Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, 541004, Guangxi, China.
CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.
BMC Biol. 2024 Oct 23;22(1):241. doi: 10.1186/s12915-024-02040-7.
The family Lauraceae is subdivided into six main lineages: Caryodaphnopsideae, Cassytheae, Cryptocaryeae, Hypodaphnideae, Laureae, and Neocinnamomeae. However, phylogenetic relationships among these lineages have been debatable due to incongruence between trees constructed using nuclear ribosomal DNA (nrDNA) sequences and chloroplast (cp) genomes. As with cp DNA, the mitochondrial (mt) DNA of most flowering plants is maternally inherited, so the phylogenetic relationships recovered with mt genomes are expected to be consistent with that from cp genomes, rather than nrDNA sequences.
The mitogenome of Machilus yunnanensis, with a length of 735,392 bp, has a very different genome size and gene linear order from previously published magnoliid mitogenomes. Phylogenomic reconstructions based on 41 mt genes from 92 Lauraceae mitogenomes resulted in highly supported relationships: sisterhood of the Laureae and a group containing Neocinnamomeae and Caryodaphnopsideae, with Cassytheae being the next sister group, followed by Cryptocaryeae. However, we found significant incongruence among the mitochondrial, chloroplast, and nuclear phylogenies, especially for the species within the Caryodaphnopsideae and Neocinnamomeae lineages. Time-calibrated phylogenetic analyses showed that the split between Caryodaphnopsideae and Neocinnamomeae dated to the later Eocene, around 38.5 Ma, Laureae originated in the Late Cretaceous, around 84.9 Ma, Cassytheae originated in the mid-Cretaceous around 102 Ma, and Cryptocaryeae originated in the Early Cretaceous around 116 Ma. From the Late Cretaceous to the Paleocene, net diversification rates significantly increased across extant clades of major lineages, and both speciation rates and net diversification rates continued steady growth towards the present.
The topology obtained here for the first time shows that mt genes can be used to support relationships among lineages of Lauraceae. Our results highlight that both Caryodaphnopsideae and Neocinnamomeae lineages are younger than previously thought, likely first diversifying in the Eocene, and species in the other extant lineages of Lauraceae dates in a long-time span from the Early Cretaceous to the Eocene, and the climate of a period of about 90 million years was relatively warm, while the extant species of Lauraceae then continuously diversified with global cooling from the Eocene to the present day.
樟科（Lauraceae）分为六个主要谱系：肉实树族（Caryodaphnopsideae）、鳄梨族（Cassytheae）、樟族（Cryptocaryeae）、暗罗族（Hypodaphnideae）、樟族（Laureae）和新樟族（Neocinnamomeae）。然而，由于核核糖体 DNA（nrDNA）序列和叶绿体（cp）基因组构建的树之间存在不一致，这些谱系之间的系统发育关系一直存在争议。与 cp DNA 一样，大多数有花植物的线粒体（mt）DNA是母系遗传的，因此用 mt 基因组重建的系统发育关系预计与 cp 基因组一致，而不是与 nrDNA 序列一致。
Machilus yunnanensis 的线粒体基因组长 735392bp，与已发表的木兰类线粒体基因组相比，其基因组大小和基因线性顺序差异很大。基于 92 个樟科线粒体基因组中的 41 个 mt 基因进行的系统基因组重建得到了高度支持的关系：樟族和包含新樟族和肉实树族的一个组是姐妹群，鳄梨族是下一个姐妹群，其次是樟族。然而，我们发现线粒体、叶绿体和核系统发育之间存在显著的不一致，尤其是在肉实树族和新樟族的物种中。时间校准的系统发育分析表明，肉实树族和新樟族的分裂发生在始新世晚期，约 38.5 百万年前，樟族起源于白垩纪晚期，约 84.9 百万年前，鳄梨族起源于白垩纪中期，约 102 百万年前，樟族起源于白垩纪早期，约 116 百万年前。从白垩纪晚期到古近纪，现存主要谱系的分支净多样化率显著增加，种形成率和净多样化率一直持续到现在。
这里首次获得的拓扑结构表明，mt 基因可用于支持樟科各谱系之间的关系。我们的结果表明，肉实树族和新樟族的谱系都比以前认为的年轻，可能最早在始新世多样化，而樟科现存其他谱系的物种在从早白垩世到始新世的很长一段时间内都有记载，大约 9000 万年的气候相对温暖，而现存的樟科物种则随着从始新世到现在的全球变冷而不断多样化。
