Michael Donoghue, Ph.D. - US grants

During the last four years the Department of Ecology and Evolutionary Biology has successfully sought to attract new faculty members who are active researchers in several developing areas of molecular evolution. In addition, a number of new and established researchers are increasingly beginning to molecular techniques t answer evolutionary questions. Collaborations with researchers in other departments such as Molecular and Cellular Biology and Biochemistry are also increasing. These trends are expected accelerate in the future resulting in even greater interest in utilizing the most modern techniques which are applicable to evolutionary research in a broad range of areas. The renovation and equipping of laboratories to meet these new research needs has involved major capital expenditure which has largely been met through departmental set.up funds for new faculty members and equipment purchased on the grants of individual investigators. However, one major item of equipment, a preparative ultracentrifuge, is still not available in the department. This equipment is currently being borrowed from members of the Departments of Molecular and Cell Biology and Biochemistry and Veterinary Science (located in another building). This is an increasing unsatisfactory arrangement for all concerned. There are serious problems of availability and scheduling and the goodwill of colleagues in other departments is being taxed. An ultracentrifuge for the shared use of members of the Department of Ecology and Evolutionary Biology is therefore an urgent necessity.

Dr. Michael Donoghue of the University of Arizona, working initially with colleague Dr. Kenneth Sytsma at University of Wisconsin, plans to study evolutionary relationships within the flowering plant genus Viburnum and relationships to other groups, emphasizing characters obtained from chloroplast DNA. The chloroplast genome will be digested with a battery of restriction enzymes, each of which cleaves the molecule at specific sites, and the exact position of these sites on the molecule will be determined. Comparison of nucleotide site similarities and differences among the species will allow determination of the evolutionary pattern of mutations separating taxa. In assessing more distant relationships, between genera and families, complete nucleotide sequences of chloroplast genes will be obtained and compared, using computer-aided methods. Phylogenies derived from molecular data will be compared to trees obtained previously based on morphological characteristics, and the nature and extent of congruence will be evaluated. Molecular data are likely to resolve relationships that remain equivocal based on morphology alone. Further, resolved phylogenetic trees will provide a framework for study of the evolution of particular morphological traits of interest. This will be especially vaulable in the case of fruit characters, because these have recently been studied in detail by Dr. Donoghue and developmental data are available for these. The use of phylogenetic information to analyze developmental changes will contribute to emerging analyses of the evolution of form and function in organisms.

9318325 Donoghue The rate of publication of phylogenetic studies has increased dramatically in recent years. Access to phylogenetic trees, and to the data underlying those trees, is needed for a wide variety of purposes, including comparative studies of morphological and molecular evolution, biogeography, coevolution, and studies of the congruence of different sources of evidence. Such data are also needed to monitor progress in phylogenetic research, to test new methods of taxometric analysis, and to address immediate practical problems in conservation of biodiversity. The aim of the project is to establish a prototype database of phylogenetic studies designed to make published information readily accessible, and thereby to explore the feasibility of developing an internationally comprehensive database. Development of a prototype will involve examination of alternative strategies for obtaining phylogenetic studies from the literature and from authors via electronic submission of data. Consultation with colleagues will help delimit a core of essential information to be included in the prototype database, including data matrices on characters, basic information on taxa, bibliographic citations, and phylogenetic trees. %%% Software will be developed for electronic transfer of taxonomic data sets, for data entry, for retrieval and manipulation of data sets and for importing and exporting data sets to phylogenetic and analy tical programs. The database will be designed to allow flexibility to incorporate additional information and to export data to future implementations on other platforms or software environments. The prototype will stimulate community discussion on the development of a comprehensive phylogenetic database for all groups of organisms.

9317625 Hartl Five senior faculty at Harvard University are applying for an Applied Biosystems Model 373A-01 Automated DNA Sequencer with associated hardware and software. Harvard is in a unique position to lead a new synthesis of molecular biology and evolutionary biology because of its long tradition of excellence in both fields. Indeed, among the priorities for academic growth and development in the life sciences is the overlap between molecular biology and evolutionary biology. The Department of Organismic and evolutionary Biology (OEB) at Harvard is already expanding with new faculty representing this type of integration. Among the five OEB faculty participating, four (Hartl, Donoghue, Kellogg, and Pierce) are new to Harvard, and three (Hartl, Donoghue, and Pierce) are senior appointments. The need for automated DNA sequencing in the participating groups is immediate and acute. There is no automated DNA sequencer available for shard use. Among the applicants, no group alone is large enough or its needs extensive enough to justify purchase, maintenance, and exclusive use of an automated sequencer. However, in the aggregate, the groups can make use of an automated sequencer essentially to full capacity (estimated sequencing needs approximately 1 million bp per year). The automated DNA sequencer will be set up in the Hartl laboratory, which is centrally located among the participating users, and will be supervised by Dr. Elena Lozovskaya, a member of the Hartl group who has extensive practical experience in automated DNA sequencing. Most of the participating groups have already had relevant experience using automated DNA sequencers and their projects are funded and ready to be implement. Therefore, the automated DNA sequencer is a familiar piece of equipment that will be set up in a central location among the users, supervised by an experienced investigator, and used immediately to essentially full capacity. OEB will contribute to the purchase of the instrument and support of the major portion of the recurring service contract. at Harvard University are applying for an Applied Biosystems Model 373A-01 Automated DNA Seq ! F $ $ ( Times New Roman Symbol & Arial " h E E E + < ! = abstract Deseree King, BIR Deseree King, BIR

GER-9554522 Donoghue This program will provide broad graduate training in plant systematics, thereby addressing widely recognized needs in plant biology and environmental biology. The Department of Organismic and Evolutionary Biology (OEB) is ideally suited to provide this training. Eight OEB faculty (three newly appointed) will be primary participants in the program, along with five associated personnel from outside the department. New molecular laboratories complement the strengths, and growing interest on the part of outstanding applicants, the development of a plant systematics program has been hindered by limitations on internal funding. The program will bring eight new students into the department and will provide flexible funding for other students to ensure broad training and timely completion of the PhD. A rotation scheme and several new courses will be initiated, targeting morphological and molecular techniques and the teaching of plant systematics. Harvard will augment NSF funding by supplementing tuition and providing field research assistantships, herbarium traineeships, and resources for the new courses, workshops, rotations, and recruitment activities. The participating faculty will allocate GRT funds to meet these goals and will coordinate efforts to recruit and retain underrepresented minority students.

