Robert P. Guralnick - US grants

Museum collections are the main repository for past and current baseline biodiversity information. In order to utilize that baseline information as fully as possible for research and management decisions, the information must be available. This project will convert separate collections in Colorado into one distributed biodiversity database and research toolkit for the southern and central Rockies and adjacent plains. This area features tremendous biological diversity and has experienced and continues to experience many environmental changes that impact biodiversity. The collection involves almost 300,000 biological specimens. The format relies upon linking data to a geographic information system database. The system will allow for the query, analysis and synthesis of local and network information through a web interface, for researchers, managers and educators, as well as the public.

A collaborative grant has been awarded to Colorado State University under the direction
of Dr. Mark Simmons; University of Colorado at Boulder under the direction of Drs.
Thomas Ranker and Robert Guralnick; University of Northern Colorado under the
direction of Dr. Neil Snow; and University of Wyoming under the direction of Dr. Ronald
Hartman to produce an online distributed database of collections of vascular plants from
the Southern Rocky Mountain Region (SRMR) and create an online, interactive
identification key for vascular plants from the SRMR. The region covered by this project
includes the entire State of Colorado, nine counties from southern Wyoming, and eight
counties from northcentral New Mexico. The SRMR as defined here is a reasonably
coherent ecoregion based on many shared geological and biological features, such as a
number of mountain chains of Laramide orogeny, and many vascular plant species are
restricted to this region. The SRMR is characterized by a rich diversity of ecosystems,
ranging from semi-arid grasslands to the east, through montane pine, subalpine
spruce-fir forests, and alpine tundra in the center, to canyons and mesas in the west.
Unique wetland and riparian ecosystems exist on the plains, and nutrient-poor streams
and lakes are frequent in the mountains. This broad range of ecosystems fosters a
diverse flora, and is reflective of strong topographic forcings and steep climatic
gradients. In addition to herbarium specimens at the Colorado State University
Herbarium, the Rocky Mountain Herbarium, the University of Colorado Herbarium, and
the University of Northern Colorado Herbarium, the distributed database will incorporate
specimens from the SRMR that have been databased at other regional and national
herbaria.
The interactive key will be produced using Lucid Professional version 2.1, which is
intended primarily for use online. Each of the approximately 4,000 species treated in
the key will have associated windows describing its associated names, distribution,
voucher specimens, and images. For the specimen database, a Federation of
Databases that communicate with each other will be created. The Federation of
Databases will be implemented by following the specifications suggested by the Digital
Generic Information Retrieval group. Georeferencing is crucial for the production of
static or dynamic species maps or atlases and for the import of data into Geographic
Information Systems. All specimens will be georeferenced as part of this project. Each
step in the process of creating linked databases and the interactive key will be
documented. Clear documentation will also be provided for becoming part of the initial
database federation to future investigators.
The specimen database established by this project will document and locate the
vascular plant diversity that currently exists in this region, and help track the rate and
magnitude of change in biodiversity patterns caused by urban development over the
next several decades. It will be useful for discerning areas of high biodiversity,
determining the point of introduction and the spread of invasive species, locating
voucher specimens, and as a coverage in geographic-information-systems applications.
The educational implications of the proposal will extend the usefulness of this project.

The University of Colorado at Boulder has been awarded a grant to support student participation in the 2004 Taxonomic Databases Working Group annual meeting in Christchurch, New Zealand, Oct 10-17, 2004. There is a potential for intellectual growth for the individual student participants as well as securing continued intellectual growth in the field by bringing the next generation of biodiversity informaticians into the community. Students from a diverse group of students, both male and female, and from different cultural and ethnic backgrounds will participate. Because training occurs during all phases of student development, and professional meetings early in careers can help shape later choices, there will be a wide range of expertise represented in the students chosen, including undergraduate, Masters, PhD and post-doctoral students. A national competition for open slots will provide an opportunity for deserving students, who couldn't otherwise afford to attend TDWG, a chance to participate.

The diversity of leaf shapes in the natural world drove early naturalists to pose questions about how and why they differ among the many groups of plants on earth. Charles Darwin (1859) described the study of morphology as ".the most interesting department of natural history, and may be said to be its very soul." This project examines the evolution and development of leaves in the fern genus Pleopeltis (in the family Polypodiaceae). As recently reported in the journal Nature and discussed on National Public Radio (April 2004), the Polypodiaceae is a relatively young and very diverse group, second in size only to flowering plants. Even though they evolved very recently, the species in Pleopeltis have a set of leaf shapes nearly as varied as those seen in all plants, living and extinct. How did evolution rapidly generate this diversity of morphology? This research has three components: 1) examining mature leaf forms, 2) examining leaf development, and 3) placing this information in an evolutionary context. NSF funding will support travel to make field collections from natural populations in Ecuador and Mexico, to complement collections already made in Costa Rica. In these three regions, taken together, one can find nearly all of the species in Pleopeltis.

