Abstract
A major current molecular evolution challenge is to link comparative genomic patterns to species' biology and ecology. Breeding systems are pivotal because they affect many population genetic processes and thus genome evolution. We review theoretical predictions and empirical evidence about molecular evolutionary processes under three distinct breeding systems-outcrossing, selfing, and asexuality. Breeding systems may have a profound impact on genome evolution, including molecular evolutionary rates, base composition, genomic conflict, and possibly genome size. We present and discuss the similarities and differences between the effects of selfing and clonality. In reverse, comparative and population genomic data and approaches help revisiting old questions on the long-term evolution of breeding systems.
Highlights
In-depth investigations on genome organization and evolution are increasing and have revealed marked contrasts between species, e.g., evolutionary rates, nucleotide composition, and gene repertoires
The effective population size strongly affects the outcome of natural selection
In the selfer Arabidopsis thaliana, selection efficacy against TEs seems to be reduced compared to its outcrossing sister species A. lyrata [139, 140], but comparison of the two complete genomes revealed a higher load of TE in A. lyrata and a recent decrease in TE in number in A. thaliana, in agreement with the date of transition to selfing [141]
Summary
In-depth investigations on genome organization and evolution are increasing and have revealed marked contrasts between species, e.g., evolutionary rates, nucleotide composition, and gene repertoires. As for selfing, clonality can be partial, with sexual reproduction occurring in addition or in alternation with asexual reproduction In addition to this common form of asexuality, other forms such as automixis imply a modified meiosis in females where unfertilized diploid eggs produce offspring potentially diverse and distinct from their mother, leading to different levels of heterozygosity [13]. This diversity of reproductive systems should be kept in mind, but for clarity we will mainly compare outcrossing, diploid selfing, and clonality. TE transposable element abundance, LD linkage disequilibrium breeding systems on genome evolution and discuss and re-evaluate how evolutionary genomics shed new light on the old question of breeding system evolution
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