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

北方针叶树是自然分布最广的生物之一。它们通常具有较高的遗传多样性和基因流动的特点。我们已经证明，在形成这种多样性的过程中，历史是一个重要因素，因为在种内水平上存在着不同的遗传谱系，这些遗传谱系是在冰河期变异的结果。这种隔离也可能导致不同的适应，因为不同的气候特征是冰川避难所，除了最近的自然选择在全新世，冰川退缩和重新殖民。我们还表明，这种冰川后的定殖也导致杂交物种之间和种内谱系之间存在接触带，分别称为杂交带或缝合带。因此，遗传多样性可以在这些区域高度结构化，在不同的基因组中甚至在核基因组的基因组区域中观察到不同的模式。我们的研究计划的长期目标是破译遗传适应的基因组结构在长寿命的广泛分布的未驯化生物中，如北方针叶树，以及它与物种形成的关系。一个主要的目标是确定中性和适应性遗传变异是如何在接触区形成的，以及物种和谱系如何在持续的基因流动中保持其完整性。另一个目标是确定负责适应气候等非生物因素的基因、基因家族和网络，以及这些基因是如何在针叶树中保存的。通过与环境因子和适应性状的关联研究，我们将在种间水平上对针叶树的适应性分子变异进行比较分析。我们将对北方云杉这样做，但也将对亚热带山地和北方冷杉进行比较。我们将进一步研究杂交区和种内缝合区，以评估基因组通透性，并确定哪些基因组区域和核位点负责可能导致物种形成的遗传分化。我们将进一步评估渗透区域如何受到渗透和可能的方向性的影响。我们将在比较的背景下进一步开展这些研究，将在种内水平上获得的结果与冰川谱系和杂交针叶树同属物种之间的结果联系起来。研究结果将有助于更好地监测适应性遗传变异和影响其短期和长期进化的因素，从而更好地了解物种如何在存在遗传接触的情况下保持遗传完整性和适应性分化的进化。在气候日益不稳定和变化的背景下，这些结果将有助于自然遗传资源的管理和树木育种目的。

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.