Probably, the key message is that viral evolution is a complex network of relationship that involves both numerous gene exchanges and intervals of vertical evolution of gene modules[ 28, 29].
On the one hand, various evolutionary processes from fields in physics, population dynamics, aeronautics, economics, and engineering are characterized by the fact that they undergo abrupt changes of state at certain moments of time between intervals of continuous evolution.
These long periods of stasis are punctuated by shorter intervals of rapid evolution under positive selection during which new dominant lineages quickly displace previously coexisting ones.
The preponderance of positive selection during intervals of rapid evolution is supported by the dramatic excess of amino acid replacements in the epitope regions of HA compared to replacements in the rest of the HA molecule.
A substantial excess of intron gains has been detected only for those intervals of eukaryotic evolution that are associated with major evolutionary innovations, such as the origin of eukaryotes and animals [ 5, 12- 14].
The interval of niche evolution continued throughout the invasion and at least the first million years of the post-invasion interval, as niche stability increased very slightly post-invasion but remained substantially below pre-invasion stability levels (Malizia and Stigall 2011).
The apparent time interval between initiation of evolution of the aVDPVs and the Sabin 2/Sabin 1 recombination event might be explained by re-exposure of a chronically infected infant with trivalent OPV at age 5 to 6 or by contact with immunized siblings.
A geomagnetic jerk represents a sudden V-shaped change in the field first time-derivative, or a step change in the second time-derivative (field acceleration), separating two time intervals of quasi-constant evolution (Courtillot et al., 1978).
Unexpectedly, it was found that the evolution of H3N2 HA includes long intervals of generally neutral sequence evolution without apparent substantial antigenic change ("stasis" periods) that are characterized by an excess of synonymous over nonsynonymous substitutions per site, lack of association of amino acid replacements with epitope regions, and slow extinction of coexisting virus lineages.
As described in [56], we then estimated (with confidence intervals) the evolution of the hidden learning state from the sequence of observed outcomes.
