Abstract
ABSTRACTAmong the most fundamental questions in viral evolutionary biology are how fast viruses evolve and how evolutionary rates differ among viruses and fluctuate through time. Traditionally, viruses are loosely classed into two groups: slow-evolving DNA viruses and fast-evolving RNA viruses. As viral evolutionary rate estimates become more available, it appears that the rates are negatively correlated with the measurement timescales and that the boundary between the rates of DNA and RNA viruses might not be as clear as previously thought. In this study, we collected 396 viral evolutionary rate estimates across almost all viral genome types and replication strategies, and we examined their rate dynamics. We showed that the time-dependent rate phenomenon exists across multiple levels of viral taxonomy, from the Baltimore classification viral groups to genera. We also showed that, by taking the rate decay dynamics into account, a clear division between the rates of DNA and RNA viruses as well as reverse-transcribing viruses could be recovered. Surprisingly, despite large differences in their biology, our analyses suggested that the rate decay speed is independent of viral types and thus might be useful for better estimation of the evolutionary time scale of any virus. To illustrate this, we used our model to reestimate the evolutionary timescales of extant lentiviruses, which were previously suggested to be very young by standard phylogenetic analyses. Our analyses suggested that these viruses are millions of years old, in agreement with paleovirological evidence, and therefore, for the first time, reconciled molecular analyses of ancient and extant viruses.IMPORTANCE This work provides direct evidence that viral evolutionary rate estimates decay with their measurement timescales and that the rate decay speeds do not differ significantly among viruses despite the vast differences in their molecular features. After adjustment for the rate decay dynamics, the division between the rates of double-stranded DNA (dsDNA), single-stranded RNA (ssRNA), and ssDNA/reverse-transcribing viruses could be seen more clearly than before. Our results provide a guideline for further improvement of the molecular clock. As a demonstration of this, we used our model to reestimate the timescales of modern lentiviruses, which were previously thought to be very young, and concluded that they are millions of years old. This result matches the estimate from paleovirological analyses, thus bridging the gap between ancient and extant viral evolutionary studies.
Highlights
Among the most fundamental questions in viral evolutionary biology are how fast viruses evolve and how evolutionary rates differ among viruses and fluctuate through time
We demonstrated the use of our time-dependent rate phenomenon (TDRP) model by estimating the evolutionary timescale of extant lentiviruses, which has always been severely underestimated by standard phylogenetic analyses
As shown previously [26, 27], our analyses suggested that viral evolutionary rate estimates are negatively correlated with their measurement timescales (P value of Ͻ0.05 in 1,000/1,000 subanalyses; combined P value, Ͻ0.001)
Summary
Among the most fundamental questions in viral evolutionary biology are how fast viruses evolve and how evolutionary rates differ among viruses and fluctuate through time. As a demonstration of this, we used our model to reestimate the timescales of modern lentiviruses, which were previously thought to be very young, and concluded that they are millions of years old This result matches the estimate from paleovirological analyses, bridging the gap between ancient and extant viral evolutionary studies. RNA viruses are generally characterized by frequent cross-species transmissions in nature; as a result, it is often difficult to calibrate their evolutionary rates using host evolutionary timescales Their rates are often calculated by using molecular sequences collected at different time points (heterochronous molecular data sets). The differences among sampling times provide the timescales for the observed genetic divergence Based on these analyses, their rates are commonly estimated to be between 10Ϫ2 and 10Ϫ5 s/n/y [8,9,10,11], 2 to 7 orders of magnitude higher than the typical rates of dsDNA viruses. On the other hand, when the cospeciation assumption is applicable to RNA viruses, such as deltaretroviruses, hantaviruses, 7184 jvi.asm.org
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.