Integration of Morphological and Stratigraphic Information in Phylogenetics and Applications in Palaeontology

The role of the fossil record in Natural Sciences and its relevance in the investigation of the tempo and mode of evolution have been commonly split between a stratigraphic approach and a phylogenetic approach. A recently introduced methodology aims to integrate the stratigraphic and morphological information in phylogenetic analysis of fossil clades. In this thesis, a modified version of this new methodology is introduced and applied to the analysis of extinct clades of marine and terrestrial vertebrates. Furthermore, novel applications of this phylogenetic method beyond the mere reconstruction of ultrametric topologies have been explored and discussed. This novel method represents an innovative and useful tool in the following research areas: Quantitative estimation of the rates of phenotipic evolution among fossil lineages: the identification of heterogeneity in morphological transitions, and the estimation of “hot spots” of phenotype evolution, provide a testable framework for the investigation of the tempo and mode of Life history in the geological past. Realization of ultrametric frameworks for palaeobiogeographic inference, in particular for analyses requiring branch lengths in ancestral area reconstruction: this method provides a quantitatively-defined base for the integration of palaeogeographic models in the reconstruction of clade history. Comparison between the phylogenetic patterns among distinct lineages sharing palaeogeographic and stratigraphic ranges: this approach allows for testing whether environmental evolution constrained the biological evolution along shared trajectories. Inference on the taxonomic diversity among a sample of individuals collected from the same stratigraphic unit: this application of Bayesian phylogenetic methods uses, as terminal units, individual specimens instead of clades. This approach allows for testing taxonomic hypotheses in the fossil record. Auxiliary and independent test of stratigraphic relationships among fossil localities sharing the same fossil groups: this application stems from the previous approach, and provides testable hypotheses on the relative stratigraphic relationships among a series of fossil-bearing localities.