Shu Jiang-Ping, Wang Hao, Shen Hui, Wang Rui-Jiang, Fu Qiang, Wang Yong-Dong, Jiao Yuan-Nian, Yan Yue-Hong
Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China.
Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
Plants (Basel). 2022 Jun 7;11(12):1529. doi: 10.3390/plants11121529.
Phylogenetic conflicts limit our understanding of the evolution of terrestrial life under multiple whole genome duplication events, and the phylogeny of early terrestrial plants remains full of controversy. Although much incongruence has been solved with so-called robust topology based on single or lower copy genes, the evolutionary mechanisms behind phylogenetic conflicts such as polyploidization remain poorly understood. Here, through decreasing the effects of polyploidization and increasing the samples of species, which represent all four orders and eight families that comprise early leptosporangiate ferns, we have reconstructed a robust phylogenetic tree and network with 1125 1-to-1 orthologs based on both coalescent and concatenation methods. Our data consistently suggest that Matoniales, as a monophyletic lineage including Matoniaceae and Dipteridaceae, should be redefined as an ordinal rank. Furthermore, we have identified and located at least 11 whole-genome duplication events within the evolutionary history of four leptosporangiates lineages, and associated polyploidization with higher speciation rates and mass extinction events. We hypothesize that paleopolyploidization may have enabled leptosporangiate ferns to survive during mass extinction events at the end Permian period and then flourish throughout the Mesozoic era, which is supported by extensive fossil records. Our results highlight how ancient polyploidy can result in rapid species radiation, thus causing phylogenetic conflicts yet allowing plants to survive and thrive during mass extinction events.
系统发育冲突限制了我们对多次全基因组复制事件下陆地生命进化的理解，早期陆地植物的系统发育仍然充满争议。尽管许多不一致性已通过基于单拷贝或低拷贝基因的所谓稳健拓扑结构得到解决，但多倍体化等系统发育冲突背后的进化机制仍知之甚少。在这里，通过减少多倍体化的影响并增加物种样本，这些物种代表了构成早期薄囊蕨类植物的所有四个目和八个科，我们基于溯祖法和串联法，用1125个直系同源基因重建了一个稳健的系统发育树和网络。我们的数据一致表明，Matoniales作为一个包括Matoniaceae和Dipteridaceae的单系类群，应重新定义为一个目级分类单元。此外，我们在四个薄囊蕨类植物谱系的进化历史中识别并定位了至少11次全基因组复制事件，并将多倍体化与更高的物种形成率和大规模灭绝事件联系起来。我们假设古多倍体化可能使薄囊蕨类植物在二叠纪末期的大规模灭绝事件中得以幸存，然后在整个中生代繁荣发展，这得到了大量化石记录的支持。我们的结果突出了古代多倍体如何导致物种快速辐射，从而引发系统发育冲突，但同时也使植物在大规模灭绝事件中得以生存和繁荣。
