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，历史是形成这种多样性的一个重要因素，因为存在不同的遗传差异。 在种内水平的谱系，已经出现了作为冰河时期的地理隔离的结果。这种隔离也可能导致差异适应， 不同的气候特征冰川避难所，除了最近的自然选择在全新世，继冰川退缩， 去离子化。我们还表明，这种后冰川殖民也导致了杂交物种之间的接触区的存在， 种内谱系之间，分别称为杂交或缝合带。因此，遗传多样性可以在这些区域中高度结构化，对于不同的基因组甚至在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分布广泛的长寿未驯化生物的遗传适应的基因组架构 例如北方针叶树，以及它与物种形成的关系。一个主要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， 物种和谱系如何在持续的基因流中保持其完整性。另一个目的是识别基因、基因家族和 网络负责适应非生物因素，如气候，以及这些是如何保存在针叶树。 利用环境因子和适应性性状的关联研究，我们将在种间进行适应性分子变异的比较分析， 在针叶树之间。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。我们将进一步研究缝合线的杂交区和种内区， 渗透性，并确定哪些基因组区域和核基因座负责可能导致物种形成的遗传分歧。我们将进一步评估渗透区域 受到基因渗入和可能的方向性的影响。我们将进一步在比较的背景下进行这些研究， 种内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 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.