9521944 Pfister Despite their ecological importance in decay and decomposition of organic matter and their occasional pathogenicity in plants and animals, fungi as a group remain poorly known, with few specialists able to identify the taxonomic entities or to pursue further biological investigations. One especially difficult complication lies in the fact that fungal organisms may live and reproduce asexually, through specialized spores, for years, without showing evidence of the sexual reproductive or "fruiting" structures that make possible accurate taxonomic identification and phylogenetic analysis. Dr. Donald Pfister at Harvard University, a mycologist with a long and productive record of research on ascomycete fungi, is teaming with colleague Dr. Michael Donoghue, with interests in theoretical aspects of systematic and phylogenetic research, in a study of filamentous fungi placed in the suborder Sarcoscyphinae. These are largely wood decomposers or saprobes, although some are known plant pathogens; many species are estimated yet to be described, especially from tropical environments. A major emphasis of their five-year program is on the integration of traditional morphological studies with two additional lines of evidence: molecular analyses of DNA sequences of fungal samples, and laboratory culturing to asqess mating behavior between geographic isolates. Training in both practical and theoretical aspects of fungal systematics will involve undergraduate and graduate students, as well as postdoctoral associates. Colleagues in South America will also participate in the work. The University provides superb laboratory and collections facilities, and computerization is a hallmark of all aspects of the research, including specimen databasing, taxonomic and phylogenetic analysis, and Internet linkage to major fungal resources.

9705795 Donoghue et al. This project will inventory plant and fungal diversity in western Sichuan and eastern Xizang (Tibet) provinces of China. This area is one of extreme topographic complexity caused by the parallel, very deep valleys of the major rivers that drain the Asian plateau. Lower elevations of the region are characterized by tropical forests, while higher elevations are dominated by conifers and alpine vegetation. Preliminary work has shown that vascular plant diversity in this area is far greater than in any other region of comparable size in the Earth's temperate zones. It is reasonable to hypothesize that high levels of diversity will also be found among the non-vascular plants and fungi, although current knowledge of these groups is very poor for this region. Expeditions to collect plants and fungi will be undertaken in 1997, 1998, and 1999; these will be in close collaboration with Chinese colleagues from Beijing and the Chengdu Institute of Biology in Sichuan. Spciemens will be distributed to relevant institutions within and outside of China, and will be made available particularly quickly to experts in various groups. The specimen data will be made available electronically, as quickly as it can be provided via the WWW. This project is funded as a partnership among the International Programs and Biotic Surveys & Inventories Program of the NSF, Harvard University, the Chengdu Institute and other Chinese institutions and agencies, and the Royal Botanic Gardens, Edinburgh. Through the course of the project, both American and Chinese students will be trained and have the opportunity for international travel and collaboration. In addition, this project will establish long-term collaborative edforts to assess the biodiversity of China.

9801259 Donoghue Phylogenetic and comparative analyses will be used to examine the evolution of interactions between dioecious figs (Moraceae: Ficus subg. Ficus) and their pollinating fig wasps (Hymenoptera: Agaoninae). Paired collections of dioecious figs and fig wasps from the field were made by Weiblen during 1995-1997. Morphological and molecular data from these collections will be used in parallel phylogenetic analyses. The internal transcribed spacer (ITS) region of nuclear ribosomal DNA from selected fig species and the 3' end of mitochondrial cytochrome oxidase I (COI) from fig wasps will be sequenced. The extensive fig wasp collections at the Rijksmuseum van Natuurlijke Historie, Leiden, The Netherlands, will be used to confirm the identities of selected pollinator species and to explore morphological characters. Scanning electron microscopy will document fig and fig wasp morphological characters used in phylogenetic and comparative analyses. Comparative studies are designed to evaluate coevolutionary hypotheses in a phylogenetic context, including parallel diversification and cases of reciprocal adaptations between interacting lineages.

9903835
Hibbett and Donoghue
Homobasidiomycetes include the mushroom-forming fungi and their relatives. About 13,500 species have been described, which is about 23% of all known species of fungi. The fruiting bodies of homobasidiomycetes include conspicuous, developmentally integrated structures such as mushrooms and puffballs, as well as very simple forms such as the crust-like fruiting bodies of "corticioid" fungi. Homobasidiomycetes play major roles in carbon cycling in terrestrial ecosystems; they comprise the majority of wood-decay fungi and ectomycorrhizal fungi (associated with tree roots); and they also include mycoparasites, insect symbionts, lichens, and litter decomposers. Although individual groups of these fungi have been studied intensively, their overall pattern of morphological and ecological evolution has not been determined because to date there has existed no broad well-supported phylogenetic framework for the group.
Over the last few years, considerable progress has been made in understanding homobasidiomycete phylogeny through the use of new DNA sequence characters, particularly the genes encoding nuclear and mitochondrial ribosomal RNA (rDNA). This project will expand the database of nuclear and mitochondrial rDNA sequences and add new data from protein-coding genes under study, such as the tubulins or RNA polymerases. Taxon sampling will target problematic groups such as the polyporoid, hymenochaetoid, and cantharelloid groups of fungi, whose relationships remain weakly supported by the existing molecular data. Conventional protocols for phylogenetic analyses will be employed, and in addition the investigators will explore the use of "supertrees" for combining or collating independent phylogenetic trees with overlapping sets of taxa in order to construct a composite phylogenetic hypothesis. The trees will be used to construct phylogenetic classifications and to study historical patterns of evolution in selected morphological and ecological characters. Specific characters to be investigated include: corticioid versus erect fruiting bodies; brown rot versus white rot modes of wood decay; and ectomycorrhizal versus saprotrophic and pathogenic modes of nutrition. A broad framework phylogeny for the homobasidiomycetes will facilitate, for example by identifying sister groups and nearest outgroups, more intensive analyses of morphological and physiological changes in these fungi.