This research will provide important experience and training for a doctoral student, and it will support international collaboration with researchers in Ecuador and Mexico. The resulting comprehensive living collection of Pleopeltis species will make possible numerous research projects that could be undertaken by high school, undergraduate, or graduate researchers. Living plants will also be made available to students as part of the teaching collection. Pressed specimens of field-collected plants will become part of the research and teaching collections in the University of Colorado Museum, as well as at institutions in Ecuador and Mexico. Results of this research will be presented at professional conferences and to the general public through the University of Colorado Museum and the Denver Museum of Nature and Science. Understanding leaf development and evolution is of broad scientific interest, yet has important applications, such as the improvement of crop plants. Studying ferns is essential, since this major group has been understudied compared to flowering plants, even though many fern species are economically important, either as crop plants or as invasive weeds. Ultimately, this research will provide a deeper understanding of the evolution and development of leaf form throughout the plant kingdom.

A grant has been awarded to the University of Colorado under the direction of Dr. M. Deane Bowers for partial support of a project to curate and database the Gordon Alexander collection of grasshoppers. This collection is composed of over 19,000 grasshoppers from the Rocky Mountain and plains regions of Colorado that were originally collected under the auspices of a 1958 - 1960 NSF grant. Approximately 75% of this collection is composed of representative specimens from over 65,000 grasshoppers, representing 95 different species, that were processed during the tenure of this grant. The remaining 25% is composed of specimens from other studies conducted in Colorado and neighboring states during the 1930's to 1960's. Given the recent and dramatic impacts of humans in this region, this collection is of particular importance for understanding the communities in existence before these changes occurred. The goals of this project are 1) to curate the collection in order to preserve it and make it accessible to researchers; 2) to database the collection; and 3) to make the information from this collection available to researchers as well as lay-people by publishing the data from this collection online. In order to accomplish these goals, the Entomology section requires funds to support curatorial staff and students to coordinate and implement the project. The Entomology section also requires additional curatorial supplies, a microscope and computer equipment, to properly curate and database all specimens.

The Alexander grasshopper collection will be curated and databased and information from this historically important collection will be posted online via a new website developed under the auspices of the grant and through publishing the data on global biodiversity networks. The Alexander collection will be made available in a format that will allow professional researchers and the public access to data that can be used for education and outreach-related projects. Participation in this project by students will be extensive. Graduate students will be trained in museum skills, insect taxonomy, curation, databasing, and use of computer programs that are important for making collection data available over the internet. Undergraduates and the general public will have also have access, via the internet, to a relational database that will allow them to examine Alexander's survey and collection data,

This project will make the Alexander Collection readily available to researchers, land managers, educators and students. In addition to making the collection and its specimen information available for study, the data can be used by researchers to examine the effects of land use practices and climate change on communities and species. Furthermore, the Education section of the Museum will ensure that the collection and the internet material will be used in public outreach and education to the public.

University of Colorado at Boulder is granted an award to support student participation in the 2005 Taxonomic Databases Working Group annual meeting in Saint Petersburg Russia during September 11-18. Funding will support 7 students to attend TDWG2005 based on a competitive application process and the PI to be a mentor for the students before, during, and after the workshop. The merit is the potential for intellectual growth for the individual student participants, securing continued research growth in the field by bringing the next generation of biodiversity informaticians into the community, and to provide cross-disciplinary training, community-building, and contacts with the leaders in the field for a new cadre of biodiversity informaticians. Student participation is solicited from a diverse group of students both male and female, and from different cultural and ethnic backgrounds. Because training occurs during all phases of student development, participants from all stages in their student careers including undergraduate, Masters, PhD and post-doctoral students will be eligible to apply. The national competition for open slots will provide an opportunity for deserving students who couldn't otherwise afford to attend TDWG a chance to participate. Preference will be given to students who help assure continued ethnic and gender diversity.

There is a compelling societal need to understand how climate change is affecting the world's biota. The proposed project will use the Gordon Alexander grasshopper collection and a new resurvey program to measure the effects of climate change on the grasshoppers found along the Front Range of Colorado. The Alexander collection is composed of over 24,000 pinned and labeled grasshoppers collected during the 1930's to the 1960's from the Rocky Mountain and plains regions of Colorado. During the survey years of 1958-1960, Alexander recorded the presence of over 65,000 grasshoppers from repeatedly sampled sites along an elevational gradient from Boulder to Niwot Ridge, Colorado. By resurveying Alexander's elevational transect, the proposed project will study the effects of a changing climate on the timing of life history events, elevational ranges and body sizes of a well studied and economically important group of organisms.

