Collaborative Research: Advancing Bayesian phylogenetic methods for synthesizing paleontological and neontological data

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Combining data from living species and the fossil record provides a rich perspective for understanding the evolutionary processes responsible for generating the biodiversity observed in nature. Although methods for combining these data have made significant advances, these approaches still do not consider the completeness and sampling of the fossil record or the geographical distributions of living and fossil species. For this project, the investigators will integrate statistical models for describing how fossils are sampled over time and where species are found. These models for estimating species relationships will be developed in widely used software packages, making them broadly accessible to other researchers. These new methods will be tested using both simulated and real datasets. Specifically, two vertebrate groups with rich fossil records will be studied: penguins and crocodyliforms (crocodiles, alligators, gharials, and extinct relatives). This work will help to uncover how rates of speciation and extinction have changed over time for these species. The methods developed as part of this project will be taught in workshops for evolutionary biologists. Additionally, results from analyses of data from living and fossil penguins will be contributed to a public museum exhibit at the Bruce Museum in Greenwich, CT. In recent years, advances in phylogenetic inference methods have provided ways to integrate fossil and extant taxa. These approaches allow simultaneous estimation of the divergence times and phylogenetic relationships of extant and fossil species, thus making full use of morphological and temporal data, rather than just molecular sequence data from living species. Approaches combining fossil and extant taxa have opened the door for fully integrative phylogenetic methods that use more sources of biological data, including stratigraphy, sampling, and biogeography. Thus, there is a need for comprehensive statistical models and methods that accommodate this information. The investigators will develop new, Bayesian statistical models, extensions of stochastic birth-death processes, that will integrate information about the fossil record and biogeography for use in phylogenetic methods that consider both extant and fossil taxa. The new models will be implemented in the program RevBayes. The performance and adequacy of new and previously described models will be evaluated using simulated and empirical datasets. New methods will be used to investigate macroevolutionary patterns in two exemplar clades: Sphenisciformes (penguins) and Crocodyliformes, addressing key hypotheses about phylogenetic relationships, lineage diversification, and biogeography.