Molecular Phylogenetic Reconstruction And Biogeography Of Orchidaceae

Orchidaceae is one of the families with the largest and most diverse species,accounting for approximately 10%of seed plants,with particular diversity in wet tropical regions,but absent in the Polar Regions and the driest deserts.This complex family presents a considerable challenge to systematists interested in phylogenetic reconstruction and classification.Previous studies have established the suprageneric level phylogenetic framework based on molecular data,however,relationships among or within several tribes/subtribes were not well resolved due to limited taxon/molecular markers sampling,especially ignoring the ancient and complex origin of Asia taxa.Until recently,molecular dating of Orchidaceae has been also challenging due to the incompleteness of reliable orchid fossils,and the biogeographic history of this fascinating group is still controversial.In this study,the Asia taxa were added to reconstructed the infragenetic phylogeny of the Orchidaceae with multiple coding chloroplast and low copy nuclear genes,and the origin,diversified history and biogeography of orchids were discussed based on the phylogeny,divergence time estimation and ancestral area reconstruction.1.Molecular systematicsA total of 1475 orchid species,which represent 689 genera(accounting for approximately 90%genera)were sampled.The suprageneric phylogeny,including 412 genera and 617 species,was reconstructed using the sequence of pasB,rbcL,matK,ycfl and Xdh based on the results of generic phylogeny which was constructed using the squences of rbcL,matK,ycf1,trnL-F,Xdh and ITS.The suprageneric phylogenetic trees are in strong agreement and show significant support for many key clades.Many previously proposed relationships among subfamilies,tribes and subtribes are well supported,and some new relationships in Orchidoideae and Epidendroideae are revealed.The new relationships include:1)Orchidoideae are divided into two clades.Codonorchideae and Orchideae belong to one clade;Diurideae and Cranichideae belong to the other one.Disinae,Caladeniinae,and Cranichidinae are confirmed as polyphyletic subtribes;Coryciinae,Megastylidinae and Pterostylidinae are paraphyletic subtribes.2)The tribal relationships within Epidendroideae have been much clarified.The Thaieae is sister to Higher Epidendroideae and seven clades within the Higher Epidendroideae are recognized:Arethuseae,Malaxideae,Cymbidieae,Epidendreae,Vandeae,Podochileae and Collabieae.Eulophiinae,Adrorhizinae and Polystachyinae are confirmed as paraphyletic subtribes.The tribes and subtribes of Orchidoideae and Epidendroideae are revised based on molecular,morphological characters,geographical evidences,and divergence time.1)In Orchidoideae,Achlydosinae is recognized;Coryciinae and Disinae are combined under Orchidinae;Megastylidinae,Drakaeinae and Aporostylis are combined under Thelymitrinae;Galeottiellinae,Mannielinae,Discyphusinae and Cranichidinae are combined under Spiranthinae.2)In Epidendroideae,a new tribe,Agrostophyllieae M.H.Li,Z.J.Liu&S.R.Lan,and three subtribes,Dipodiinae M.H.Li,Z.J.Liu&S.R.Lan,Eriodiinae M.H.Li,Z.J.Liu&S.R.Lan and Spathoglottiinae M.H.Li,Z.J.Liu&S.R.Lan are proposed to be established.Dendrobieae tribe,Anthogoniinae,Arundininae,Bromheadiinae,Ridleyellinae,Coeliinae,Corallorhizinae,Thelasinae,Eriinae,Chysoglossinae and Calanthinae subtribes are recognized.Eriopsidinae,Maxillariinae,Coeliopsideae,Stanhopeinae and Zygopetalinae are combined under Oncidiinae;and Hederorkis is combined under Adrorhizinae.2.Origin and diversificationIn this study,the crown ages(152.1-118.1 Ma)between Asparagales and Poales based on the previous genomic analysis of Phalaenopsis equestris are used for age estimation.According to molecular clock estimates,the most recent common ancestor of five subfamilies could be dated back to the Early Cretaceous,and four rapid diversification and extinction patterns are highly synchronous with the Aptian extinction,Gondwana breakup,K/T boundary extinction,and India&Asia collision.This impulse response provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among the subfamilial,tribal and generic diversification of orchids.3.BiogeographyAncestral area reconstruction indicates that the orchids originated in Laurasia and the pantropical distribution pattern is mainly responsible for the Gondwana breakup and fragmentation of the boreotropical flora.The former includes Orchidoideae,Cymbidieae,Agrostophyllinae,Podochileae and Vandeae;the latter includes Apostasioideae,Vanilloideae,Cypripedioideae,Lower Epidendroideae,Arethuseae,Malaxideae,Epidendreae(except Agrostophyllinae)and Collabieae.In addition,the Orchidinae and Aeridinae subtribes originated from continental Africa in the Paleocene and late Cretaceous,and they reached Asia independently in the Eocene by land bridges of Tethys and rafting on the Indian plate,respectively.This study sheds light on mechanisms underlying in the orchid family and tropical disjunctions of plant groups.