); seed germination conditions, i.e. the relationship with mycorrhizal fungi . sample host trees completely for epiphytic orchids. For each point .. generation in schools, for example, will be essential to reach this goal. The symbiotic relationship that occurs between an orchid and a tree would be classified as commensalism. Most orchids are epiphytes, which mean that that. An epiphyte is a plant that grows on another plant or tree but is not relationship between an epiphytic orchid and its host tree is what we Helping clients create better portfolios in line with their financial goals and needs;.
As structural elements of forests, these epiphytes are important for maintaining biological diversity and abundance because they provide food and habitats for numerous birds, insects and mammals in the forest canopy Nadkarni and Matelson ; Sillett ; Treseder et al.
Unlike terrestrial plants, their roots have no contact with the soil. Therefore, water stress is a major limitation to their survival, growth and distribution Zotz and Hietz ; Laube and Zotz ; Zotz and Bader For adapting to limited water availability, vascular epiphytes utilize suites of morphological and anatomical adaptations in their leaves, stems and roots, including thickened cuticles, stomata surrounded by trichomes, a reduction in transpiring surfaces through symodial growth, and development of aerial root systems Moreira et al.
The leaf cuticles of vascular epiphytes may act as efficient barriers against water loss after their stomata close Helbsing et al. Furthermore, these types of epiphytes have greater capacity for foliar water uptake and tend to have thinner hydrenchymal and cuticle layers Gotsch et al. Other mechanisms for storing water might involve the production of tissues such as succulent leaves and pseudobulbs, which are common features in vascular epiphytes Sinclair ; Zimmerman ; Stern and Morris The hydrenchyma in succulent leaves from numerous epiphytes can store water to buffer the effects of reduced water supplies during periods of drought Zotz and Bader ; Ogburn and Edwards In addition to these multiple morphological and anatomical adaptations to water shortage, vascular epiphytes demonstrate differences in their phenology and photosynthetic pathways.
In Orchidaceae, some deciduous epiphytic orchids may react to relatively long-lasting drought by shedding their leaves to reduce the surface area available for transpiration. When compared with the performance of C 3 photosynthesis, crassulacean acid metabolism CAM in many epiphytes plays an important role in improving carbon gains and water use Motomura et al. In some orchids, pseudobulbs are very short, thick and bulb-shaped stems that can bear one or more leaves at the top or along the stem axes.
These structures are present among most of the epiphytic orchids in tropical and subtropical regions. As storage organs for water, carbohydrates and minerals, pseudobulbs are of central importance to the growth and survival of those orchids Goh and Kluge ; Ng and Hew Furthermore, they have critical roles during the processes of vegetative growth, flowering and reproduction Zimmerman ; Blanchard and Runkle For trees, internal water stored in the stems contributes significantly to regulating their daily transpirational water losses Goldstein et al.
Likewise, water stored in the pseudobulbs of the epiphytic orchids may constitute an effective reservoir for protecting those plants against the effects of short- or long-term water deficits. Despite the recognized value of pseudobulbs, however, most published studies on the water relations of vascular epiphytes have historically focused primarily on their leaves e.
The Orchidaceae is the largest and most varied families of epiphytic vascular plants, particularly because of their life forms, habitats, and morphological and physiological traits Benzing Most members of Dendrobium are naturally distributed throughout South- East- and Southeast Asia, as well as the Southwest Pacific islands.
Some have argued that indels are more reliable characters than base changes Lloyd and Calder Freudenstein and Chase found them to be a particularly important component of the nad1b-c dataset. At present, we have implemented the automated workflow procedure only for base substitutions, but we plan to incorporate a module that codes indels as well according to the simple gap scoring procedure of Simmons and Ochoterenabecause the complex approach, relying on step-matrices, would be potentially intractable for such large datasets with their high numbers of indel character states.
The computations needed for this project will be carried out using a general purpose system for the parallel execution of bioinformatic workflows under development by one of the PIs ML. A prototype of the system has already been built and it was used for the preliminary experiments reported in this proposal.