The Alexander resurvey project will make information about climate change and the importance of museums and biodiversity readily available to a wide audience via a project related website. This project will also train undergraduate and graduate students in the techniques of curating, maintaining and databasing collections, as well as the use of collections and their associated data to test ecological questions.

"This award is funded under the American Recovery and Reinvestment Act of 2009
(Public Law 111-5)."


The University of Colorado has been awarded a grant to develop cyberinfrastructure to track the geographic distribution of changes in virus genetics. The second part of the 20th century was notable for the development of earth observation systems providing an unparalleled view of a changing world. In the 21st century, a new frontier is real time monitoring biological systems and how those systems are changing over space and time. Biological systems provide an added challenge because organisms continue to evolve, responding to biotic and abiotic changes to the overall earth system. Therefore, it is not simply enough to monitor spatiotemporal trends in species or ecosystems. If scientists are to become better able to predict future changes to biological systems, they must understand the underlying changes to the genomes of organisms, how those genetic changes translate to phenotypic changes, and which phenotypes are successful in relation to a changing environment.

The pipeline of genetic data available for such predictions has increased rapidly but the ability to analyze these data has lagged behind. This project is a groundbreaking evolutionary-based biomonitoring program. The prototype system would begin to close this gap by utilizing an automated analysis workflow that provides essential information about organismal evolution usable by the research, education and policy-making community. This proof of concept will be tested especially on evolution of influenza A viruses to rapidly detect evolution of drug resistance, a timely and time-sensitive issue. Users will be able to select a taxon and gene or genome of interest and our system will automatically harvest those data and produce an evolutionary tree. By tying locality data of the sequence data to the evolutionary tree, the system can project that tree onto a virtual globe producing a sharable geophylogeny. The system will also automate detection of selection pressure on protein coding genes as another output. Most importantly, once a workflow is set up by a user, it can be set to persist so that as new data becomes available, new analyses are consistently run and new knowledge about the state of the biological world returned to interested users. For the research and policy community, near-real-time monitoring will provide a useful, customizable and ultimately predictive tool. For education and outreach communities, geophylogenies offer a powerful visual tool for exploring and learning about evolutionary changes occurring across the environment. Information about the project can be found at http://biodiversity.colorado.edu/.

Yale University and the University of Colorado Boulder are awarded grants to develop an interactive, online species distribution workbench and knowledge-base, the "Map of Life", as the fundamental mechanism for documentation, integration, and advance of human biodiversity distribution knowledge. Despite hundreds of years of active exploration, human knowledge of the distribution of biodiversity remains very limited. A fundamental factor in this shortcoming is that the majority of direct and indirect information about species' distributions has not been mobilized and integrated. While researchers can readily access fine-scale environmental data with global coverage, access to integrated species distribution information at validated precision remains elusive. This collaborative project will develop a conceptual and cyberinfrastructure framework for provisioning and improving reliable species geographic range information. Map of Life will combine on a single website expert range maps, survey data, and range maps adjusted for species habitat suitability initially for terrestrial vertebrate species, with extensions planned for other animal and plant groups. It will therefore serve the needs of all those requiring estimates of species geographic ranges across taxonomic groups and regions, such as scientists, land-managers, governments, policy-makers and the general public. Users can upload data, edit input or output and directly improve or comment on existing maps which will iteratively lead to more advanced species distribution knowledge. Users can also download any and all maps in different formats directly from the application or perform batch-download for multiple species. Finally, simple richness and regional species list tools will extend the products to users with a geographic focus.

Given that species range maps are one of the most commonly used and familiar information products in biology, the potential broader impacts and benefits of Map of Life to society are remarkable. Unlike printed range maps, the dynamic nature of editable online range maps encourages the public to move from roles of passive consumers to "prosumers"; they can both produce and consume information and generate new knowledge. The Map of Life project also presents a unique cross-disciplinary training opportunity in macroecology and biodiversity informatics. Dedicated lab exchanges between Yale and the University of Colorado, along with workshops and symposia at professional meetings will allow extensive cross-fertilization of ideas. The PIs will also develop targeted map and web tutorials illustrating the notion of human understanding of a species' geographic range and will showcase those products at the Yale Peabody Museum and the University of Colorado Museum of Natural History. Further information about the Map of Life may be found at http://www.yale.edu/mapoflife.

