Article

A New Myco-Heterotrophic Genus, Yunorchis, and the Molecular Phylogenetic Relationships of the Tribe Calypsoeae (Epidendroideae, Orchidaceae) Inferred from Plastid and Nuclear DNA Sequences

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We identified a new holomycotrophic orchid that is related to the myco-heterotrophic Calypsoeae. Because chloroplast genes are primarily lacking or are highly divergent, key morphological characters are either reduced or lost from many myco-heterotrophs, and the phylogenetic relationships of weakly supported paraphyletic Calypsoeae within Epidendroideae have been poorly understood in previous molecular systematic studies. Using chloroplast rbcL, psaB, and matK and nuclear Xdh and ITS sequences, we determined the circumscription and systematic positions of the new orchid and the tribe. The results indicate that the epidendroid taxa include most of the clades that are successively sister to the grade of clades representing previously recognized tribes. Calypsoeae comprising four well-supported clades with 12 genera (except for the previous temporarily placed Wullschlaegelia) is supported as a monophyletic and sister clade to Epidendreae (excluding Coeliinae). The new orchid is nested in Calypsoeae and is a sister to Dactylostalix and/or Calypso. This new holomycotrophic orchid presents a subumbel inflorescence that grows underground, and flower with a long pedicel reputing the ground to open and two fragments at the base of the hook, which are obviously morphologically different from those of Calypsoeae. To accommodate this species in the current generic circumscription, a new genus Yunorchis was created.
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... Most recently, two new leafless genera were proposed and one genus has been subsumed under another. The two new genera, Danxiaorchis and Yunorchis, were published in association with phylogenetic analyses of the subtribe by Zhai et al. (2013) and Zhang et al. (2015), respectively. Zhai et al. (2013) analyzed the subtribe based on ITS, matK and rbcL sequences, as well as morphology. ...
... Their tree had poor support for much of its backbone, leaving fundamental relationships in the group unclear. Zhang et al. (2015) named Yunorchis based in part on the position of this new taxon in their phylogenetic analysis. The new genus is morphologically highly similar to Yoania, but their analysis suggested that it is only relatively distantly related to Yoania. ...
... Cremastra aphylla was not included in their analysis, but the placement of Cremastra in the tree would necessitate a second origination of holomycotrophy in this genus. Zhang et al.'s (2015) analysis placed Danxiaorchis + Yoania japonica as sister to Oreorchis with poor support and placed their newly described genus, Yunorchis, as sister to Dactylostalix, also with poor support. Yunorchis in that case would represent a separate loss of leaves and Cremastra aphylla would represent a third, with Corallorhiza then a fourth instance of leaf loss in the group. ...
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Article
Calypsoinae are a small, largely temperate subtribe that are diverse with respect to trophic strategy (many species have an unusual winter leaf and several are leafless) and pollinium stalk morphology. Here we sought to re-evaluate the placement of Yoania and recently proposed genera and to examine trophic strategy, pollinium stalk type, and geographic distribution in a phylogenetic context. We analyzed ITS and matK sequences from all accepted genera using maximum likelihood and parsimony on individual and combined data sets. The only supported disagreement among trees was between the combined ML and parsimony analyses for the placement of Dactylostalix and Ephippianthus; the trees from one analysis reflected the nuclear pattern, while the other resembled the plastid pattern. A group of genera related to Calypso and a group related to Corallorhiza were resolved. Yoania is closely related to Calypso; the recently proposed Yunorchis is a species of Yoania, while Didiciea is part of Tipularia. Examining leaf morphology on the tree revealed two originations of the winter leaf morphology and four losses of leaves (and shifts to mycoheterotrophy). Pollinium stalks evolved in three directions, two of which resulted in epidermally-derived stalks (tegulae) and one that comprises the entire rostellum (a hamulus). Biogeographic analysis suggests a New World origin for the subtribe, with two major shifts to the Old World and one shift back to the New World.
... The newly described orchids included 23 more genera (29 new genera and six combined genera) and 141 more species than FRPS. Subsequently, more than 10 combined genera and 20 new or newly recorded genera (e.g., Chen & Liu, 2010;Li et al., 2011Li et al., , 2014aLi et al., , 2015Liu et al., 2011;Huang et al., 2012;Xiang et al., 2012;Yang et al., 2013;Zhai et al., 2013Zhai et al., , 2014Zhang et al., 2013Zhang et al., , 2015aJin et al., 2014Jin et al., , 2015Tang et al., 2015a), and 60 species (e.g., Hu et al., 2013Hu et al., , 2014Jin et al., 2013;Li & Yan, 2013;Peng et al., 2013;Guan et al., 2014;Li et al., 2014b;Meng et al., 2014;Tian et al., 2014;Xu et al., 2014;Zou et al., 2014;Su et al., 2015) have been reported in recent years. The completion of the FRPS, Flora of China, and the updated taxa of orchids have contributed greatly to the understanding of Chinese orchid classification and diversification. ...
