitutions occur over the course of evolution and that such changes should be considered in evaluating and dating viral phylogenies.
Highlights
Phylogenetic analyses reveal probable patterns of divergence of present day organisms from common ancestors
Datasets Six datasets were assembled from sequences available in GenBank/EMBL/DDBJ for coding regions for the large subunit of ribulose bisphosphate carboxylase from red algae, the small subunit of the same enzyme from cereals, reverse transcriptase (RT) coding sequences from retroelements of a diversity of sources
It may not be valid to apply substitution frequencies calculated from recently diverged pairs to evolution of species. These observations suggest strongly that the probabilities of particular substitutions are different at different stages of evolution
Summary
Phylogenetic analyses reveal probable patterns of divergence of present day organisms from common ancestors. Substitution frequencies calculated from analysis of strains of single viral species suggest that many viruses are evolving so rapidly that any traces of distant evolutionary events should be obscured [1,2]. Evidence has been presented [3,4,5,6,7] that phylogenetic trees of larger taxa often mirror those of their hosts, implying codivergence of virus with host. This implication is consistent with conclusions from analysis of viral hallmark genes that viruses existed at the time that cellular life evolved [8]. A recent review [10] suggests, by way of reconciliation of the two views, that different evolutionary mechanisms are at work in viral speciation than in the evolution of viral strains of individual species
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