Scientific specimens, typically found in museum collections, serve as the anchor for an expanding array of information that grows and changes over time. This information, about specimens and the species that the specimens represent, is often scattered geographically across institutions and across independent computer systems, making it difficult to access or synthesize. The goal of this project is to develop a two-way system of linking and tracking scientific specimens and specimen-related data across biological collections, and to make this system widely available to the scientific community and the public. This system would employ globally unique identifiers, or GUIDs, to tag and update information associated with specimens, allowing communication between end users and collections. This project will improve data quality and quantity for non-scientists and scientists, and will actively engage use communities through training workshops, summer student internships, and community BioBlitz enhancements.

The ability to integrate specimen data and associated information across biological collections will enable critical studies related to systematics, biogeography, and changing species distributions. These in turn have implications for climate change, changing land use, and other questions key to understanding the past, placing changes in an historical context, and predicting the future of species and environments. This project is part of a 10-year effort to digitize and mobilize the scientific information associated with biological specimens held in U.S. research collections. The images and digitized data from this project will be integrated into the online national resource as outlined in the community strategic plan available at http://digbiocol.files.wordpress.com/2010/05/digistratplanfinaldraft.pdf.

The American pika is a small mammal that inhabits high-elevation rock slopes throughout the western United States. Reports that pika populations are declining in the Great Basin region have raised concerns that these populations may be particularly sensitive to climate change, in part because high-elevation ecosystems are disproportionately threatened by warming temperatures. Two years of preliminary data across 69 sites suggest that precipitation patterns impact pika distribution in the southern Rocky Mountains. This research will be extended through focused monitoring of climate and pika densities at 25 sites. Gene frequencies will be compared among pika populations to determine how climate and habitat may have constrained the dispersal of pikas across this region. The intellectual merit of the proposed research lies in its investigation of why climate is impacting the pika and similar sensitive species.

This research will have several broader impacts. It will inform conservation efforts for the pika and other species that may be threatened by climate change. Mechanistic studies such as this are critical to developing the understanding needed for sustainable management of biological resources in a changing world. Second, undergraduate students will continue to play an integral role in this research. Finally, it will support develoment of a Colorado pika citizen science program that will empower local citizens to get involved in science and conservation.

This collaborative award is made to implement an innovative model for biodiversity networks and data sharing called VertNet (http://vertnet.org). Biodiversity is in a crisis caused by multiple human impacts on the environment, and documentation of spatial and temporal biodiversity changes is immediately and urgently needed in order to address this crisis. The community of vertebrate natural history collections has begun to meet this need by establishing social and technological infrastructures that provide open access to data describing planetary occurrences of biological specimens. Taxon-specific data sharing initiatives such as MaNIS, ORNIS, HerpNET and FishNet 2 currently provide, in total, over 85 million records documenting where vertebrates occur. Together these networks include 171 collections from 12 countries, with an additional 52 collections (20 countries) committed to participation. Already, they are accessed at a rate of nearly 2.5 million records per week. Participation in each of these networks has far exceeded expectations, resulting in growing issues of scalability, performance, sustainability, and ability to incorporate new members. VertNet will solve these impediments by moving to a cloud computing solution in which providers and users synchronize changes to a cloud-based network of vertebrate biodiversity data. Cloud computing is a pay-per-use model utilizing internet-based, third party computing resources that are fast and dynamically scalable. The new VertNet model removes the requirement and cost to contributors to buy or maintain their own servers while leveraging all of the data integrity and replication services provided by the cloud. Under the new model, contributors will use a web-based administrative interface to create a "provider" in the cloud. Subsequent updates will use the same local application to publish differences (additions, changes, deletions) since initial publishing. Data storage in the cloud will contain the primary data published from all contributors as persistently and uniquely available records. In addition, it will contain summary information about data aggregations, and will incorporate data from other sources such as auxiliary data look-ups, user feedback, and data quality assessments. VertNet will provide open access to data with new capabilities for discovery and visualization, and will integrate with several existing biodiversity and collection management applications. Development of VertNet will transform the use of vertebrate biodiversity data for cross-disciplinary research, conservation, and policy-making.

The four predecessor projects (MaNIS, ORNIS, HerpNET, FishNet 2) have built a strong tradition of biodiversity informatics training and community-building. VertNet will continue this tradition, with impacts extending beyond the funded institutions. Specifically, VertNet will engage students from across the United States in two Summer Internships in Biodiversity Informatics and two Workshops in Biodiversity Informatics. In addition, undergraduate students will be offered volunteer apprenticeships through existing programs at UC Berkeley. An additional workshop that involves the broader community will address strategies for long-term sustainability of digitization and data-sharing efforts.