... Within the higher epidendroids, support for the relationships of these clades is not high, and the sequences of certain genera are lacking; thus, the relationships among the tribes and monophylies of Epidendreae are not clearly refuted on the basis of the TL results. The topology of the RT is nearly consistent with previous molecular analyses (G orniak et al., 2010;Luo et al., 2014;Givnish et al., 2015;Zhang et al., 2015a) and the classification of Chase et al. (2015) and the tribe and subtribe levels are successively sister to the next; thus, we chose the results of the RT to elucidate the arrangement of the suprageneric levels. ...
... The bestsampled analysis in terms of data was carried out by , who provided a mixed result depending on the type of analysis (ML vs. MP). Based on the combined chloroplasts of rbcL, matK, and psaB, and the nuclear Xdh, the results of Zhang et al. (2015a) showed that Arundina is sister to Coelogyninae. ...
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We estimated the molecular phylogenetic relationships of the Chinese members of the family Orchidaceae. Within the Tree of Life for the Genera of Chinese Vascular Plants using atpB, rbcL, matK, ndhF, and matR, the currently delimited subfamilies, tribes, and subtribes are highly supported as monophyletic except for the perplexing Epidendroideae. Five genes (rbcL, matK, psaB, ycf1, and Xdh), which are more universally used in Orchidaceae, were further analyzed to reconstruct the phylogeny of Epidendroideae. The reconstructed trees were in strong agreement and showed significant support for the tribal and subtribal clades. Based on the highly supported circumscription and arrangement of the suprageneric levels in the Tree of Life and reconstructed trees, we have proposed a new phylogenetic classification of Chinese Orchidaceae that includes five subfamilies, 17 tribes, and 21 subtribes.
... Phylogenetic analyses based on combined DNA sequences (ITS, matK and rbcL) and morphological characters matrix indicated that Danxiaorchis is a member of the tribe Calypsoeae in the subfamily Epidendroideae (Zhai et al. 2013). Under Calypsoeae, Danxiaorchis was inferred to be most closely related to Yoania Maximowicz (1873: 68), and this relationship was subsequently confirmed by Zhang et al. (2015). However, the only sequence for Yoania included in both Zhai et al. (2013) and Zhang et al. (2015) data sets was a partial rbcL sequence of 222 bp out of the full length of 1428 bp, and Freudenstein et al. (2017) noted that such a high proportion of missing data of Yoania would output a spurious relationship for Danxiaorchis and Yoania. ...
... Under Calypsoeae, Danxiaorchis was inferred to be most closely related to Yoania Maximowicz (1873: 68), and this relationship was subsequently confirmed by Zhang et al. (2015). However, the only sequence for Yoania included in both Zhai et al. (2013) and Zhang et al. (2015) data sets was a partial rbcL sequence of 222 bp out of the full length of 1428 bp, and Freudenstein et al. (2017) noted that such a high proportion of missing data of Yoania would output a spurious relationship for Danxiaorchis and Yoania. After including more representatives and sequences of Yoania and reanalyzing generic relationships among subtribe Calypsoinae, Freudenstein et al. (2017) found that Danxiaorchis emerges in Corallorhiza (Gagnebin 1755: 61) clade and is sister to Oreorchis (Lindley 1859: 26) + Corallorhiza, while Yoania emerges in Calypso (Salisbury 1807: 89) clade. ...
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Article
Danxiaorchis yangii (Calypsoinae, Epidendreae, Epidendroideae), a holomycotrophic new species from Jinggangshan National Nature Reserve, western Jiangxi, eastern of China, is here illustrated and described based on both morphological and phylogenetic evidences. The new species can be easily distinguished from D. singchiana by its much smaller flowers and larger Y-shaped callus adaxially bearing a additional obovoid appendage, and by its four pollinia narrowly elliptic in shape and equal in size.
... including new genera Danxiaorchis [14], Hsenhsua [15], Shizhenia [16] and Yunorchis [17], the newly recorded genus Thaia [18] [33]; plastid phylogenomic resolution of subtribes Aeridinae [19] and Goodyerinae [34]; genera phylogenetics such as Dendrobium [35], Cymbidium [36], Holcoglossum [37] and Paphiopedilum [38] In parallel with the examination of plant's organelle genomes, opportunities are rising for using transcriptomic data for orchid phylogenetics. Several orchid phylotranscriptomics have been performed for addressing either broad-scale or shallow-scale orchid relationships including species diversification and genome evolution, as well as key traits like sexual deception [39][40][41][42][43]. ...
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Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology and pollination syndromes that exhibit exclusive specializations than any other plants on earth. These intrinsic factors together with human influences also make it a keystone group in biodiversity conservation. The advent of sequencing technologies and transgenic techniques represents a quantum leap in orchid research, enabling molecular approaches to be employed to resolve the historically interesting puzzles in orchid basic and applied biology. To date, 15 different orchid genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae and Orchidoideae) have been released. These genome projects have given rise to massive data that greatly empowers the studies pertaining to key innovations and evolutionary mechanisms for the breadth of orchid species. The extensive exploration of transcriptomics, comparative genomics, and recent advances in gene engineering have linked important traits of orchids with a multiplicity of gene families and their regulating networks, providing great potential for genetic enhancement and improvement. In this review, we summarize the progress and achievement in fundamental research and industrialized application of orchids with a particular focus on molecular tools, and make future prospects of orchid molecular breeding and post-genomic research, providing a comprehensive assemblage of start-of-art knowledge in orchid research and industrialization.
