Comprehensive phylogenetic analyses of Orchidaceae using nuclear genes and evolutionary insights into epiphytism
摘要Orchidaceae(with>28,000 orchid species)are one of the two largest plant families,with economically and ecologically important species,and occupy global and diverse niches with primary distribution in rain-forests.Among orchids,70%grow on other plants as epiphytes;epiphytes contribute up to~50%of the plant diversity in rainforests and provide food and shelter for diverse animals and microbes,thereby contributing to the health of these ecosystems.Or-chids account for over two-thirds of vascular epi-phytes and provide an excellent model for studying evolution of epiphytism.Extensive phylogenetic studies of Orchidaceae and subgroups have;been crucial for understanding relationships among many orchid lineages,although some uncertainties remain.For example,in the largest subfamily Epidendroideae with nearly all epiphytic orchids,relationships among some tribes and many subtribes are still con-troversial,hampering evolutionary analyses of epi-phytism.Here we obtained 1,450 low-copy nuclear genes from 610 orchid species,including 431 with newly generated transcriptomes,and used them for the reconstruction of robust Orchidaceae phyloge-netic trees with highly supported placements of tribes and subtribes.We also provide generally well-supported phylogenetic placements of 131 genera and 437 species that were not sampled by previous plastid and nuclear phylogenomic studies.Molecular clock analyses estimated the Orchidaceae origin at~132 million years ago(Ma)and divergences of most subtribes from 52 to 29 Ma.Character reconstruction supports at least 14 parallel origins of epiphytism;one such origin was placed at the most recent common ancestor of~95%of epiphytic orchids and linked to modern rainforests.Ten occurrences of rapid increase in the diversification rate were de-tected within Epidendroideae near and after the K-Pg boundary,contributing to ~80% of the Orchidaceae diversity.This study provides a robust and the largest family-wide Orchidaceae nuclear phylo-genetic tree thus far and new insights into the evo-lution of epiphytism in vascular plants.
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