Collaborative Research: ABI Innovation: Connecting resources to enable large-scale biodiversity analyses

University Of Florida, Gainesville FL

Investigators

Abstract

Extracting biological knowledge from complex datasets such as those now being compiled requires integration of powerful computational tools. Recent developments in computational biology as well as rich new data sources provide novel opportunities for integrating massive amounts of biological data. This perfect storm of new data and advanced data acquisition, management, and integration afford the unique opportunity to drive the discovery of new, complex patterns in biology. The project will leverage NSF's considerable investment in biodiversity tools provided by Open Tree of Life (the framework for the project), Lifemapper (which handles geospatial data), iDigBio (data from ~1 billion museum specimens that carry locality data and their ecological information), and Arbor (computer tools that permit new analyses from the sources noted). It will create much needed computational connections among these tools. It will then build upon these new linkages and tools, enabling novel research in biodiversity. These linkages will provide researchers the opportunity to rapidly synthesize datasets and use them to address diverse evolutionary questions. The tools and infrastructure the project will build will connect species relationships with species distribution models, climate projections, genes and traits. The project will transform future studies of biodiversity; it will provide a global integration of powerful tools that will permit new data-driven discovery in "next generation" biodiversity science. It will provide interdisciplinary post-doc and graduate student training in bioinformatics, use of digitized specimen data, and complex analyses (e.g. ecological analyses), preparing the biodiversity scientists of the future. The project will recruit underrepresented students and women and develop an undergrad course that will help train students with the integrative skills (field biology to computational biology) needed in the workforce. We will further develop this module for wider classroom use. We will introduce an annual week-long course at University of Florida (UF) for students and post-docs on the use of the resources developed. With education specialists at UF, the project will produce video materials and a coordinated display for general audiences on the importance of digitized specimen data, and their utility for studies of climate change. The project will develop a computational framework linking diverse data (trees of species relationships, morphology, ecology, fossils, geography, and climate) across research tools used by the biological community, including Open Tree of Life, which will serve as the framework to which all other biological data - traits, genes, genomes, and especially specimens - will be linked, as well as Lifemapper, iDigBio, and Arbor. Use of the large, hyper-diverse plant group Saxifragales will provide precisely what is needed to drive the development of these tools--a comprehensive dataset that covers morphology, ecology, geography, fossils, and climate provides a test case for refining the tools the project will develop and their integration. The project will: 1. Facilitate new synergistic research of broad utility at the interface of phylogenetics, ecology, evolutionary biology, biogeography and biodiversity science, enabling scientists to address novel questions relating phenotypic and ecological biodiversity, spatial and temporal variation, community assembly, and diversification across landscapes and through time. 2. Increase visibility and accessibility of iDigBio, Open Tree of Life, Arbor, and Lifemapper resources by linking them together and making them available through multiple access points (e.g., pre-existing tools associated with Arbor and Lifemapper) in a variety of appropriate formats. 3. Develop a complete, multifaceted species-level dataset for a large clade (Saxifragales), which will not only fill in this branch on the ToL, but will produce a resource of great utility for the scientific community to explore. 4. Demonstrate the utility of iDigBio, Open Tree, Lifemapper, and Arbor resources with a comprehensive analysis using near complete sampling of Saxifragales, for which we will add the following data layers: DNA sequences, morphology, fossils, ontologies, geospatial and environmental data, digitized voucher specimens, and link to the Encyclopedia of Life (EOL). The project will: 1) provide interdisciplinary post-doc and graduate student training in bioinformatics, large-scale phylogeny reconstruction, use of digitized specimen data, and complex post-tree analyses (e.g. niche modeling, niche diversification), preparing the integrative biodiversity scientists of the future; 2) recruit underrepresented students and women; 3) developed an undergrad course that uses field collection, herbarium specimens, digitized data (iDigBio), and niche modeling (with climate change; 4) introduce an annual week-long course (UF) for students and post-docs on the use of the resources produced; 5) produce video materials and a coordinated display for general audiences on the importance of digitized specimen data, their utility for modeling niche evolution through time and implications for climate change. The project will provide a platform that will enable other researchers to take the same integrated approach in other groups. It will also establish web links to EOL and 1) build species pages; 2) place morphological and other trait data on TraitBank, making these widely available; 3) work with EOL and iNaturalist to engage citizen scientists.