Abstract
Mating systems are thought to play a key role in molecular evolution through their effects on effective
population size (N e ) and effective recombination rate. Because of reduced N e , selection in self-fertilizing
species is supposed to be less efficient, allowing fixation of weakly deleterious alleles or lowering adap-
tation, which may jeopardize their long-term evolution. Relaxed selection pressures in selfers should be
detectable at the molecular level through the analyses of the ratio of nonsynonymous and synonymous
divergence, D n /D s , or the ratio of nonsynonymous and synonymous polymorphism, p n /p s . On the other
hand, selfing reveals recessive alleles to selection (homozygosity effect), which may counterbalance the
reduction in N e . Through population genetics models, this study investigates which process may prevail in
natural populations and which conditions are necessary to detect evidence for relaxed selection signature
at the molecular level in selfers. Under a wide range of plausible population and mutation parameters,
relaxed selection against deleterious mutations should be detectable, but the differences between the two
mating systems can be weak. At equilibrium, differences between outcrossers and selfers should be more
pronounced using divergence measures (D n /D s ratio) than using polymorphism data (p n /p s ratio). The
difference in adaptive substitution rates between outcrossers and selfers is much less predictable because
it critically depends on the dominance levels of new advantageous mutations, which are poorly known.
Different ways of testing these predictions are suggested, and implications of these results for the evo-
lution of self-fertilizing species are also discussed.
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