9972612
Donoghue and Ree
Graduate student Richard Ree, under the direction of Dr. Michael Donoghue at Harvard University, is studying the phylogenetic relationships and patterns of evolution in morphological characters in the genus Pedicularis (louseworts, of family Scrophulariaceae), a northern hemisphere lineage of flowering plants that has undergone extraordinary diversification in the mountains of south-central China and neighboring regions. Conflicting taxonomic classifications of the numerous species in this genus (ca.. 500 described species in total) have resulted from differing emphases on floral features versus vegetative characters by taxonomists in their mostly intuitive assessments of similarity between species. The primary aim of the project is to test the hypothesis that major differences among classifications of Pedicularis reflect differential rates of evolutionary change in vegetative versus flower characters. Molecular data from nuclear and chloroplast DNA sequences, supplemented with morphological data, will be used to construct a phylogenetic (genealogical) framework for a sample of ca. 90 of the estimated 270 Asiatic species of the genus. Patterns and rates of character change will then be explored using methods of inferring ancestral states and assessing heterogeneity in rates across lineages.
The project is the first effort to apply modern, explicit phylogenetic methods to the study and interpretation of floral and vegetative diversity in the genus Pedicularis, and it will provide a framework for extended analyses on other species in the genus and in related Scrophulariaceae. Furthermore, the research targets one of the most species-rich regions in the eastern Himalayan biodiversity "hotspot" and hence will provide insights into the processes that have made this remote region the most diverse in the northern temperate zone.

New Haven has been identified as one of the most needy districts for science reform with only 10.8% of urban students meeting state goals in science. In 1997, the Peabody Museum of Natural History of Yale University and the New Haven Public Schools joined forces to improve the quality of science teaching and learning in the New Haven community by establishing the Peabody Fellows Program. The well-documented success and excitement of this initiative and the request of New Haven Public School administrators to integrate science and health issues compelled us to propose the development and implementation of a new program, the Peabodv Fellows Biodiversity and Human Health Program. Data show that 78% of K-6 New Haven teachers do less than two hours per week of hands-on science in the classroom and 70% of those teachers receive less than five hours of staff development in science. Accordingly, this Program is designed to be a rigorous teacher-training program that involves teacher- designed science curriculum and the use of interactive mobile science units, BioAction Lab I and ll. The target audience is New Haven science teachers and students (90% minority, 50% female) and their families. The scientific content of the newly designed Peabody Fellows Program is focused on the fundamental relationship between biodiversity and human health. Specifically, the Program aims to build science literacy and demonstrate how the study of science can contribute to human health and well being. Consortium members represent the following institutions: Yale University (Peabody Museum of Natural History, School of Epidemiology & Public Health in Yale University School of Medicine, Yale Child Study Center, Yale University Health Services Center), New Haven Public School System, Connecticut Agricultural Experiment Station, New Haven Natural Guard and Connecticut Academy for Education in Math, Science and Technology. Together, this consortium will work to educate and train teachers and students in four broad themes that link biodiversity and health: (l) Plant Biodiversity/Medicinal and Food Resources; (2) Vertebrate Biodiversity/Food Resources; (3) Invertebrate Biodiversity/Pathogens; (4) Environmental Changes/Health Risks. Extensive formative and summative evaluations conducted in collaboration with the Yale Child Study Center will assist in the Program's development. All curriculum designed as a result of this Program will be an integral part of New Haven School District's science curriculum for grades 3-8 and serve as a model for the writing of additional curriculum units. In Year IV, the Peabody Fellows Biodiversity and Human Health Program and its associated curriculum will be placed on the Museum website for maximum dissemination and accessibility.

0073299
Baum, Donoghue, and Davis
Malpighiaceae are a family of flowering plants that are an important element of forests and savannas in the Old and New World tropics. New World Malpighiaceae are pollinated by specialized oil-collecting bees (anthophorid females) and exhibit a highly conserved floral morphology despite tremendous diversity in fruit morphology and habit. These oil-collecting bees are absent from the Old World. Some Old World clades, like Acridocarpus, are presumed to be derived from New World lineages and they exhibit a combination of features associated with oil-bee pollination and with "buzz" pollination. These groups provide an opportunity to examine the consequences of the loss of specialized pollinators. The goals of this study by graduate student Charles Davis, under the direction of Drs. David Baum and Michael Donoghue, are (1) to infer the phylogenetic relationships within Malpighiaceae using chloroplast and nuclear DNA sequences, (2) to infer the phylogeny or genealogy of Acridocarpus species in order to examine patterns of floral morphological evolution associated with pollinator shifts, and (3) to document the pollination of Acridocarpus in African habitats.
Preliminary molecular data indicate that Old World genera of Malpighiaceae belong to several separate lineages, suggesting that morphologies associated with buzz pollination have evolved more than once independently. However, several areas of the phylogeny remain poorly resolved. Furthermore, several additional Old World lineages need to be added to existing datasets. Analyses of Acridocarpus using ribosomal DNA sequences reveal two major clades, one including species endemic to Madagascar and New Caledonia and the other consisting of species distributed across Africa. Oil glands appear to be entirely absent in species from Madagascar and New Caledonia, but appear in some African species. Fieldwork in Africa indicates that species of Acridocarpus are pollinated by large xylocopine bees that buzz the anthers, and the floral glands produce sugars rather than oils. Resolving the phylogeny of Malpighiaceae with additional chloroplast DNA sequences, along with sequences of a nuclear phytochrome gene, will clarify the origin and relationships of the Old World species. Further phylogenetic work will allow an evaluation of whether Old World species with similar morphologies have evolved independently, and whether such floral evolution is associated with the loss of oil-collecting pollinators. This study will shed light on the patterns and mechanisms of morphological change following a shift in pollination system.

