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，鉴于不同基因的存在，历史是形成这种多样性的重要因素。 种内水平的谱系，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 冰川避难所的不同气候特征，以及全新世期间较新的自然选择，在冰川消退和 重新殖民。我们还表明，这种冰川后的殖民也导致了杂交物种和 种内谱系之间，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，在不同的基因组甚至核基因组内的基因组区域中观察到不同的模式。 我们研究计划的长期目标是破译广泛分布的长寿未驯化生物的遗传适应的基因组结构。 例如北方针叶树，以及它与物种形成的关系。一个主要目标是确定中性和适应性遗传变异是如何在接触区和 物种和谱系如何在持续的基因流动中保持其完整性。另一个目标是识别基因、基因家族和 负责适应气候等非生物因素的网络，以及这些因素在针叶树中的保护情况。 利用与环境因素和适应性性状的关联性研究，我们将在种间进行适应性分子变异的比较分析。 针叶树之间的水平。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。我们将进一步研究缝合线的杂交区和种内区，以评估基因组 并确定哪些基因组区域和核基因座是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性地区的 受入渗和可能的方向性影响。我们将在比较的情况下进一步进行这些研究，将在 冰川谱系之间和杂交针叶树同属种之间的种内水平。 这些结果将有助于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，更好地了解物种如何在遗传接触存在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。

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.