... including new genera Danxiaorchis [14], Hsenhsua [15], Shizhenia [16] and Yunorchis [17], the newly recorded genus Thaia [18] [33]; plastid phylogenomic resolution of subtribes Aeridinae [19] and Goodyerinae [34]; genera phylogenetics such as Dendrobium [35], Cymbidium [36], Holcoglossum [37] and Paphiopedilum [38] In parallel with the examination of plant's organelle genomes, opportunities are rising for using transcriptomic data for orchid phylogenetics. Several orchid phylotranscriptomics have been performed for addressing either broad-scale or shallow-scale orchid relationships including species diversification and genome evolution, as well as key traits like sexual deception [39][40][41][42][43]. ...
Full-text available
Article
Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology and pollination syndromes that exhibit exclusive specializations than any other plants on earth. These intrinsic factors together with human influences also make it a keystone group in biodiversity conservation. The advent of sequencing technologies and transgenic techniques represents a quantum leap in orchid research, enabling molecular approaches to be employed to resolve the historically interesting puzzles in orchid basic and applied biology. To date, 15 different orchid genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae and Orchidoideae) have been released. These genome projects have given rise to massive data that greatly empowers the studies pertaining to key innovations and evolutionary mechanisms for the breadth of orchid species. The extensive exploration of transcriptomics, comparative genomics, and recent advances in gene engineering have linked important traits of orchids with a multiplicity of gene families and their regulating networks, providing great potential for genetic enhancement and improvement. In this review, we summarize the progress and achievement in fundamental research and industrialized application of orchids with a particular focus on molecular tools, and make future prospects of orchid molecular breeding and post-genomic research, providing a comprehensive assemblage of start-of-art knowledge in orchid research and industrialization.
... Thus, setae are found on the labellum of Calypso Salisb. (Zhang et al. 2015), Catasetum (Franken et al. 2016) and Pterostylis R.Br. (Janes et al. 2010), which use food deception (Tuomi et al. 2015), perfume rewarding (Milet-Pinheiro and Gerlach 2017) and sexual deception (Phillips et al. 2013) as pollination strategies, respectively. ...
Article
Floral innovations are key for pollinator specialization and play a significant role in plant diversification. Orchidaceae present many examples of floral innovations that allow its high degrees of pollinator specialization and promoted speciation. The rich neotropical genus Telipogon evolved an uncinate (=hook-like) viscidium on the pollinarium and setae-bearing flowers, which are uncommon in Orchidaceae; however, the importance of them on pollination success and whether they are floral innovations or exaptations in Telipogon have not been investigated. Here we investigate the morphology of the viscidium and floral setae within the Telipogon alliance (including the genera Hofmeisterella, Trichoceros and Telipogon), test their significance in pollination, and their occurrence and evolution across the Oncidiinae. We used Telipogon peruvianus as a model species to test whether uncinate viscidium and floral setae increased pollination success compared with a cochleariform (=spoon-like) viscidium and lack of floral setae condition. We show that the uncinate viscidium is a synapomorphy for Telipogon; setae-bearing flowers are not universally found among all species of Telipogon and evolved once in the Telipogon alliance. Furthermore, Telipogon peruvianus flowers with an uncinate viscidium have achieved higher pollinia export than those with cochleariform viscidium (ancestral condition), whereas flowers with setae have both higher success in pollinia removal, although not significant, and pollinia deposition than those lacking of setae (ancestral condition). We demonstrate that uncinate viscidia and floral setae in Telipogon are a key innovation and exaptation, respectively, that enhance pollination success and they might act as drivers of diversification and pollinator specialization in this genus.
... The analysis of a partial sequence of rRNA gene is considered an efficient molecular tool for species identification which can indorse the phenotype-based methods which sometimes produce refuted results (Jagielski et al., 2013). The small subunit, SSU rRNA is a common molecular marker frequently used in diversity research (Lindeque et al., 2013;Fonseca et al., 2014;Wu et al., 2015) and phylogenetic studies (Petrov et al., 2014;Zhang et al., 2015). The SSU rRNA are widely used for identification of species from different taxonomic groups from bacteria to higher animals (Jagielski et al., 2013;Wu et al., 2015). ...
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Ostracods are microscopic crustaceans living in a wide variety of environments. They are very important as the key food item for fish and benthic macro-invertebrates and are used as bio-indicators for environmental changes and pollution. The identification and taxonomy of the Heterocypris species are so challenging issues because of their morphological plasticity that is often related to environmental factors. The studied species is recorded for the first time in Egypt. Therefore, Morphological evidences for the identification of this species were thoroughly recorded using the scanning electron and stereo microscopes. Furthermore, DNA barcoding was used to confirm the morphological identification. The morphological examination identified the species as Heterocypris salina, where it revealed an accurate description for its carapace, valves and appendages. However, few dissimilarities with the description of that species by other authors were noted. The sequencing of partial sequences of 28S, 18S rRNA genes confirmed the results of the morphological identification. New barcodes for 28S, 18S rRNA genes and cytochrome oxidase subunit 1, COI gene, of H. salina were added to GenBank databases. Based on morphological and genetic evidences, this study adds new species to the biodiversity inventory of the aquatic environment of Egypt. Furthermore, COI sequence for Heterocypris salina has been submitted on the GenBank databases for the first time to be used as a marker for identification of such species in the future.
