Presented here is an analysis of the molecular evolutionary dynamics of the
P gene among 76 representative sequences of the Paramyxoviridae and Rhabdo
viridae RNA virus families. In a number of Paramyxoviridae taxa, as well as
in vesicular stomatitis viruses of the Rhabdoviridae, the P gene encodes m
ultiple proteins from a single genomic RNA sequence. These products include
the phosphoprotein (P), as well as the C and V proteins. The complexity of
the P gene makes it an intriguing locus to study from an evolutionary pers
pective. Amino acid sequence alignments of the proteins encoded at the P an
d N loci were used in independent phylogenetic reconstructions of the Param
yxoviridae and Rhabdoviridae families. P-gene-coding capacities were mapped
onto the Paramyxoviridae phylogeny, and the most parsimonious path of mult
iple-coding-capacity evolution was determined. Levels of amino acid variati
on for Paramyxoviridae and Rhabdoviridae P-gene-encoded products were also
analyzed. Proteins encoded in overlapping reading frames from the same nucl
eotides have different levels of amino acid variation. The nucleotide archi
tecture that underlies the amino acid variation was determined in order to
evaluate the role of selection in the evolution of the P gene overlapping r
eading frames. In every case, the evolution of one of the proteins encoded
in the overlapping reading frames has been constrained by negative selectio
n while the other has evolved more rapidly. The integrity of the overlappin
g reading frame that represents a derived state is generally maintained at
the expense of the ancestral reading frame encoded by the same nucleotides.
The evolution of such multicoding sequences is likely a response by RNA vi
ruses to selective pressure to maximize genomic information content while m
aintaining small genome size. The ability to evolve such a complex genomic
strategy is intimately related to the dynamics of the viral quasispecies, w
hich allow enhanced exploration of the adaptive landscape.