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体之一。它们通常具有高度的遗传多样性和基因流动的特点。我们已经证明，历史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，这些谱系是冰河时代更替的结果。这种隔离也可能导致不同的适应，因为冰川避难所*具有*不同的气候特征，此外，在冰川消退和*重新殖民之后，在全新世期间进行了较新的自然选择。我们还表明，这种冰期后的殖民也导致了杂交物种之间和种内谱系之间存在接触区，分别称为杂交区或缝合区。因此，遗传多样性可以在这些区域高度结构化，不同的基因组甚至核基因组内的基因组区域观察到不同的模式。*我们研究计划的长期目标是破译广泛分布的长寿命未驯化生物的遗传适应的基因组结构*如北方针叶树，以及它与物种形成的关系。一个主要目标是确定接触区中性和适应性遗传变异是如何形成的，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，以及这些在针叶树中是如何保守的。*利用与环境因素和适应特性的关联研究，我们将在种间水平上进行针叶树适应分子变异的比较分析。我们将对北方云杉这样做，但也会比较亚热带山区和北方冷杉。我们将进一步研究杂交区和种内缝合区，以评估基因组*渗透性，并确定哪些基因组区域和核基因座是导致可能导致物种形成的遗传差异的原因。我们将进一步评估渗透区域*如何受到入渗和可能的方向性的影响。我们将在比较的情况下进一步进行这些研究，将在种内水平上冰川谱系之间和杂交针叶树同属物种之间所获得的结果联系起来。*这些结果将允许更好地监测适应性遗传变异及其短期和长期进化的影响因素，以更好地了解物种如何在存在遗传接触的情况下保持其遗传完整性和适应性分化的进化。在气候不稳定和气候变化日益加剧的背景下，研究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 genetic*lineages 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 the*different climates characterizing glacial refugia, in addition to more recent natural selection during Holocene, following the retreat of glaciers and*recolonization. We have also shown that this post-glacial colonization has also resulted in the existence of contact zones between hybridizing species and*between 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 distribution*such 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 and*how species and lineages conserve their integrity in spite of ongoing gene flow. Another aim is to identify genes, gene families and*networks 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 interspectific*level 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 genomic*permeability and identify which genomic regions and nuclear loci are responsible for genetic divergence potentially leading to speciation. We will further evaluate how permeable regions*are affected by introgression and possible directionality. We will further conduct these studies in a comparative context by relating the results obtained at the*intraspecific 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.**