Based on the distribution of selfing species on phylogenies, selfing is often considered to be of recent origin. However, except for well-documented and specific cases (such as Capsella rubella [1,2,3]) it is difficult to date precisely the origin of selfing. Indeed the shift from outcrossing to selfing does not necessarily coincide with the formation of a new species.
Selfing strongly affects population genetic parameters such as homozygosity, effective size and effective recombination rate, which, in turn, affect patterns of polymorphism and genome evolution [reviewed in 4,5]. Contemporary or very recent selfing rates can be estimated using genetic markers, but it is not clear if more ancient selfing rate, and especially the shift in selfing rates, could also be inferred from population genetic data. An alternative approach would be to use the signature of the effect of selfing that can last on a genome for longer time periods and that could be recorded in patterns of divergence among species.
A strong candidate is GC content that is affected by GC-biased gene conversion (gBGC) in many species [6,7]. gBGC is a recombination-associated process mimicking selection in favour of G and C bases . During recombination mismatches induced by pairing heterozygotes during heteroduplex formation are preferentially corrected towards G or C instead of A or T. gBGC is supposed to be the main driver of the frequently-observed correlation between recombination and GC content and one of the main driver of variation of base composition within and among genomes [6,9]. Because gBGC occurs on heterozygote sites it is thus expected to be absent or nearly absent in highly selfing species  and a decline in GC content in selfing species has been observed both at the divergence and polymorphism levels [11,12,13,14]. GC-content and gBGC also vary along genes, likely as a function of recombination gradients, first exons and introns being GC-richer than others [15,16,17,18].
The aim of the project is to use the dynamics of GC-content evolution among closely related species with different mating systems to date the shift from outcrossing to selfing by combining information from genomic regions with contrasted GC content (for example first exons versus last ones). The principle of the method is already developed but remains to be tested and applied. The project will include two parts:
(i) a simulation part to assess the power and the robustness of the method and (ii) a data-analysis part where the method will be applied to empirical datasets for which genome-wide data are already available. Possible datasets are:
– Arabidopsis thaliana: the age of selfing in this model species is likely much more recent that the divergence with its outcrossing relative A. lyrata but is it still debated [e.g.19].
– Capsella orientalis: the Capsella genus, on which we work in the lab, is interesting to study the evolution of mating systems. C. rubella is a very recent species (20,000/50,000 yrs) and the transition to selfing is concomitant to speciation [1,2,3]. C. orientalis is much older (~1 Myrs) but we don’t know if the transition occurred at the speciation time as in C. rubella or much later as in A. thaliana.
– Oryza genus (AA clade): among the rice species close to the domesticated ones, there is variation in mating systems from outcrossing to different level of selfing and the age and number of transition are unclear. All species of the group are fully sequenced .
– Caenorhabiditis nematodes: selfing evolved three times independently in this genus and, as for C. orientalis, the age of transition is still unknown and could differ among the three species [21,22]
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