The design objectives of this system are: These objectives are met by an architecture that integrates a graphical user interface GUI with state-of-the-art Grid scheduling technology and implemented entirely in Python. Based on our experience with the prototype, there are a number of design issues that need to be solved in adapting Grid technology to the execution of large scale bioinformatic workflows and that we will study as part of this proposal. Specifically, we will seek solutions to the issues of the heterogeneity of middleware software, optimal interfacing to queuing systems such as PSB and Maui commonly found in production supercomputers, the load balancing of multi-site computations using supercomputers at different institutionsand robustness to failures in subtask execution.
The issues described above are not adequately addressed by existing workflow management tools. Pegasys Shah et al. However the parallelization is at the level of the individual components of the workflow; customization here also requires Java programming skills. GridAnt Amin et al. It does not have a graphical interface and only runs in the Globus environment.
Its use also requires Java and Globus programming skills. This demonstrates the feasibility of the analysis approach, since essentially unlimited run time is available to us for larger data sets on clusters with many more nodes see facilities statements.
It directs us to which alignments should be examined for the cause of variation among even these similar alignments, however. We expect to see more significant variability among ITS alignments, for example, where this approach will be particularly important.
We will analyze each dataset individually, combined by genome, and combined in a total analysis under our 2-tier approach.
What is an Epiphyte? | Arnerich Massena Blog Home Page
Conducting individual and various combined analyses will allow us to determine whether there is conflict at the level of locus or genome.
Previous phylogenetic analyses of Orchidaceae utilizing sequences from the three genomes have not revealed notable incongruence e. However, we will examine the data sets for incongruence using the ILD test Farris et al. If we find incongruence we will attempt to localize it to particular taxa by performing an Adams consensus Adams on trees from analyses for each gene locus done separately, since that procedure allows individually conflicting terminals to drop to the node of conflict without losing the remaining structure in the tree.
This will allow us to identify and reexamine problematic taxa to determine if lab errors could be responsible for data disagreement. Heuristic searches will be performed using strategies to explore the data as completely as possible to search for islands of most parsimonious trees Maddisongiven that the problem of local optima can be particularly troublesome for very large data sets Goloboff In particular, TNT has implemented a number of innovative strategies such as the Parsimony Ratchet Nixon,sectorial searches, tree-drifting, and tree-fusing Goloboff that improve the thoroughness of tree search.
Given that each data set will undoubtedly have homoplasy, this can be important in revealing "underlying signal" among the data sets. This is done with the knowledge that independent genomes could be functioning essentially as single characters Doyle ; de Queiroz and that they may be reflecting different patterns due to incongruent transmission and fixation.
Nonetheless, the combined analysis will represent our best phylogenetic estimate.
Symbiotic Relationship Between an Orchid & a Tree
Because of the size of the datasets we will be analyzing, model-based approaches such as Maximum Likelihood ML and Bayesian analysis are computationally more problematic for use as primary tree search methods.
However, we will employ these approaches in particular cases in which their properties might be especially useful. These include situations where long branches are to be expected as with the leafless mycoheterotrophic taxa and where the parsimony analyses indicate significant rate heterogeneity among branches.
In these cases, smaller clades with potentially problematic taxa will be submitted for model-based analyses. Bayesian implementation of likelihood in MrBayes version 3. Assessing tree robustness and support: Jackknife analysis Farris et al. A minimum of replicates will be performed, each of which will include a small amount of branch swapping in each jackknife replicate, as it can significantly improve results Freudenstein et al. As stated above, Bayesian analysis also provides an indication of support in its posterior probability values.
Sensitivity analysis will be used to explore the datasets for robustness to alignment variation, as described above.
Project Description - Assembling the Tree of Life: Orchidaceae
Analytical and informatics resources and expertise: Each also can perform routine phylogenetic analysis on desktop PCs and Macintoshes see Facilities statements for details. Our primary resources for performing large analyses such as the combined alignment and tree search runs and analyses with large numbers of taxa are processor clusters and the supercomputers located at Ohio State University. Our Computer Science PI, Mario Lauria, will supervise use of this hardware and will develop the software infrastructure for the parallel execution of bioinformatic workflows linking free-standing programs Clustal, TNT.
Servers dedicated to the construction and maintenance of our website will be purchased by PI Williams for installation at the University of Florida. Dissemination of results and archiving of data products: Results will be disseminated in a number of ways.
