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2016 ; 90
(16
): 7184-95
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Time-Dependent Rate Phenomenon in Viruses
#MMPMID27252529
Aiewsakun P
; Katzourakis A
J Virol
2016[Aug]; 90
(16
): 7184-95
PMID27252529
show ga
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. 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.
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