干旱区生态环境知识资源中心(Arid): Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae)

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DOI	10.1016/j.ympev.2019.05.016
	Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae)
	Kao, Tzu-Tong 1; Pryer, Kathleen M.1; Freund, Forrest D.2,3; Windham, Michael D.1; Rothfels, Carl J.2,3
通讯作者	Kao, Tzu-Tong
来源期刊	MOLECULAR PHYLOGENETICS AND EVOLUTION
ISSN	1055-7903
EISSN	1095-9513
出版年	2019
卷号	138 页码:139-155
英文摘要	Notholaenids are an unusual group of ferns that have adapted to, and diversified within, the deserts of Mexico and the southwestern United States. With approximately 40 species, this group is noted for being desiccation-tolerant and having farina-powdery exudates of lipophilic flavonoid aglycones-that occur on both the gametophytic and sporophytic phases of their life cycle. The most recent circumscription of notholaenids based on plastid markers surprisingly suggests that several morphological characters, including the expression of farina, are homoplasious. In a striking case of convergence, Notholaena standleyi appears to be distantly related to core Notholaena, with several taxa not before associated with Notholaena nested between them. Such conflicts can be due to morphological homoplasy resulting from adaptive convergence or, alternatively, the plastid phylogeny itself might be misleading, diverging from the true species tree due to incomplete lineage sorting, hybridization, or other factors. In this study, we present a species phylogeny for notholaenid ferns, using four low-copy nuclear loci and concatenated data from three plastid loci. A total of 61 individuals (49 notholaenids and 12 outgroup taxa) were sampled, including 31 out of 37 recognized notholaenid species. The homeologous/allelic nuclear sequences were retrieved using PacBio sequencing and the P-URC bioinformatics pipeline. Each dataset was first analyzed individually using maximum likelihood and Bayesian inference, and the species phylogeny was inferred using *BEAST. Although we observed several incongruences between the nuclear and plastid phylogenies, our principal results are broadly congruent with previous inferences based on plastid data. By mapping the presence of farina and their biochemical constitutions on our consensus phylogenetic tree, we confirmed that the characters are indeed homoplastic and have complex evolutionary histories. Hybridization among recognized species of the notholaenid clade appears to be relatively rare compared to that observed in other well-studied fern genera.
英文关键词	Allopolyploidy Cheilanthoids Missing diploids Notholaena PacBio sequencing Phylogenetics P-URC bioinformatics pipeline
类型	Article
语种	英语
国家	USA
开放获取类型	Green Published
收录类别	SCI-E
WOS记录号	WOS:000475550000011
WOS关键词	CHEILANTHOID FERNS ; FROND EXUDATE ; PHYLOGENETIC-RELATIONSHIPS ; FLAVONOID AGLYCONES ; GENE TREES ; INFERENCE ; CHLOROPLAST ; DNA ; DIVERSIFICATION ; HYBRIDIZATION
WOS类目	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS研究方向	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
来源机构	University of California, Berkeley
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/217671
作者单位	1.Duke Univ, Dept Biol, Durham, NC 27708 USA; 2.Univ Calif Berkeley, Univ Herbarium, Berkeley, CA 94720 USA; 3.Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA
推荐引用方式 GB/T 7714	Kao, Tzu-Tong,Pryer, Kathleen M.,Freund, Forrest D.,et al. Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae)[J]. University of California, Berkeley,2019,138:139-155.
APA	Kao, Tzu-Tong,Pryer, Kathleen M.,Freund, Forrest D.,Windham, Michael D.,&Rothfels, Carl J..(2019).Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae).MOLECULAR PHYLOGENETICS AND EVOLUTION,138,139-155.
MLA	Kao, Tzu-Tong,et al."Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae)".MOLECULAR PHYLOGENETICS AND EVOLUTION 138(2019):139-155.