First, the most up-to-date results will be posted on our website "OrchidTree" that will convey the results of our project using the large-scale phylogeny as an organizing tool. Because of the large number of taxa and nodes, we have chosen to employ special software to make viewing the tree and recovering information from it as easy as possible.
Inxight VizServer software already purchased at UF allows users to navigate easily through the tree using a hyperbolic tree. By clicking and dragging on nodes, users can stretch portions of the tree and follow a path of their own choosing through the tree.
See demo at http: Clicking on terminals and nodes brings up pages of information on those groups. These pages will include descriptions of the taxa, photographs of included species, literature references, links to GenBank accession numbers for individual DNA sequences, and links to other relevant orchid websites.
All data will be made available to the public as soon as they are collected and verified. DNA sequences will be deposited in GenBank and accession numbers will be provided on the appropriate taxon page on our website, which will be maintained at the University of Florida. All morphological character observations will be tied to voucher specimens, which will be documented and archived on our web site, as well as being archived on the OrchidTree website and ultimately deposited in TreeBase at http: The morphological data matrix will be input into the LucID software package University of Queensland; http: A member of our group Whitten has already assembled such a key for the orchid genus Maxillaria for Central America.
We will make available to the scientific community the software tool that we develop for the management of large scale bioinformatic workflows that is easy to use, can take advantage of a range of computational resources from collections of single PCs to production supercomputers requiring only minimal or no preinstalled supporting software, and is highly customizable by anyone with only basic script writing skills. See the "Workshops, Symposia, Presentations" section below for further details on dissemination.
One of the most important components of this proposal is the educational opportunities available for undergraduate and graduate students. Funding is requested to provide stipends for undergraduates at UF and OSU as well as assistantships for at least one graduate student position at each institution. Although specific thesis topics have not yet been formulated, these students will be trained broadly with aspects of their research being integrated into this greater Orchid Tree project.
It should be noted that the PIs have had great success attracting graduate students from Latin America. There are already a number of prospective students from Latin America who have expressed interest in pursuing graduate studies on orchids at these institutions; all efforts will be made to recruit students from this part of the world, Australasia, as well as underrepresented minorities from the United States.
To emphasize our commitment to recruiting minority and underrepresented groups, PI Williams has a commitment from UF administrators to support a minority graduate student for four years. Each year he will continue this program. See letters for elaboration. In training the next generation of plant systematists, educational opportunities will also be made available for two postdoctoral researchers - one under the direct supervision of Cameron and one working with Freudenstein, but both interacting with the entire team.
Unlike the graduate research activities described above, these postdoctoral fellowships will be advertised to attract individuals for specific research topics that have been developed from the results of the Orchid Tree project. These are as follows: This person will not simply be used as a technician to gather and code morphological data -- quite the contrary.
We expect this postdoc to B employ the resulting phylogenetic trees in order to investigate the evolution of key morphological orchid features. At the same time as these trends in character evolution are evaluated, the postdoc will seek to identify correlations among these characters of form, life history, physiology, and pollination syndromes, and will seek correlations with species richness, in order to relate character transformation to diversification.
The computer program DISCRETE Pagel has been used to document the phenomenon of concerted convergence in monocots among such characters as climbing habit, reticulate leaf venation, and fleshy fruits Givnish The software looks at the evolution of pairs of binary characters to test for significant correlations. This approach should uncover whether characters suspected to be correlated in Orchidaceae e.
I am sure there will be many, and. We expect that the ideal candidate for this position may or may not have an exclusive background in plant biology, but instead would be equally likely to hold a degree in museum science, children's education, or horticulture.
Past reviewers of our proposal considered this to be "an interesting and innovative approach. For example, NYBG's Everett Children's Adventure Garden welcomes more thanchildren, their parents and teachers each year to learn basic information about plants and their role in our world. The postdoc would be expected to A develop at least one orchid diversity educational module directed toward K school children. For example, a weeklong program focused on "Vanilla: In a similar vein, both gardens organize an annual orchid show.
