Time dependency of foamy virus evolutionary rate estimates

Area of Science:

• Evolutionary Biology
• Virology
• Phylogenetics

Background:

• Viral substitution rate estimates vary with measurement timescale; shorter timescales yield higher estimates.
• Foamy viruses exhibit long co-speciation histories and low long-term evolutionary rates, but rapid short-term rates, suggesting time-dependency.
• The time-dependent rate phenomenon (TDRP) complicates accurate evolutionary rate estimation.

Purpose of the Study:

• To empirically describe the TDRP using foamy viruses as a case study.
• To determine the best empirical model for correcting TDRP-affected rate estimates.
• To investigate the impact of molecular clocks on TDRP correction within phylogenetic frameworks.

Main Methods:

• Investigated four empirical models: vertically-translated exponential, simple exponential, vertically-translated power-law, and simple power-law rate decay.
• Analyzed foamy virus data to assess model performance in correcting for TDRP.
• Evaluated the efficacy of current molecular clocks in addressing TDRP within Bayesian phylogenetic analyses.

Main Results:

• The TDRP significantly explains discrepancies in foamy virus short-term and long-term rate estimates.
• The simple power-law rate decay model proved most effective for inferring evolutionary timescales.
• Existing molecular clocks can introduce severe biases in evolutionary date estimates when TDRP is not accounted for.
• TDRP dynamics may vary across viral lineages, potentially biasing estimates if unaddressed.

Conclusions:

• Evolutionary rate estimates must be interpreted within their measurement timescale context.
• Extrapolation of rate estimates across timescales can lead to significant biases in evolutionary inferences.
• Reconsideration and re-estimation of viral timescales are necessary due to the widespread nature of TDRP.
• Developed models can serve as a basis for improving phylogenetic inference tools.