State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
Mol Phylogenet Evol. 2022 Dec;177:107606. doi: 10.1016/j.ympev.2022.107606. Epub 2022 Aug 9.
After the merger of the former Taxodiaceae and Cupressaceae s.s., currently the conifer family Cupressaceae (sensu lato) comprises seven subfamilies and 32 genera, most of which are important components of temperate and mountainous forests. With the exception of a recently published genus-level phylogeny of gymnosperms inferred from sequence analysis of 790 orthologs, previous phylogenetic studies of Cupressaceae were based mainly on morphological characters or a few molecular markers, and did not completely resolve the intergeneric relationships. In this study, we reconstructed a robust and well-resolved phylogeny of Cupressaceae represented by all 32 genera, using 1944 genes (Orthogroups) generated from transcriptome sequencing. Reticulate evolution analyses detected a possible ancient hybridization that occurred between ancestors of two subclades of Cupressoideae, including Microbiota-Platycladus-Tetraclinis (MPT) and Juniperus-Cupressus-Hesperocyparis-Callitropsis-Xanthocyparis (JCHCX), although both concatenation and coalescent trees are highly supported. Moreover, divergence time estimation and ancestral area reconstruction indicate that Cupressaceae very likely originated in Asia in the Triassic, and geographic isolation caused by continental separation drove the vicariant evolution of the two subfamilies Cupressoideae and Callitroideae in the northern and southern hemispheres, respectively. Evolutionary analyses of some morphological characters suggest that helically arranged linear-acicular leaves and imbricate bract-scale complexes represent ancestral states, and the shift from linear-acicular leaves to scale-like leaves was associated with the shift from helical to decussate arrangement. Our study sheds new light on phylogeny and evolutionary history of Cupressaceae, and strongly suggests that both dichotomous phylogenetic and reticulate evolution analyses be conducted in phylogenomic studies.
在以前的杉科和柏科 s.s. 合并之后，目前的柏科（广义）包括七个亚科和 32 个属，其中大多数是温带和山地森林的重要组成部分。除了最近发表的基于 790 个直系同源序列分析推断的裸子植物属级系统发育外，以前对柏科的系统发育研究主要基于形态特征或少数分子标记，并没有完全解决属间关系。在这项研究中，我们使用从转录组测序中生成的 1944 个基因（Orthogroups），重建了一个由 32 个属组成的柏科的强大而分辨率高的系统发育。网状进化分析检测到在 Cupressoideae 的两个亚科祖先之间可能发生了一次古老的杂交，包括 Microbiota-Platycladus-Tetraclinis (MPT) 和 Juniperus-Cupressus-Hesperocyparis-Callitropsis-Xanthocyparis (JCHCX)，尽管联合和合并树都得到了高度支持。此外，分化时间估计和祖地重建表明，柏科很可能起源于三叠纪的亚洲，大陆分离引起的地理隔离导致了两个亚科 Cupressoideae 和 Callitroideae 在南北半球的分歧进化。对一些形态特征的进化分析表明，螺旋排列的线性针叶和覆瓦状的苞片复合体代表了原始状态，从线性针叶到鳞片状叶的转变与从螺旋状到交叉排列的转变有关。我们的研究为柏科的系统发育和进化历史提供了新的视角，并强烈建议在系统发育基因组学研究中同时进行二叉系统发育和网状进化分析。