... The outgroup included one genus from the tribe Vandeae Lindley (1826: 14) and two genera from Epidendreae Lindley (1826: 16). The selection of outgroups was based on the phylogenetic analysis of Zhang et al. (2015), which placed the clade Malaxideae-Vandeae-Epidendreae as sister to Cymbidieae based on Xdh, psaB, rbcL and matK. ...
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The subtribal delimitation and relationship of Old World Cymbidiinae and Eulophiinae within Cymbidieae remain unresolved. Relationships among all subtribes of Cymbidieae (Orchidaceae: Epidendroideae) were estimated using the coding genes psaB, rbcL, matK, ycf1 and Xdh for 103 taxa. The results indicate that most of the clades are successively sister to the grade of clades representing previously recognized subtribes, and Dipodium does not belong in its previous classification of Cymbidiinae and Eulophiinae. Instead, this genus represents an additional isolated lineage.
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Recently, two new genera of mycoheterotrophic orchids were described from China: Danxiaorchis Zhai, Xing & Liu (2013: e60371) and Yunorchis Liu, Zhang & Li (2015: e123382). Both were considered to be monospecific, and in each case the descriptions were accompanied by a phylogenetic analysis. It was inferred that Danxiaorchis is the sister genus of another mycoheterotrophic genus, Yoania Maximowicz (1873: 68), whereas Yunorchis was found to be closely related to the autotrophic genera Calypso Salisbury (1807: Tab. 89) and Dactylostalix Reichenbach (1878: 74). Support for the sister-group relationship of Danxiaorchis and Yoania appeared to be strong, and the clade consisting of Calypso, Dactylostalix and Yunorchis had a high Bayesian posterior probability. These analyses suggested that Yunorchis and Yoania were only distantly related. However, based on additional molecular analyses, Freudenstein et al. (2017) found that Yunorchis and Yoania formed a clade. They also argued, and we would agree, that Yunorchis and Yoania do not significantly differ morphologically.
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An expanded plastid DNA phylogeny for Orchidaceae was generated from sequences of rbcL and matK for representatives of all five subfamilies. The data were analyzed using equally weighted parsimony, and branch support was assessed with jackknifing. The analysis supports recognition of five subfamilies with the following relationships: (Apostasioideae (Vanilloideae (Cypripedioideae (Orchidoideae (Epidendroideae))))). Support for many tribal-level groups within Epidendroideae is evident, but relationships among these groups remain uncertain, probably due to a rapid radiation in the subfamily that resulted in short branches along the spine of the tree. A series of experiments examined jackknife parameters and strategies to determine a reasonable balance between computational effort and results. We found that support values plateau rapidly with increased search effort. Tree bisection-reconnection swapping in a single search replicate per jackknife replicate and saving only two trees resulted in values that were close to those obtained in the most extensive searches. Although this approach uses considerably more computational effort than less extensive (or no) swapping, the results were also distinctly better. The effect of saving a maximal number of trees in each jackknife replicate can also be pronounced and is important for representing support accurately.
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Phylogenetic relationships within the epidendroid orchids with emphasis on tribes Epidendreae and Arethuseae were assessed with parsimony and model-based analyses of individual and combined DNA sequence data from ITS nuclear ribosomal DNA and plastid trnL intron, the trnL-F spacer, matK (gene and spacers), and rbcL regions. Despite the absence of boostrap support for some of the relationships, a well-resolved and supported consensus was found, for which most clades were present in more than one individual analysis. Most clades of this consensus attained high posterior probabilities with a Bayesian approach. Circumscription of Arethuseae and Epidendreae are different from most orchid systems based on morphology, but they correspond to a combination of patterns from several less comprehensive orchid phylogenetic analyses previously published. A new circumscription of Epidendreae includes only Neotropical subtribes (Bletiinae, Chysiinae, Laeliinae, Ponerinae, and Pleurothallidinae), whereas Arethuseae include Coelogyninae (all Old World) and Arethusinae (pantropical). Many previously included genera will need to be moved to other tribes. Taxa previously assigned to be Old World Epidendreae are related to different groups of Old World orchids, and this study can serve as a guide for sampling strategies in future studies to resolve troublesome epidendroid orchid clades.
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Since the endosymbiotic origin of chloroplasts from cyanobacteria 2 billion years ago, the evolution of plastids has been characterized by massive loss of genes. Most plants and algae depend on photosynthesis for energy and have retained ∼110 genes in their chloroplast genome that encode components of the gene expression machinery and subunits of the photosystems. However, nonphotosynthetic parasitic plants have retained a reduced plastid genome, showing that plastids have other essential functions besides photosynthesis. We sequenced the complete plastid genome of the underground orchid, Rhizanthella gardneri. This remarkable parasitic subterranean orchid possesses the smallest organelle genome yet described in land plants. With only 20 proteins, 4 rRNAs, and 9 tRNAs encoded in 59,190 bp, it is the least gene-rich plastid genome known to date apart from the fragmented plastid genome of some dinoflagellates. Despite numerous differences, striking similarities with plastid genomes from unrelated parasitic plants identify a minimal set of protein-encoding and tRNA genes required to reside in plant plastids. This prime example of convergent evolution implies shared selective constraints on gene loss or transfer.