Plant MADS-box genes encode transcriptional regulators that are required for a variety of critical developmental processes, including organ identity, flowering, fruit development, root development, and pattern formation. This family of genes has diversified dramatically during the evolution of vascular plants, and especially within the angiosperms, resulting in the large number of these genes in modern flowering plant species. The problem at hand is to define the roles of these MADS-box genes, as well as to understand the evolutionary changes that resulted in their great diversity of functions. Cloning and sequencing MADS-box genes in a variety of plant species will lay the groundwork to address this question. These sequences will be used in a series of phylogenetic analyses to determine the relationships among these genes. Understanding the diversity of functions encoded by the MADS-box genes, coupled with knowledge of how these processes have been modified through the evolution of vascular plants, will be key in developing targeted strategies for manipulating the growth and development of non-model plant species.

Evolutionary biologists and ecologists have long been fascinated by explosive radiations of species that exhibit tremendous morphological diversity and occupy a wide range of habitats. The flowering plant lineage Valerianaceae contains 300-350 species that have been placed in 14-17 genera, with nearly 200 of the species being endemic to South America. These species exhibit a striking range of floral and vegetative forms. It has been hypothesized that the South American species represent a recent radiation. The availability of fossils will allow us to explicitly test biogeographic hypotheses and investigate rates of speciation within this group. The goals of this study are: 1) to infer the phylogeny of Valerianaceae using several DNA sequence data sets, 2) to examine morphological character evolution, 3) to elucidate the biogeographic history of Valerianaceae, and 4) to assess rates of speciation, with an emphasis on the South American radiation.

This will be the first phylogentic analysis of Valerianaceae to include a broad sample of species from each of the genera and will also provide an empirical application of several new methods for the study of rates of evolution and speciation. Specifically we will test the hypothesis that over 200 species of Valerianaceae have originated since the formation of the Isthmus of Panama some 3-6 million years ago. This project will compliment ongoing studies of other lineages of the Dipsacales and will enhance our understanding of Northern Hemisphere biogeography and the origin of the South American flora. While our main aim is to address questions of broad evolutionary significance, there is an element of urgency to this research from the standpoint of conservation. Specifically, the enormous diversity now found in the Andes of South America is threatened by human impacts on the high elevation "paramo" vegetation.

Phylogenetic Structure of Woody-Plant Communities

Webb, Ackerly, & Donoghue; NSF proposal 0212873

The ecological communities of organisms found in nature have usually been treated as collections of independent species. However, the great advances made recently by phylogenetic biologists in understanding the "tree of life" mean that ecologists can now examine the evolutionary relationships among the species in their communities. Knowing this phylogenetic structure also enables ecologists to detect the processes organizing species membership in the communities, and thus provides a powerful new tool to understand species-rich systems. In the proposed research software tools will be developed for assembling and analyzing community phylogenetic structure, and will be applied to an endangered, rain forest tree community in Borneo, and to the Californian flora. A comparative survey of the phylogenetic structure of other plant communities around the world will also be performed. The proposed research will promote a closer integration of evolutionary biology and community ecology.
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A grant has been awarded to Dr. Michael J. Donghue of Yale University to investigate green plant evolution. Humans rely on green plants for food, shelter, clothing, and for providing the oxygen that is essential to life. From a biological perspective and as one of the oldest and most diverse branches of the tree of life, green plants provide an unparalleled system in which to explore interrelationships of living organisms and to approach some of the most significant and intriguing questions concerning the diversification of life on earth. Many of these questions relate to fundamental evolutionary events, such as the transition of organisms from single-celled to multicellular body plans, the colonization of land, and the derivation of different life-cycle modes. Accordingly, understanding their evolutionary history is a critical component in the NSF's Assembling the Tree of Life program.

This grant is part of a collaborative project, including principal investigators from the Bigelow Laboratory for Ocean Sciences, the University of California at Berkeley, Southern Illinois University, Utah State University, the University of Washington, and Yale University, the focus will be: 1) resolving the primary pattern of diversification among green plants; 2) investigating questions relating to the long evolutionary history of these organisms; 3) providing a model for analysis that will be applicable to other groups of organisms with extensive evolutionary histories. The team will emphasize the development of novel analytical methods that make it possible to conduct analyses across multiple scales and to use all of the available data from heterogeneous sources. A solid backbone of relationships based on genomes and structure for 50-100 plants, representing the critical deep-branching lineages, will enable the integration of previous and ongoing studies of many more plants into a comprehensive picture of green plant genealogy. The primary objectives of the project are: 1) complete a matrix of whole genome sequences for chloroplasts and mitochondria, and develop Bacterial Artificial Chromosome (BAC) nuclear genome libraries; 2) produce a comprehensive set of comparable morphological and ultrastructural data for the same plants; and 3) incorporate inferences from across the phylogenetic hierarchy in green plants using methods designed to permit scaling across studies. Multiple integrated training, educational and outreach activities will result in continual dissemination of the activities and progress of this research group to the scientific community and beyond.

Michael Donoghue will have primary responsibilities for phylogenetic analysis, including supertree construction, analysis of character evolution and macroevolution, and archiving trees and other phylogenetic products.

