College of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China.
Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA.
J Integr Plant Biol. 2023 May;65(5):1183-1203. doi: 10.1111/jipb.13466. Epub 2023 Mar 24.
The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species. Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene, followed by widespread extinction and survival of relicts in the tropical New World. During the climate warming in the early Miocene, a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region. We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis. Furthermore, the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes. Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis, which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere. The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene.
北温带在始新世前气候温暖，嗜热植物区系丰富，但在全球气候变化和生物群区系转变下，温带生物群区的早期多样化仍然不确定。此外，杂交/基因渗入正在成为植物多样性形成的一个重要驱动力，这一点变得越来越明显。在这里，我们应用生物地理学和系统发育网络分析，根据来自新世界葡萄属（Vitis）的基因组数据来解释基因渗入和不完全谱系分选，新世界葡萄属是北温带北美植物群系的一个迷人组成部分，具有已知和可疑的物种间基因流。生物地理学推断和化石证据表明，在古新世到始新世期间，葡萄广泛分布于从北美洲到欧洲，随后在热带新世界广泛灭绝，仅有残遗种幸存。在中新世早期气候变暖期间，葡萄的一个祖先从避难所向北迁移，随后在北美地区多样化。我们发现，在新世界葡萄属的近期和远古谱系中，核基因之间存在广泛的不一致和网状进化的有力证据。此外，细胞器基因组与从核基因组推断的物种树之间存在强烈冲突。我们的系统基因组分析为新世界葡萄属中广泛存在的网状基因渗入提供了重要评估，这可能是适应新近纪全球气候变冷和波动的北温带北美甚至整个北温带开花植物多样化的最重要机制之一。我们报告的情景可能是适应新近纪全球气候变冷和波动的北温带开花植物多样化的常见模式。
