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。它们通常具有高度的遗传多样性和基因流动。我们已经表明，历史一直是形成这种多样性的一个重要因素，因为在种内水平上存在着不同的遗传谱系，这些谱系是冰河时期由于地理分隔而出现的。这种隔离也可能导致了不同的适应，因为不同的气候是冰川避难所的特征，除了在全新世期间，随着冰川的退缩和冰川化，最近的自然选择。我们还表明，这种冰后期的殖民也导致了杂交物种之间和种内谱系之间的接触区的存在，分别称为杂交区或缝合区。因此，遗传多样性可以高度结构化，在这些区域，不同的基因组，甚至在核基因组内的基因组区域观察到不同的模式，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，在长寿的非驯化生物广泛distributionsuch如北方针叶树，以及它是如何与物种形成。一个主要的目的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。另一个目的是确定基因，基因家族和网络负责适应非生物因素，如气候，以及如何在针叶树中保守，使用与环境因素和适应性状的关联研究，我们将追求适应分子变异的比较分析，在种间水平的针叶树。我们将这样做的北方云杉，但也通过比较亚热带山区和北方冷杉。我们将进一步研究杂交带和种内缝合带，以评估基因组渗透性，并确定哪些基因组区域和核位点负责遗传分歧可能导致物种形成。我们将进一步评估渗透区域如何受到渗入和可能的方向性的影响。我们将进一步进行这些研究在比较的背景下，通过相关的结果在theintraspecific水平之间的冰川谱系和杂交针叶树同属物种。研究结果将有助于更好地监测适应性遗传变异及其影响短期和长期进化的因素，更好地了解物种如何保持其遗传完整性以及在遗传接触的情况下适应性分歧的进化。研究结果将有助于在气候日益不稳定和变化的情况下管理自然遗传资源和树木育种。

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.