Effects of ploidy and life history traits on the footprints of selection and demographic events in forest trees genomes

Selection and demography are fundamental processes that affect the genetic diversity of a species, but the interaction of these processes with the life history traits of a species ultimately shapes the observed patterns of genetic diversity. Life history traits such as mating system and dispersal strategy can contribute to efficient gene flow, which can buffer against the loss of genetic diversity. Having a lengthy haploid stage in the life cycle may contribute to efficient purging of deleterious mutations. In this thesis, analyses of gene expression in tissues with different ploidy levels identified hundreds of genes with patterns of tissue-specificity in Pinus sylvestris growing
under natural conditions. Comparing the efficacy of selection on haploid and diploid tissue-specific genes demonstrated that purifying selection on genes expressed specifically in the female derived haploid tissues of P. sylvestris is strong. The work presented here is the first report of haploid selection in a tree, and one of the few studies to demonstrate the efficacy of purifying selection on the female gametophyte in plants. Last, reconstruction of the demographic history of seven outcrossing, wind pollinated European trees showed that their effective population size has been relatively stable through time, and that these tree species have retained high levels of genetic diversity through the climatic oscillations of the Pleistocene. The findings of the work done in this thesis highlight the influence of the life cycle and life history traits in shaping levels of genetic diversity as a response to purifying selection and demographic events.