The evolution of adaptive genetic variation in relation to speciation divergence and introgression in conifers

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Boreal conifers are among the living organisms with largest natural distributions. They are usually characterized by high genetic diversity and gene flow. We have shown that history has been an important factor in shaping this diversity given the existence of distinct geneticlineages at the intraspecific level, that have emerged as a result of vicariance during ice ages. This isolation may also have resulted in differential adaptation given thedifferent climates characterizing glacial refugia, in addition to more recent natural selection during Holocene, following the retreat of glaciers andrecolonization. We have also shown that this post-glacial colonization has also resulted in the existence of contact zones between hybridizing species andbetween intraspecific lineages, respectively called hybrid or suture zones. Therefore, genetic diversity can be highly structured in these zones, with different patterns observed for different genomes and even among genomic regions within the nuclear genome.The long-term goal of our research program is to decipher the genomic architecture of genetic adaptation in long-lived undomesticated organisms with wide distributionsuch as boreal conifers, and how it is related to speciation. One major aim is to identify how neutral and adaptive genetic variation are shaped in contact zones andhow species and lineages conserve their integrity in spite of ongoing gene flow. Another aim is to identify genes, gene families andnetworks responsible for adaptation to abiotic factors such as climate, and how these are conserved among conifers.Using association studies with environmental factors and adaptive traits, we will pursue the comparative analysis of adaptive molecular variation at the interspectificlevel among conifers. We will do so for boreal spruces but also by comparing subtropical mountain and boreal firs. We will further study hybrid zones and intraspecific zones of suture to evaluate genomicpermeability and identify which genomic regions and nuclear loci are responsible for genetic divergence potentially leading to speciation. We will further evaluate how permeable regionsare affected by introgression and possible directionality. We will further conduct these studies in a comparative context by relating the results obtained at theintraspecific level between glacial lineages and between hybridizing conifer congeneric species. The results will allow to better monitor adaptive genetic variation and the factors affecting its short- and long-term evolution, to better understand how species are maintaining their genetic integrity and the evolution of adaptive divergence in the presence of genetic contact. The results will be useful for the management of natural genetic resources and for tree breeding purposes, both in the context of increasing climate instability and change.