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Myco-heterotrophic plants are partly or entirely non-photosynthetic plants that obtain energy and nutrients from fungi. These plants form a symbiosis with arbuscular mycorrhizal, ectomycorrhizal or saprotrophic fungi to meet their nutrient demands. This Botanical Briefing summarizes current knowledge about myco-heterotrophy, discusses its controversial aspects and highlights future directions for research. Considerable recent progress has been made in terms of understanding the evolutionary history, germination and nutrition of myco-heterotrophic plants. Myco-heterotrophic plants: (1) are diverse and often ancient lineages that have coevolved with fungi, (2) often demonstrate unusually high specificity towards fungi during germination and maturity, and (3) can either cheat common mycorrhizal networks supported by neighbouring photosynthetic plants to satisfy all or part of their energetic and nutritional needs, or recruit free-living saprotrophic fungi into novel mycorrhizal symbioses. However, several fundamental aspects of myco-heterotrophy remain controversial or unknown, such as symbiotic costs and physiology.
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Mycoheterotrophic orchids have adapted to shaded forest understory by shifting to achlorophylly and receiving carbon from their mycorrhizal fungi. In temperate forests, they associate in a highly specific way with fungi forming ectomycorrhizas on nearby trees, and exploiting tree photosynthates. However, many rainforests lack ectomycorrhizal fungi, and there is evidence that some tropical Asiatic species associate with saprotrophic fungi. To investigate this in different geographic and phylogenetic contexts, we identified the mycorrhizal fungi supporting two tropical mycoheterotrophic orchids from Mascarene (Indian Ocean) and Caribbean islands. We tested their possible carbon sources by measuring natural nitrogen ((15)N) and carbon ((13)C) abundances. Saprotrophic basidiomycetes were found: Gastrodia similis associates with a wood-decaying Resinicium (Hymenochaetales); Wullschlaegelia aphylla associates with both litter-decaying Gymnopus and Mycena species, whose rhizomorphs link orchid roots to leaf litter. The (15)N and (13)C abundances make plausible food chains from dead wood to G. similis and from dead leaves to W. aphylla. We propose that temperature and moisture in rainforests, but not in most temperate forests, may favour sufficient saprotrophic activity to support development of mycoheterotrophs. By enlarging the spectrum of mycorrhizal fungi and the level of specificity in mycoheterotrophic orchids, this study provides new insights on orchid and mycorrhizal biology in the tropics.
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Despite recent advances achieved by application of high-performance computing methods and novel algorithmic techniques to maximum likelihood (ML)-based inference programs, the major computational bottleneck still consists in the computation of bootstrap support values. Conducting a probably insufficient number of 100 bootstrap (BS) analyses with current ML programs on large datasets-either with respect to the number of taxa or base pairs-can easily require a month of run time. Therefore, we have developed, implemented, and thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated Maximum Likelihood) that are more than an order of magnitude faster than current algorithms. These new heuristics can contribute to resolving the computational bottleneck and improve current methodology in phylogenetic analyses. Computational experiments to assess the performance and relative accuracy of these heuristics were conducted on 22 diverse DNA and AA (amino acid), single gene as well as multigene, real-world alignments containing 125 up to 7764 sequences. The standard BS (SBS) and rapid BS (RBS) values drawn on the best-scoring ML tree are highly correlated and show almost identical average support values. The weighted RF (Robinson-Foulds) distance between SBS- and RBS-based consensus trees was smaller than 6% in all cases (average 4%). More importantly, RBS inferences are between 8 and 20 times faster (average 14.73) than SBS analyses with RAxML and between 18 and 495 times faster than BS analyses with competing programs, such as PHYML or GARLI. Moreover, this performance improvement increases with alignment size. Finally, we have set up two freely accessible Web servers for this significantly improved version of RAxML that provide access to the 200-CPU cluster of the Vital-IT unit at the Swiss Institute of Bioinformatics and the 128-CPU cluster of the CIPRES project at the San Diego Supercomputer Center. These Web servers offer the possibility to conduct large-scale phylogenetic inferences to a large part of the community that does not have access to, or the expertise to use, high-performance computing resources.
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Advocates of conditional combination have argued that testing for incongruence between data partitions is an important step in data exploration. Unless the partitions have had distinct histories, as in horizontal gene transfer, incongruence means that one or more data support the wrong phylogeny. This study examines the relationship between incongruence and phylogenetic accuracy using three tests of incongruence. These tests were applied to pairs of mitochondrial DNA data partitions from two well-corroborated vertebrate phylogenies. Of the three tests, the most useful was the incongruence length difference test (ILD, also called the partition homogeneity test). This test distinguished between cases in which combining the data generally improved phylogenetic accuracy (P > 0.01) and cases in which accuracy of the combined data suffered relative to the individual partitions (P < 0.001). In contrast, in several cases, the Templeton and Rodrigo tests detected highly significant incongruence (P < 0.001) even though combining the incongruent partitions actually increased phylogenetic accuracy. All three tests identified cases in which improving the reconstruction model would improve the phylogenetic accuracy of the individual partitions.