This collaborative project aims to establish a national computational resource to move the research community much closer to the realization of the goal of the Tree of Life initiative, namely, to reconstruct the evolutionary history of all organisms. This goal is the computational Grand Challenge of evolutionary biology. Current methods are limited to problems several orders of magnitude smaller, and they fail to provide sufficient accuracy at the high end of their range.

The planned resource will be designed as an incubator to promote the development of new ideas for this enormously challenging computational task; it will create a forum for experimentalists, computational biologists, and computer scientists to share data, compare methods, and analyze results, thereby speeding up tool development while also sustaining current biological research projects.

The resource will be composed of a large computational platform, a collection of interoperable high-performance software for phylogenetic analysis, and a large database of datasets, both real and simulated, and their analyses; it will be accessible through any Web browser by developers, researchers, and educators. The software, freely available in source form, will be usable on scales varying from laptops to high-performance, Grid-enabled, compute engines such as this project's platform, and will be packaged to be compatible with current popular tools. In order to build this resource, this collaborative project will support research programs in phyloinformatics (databases to store multilevel data with detailed annotations and to support complex, tree-oriented queries), in optimization algorithms, Bayesian inference, and symbolic manipulation for phylogeny reconstruction, and in simulation of branching evolution at the genomic level, all within the context of a virtual collaborative center.

Biology, and phylogeny in particular, have been almost completely redefined by modern information technology, both in terms of data acquisition and in terms of analysis. Phylogeneticists have formulated specific models and questions that can now be addressed using recent advances in database technology and optimization algorithms. The time is thus exactly right for a close collaboration of biologists and computer scientists to address the IT issues in phylogenetics, many of which call for novel approaches, due to a combination of combinatorial difficulty and overall scale. The project research team includes computer scientists working in databases, algorithm design, algorithm engineering, and high-performance computing, evolutionary biologists and systematists, bioinformaticians, and biostatisticians, with a history of successful collaboration and a record of fundamental contributions, to provide the required breadth and depth.

This project will bring together researchers from many areas and foster new types of collaborations and new styles of research in computational biology; moreover, the interaction of algorithms, databases, modeling, and biology will give new impetus and new directions in each area. It will help create the computational infrastructure that the research community will use over the next decades, as more whole genomes are sequenced and enough data are collected to attempt the inference of the Tree of Life. The project will help evolutionary biologists understand the mechanisms of evolution, the relationships among evolution, structure, and function of biomolecules, and a host of other research problems in biology, eventually leading to major progress in ecology, pharmaceutics, forensics, and security.

The project will publicize evolution, genomics, and bioinformatics through informal education programs at museum partners of the collaborating institutions. It also will motivate high-school students and college undergraduates to pursue careers in bioinformatics. The project provides an extraordinary opportunity to train students, both undergraduate and graduate, as well as postdoctoral researchers, in one of the most exciting interdisciplinary areas in science. The collaborating institutions serve a large number of underrepresented groups and are committed to increasing their participation in research.

These activities build upon an existing collaboration between 1998, Yale University's Peabody Museum of Natural History and the New Haven Public School (NHPS) District, the Peabody Teachers Program, a professional development program. Participating teachers produce inquiry-based science curricula that use Peabody Museum specimens in the mobile BioAction Lab for hands-on exploration of biological diversity and its impacts on human affairs. This draws on the expertise and materials resident in Yale's Peabody Museum, and provides stimulating subject matter upon which basic science competencies can be developed. The project proposed here is designed to build upon the already-existing strengths of the Peabody Teachers Program to enhance the professional development of middle school teachers and Yale graduate students, as well as to enrich the science-learning environment for New Haven middle school students. The Fellows work closely with participating teachers throughout the year to provide technical assistance as they develop curriculum units, in part to help ensure the scientific accuracy of the content. Working with the teachers and with children in their classrooms improves the science communication skills of the Graduate Fellows. Training and on-site supervision of the Graduate Fellows is provided by the PIs, by the staff of the program, and by the Yale Teacher Preparation Program. In addition, Master Peabody Teachers serve as mentors for pedagogical and classroom management techniques. All curriculum units designed in connection with this program are being incorporated into the middle school science curriculum and will also be disseminated broadly via the Peabody Museum's website. All aspects of the program are overseen by an Advisory Council and a Working Committee, including evaluations of the efficacy of the program. The broader impacts of the project affect a spectrum of beneficiaries. Participating teachers are increasing their scientific knowledge and developing new content-rich curricula. Their students (90% minority, 50% female, 75% on subsidized lunch programs) are benefiting from exposure to scientific subject matter and approaches of relevance to their daily lives, as well as to new role models. Yale graduate students are directly exposed to educational issues at the middle school level, and to the challenges of communicating the wonder of nature and the excitement and importance of science. This initiative strengthens Yale University's graduate programs and its commitment to providing resources for the enhancement of science education in the local school system.

Title: Yale University Graduate Teaching Fellows in Biodiversity
Institution: Yale University, Peabody Museum of Natural History
School Partners: New Haven Public
PI: Michael J. Donoghue, Leonard E. Munstermann
Fellows/yr: 4 Graduate year 1, 6 in years 2 and 3, 2 Undergraduate Target: Middle School (grades 4-8)
Setting; Urban
Disciplines: Biological sciences

Proposal # DBI-BDI: 0345341
PI: Beaman


Abstract

Yale University has been awarded a grant in collaboration with the New York Botanical Garden and the University of Illinois to create a system to image specimens in natural history collections (plant specimens in this case), use Optical Character Recognition (OCR), Natural Handwriting Recognition (NHR) and Natural Language Processing (NLP) to read the labels on the specimens and parse the label data into its component fields, then enter the data into a database. Modular, configurable, open source web services will provide interoperability and scalability in mirrored, distributed environments. This project will make the data capture of natural history collections much more efficient and lower the associated time and costs per specimen digitized.

