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Abstract

Long term reduction in effective population size will lead to major shift in genome evolution. In
particular, when effective population size is small, genetic drift becomes dominant over natural
selection. The onset of self-fertilization is one evolutionary event considerably reducing effective size
of populations. Theory predicts that this reduction should be more dramatic in organisms capable for
haploid than for diploid selfing. Although theoretically well-grounded, this assertion received mixed
experimental support. Here we test this hypothesis by analyzing synonymous codon usage bias of
genes in the model moss Physcomitrella patens frequently undergoing haploid selfing. In line with
population genetic theory, we found that the effect of natural selection on synonymous codon usage
bias is very weak. Our conclusion is supported by four independent lines of evidence: a) Very weak or
nonsignificant correlation between gene expression and codon usage bias; b) No increased codon
usage bias in more broadly expressed genes; c) No evidence that codon usage bias would constrain
synonymous and nonsynonymous divergence; d) Predominant role of genetic drift on synonymous
codon usage predicted by a model-based analysis. These findings show striking similarity to those
observed in AT-rich genomes with weak selection for optimal codon usage and GC content overall.
Our finding is in contrast to a previous study reporting adaptive codon usage bias in the moss P.
patens.