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MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters. Availability: http://morphbank.ebc.uu.se/mrbayes Contact: fredrik.ronquist@ebc.uu.se * To whom correspondence should be addressed.
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Nonphotosynthetic mycorrhizal plants have long attracted the curiosity of botanists and mycologists, and they have been a target for unabated controversy and speculation. In fact, these puzzling plants dominated the very beginnings of the field of mycorrhizal biology. However, only recently has the mycorrhizal biology of this diverse group of plants begun to be systematically unravelled, largely following a landmark Tansley review a decade ago and crucial developments in the field of molecular ecology. Here I explore our knowledge of these evolutionarily and ecologically diverse plant-fungal symbioses, highlighting areas where there has been significant progress. The focus is on what is arguably the best understood example, the monotropoid mycorrhizal symbiosis, and the overarching goal is to lay out the questions that remain to be answered about the biology of myco-heterotrophy and epiparasitism.
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The ancient arbuscular mycorrhizal association between the vast majority of plants and the fungal phylum Glomeromycota is a dominant nutritional mutualism worldwide. In the mycorrhizal mutualism, plants exchange photosynthesized carbohydrates for mineral nutrients acquired by fungi from the soil. This widespread cooperative arrangement is broken by 'cheater' plant species that lack the ability to photosynthesize and thus become dependent upon three-partite linkages (cheater-fungus-photosynthetic plant). Using the first fine-level coevolutionary analysis of mycorrhizas, we show that extreme fidelity towards fungi has led cheater plants to lengthy evolutionary codiversification. Remarkably, the plants' evolutionary history closely mirrors that of their considerably older mycorrhizal fungi. This demonstrates that one of the most diffuse mutualistic networks is vulnerable to the emergence, persistence and speciation of highly specific cheaters.
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Myco-heterotrophy evolved independently several times during angiosperm evolution. Although many species of myco-heterotrophic plants are highly endemic and long-distance dispersal seems unlikely, some genera are widely dispersed and have pantropical distributions, often with large disjunctions. Traditionally this has been interpreted as evidence for an old age of these taxa. However, due to their scarcity and highly reduced plastid genomes our understanding about the evolutionary histories of the angiosperm myco-heterotrophic groups is poor. We provide a hypothesis for the diversification of the myco-heterotrophic family Burmanniaceae. Phylogenetic inference, combined with biogeographical analyses, molecular divergence time estimates, and diversification analyses suggest that Burmanniaceae originated in West Gondwana and started to diversify during the Late Cretaceous. Diversification and migration of the species-rich pantropical genera Burmannia and Gymnosiphon display congruent patterns. Diversification began during the Eocene, when global temperatures peaked and tropical forests occurred at low latitudes. Simultaneous migration from the New to the Old World in Burmannia and Gymnosiphon occurred via boreotropical migration routes. Subsequent Oligocene cooling and breakup of boreotropical flora ended New-Old World migration and caused a gradual decrease in diversification rate in Burmanniaceae. Our results indicate that extant diversity and pantropical distribution of myco-heterotrophic Burmanniaceae is the result of diversification and boreotropical migration during the Eocene when tropical rain forest expanded dramatically.
Book
In Volume Two of Genera Orchidacearum, three of the seven tribes found in the subfamily Orchidoideae-Orchideae, Diurideae, and Diseae are thoroughly described. Each of the 101 genera in this volume receive separate treatment with sections on nomenclature and synonymy, distribution, anatomy, palynomy, embryology, cytogenetics, ecology, phytochemistry, phylogenetics, pollination, taxonomic notes, and economic uses. For those genera found in hobbyist's collections, cultivation notes emphasizing aritificial propagation are provided.This book features distribution maps of each genus with details on the dispersion of the flowers; superb illustrations with over 120 color photographs and line drawings; cultivational details for orchid enthusiasts and growers; contributions from over 50 international orchid experts; and diagnostic illustrations that detail each genus.
Article
Resumen Calypsoeae represent a small tribe of anatomically little-known orchids with a wide distribution in the Western Hemisphere. Leaves are present in all genera, except Corallorhiza and Wullschlaegelia both of which are subterranean taxa. Stomata are abaxial (ad- and abaxial in Aplectrum) and tetracytic (anomocytic in Calypso). Fiber bundles are absent in leaves of all taxa examined except Govenia tingens. Stegmata are present in leaves of only Cremastra and Govenia. Roots are velamentous, except in filiform roots of Wullschlaegelia. Vegetative anatomy supports a relationship between Wullschlaegelia and Corallorhiza but does not support the grouping of winter-leaved Aplectrum and Tipularia nor proposed groupings of genera based on pollinarium features.