Intellectual Merit: Flowering plants (angiosperms) are the largest (>270,000 species), most diverse, and economically most important group of green plants. Understanding the origin, patterns of variation, and relationships among angiosperms is challenging. Despite progress, relationships among major groups remain unclear, as do relationships within major subgroups (e.g., roses and allies). Our multigene and genomics approaches target 12 problematic groups and subgroups; their resolution should clarify the framework for angiosperm phylogeny. We also will develop the first comprehensive non-DNA database for angiosperms and populate it with key morphological features. Together, our approaches will lay groundwork for collaboratively building the tree of all 12,000 genera of angiosperms.

Broader Impacts: The angiosperm tree will be useful to comparative biologists including physiologists, ecologists, paleobiologists, and genomicists. The Botany Browser we develop will provide an informatics infrastructure to bring many data resources to users' desktops. The Angiosperm MorphBank will facilitate group diagnosis, analyses of character distributions, and study of fossils. Our interdisciplinary training of postdoctoral fellows and students will emphasize recruitment of minorities. Our website on angiosperm diversity will be valuable to researchers, K-12 teachers, and students. We will construct pages for the Tree of Life Web Project including TreeHouses designed for K-12 students and teachers. A movable museum exhibit highlighting advances in our understanding of plant phylogeny will be distributed to museums represented in our project. Posters detailing the angiosperm tree will be designed and distributed and made available on CD. Additional outreach will be provided through presentations to local public schools.

This study investigates evolutionary patterns in the cedar apple rust fungi. These parasites have a complex life cycle in which they alternately live on two different plant species in order to reproduce. The factors that direct and constrain the evolution of new species of cedar apple rust are not well understood. This study seeks to understand the importance of three crucial aspects of parasite evolution in this group. These are cospeciation, in which a parasite evolves new species in tandem with its host plant, the evolution of life cycle complexity, and the degree of specialization on particular host species.

Rust pathogens cause major damage worldwide to such important crops as wheat, soybeans, and coffee. Cedar apple rusts in particular cause damage to fruit trees such as apples, pears, and quince. The evolution of new and virulent species of rusts is of particular concern. This study will increase understanding of evolutionary processes in rusts and the cospeciation and character analyses will have broad relevance in understanding fungal-plant relations and plant parasitism. The study will include Japanese as well as North American species of cedar apple rust. The collaborative ties with Japanese scientists that have been established will serve to promote the expansion and exchange of knowledge on plant pathogenic fungi.

This award provides support to enable the purchase of a high throughput DNA analyzer, thermocycler and robotic workstation to be placed in a core microchemistry facility where it will be used and maintained by facility staff. This set of equipment is now a mainstay of research programs requiring high throughput DNA sequencing, microsatellite analysis, and single-nuculeotide polymorphism surveys. Investigators whose research and training efforts require use of the equipment will be charged using a set fee for service schedule. Placement of such equipment in a core facility fosters communication among different research groups who use the equipment leading to the sharing of ideas, information, and technical innovations. It also maximizes the use of the equipment by making the equipment available to a large number of other users from different disciplines and departments across campus. The equipment will allow the PI and her colleagues to expand their capacity for population-level analysis via enhancement of fragment analysis (e.g., microsatellite DNA), and more importantly, via single nucleotide polymorphism survey. The requested equipment will be housed in the Yale Institute for Biospheric Studies - Molecular Systematics and Conservation Genetic laboratory (YIBS - MSCG) which trains students in molecular techniques applied to environmental and organismal level questions. Since its inception, the YIBS - MSCG has trained students via research rotations, formal laboratory courses, dedicated seminars, and workshops. The equipment will enhance training by allowing students to obtain genetic information from large data sets in a time frame that is appropriate to their academic schedules, and do so within the budget available for training. It will also expose them early in their scientific life to state of the art equipment. The equipment is also expected to impact joint efforts of YIBS - MSCG with the Yale Peabody Museum in a science literacy partnership with the public school district of New Haven. Via this program, middle schools characterized by underachieving minority students from low-income families are targeted for educational outreach. The partnership, begun two years ago, plans to integrate the YIBS-MSCG laboratory as a means for offering additional opportunities for learning and hands-on training.

Evolution of a novel floral organ in Dipsacaceae: Consequences for dispersal and diversification

This project is designed to elucidate the origin and consequences of morphological novelty using the flowering plant group Dipsacaceae (Dipsacales) as a study system. Dipsacaceae are characterized by an "epicalyx," a novel organ that subtends the flower and functions in fruit dispersal. Much of the diversity in Dipsacaceae relates directly to the epicalyx and different morphologies are associated with different dispersal mechanisms. These observations suggest that the epicalyx functioned as a "key innovation" that spurred the adaptive radiation of the Dipsacaceae around the Mediterranean basin. A detailed molecular phylogenetic study of the Dipsacaceae will be conducted to critically test this "key innovation" hypothesis, while also taking into account the possible influence of biogeography on the evolution of morphological characters and the rate of diversification.

