Arch Virol (2006) 151: 1625–1633
Analyses on mutation patterns, detection of population
bottlenecks, and suggestion of deleterious-compensatory
evolution among members of the genus Potyvirus
H. Wang, L. F. Huang, and J. I. Cooper
NERC/Centre for Ecology and Hydrology-Oxford
, Oxford, U.K.
Received October 5, 2005; accepted January 31, 2006
Published online March 16, 2006
Summary. Viruses of the family Potyviridae exhibited a robust single-nucleotide
polymorphism proﬁle at the between-species level, conforming to the neutral the-
ory rule. However, the ratios of nonsynonymous to synonymous mutations (Ka/Ks)
were relatively greater between-species than within-species in viral cistrons exam-
ined from members of the genus Potyvirus, indicating a relaxation on constraint.
Judged by the McDonald and Kreitman’s test, the ﬁxation frequencies for nonsyn-
onymous mutations across the genomes of closely related potyviruses were greater
than expected, suggesting population bottlenecks at speciation. These mutation
patterns are best explained by a deleterious-compensatory model.
The neutral theory of molecular evolution proposes that most observed within- and
between-species variations are functionally neutral. Synonymous substitutions
are assumed relatively neutral whereas nonsynonymous substitutions may be
advantageous or deleterious or neutral. Advantageous mutagenesis is rare, and
most nonsynonymous mutation is deleterious, so tends to be eliminated from
large populations. Fixation of neutral mutations is governed by genetic drift. The
nearly neutral theory emphasizes that slightly deleterious mutations may also be
ﬁxed as effectively neutral variants in small populations, and the importance of
near neutrality is increasingly supported by evidence .
Combining the concepts of slightly deleterious mutation, Muller’s ratchet
(genetic melt-down via transmission bottleneck) , and compensatory mutation
Formerly Institute of Virology and Environmental Microbiology.