Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Key Laboratory for Plant Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
Key Laboratory for Plant Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
Mol Phylogenet Evol. 2019 May;134:74-86. doi: 10.1016/j.ympev.2018.12.023. Epub 2019 Feb 5.
The Caryophyllales includes 40 families and 12,500 species, representing a large and diverse clade of angiosperms. Collectively, members of the clade grow on all continents and in all terrestrial biomes and often occupy extreme habitats (e.g., xeric, salty). The order is characterized by many taxa with unusual adaptations including carnivory, halophytism, and multiple origins of C photosynthesis. However, deep phylogenetic relationships within the order have long been problematic due to putative rapid divergence. To resolve the deep-level relationships of Caryophyllales, we performed phylogenomic analyses of all 40 families of Caryophyllales. We time-calibrated the molecular phylogeny of this clade, and evaluated putative correlations among plastid structural changes and rates of molecular substitution. We recovered a well-resolved and well-supported phylogeny of the Caryophyllales that was largely congruent with previous estimates of this order. Our results provide improved support for the phylogenetic position of several key families within this clade. The crown age of Caryophyllales was estimated at ca. 114.4 million years ago (Ma), with periods of rapid divergence in the mid-Cretaceous. A strong, positive correlation between nucleotide substitution rate and plastid structural changes was detected. Our study highlights the importance of broad taxon sampling in phylogenomic inference and provides a firm basis for future investigations of molecular, morphological, and ecophysiological evolution in Caryophyllales.
石竹目包含 40 个科和 12500 个物种，代表了一个庞大而多样化的被子植物分支。该分支的成员共同生长在所有大陆和所有陆地生物群系中，并且经常占据极端的栖息地（例如干旱、含盐）。该目以许多具有不寻常适应性的类群为特征，包括肉食性、盐生植物和 C 光合作用的多种起源。然而，由于假定的快速分化，该目内的深层系统发育关系长期以来一直存在问题。为了解决石竹目的深层关系，我们对石竹目的所有 40 个科进行了系统基因组分析。我们对这个分支进行了分子系统发育的时间校准，并评估了质体结构变化和分子替代率之间的潜在相关性。我们恢复了一个石竹目得到良好解决和支持的系统发育，与该目之前的估计基本一致。我们的结果为该分支内的几个关键科的系统发育位置提供了更好的支持。石竹目的冠层年龄估计约为 1.144 亿年前（Ma），在白垩纪中期有快速分化的时期。在核苷酸替代率和质体结构变化之间检测到强烈的正相关性。我们的研究强调了在系统基因组学推断中广泛的分类群采样的重要性，并为未来对石竹目分子、形态和生理生态进化的研究提供了坚实的基础。