Book
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
Article
Development of anthers in three subfamilies of Orchidaceae was studied anatomically to examine homology hypotheses for pollinium number characters and to produce a model of pollinium development for the family. Serial sections of plastic-embedded embryonic inflorescences revealed that anther primordia were either flattened or ovoid; subsequent expansion of thecae and their inward (adaxial) reorientation (''rotation''), achieved by differential cell division and elongation in the connective, result in a mature anther with strongly introrse morphology and pollinia oriented side by side (juxtaposed). Strongly introrse anthers occur in at least some members of all subfamilies and are probably the basal state for the family. All anthers examined (from Orchidoideae, Spiranthoideae, and Epidendroideae) showed a single meristematic region, which would later give rise to pollen, per theca at earliest stages; septation of each of these regions resulted in four or eight pollinia per anther, while lack of septation in some members of the Epidendroideae gave two pollinia. In contrast, the two bipartite pollinia found in many Spiranthoideae and Orchidoideae were produced by adherence of the contents of two locules at a late ontogenetic stage, and should be recognized as a distinct character state. Eight pollinia result from partitioning by two longitudinal septa or a longitudinal and a transverse septum; these two morphologies may also represent separate character states.
Article
As part of a phylogenetic study of Corallorhiza, a genus of ten species of leafless mycoparasitic orchids, the large single copy region (LSC) and inverted repeat of plastid DNA were examined with restriction fragment analysis to obtain information on relationships among the species, as well as to determine whether structural changes had occurred in the plastome. Deletion areas of between 1.3 and 6.0 kb were detected in the LSC of the C. maculata complex and C. striata, but most of the genome was not significantly affected. Cladistic analysis of restriction site characters produced one most parsimonious tree; additional accessions screened were shown to be most closely related to the primary accession for each species. No synapomorphy was found to unite Corallorhiza. The same topology resulted when deletion characters were added and indicates that deletions in the region of rpo and psa genes have occurred independently in the C. maculata and C. striata groups. Because of the coarse level of resolution in the probing, it is not clear to what extent the genes themselves have been affected. Only one species, the undeleted C. trifida, has been examined physiologically, and it was found to be photosynthetic. This fact, and the deletion pattern, suggest that species of Corallorhiza may show a range of levels of autotrophy.
Article
The present distribution and ecology of New Zealand plants is discussed from a historical viewpoint.It is suggested that during the Miocene a southern extension of the New Zealand archipelago supported a cool temperste flora, which gave rise to the present mountain flora after the onset of orogeny and climatic cooling in the Pliocene.As there was scarcely any simultaneous development of a distinctive flora adapted to the dry conditions which prevail to the east of the mountain axis, Cockayne§ opinion that extremely arid Pleistocene climates evoked certain characteristic life forms—notably the divaricating juvenile form of some trees—is considered to be substantially incorrect. That these life forms are adapted to still–existing conditions seems more probable.The broader features of present distribution are explllined in terms of Pleistocene glaciation and subsequent climatic amelioration.From the evidence of endemism and discontinuous distribution, it is concluded that Otago and Southland,Nelson and Marlborough, Auckland,the subantarctic regions and the Chatham Islands are areas where much of the present flora survived during the glaciation,whereas the middle portion of the South Island and the south of the North Island were characterised by extinction.Adjustment of the vegetation to post Pleistocene conditions is still incomplete, and complicated by the effect of continuing climatic fluctuations
Article
More than 400 species of vascular plants, in 87 genera, are acholophyllous and heterotrophic, but not directly parasitic upon autotrophs. They are usually, but incorrectly, described as 'saprophytes’since they are in fact nourished by means of specialized mycorrhizal associations. Although distributed world-wide, they are most abundant and show the greatest species-richness in the Neotropics and Palaeotropical regions. Their aerial parts range in size from a few centimetres to extensive liane types up to 40 m long. With few exceptions, their habitats are dense moist forests in which there is a surface accumulation of leaf litter, often in situations which are too shaded for autotrophic growth.
Article
Corallorhizinae are a small group of Old and New World temperate orchids of which a core monophyletic group comprises Govenia, Cremastra, Aplectrum, Oreorchis and the leafless Corallorhiza, and which according to phylogenetic analysis of nuclear ITS and plastid matK sequences, are related in this way: (Govenia (Cremastra (Aplectrum (Oreorchis (Corallorhiza))))). This hypothesis is consistent with the progressive deletion of the trnK intron and matK ORF. Frameshift-resulting indels yield a predicted loss of translation for the critical "domain X" region of matK and are evidence that matK is a probable pseudogene in Aplectrum, Oreorchis, and Corallorhiza. Within Corallorhiza, a previous hypothesis based on plastid DNA restriction site analysis is confirmed, with the thickened-labellum C. striata group being sister to the thin-labellum remainder of the genus, within which the circumboreal C. trifida is sister to the remainder, which then comprise two further sister groups: C. maculata + C. bulbosa + C. mertensiana and C. odontorhiza + C. wisteriana. A close relationship between C. striata and the recently described Appalachian C. bentleyi is shown; in particular, C. bentleyi is more closely allied to a southern Mexican population of C. striata than it is to northern North American C. striata populations, suggesting that two lineages, each with Mexican and northern North American populations, exist within the C. striata group.
