Integrating Fossil Data into Likelihood-based Phylogenetic Analyses with Trilobites as a Model System

1 Objectives The primary objective of the proposed research is to develop improved methods for likelihood-based phylogenetic analysis of morphological data with an emphasis on fossil taxa. Many analyses of molecular data use likelihood-based approaches, so the current lack of compelling models of character evolution for morphology is a serious impediment to integrating paleontological and neontological data. We will develop models and software that can estimate phylogenies from character data. We will use examples from the Trilobita to test our methods. Trilobita is an exceptionally diverse fossil clade that has been the subject of numerous phylogenetic analyses at several taxonomic scales (Lieberman and Karim, 2010a). Our new models of character change will be implemented in software that will estimate divergence times, and speciation and extinction rates. The results of this grant will dramatically improve researchers’ ability to put a time scale on the Tree of Life and explore evolutionary questions about the tempo of character changes and macroevolutionary processes. The proposal is structured into the following sections: Section 2 Background: a discussion of prior work and preliminary data, Section 3 Research questions and approaches: a presentation of five specific goals to be addressed and a discussion of the approaches to be taken, Section 4 Software: the details of the software to be written to enable the research, Section 5 Broader Impacts: a summary of the broader impacts of the proposed work, and Section 6 Timeline: a schedule for accomplishing the work including a discussion of the role of each researcher.