These have been so popular that now nearly every botanical garden and museum in the country, including the Atlanta Botanical Garden, Missouri Botanical Garden, and Smithsonian Institution, offer similar exhibitions.
Last year's orchid show at NYBG drew more than 66, visitors, and the Kew show is even more popular. At present, these shows contain little scientific content. To remedy this problem, our postdoc will work closely with the show organizers and the PIs to communicate the results of our Orchid Tree project to the public see letter from M.
We propose at least one specific project for the postdoc related to these orchid shows: Currently, NYBG offers a handheld wand that takes visitors on a self-guided tour of its annual exhibit. Most of the content is horticultural rather than scientific. Producer for Acoustiguide, the world's leading supplier of audiotours, has agreed to assist in working with the postdoc to develop this script see his letter of support.
- What is an Epiphyte?
Considering only the orchid shows at the New York, Smithsonian, Kew, and Atlanta Botanic Gardens, these each have a potential visitor base of tens of millions within a day's travel. See letter from Kress Smithsonian and Chase Kew. We have identified one additional outreach module for the postdoc to develop. The American Orchid Society offers to its approximately 24, members the free use of dozens of slide and video programs for local society meetings.
According to the AOS, "many smaller societies use these educational programs for a few months of meetings. A recent Education Committee initiative has made the generation of new slide programs a high priority for the AOS, including PowerPoint presentations. These will be made available at no cost, with sponsorship from NSF clearly listed, not only to the AOS for distribution to its unparalleled membership base, but also to many of the 34 other orchid societies around the world.
Our goal is to reach out to the general public and of course also to disseminate the information resulting from this project to professional plant biologists. To this end we will present results regularly at national and international scientific meetings at all stages of the project.
In addition, we will organize one workshop and two scientific symposia. The workshop will be scheduled in to coincide with the 19th World Orchid Conference in Miami, Florida.
The WOC attracts several thousand commercial orchid growers, scientists, and hobbyists from around the world with lectures, plant sales, and exhibits. The PIs will attend this meeting and organize a workshop to introduce the Orchid Tree concept and an update on the progress of the project to this diverse group. Preliminary phylogenetic trees, databases, and web sites will be demonstrated, and the principles of molecular systematics, evolution, cladistics, and phylogenetic classification will be presented.
The PIs have found that this audience of well-educated orchid enthusiasts is eager to adopt new ideas if they can be explained without the use of jargon or taught in a non-patronizing manner.
During the final year of the grant period, we will organize a formal orchid phylogeny symposium to present our research to the professional orchid systematics community. Such a meeting was held in at the Linnean Society in London.
Personal communications through M. Chase see letters indicate that the Linnean Society would be willing to host this Orchid Tree Symposium. Our intention is to invite all orchidologists who have been involved in the five-year endeavor to deliver a paper on their orchid clade of specialization.
A Proceedings or a volume of the Bot. In this way, a dozen or more orchidologists not only the PIs will be able to make a contribution to the orchid systematics literature as a result of this large AToL initiative. We will provide material for branches to insure that our work reaches the broadest possible audience. The broader impacts of this project are numerous: Because orchids are such a popular and increasingly economically important group of plants, and in view of their diversity and myriad specializations, orchids are a natural group with which to capture the interest of the public and to convey the importance of systematics, evolution, biodiversity, and especially conservation.
This project is designed to capitalize on this opportunity by providing outreach at various levels, including institutional museums, universities, elementary and middle schools, local orchid societies and most broadly through web-based tools. The project will provide for training of undergraduates, graduate students, and postdoctoral fellows, and will foster collaboration between scientists and museum outreach specialists.
It will increase collaboration among a worldwide network of orchid systematists, including professionals from throughout Latin America. Our outreach to historical black colleges will, we hope, bring underrepresented minorities into the project. From a more academic point of view, orchids have been the subject of many evolutionary studies because of their diversity of form, intimate relationships with fungi, and elaborate pollination strategies. Such studies can only be properly interpreted within a phylogenetic context, and the ATol Orchid Tree will provide that framework, as well as the basis for a phylogenetically based classification.
This will position the family well for increased opportunities for studying evolutionary and ecological questions.
The software and approach to exploring multiple alignments and their implication will be of broad use to systematists studying any group.