This study will provide key phylogenetic information for a morphologically unusual and understudied group within the Dipsacales. This will yield an excellent sampling of Dipsacales as a whole and provide a valuable model for exploring a wide range of macroevolutionary issues. This project will expand collaborative ties with Italian colleagues and provide the Co-PI with training in a wide variety of rapdily developing analytical techniques that will allow her to work across traditional disciplines

"This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5)." Terrestrial plants display remarkable variation in many aspects of leaf form. Leaves serve as main sites for photosynthesis, and are thus primary custodians of plant growth and ultimately, fitness. Previous work suggests that there are optimal values for particular leaf traits in a given environment that will maximize growth, and thus predicts that certain leaf forms will evolve under certain conditions. However, evolutionary response to external pressures such as climate may be constrained, because leaves are developmentally and functionally integrated parts of the whole plant. In spite of the long-standing interest in the role of leaves in plant ecological adaptation, few studies have successfully documented consistent evolutionary shifts in leaf traits in relation to environment. This collaborative project will develop the plant lineage Viburnum (Adoxaceae), a widespread group of approximately 168 species of woody shrubs and trees, as a model system for investigations into the ecology and evolution of leaf form. Viburnum is ideally suited for this problem as it exhibits a remarkable diversity of leaf shapes and sizes, and much is already known regarding evolutionary relationships within the group. The interdisciplinary PI team will collect physiological data from two common gardens, anatomical and environmental data from herbarium collections, and molecular sequence data for phylogenetic analyses to produce a unique, whole-lineage perspective on leaf evolution that is simultaneously detailed and broad. They will directly test several hypotheses regarding stem and leaf co-evolution, the decoupling of certain aspects of leaf water use from photosynthetic capacity, and the evolution of particular leaf traits in response to environmental conditions. One prediction is that considerable leaf shape diversity has evolved within a relatively narrow climate space, suggesting that other factors have historically been more important in shaping the evolutionary trajectory of leaf structure and function. Results from this work may be directly relevant to predicting plant response to rapid climate change. This work will also result in the development of new online community-wide teaching and research resources, such as a large leaf collection for anatomical study. In conjunction with the Peabody Museum of Natural History and public school teachers from the Providence, RI area, the PI's will also develop two 'leaf diversity' education modules targeted for elementary and high school levels in the New Haven and Providence school districts.

Herbarium specimens provide a source of historical information useful to the study of global environmental change. The goal of this project is to provide data to support studies of the nature and consequences of environmental change in the New England region over the last three centuries. This project will digitally capture specimen data and images from about 1.3 million vascular plant specimens from herbaria across New England, enhancing the data with georeferencing, habitat, and phonological information. The digitization process will integrate with existing community efforts and will develop novel high-throughput digitization technologies to increase efficiency and decrease costs. All resulting data and images will be freely available on-line.

The data from this project will be of immediate use to scientists who study climate and land-use change, and will provide a better understanding of how global changes will impact the distribution of native and introduced plant species. This project will benefit research in taxonomy, ecology, morphology, biogeography, and evolutionary history by making available data on an entire regional flora in an electronic format. The methodologies developed will provide a model for other regions around the nation. In addition the project will utilize citizen scientists, school groups, and students providing training, research, and educational opportunities. . This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biological Collections program and all data resulting from this award will be available through the national resource (iDigBio.org).

The genus Viburnum contains some 170 woody plant species in temperate and subtropical forests around the Northern Hemisphere and in Latin America and Southeast Asia. Over 70 Viburnum species are used in horticulture, and many are ecologically important. Building on years of prior research, and based directly upon herbarium specimens and new collections, the goal of this project is to resolve all remaining species-level taxonomic problems and to produce a comprehensive description of the entire group, with geographic range maps and richly-illustrated interactive identification keys that can be deployed on the web and in the field. All data will be internet-accessible and integrated into global biodiversity databases.

This project will produce a global treatment of a widespread, taxonomically confusing, and horticulturally important plant lineage. In doing so, it will generate data and informatics tools of general value to the scientific community. This work will greatly increase the value of Viburnum as a model for addressing fundamental issues in evolutionary biology, ecology, and global change. The project will be transformative in modeling the use of knowledge of evolutionary relationships in producing a species-level taxonomic monograph. It will provide hands-on training in modern, collaborative, cyber-enabled systematic biology to students at all levels.

An award is made to join the University of Minnesota (MIN) and the Yale University (YU) herbaria to the North American Lichens and Bryophytes: Sensitive Indicators of Environmental Quality and Change Thematic Collections Network (LBCC TCN). A total of 91,300 lichen and bryophyte specimens will be imaged and georeferenced. Historical records of lichens and bryophytes, along with geographic coordinates of collecting localities, are ideally suited for investigating a variety of questions related to global environmental change. The collections included in this PEN are each important regional repositories of North American specimens, and digitizing them will fill a considerable gap in the TCN's goal of digitizing nearly all lichen and bryophyte specimens in North America and add historically important specimens.

Data resulting from this project will be of immediate use to scientists who study how ecosystems respond to climate change and who use lichens and bryophytes as indicators of air quality. Societal benefits of this work include improved understanding of what causes ecosystem change and how environmental change may affect human health, our economy, and our environment. This project introduces a new generation of students to museum collections by offering internships to high school students of diverse backgrounds and by involving undergraduates and graduate students in project activities. This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biological Collections program and all data resulting from this award will be available through iDigBio.org.

Scientists have long recognized a global pattern in leaf shape between tropical and temperate climates: tropical leaves have smooth margins while plants living in cold regions have leaves with teeth or lobes, like a birch or a maple. The relationship is so strong that paleobotanists use leaf shapes in fossil floras as a proxy for temperature, allowing for estimates of climate change through time. But there is still no mechanistic understanding of why this relationship exists. The PIs hypothesize that the evolution of complex leaf margins in temperate plants results in part from the way that young, immature leaves are packed into overwintering buds. This is inspired by recent mathematical models of efficient leaf folding within buds, and by observations of within-plant differences in leaf form. Viburnum is a lineage of ~170 species of woody shrubs and trees that have shifted between tropical and temperate forests many times throughout the past 50 million years, and exhibit the expected changes in leaf shape. The PIs will document timing of growth, leaf lifespan, and patterns of leaf-packing within buds, and gather additional data on a suite of relevant morphological and physiological traits on a set of Viburnum species spanning the tropical-temperate gradient. They will also continue long-term phenological monitoring of ~30 Viburnum species in a common garden. This is a highly collaborative and interdisciplinary project, involving biologists from four other nations as well as an applied mathematician. The PIs will also develop educational modules designed for elementary school children aimed to bridge the gap between math and biology, using origami and basic geometric principles to understand common leaf shapes.

