水龙骨目的系统发育与早期演化 ——兼论质体基因组RNA编辑对系统发育重建的影响

	水龙骨目的系统发育与早期演化 ——兼论质体基因组RNA编辑对系统发育重建的影响; Phylogeny and early diversification of Polypodiales with a case study on the effect of plastid RNA editing on phylogenetic reconstruction
	杜新宇
导师	李德铢
摘要	Polypod ferns contain about 82% species diversity of extant ferns (8,700/10,600), which represent the second most species-rich lineage of vascular plants, only exceeded by angiosperms. The deep relationships of Polypodiales have been intensively investigated in the last 20 years; however, they remain as a highly dynamic research area in fern systematics. It was generally believed that polypod ferns diversified in the shadow of angiosperms in the Late Cretaceous. This hypothesis has been adopted widely since it was proposed, while it has been questioned by other some studies. However, previous time-estimates were based either on incomplete sampling or fossil recognition. We used a phylogenomic approach to resolve the relationships among the backbones of Polypodiales, and to date deepest divergences in polypod ferns with comprehensive taxon sampling, together with a good consideration of important fossil taxa, especially some well-preserved Early Cretaceous polypod fern fossils. We sampled 208 plastomes representing 199 species of 109 genera of all 28 polypod fern families, with 164 plastomes representing 160 species of 100 genera of 27 families newly generated in the present study. We also compared the diversification patterns of polypod ferns with those of angiosperms. The results showed that the plastid genomes of polypod ferns exhibited high stability in structure and gene content, and the variation in genomic structure and the changes in gene content were scattered among distant clades or individuals. Prominent features including RNA editing, IR expansion or contraction, and long noncoding sequence insertion were detected in the Polypodiales plastid genomes. The phylogeny based on 88 coding genes of 214 samples and eight analytical schemes recovered six main lineages of Polypodiales recognized as suborders; relationships at and above the familial level were largely identical. The suborders Saccolomatineae and Lindsaenieae were sister clades and in turn formed together (the SaCyLoLi clade) the sister clade to all other Polypodiales. The Dennstaedtiineae and Pteridineae were sister clades that were together sister to a clade comprising Aspleniineae (eupolypods II) and Polypodiineae (eupolypods I). The relationships among Dennstaedtiineae, Pteridineae, and eupolypods still need further investigation because of the inconsistencies between the analyses of plastid DNA and AA matrices, and between the analysis of plastid and trascriptome data. Hypodematiaceae were the first diverging clade followed by Didymochlaenaceae in the Polypodiineae clade. Cystopteridaceae were sister to the remaining Aspleniineae that comprises two clades, namely the WOBAT clade (including Athyriaceae, Blechnaceae, Onocleaceae, Thelypteridaceae and Woodsiaceae) and the RHADD clade (including Aspleniaceae, Desmophlebiaceae, Diplaziopsidaceae, Hemidictyaceae and Rhachidosoraceae) in the Aspleniineae clade. Within the RHADD clade, Rhachidosoraceae were sister to the rest familie
	2020-05
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74119
专题	昆明植物所硕博研究生毕业学位论文
推荐引用方式 GB/T 7714	杜新宇. 水龙骨目的系统发育与早期演化 ——兼论质体基因组RNA编辑对系统发育重建的影响, Phylogeny and early diversification of Polypodiales with a case study on the effect of plastid RNA editing on phylogenetic reconstruction[D],2020.

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