Utilizing likelihood models for phylogenetic reconstruction from discrete phenotypic characters

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Presently, there are two major methods for estimating phylogenetic trees from morphological data. In this study, researchers will simulate morphological data and use these data to to test the effectiveness of these methods. A strength of using simulated data is the ability to manipulate relevant parameters to create data sets that are relevant to many different types of researchers and scientific questions. The goals of this project are twofold: to provide practical recommendations and guidelines for best practices in estimating phylogenetic trees from morphological data and to understand the strengths and weaknesses of various methods for estimating phylogenetic trees.Estimating a phylogenetic tree is a common way to understand the relationships among different groups of organisms. These trees can be used to understand the evolution of a trait, to test hypotheses of biogeography, or to infer other aspects of the evolution and ecology of organisms. Fossils are the only way that scientists can directly observe long-extinct organisms, making the study of fossil data a relevant practice, even as the price of DNA sequencing falls. The results from this project can be used to inform scientists about appropriate methods for inferring phylogenetic relationships from fossilized remains.