ATOL: Collaborative Research: Deep Green Plant Phylogenetics: Novel Analytical Methods for Scaling Data from Genomics to Morphology

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A grant has been awarded to Dr. Brent Mishler of the University of California, Berkeley 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. Brent D. Mishler will have primary responsibilities for coordinating the research with DEEP GENE and other related green plant phylogenetic projects, help develop tools for phylogenetic analysis and databases, and carry out analyses of organellar genomic data and bryophyte morphological data ; Jeffrey L. Boore will supervise the shotgun cloning; as well as automated sequencing, assembly, and annotation. Alan R. Smith will assist in plant material collection and identification as well as analysis of morphological data for ferns and allies.