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It appears that substitution rate estimates co-vary very strongly with their timescale of measurement; the shorter the timescale, the higher the estimated value.
We also empirically describe the rate decay pattern, examine whether or not the TDRP can explain the discrepancy between FV short-term and long-term rates, and discuss the applications and limitations of our empirical rate decay models, as well as how the TDRP may bias evolutionary inference and rate estimate interpretation.
In total, 13 posterior distributions of (linear regression: correlation coefficient [95 % highest probability density (HPD)] = -0.577 [-0.614, -0.542]; randomisation test: number of randomization tests = 15,000, number of data points for null distribution construction in each test = 100, p Foamy virus (FV) and corresponding host phylogenies, and the relationship between node-to-tip average evolutionary rate estimate and timescale of measurement.
(a, left) FV phylogeny (taxon definitions and Gen Bank sequence accession numbers are in Additional file : Table S1).
Since the rate of evolution is a central component of evolutionary study, an accurate evolutionary inference requires that the TDRP is integrated into the analysis.
An ideal approach to this problem is to understand how the TDRP is generated, and improve evolutionary inference tools so that they can account for the factors underlying the TDRP.