Article
Using parsimony and Bayesian analyses, we estimated higher-level relationships within Orchidaceae, focusing on subfamilies and tribes. DNA sequences of part of the low-copy nuclear protein gene Xdh were obtained for 154 taxa including 126 genera of Orchidaceae and outgroup families of Asparagales. The general topology of the Xdh trees is congruent with those published previously based on plastid protein-coding genes and non-coding nuclear ribosomal DNA. The five subfamilies previously recognized are monophyletic and well supported. The results indicate that monandrous condition evolved independently in Vanilloideae and Epidendroideae/Orchidoideae. The analysis clarifies relationships between tribes of Epidendroideae such as Vandeae sensu lato to Collabieae, Epidendreae to Calypsoeae and Malaxideae to Dendrobieae. Also relationships of Bromheadia, Imerinaea, Sirhookera, and achlorophyllous species of Corallorhiza, Gastrodia, Limodorum, Neottia, Wullschlaegelia are for the first time evaluated in a broad molecular phylogenetic framework.
Article
DNA sequences of the plastid gene psaB were completed for 182 species of Orchidaceae (representing 150 different genera) and outgroup families in Asparagales. These data were analyzed using parsimony, and resulting trees were compared to a rbcL phylogeny of Orchidaceae for the same set of taxa after an additional 30 new rbcL sequences were added to a previously published matrix. The psaB tree topology is similar to the rbcL tree, although the psaB data contain less homoplasy and provide greater bootstrap support than rbcL alone. In combination, the two-gene tree recovers the five monophyletic subfamilial clades currently recognized in Orchidaceae, but fails to resolve the positions of Cypripedioideae and Vanilloideae. These new topologies help to clarify some of the anomalous results recovered when rbcL is analyzed alone. Both genes appear to be absent from the plastid genome of several achlorophyllous orchids, but are present in the form of presumably non-functional pseudogenes in Cyrtosia. This study is the first to document the utility of psaB sequences for phylogenetic studies of plants below the family level.
Article
The relative contribution of taxon number and gene number to accuracy in phylogenetic inference is a major issue in phylogenetics and of central importance to the choice of experimental strategies for the successful reconstruction of a broad sketch of the tree of life. Maximization of the number of taxa sampled is the strategy favored by most phylogeneticists, although its necessity remains the subject of debate. Vast increases in gene number are now possible due to advances in genomics, but large numbers of genes will be available for only modest numbers of taxa, raising the question of whether such genome-scale phylogenies will be robust to the addition of taxa. To examine the relative benefit of increasing taxon number or gene number to phylogenetic accuracy, we have developed an assay that utilizes the symmetric difference tree distance as a measure of phylogenetic accuracy. We have applied this assay to a genome-scale data matrix containing 106 genes from 14 yeast species. Our results show that increasing taxon number correlates with a slight decrease in phylogenetic accuracy. In contrast, increasing gene number has a significant positive effect on phylogenetic accuracy. Analyses of an additional taxon-rich data matrix from the same yeast clade show that taxon number does not have a significant effect on phylogenetic accuracy. The positive effect of gene number and the lack of effect of taxon number on phylogenetic accuracy are also corroborated by analyses of two data matrices from mammals and angiosperm plants, respectively. We conclude that, for typical data sets, the number of genes utilized may be a more important determinant of phylogenetic accuracy than taxon number.
DNA data and Orchidaceae systematics: A new phylogenetic classification Orchid conserva-tion
  • Barrett Rl Freudenstein
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Chase MW, Cameron KM, Barrett RL, Freudenstein JV. DNA data and Orchidaceae systematics: A new phylogenetic classification. In Dixon KW, Kell SP, Barrett RL, Cribb PJ, editors. Orchid conserva-tion. Natural History Publications, Kota Kinabalu, Sabah; 2003. pp. 69–89.
Can three incongruence tests predict when data should be combined? Molecular Biology and Evolution
  • C W Cunningham
Cunningham CW. Can three incongruence tests predict when data should be combined? Molecular Biology and Evolution. 1997; 14: 733-740. PMID: 9214746
Epidendroideae (Part two)
  • Am Pridgeon
  • Pj Cribb
  • Mc Chase
  • Fn Rasmussen
Phylogenetic analysis using parsimony (* and other methods). Version 4. Sinauer Associates
  • Dl Swofford
  • Paup
  • Sc Chen
  • Zh Tsi
  • Ky Lang
  • Gh Zhu
Chen SC, Tsi ZH, Lang KY, Zhu GH. Flora Reipublic Popularis Sinicae. 1999; 18. Science Press, Beijing.
  • A M Pridgeon
  • P J Cribb
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  • Genera Orchidacearum
Pridgeon AM, Cribb PJ, Chase MC, Rasmussen FN. Genera Orchidacearum: Epidendroideae (Part one), vol. 4: 89-115. Oxford University Press, New York; 2005.
Flora Reipublic Popularis Sinicae
  • S C Chen
  • Z H Tsi
  • K Y Lang
  • G H Zhu
Chen SC, Tsi ZH, Lang KY, Zhu GH. Flora Reipublic Popularis Sinicae. 1999; 18. Science Press, Beijing.
Constructing a significance test for incongruence
  • JS Farris
Genera Orchidacearum Volume 6: Epidendroideae (Part three)
  • AM Pridgeon