The Center for Research Computing (CRC) at the University of Colorado Boulder (CU-Boulder) will acquire, deploy and maintain an expandable petascale storage instrument, the CU-Boulder petaLibrary. This instrument, consisting on an integrated disk and tape system, will enable faculty, staff, postdocs, graduate and undergraduate students to build, store, share and merge large and growing data collections. The petaLibrary will be made available to all CU-Boulder researchers at no usage charge other than the cost of the media.

The petaLibrary will serve as the infrastructure for a number of data services provided by the University Libraries, the Museum, the National Snow and Ice Data Center (NSIDC) and the CRC to the CU-Boulder campus community. The services will include the deposit and discovery of a wide range of digital resources, including digital surrogates of archives and special collections materials owned by libraries and museums on campus, openly accessible resources, digital media only library resources and the scholarly output of the campus. Data-intensive projects include digital collections; high fidelity, high definition recordings of human interaction; global-scale land remote sensing; bio-digitization efforts by the Museum; as well as research programs utilizing CU-Boulder's computational resources.

The broader impacts of the project include the development of workshops on data archival and long-term data formats for researchers, research projects and educational opportunities with the CRC for graduate and undergraduate students. Other efforts will include working with The Colorado Coalition for Gender and IT (CCGIT) and the National Center for Women and Technology (NCWIT) to address the limited diversity in IT, specifically in the area of cyberinfrastructure by providing summer internship opportunities for female faculty in data management related topics.

Amazonia is Earth's most iconic center of biological diversity and endemism and is among the most important terrestrial biomes due to its contributions to global systems ecology. This project seeks to answer an overarching question in biodiversity science: How was the modern Amazonian biota and its environment assembled across space and time? The research is designed to understand the evolutionary and environmental-ecological history of late Neogene-Recent Amazonia through a comparative approach that integrates across the disciplines of systematics, population biology, ecosystem structure and function, geology, Earth systems modeling and remote sensing, and environmental history. The project also investigates how biotic and environmental change over this time-period influenced Amazonian functional diversity in biogeochemical flows, and how these, in turn, shaped the dimensions of biodiversity seen today as well as the history of global-scale changes in biogeochemical cycling.

The project, which is a collaboration with Brazilian scientists and funding agencies, represents the most integrative examination of Amazonian biodiversity and its history to date. The approaches taken describe a methodological template for analyzing information about the history of biotic and environmental change across large, ecologically complex landscapes that can be generalized to other systems. The project creates a large framework for formal and informal education including the training of students, development of a major museum exhibit on Amazonia, workshops for K-12 STEM teachers, publications in professional educational journals, and a web portal, The Evolutionary Encyclopedia of Amazonian Biodiversity, that will make all results available to the public, as well as serve as an informational platform about Amazonian biodiversity and its global importance. This award is being co-funded by NSF's Office of International Science and Engineering.

An award is made to Yale University, the University of Colorado at Boulder, and Cornell University to advance content provision and development of the existing prototype Map of Life platform. Knowledge about the geographic occurrence of species is at the heart of much of ecology, evolution and conservation, and of tremendous societal importance. While digital species distribution products exist, they remain un-integrated and cannot serve critical societal needs. The Map of Life platform was developed to begin to solve this need. A key goal of this project is to use novel approaches to mobilize and integrate diverse types of data such that their collective strengths overcome individual weaknesses. Specifically, this project will combine, on a single website, a variety of distribution data types from many different sources, range products that integrate these, deductively and inductively modeled predictions, and reports about the spatial and environmental knowledgebase for species. When completed, users from across a broad spectrum, from researchers with published data to citizen scientists, will be able to upload data, edit input or output and directly improve or comment on maps, iteratively leading to improved species distribution knowledge. Users will be able to directly query or download any redistributable content. Map of Life will thus facilitate a dramatically improved and rigorous accounting of the spatial context of species in science and will likely benefit scientists across the biological, environmental and social sciences.

Given that species range maps are one of the most commonly used and familiar information products in biology, the potential broader impacts and benefits of Map of Life to society are remarkable. Species distribution knowledge ties to one of the greatest challenges of our time: explaining the links between biodiversity, ecosystems and human health, and how ongoing global environmental changes are impacting our natural heritage and capital. Opportunity abounds for strong educational uses of the Map of Life infrastructure. An exciting step will be the production of video tutorials covering how Map of Life works and how it can serve an important role in biodiversity knowledge creation, along with explaining core concepts about species ranges, biodiversity, and how to measure its change. Such videos are scalable means to reach large audiences and will be coordinated through the PIs and their institutional outreach programs. More information about this project can be found at: www.mappinglife.org.