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In this work, we seek to empirically describe the TDRP in detail and explore the various patterns of rate decay over time by using foamy viruses (FVs) as a case study.FVs are a group of complex retroviruses that have a very stable and long co-speciation history with their hosts, stretching back more than a hundred million years .However, given a large number of potential underlying factors and our current incomplete understanding of their interactions, untangling and explicitly accounting for each of them individually would be impractical at present .One pragmatic approach to this problem is to infer evolutionary timescales by using an empirical model describing the relationship between rate estimates and their measurement timescales.nucleotide (3,351 nt) alignments under the Bayesian and maximum-likelihood frameworks.
Given that the TDRP is widespread in nature but has been noted only recently the estimated timescales of many viruses may need to be reconsidered and re-estimated.
Several empirical models have been proposed and used to correct for the time-dependent rate phenomenon (TDRP), such as a vertically-translated exponential rate decay model and a power-law rate decay model.
Nevertheless, at present, it is still unclear which model best describes the rate dynamics.
It appears that substitution rate estimates co-vary very strongly with their timescale of measurement; the shorter the timescale, the higher the estimated value.
Foamy viruses have a long history of co-speciation with their hosts, and one of the lowest estimated rates of evolution among viruses.
Here, we use 14 extant FVs (Additional file : Table S1) as a case study to present direct evidence of a smooth decay of nucleotide substitution rate estimates as the measurement timescale increases.