Many plant species are extremely variable. Even within a population, plants of the same species can differ from one another in characteristics such as leaf shape or flower color. However, almost all broad-scale studies of trait evolution ignore such variation within species and instead assign a single value to each species. Partially for this we know little about how variation within species relates to evolutionary differentiation over longer timescales. This project focuses on six closely related species of shrubs that are native to the Eastern United States. The goal is to quantify different types of variation within species and to relate the observed patterns to how these species evolved over the past 5-20 million years. Special emphasis will be placed on describing variation in a set of leaf characteristics (size, shape, leaf margins) within individual plants, within populations, across populations spanning a latitudinal gradient in growing conditions, and across species. These data will allow a better prediction of which traits are most likely to evolve and how plant species might respond to future climate change.

This project uses a new next-generation molecular method to generate phylogenetic and phylogeographic data for the Lentago lineage within the flowering plant clade Viburnum. RAD (Restriction site Associated DNA) markers will be sequenced for over 30 individuals per species to create a high-resolution phylogeny that spans across levels of divergence, linking populations that diverged only several hundred years ago to speciation events in the Miocene. This phylogenetic framework will resolve species relationships, determine the extent of hybridization within the clade, and enable the researchers to reconstruct the phylogeographic (population-level) history of each species. The resulting detailed understanding of common ancestry and migration history will provide new insight into how adaptation and gene flow generate and maintain trait variation within and among species. The project will improve understanding of the genesis of variation in morphological traits, of how types of variation translate across levels of organization, and of the emergence of the traits that mark deeper branches in the tree of life.

Much remains unknown about the genesis of biological diversity, including the origin of new species, yet such knowledge is critical to understand evolution and to make predictions about responses to rapid environmental change. This research will investigate a striking case in a group of trees and shrubs (Viburnum) in which rapid differentiation appears to have occurred repeatedly into two radically different plant forms. Major differences in the leaves of these plants appear to have resulted from adaptation to adjacent forest types that differ subtly in environmental variables. The evident replication of this process in several different mountain regions throughout the New World tropics, provides a rare opportunity to critically test a model of rapid ecological speciation. Detailed studies of adjacent plant populations will be carried out in different mountain regions in Mexico with the aim of identifying the environmental factors and the nature of the variation within populations that have favored the rapid evolution of these leaf traits. It should also be possible to identify genes that underlie these key plant characteristics by taking advantage of natural hybridization between these species. These studies will yield general insights into speciation but also into the adaptive significance of the leaf traits that differentiate related species throughout the flowering plants. This research will be carried out in collaboration with Mexican scientists and will involve multiple undergraduate and graduate students. Outreach activities have been designed to foster interactions between participants from the United States and Mexico.

This project focuses specifically on understanding the drivers of speciation in three species pairs in the mountains of Eastern and Southern Mexico. The two species in each pair differ dramatically in leaf size and shape (large and round versus small and elliptical), in leaf margins (toothed versus smooth), and in leaf pubescence (densely hairy versus lacking hairs). The research will focus on quantifying variation within individual plants, within populations, and between the species pairs, and on determining the abiotic and biotic factors that differ between their forest habitats. Hypotheses on the adaptive value of the leaf variables will be tested using transects between adjacent habitats and a reciprocal transplant experiment. In areas that have long been disturbed by indigenous agricultural practices, extensive hybridization has resulted in a wide array of intermediate leaf forms. Molecular analyses of these hybrid swarms should allow the identification of the major genes that underlie differences in leaf form.

This project is jointly funded with the Office of International Science and Engineering.

Plant structures such as flowers and fruits often develop through the fusion of component parts. For instance, the bell-shaped flower of a morning glory is the result of the fusion of five petals, while a pineapple results from the fusion of the developing fruits of multiple individual flowers. Despite organ fusion being important for generating diversity in plants, the process is understudied in many plant groups. This project aims to understand the evolution and genetic regulation of fusion using honeysuckles (genus Lonicera) as a model. Found mostly in the Northern Hemisphere, honeysuckles include approximately 180 species, many of which exhibit different types of fusion within their flowers and fruits. Fusion can be observed across pairs of leaves, between small leaf-like structures associated with the flowers, or among adjacent fruits. This project will reconstruct the evolutionary history of honeysuckles to determine how many times -- and precisely how -- fusion has occurred during the evolution of the group. Researchers will then investigate the genes that control fusion in multiple species within the group. This project will provide the first comprehensive evolutionary and genetic analysis of multiple fusion events within a group of flowering plants. The project will greatly enhance genomic resources for a widely cultivated group of plants, which also includes honeyberry (Lonicera caerulea), a crop plant grown for the high antioxidant content of its fruit. Fifteen undergraduates, a post-doctoral researcher and a graduate student will be trained in diverse laboratory analyses and gain experience working in a field setting. The botanical images produced from this research will form the foundation for developing an art exhibit, Plant Communication and the Art of Fusion, which will be displayed in the Art Gallery at The College of New Jersey and at the Arnold Arboretum of Harvard University.

The proposed research combines phylogenomic, morphological, and evolutionary-developmental approaches to test hypotheses on the evolution of fusion in Lonicera and the genes that help regulate organ fusion. The researchers will reconstruct a robust phylogeny for at least 130 of the 180 species of Lonicera using a target-enrichment next-generation sequencing strategy. Researchers will then document and reconstruct the evolutionary patterns of leaf, bracteole, and ovary fusion throughout Lonicera, with an emphasis on ontogenetic changes in a set of 22 focal species. Fused structures will be imaged and quantified to determine the extent of fusion in each species. Finally, this project will examine the phylogenetic history and expression of NAM-like fusion genes across Lonicera to identify correlations between changes in morphology and changes in gene expression.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.