Application of phylogenetic methods to studying evolutionary processes with the fossil record

Studying the fossil record allows us to trace species evolution through time, and to understand significant events, such as mass extinctions and species radiations. While the fossil record provides evidence into past ecosystems, it is associated with several biases that prevent direct interpretation. As such, palaeontologists and evolutionary biologists have developed a battery of approaches to decipher this distorted record. One such approach is to use Bayesian phylogenetics, which is becoming increasingly popular due to its flexibility in terms of data and models as well as its inherent ability to measure uncertainty. Encouraged by the introduction of the fossilised birth-death (FBD) model, the incorporation of fossils into Bayesian phylogenetics is a rapidly developing field. Within palaeo-biology we can use Bayesian phylogenetics to estimate the evolutionary relationships of fossils through morphological characteristics. In this way we can take individual fossil occurrences and fit them into the tree of life. Additionally, Bayesian phylogenetics provides a framework for estimating rates and times. Given this increased attention in the application of model-based phylogenetics with morphological data, questions have been raised regarding the limitations and suitability of these approaches. In this dissertation, I explore the use of Bayesian phylogenetic methods with data from the fossil record, as well as model-based approaches for estimating evolution in the absence of fossils. Firstly, given the complexity of morphological evolution there are a number of concerns regarding our ability to correctly model this process. These concerns have led to years of scientific debates over whether using morphological data in a Bayesian frame-work is appropriate. To address this question I explored the use of posterior predictive simulations, a model adequacy approach, which provides a measure of the absolute fit of a model to a data set. Through simulations I validated the use of this approach with morphological models and subsequently applied this to a number of empirical datasets. Here I showed how current models of morphological evolution are able to capture the underlying dynamics of empirical data, thus supporting the use of morphological models for phylogenetic inference. Following this, I used the validated PPS pipeline for a dataset of Paleozoic stalked echinoderms. This dataset was used as a case study, as it was representative of many Paleozoic invertebrate datasets in that it was small in terms of the number of taxa (14) and the number of characters (28). Using this dataset I show how a number of morphological models are adequate. Additionally, I explored the impacts of incorporating temporal information into an inference using the FBD model. The results from this study show how tree topology and divergence time estimates are sensitive to morphological model choice, even using such a small dataset. Moreover, we demonstrate how despite the uncertainty in topology, the analysis has important implications for echinoderm body plan evolution. Since the introduction of the FBD model it has been used many times and across the tree of life for divergence time estimation. Carrying out an inference correctly using this model however requires a lot of knowledge, both in terms of the data and the model. As such these analyses are often set up using incorrect data, without fully appreciating the assumptions of the model. To explore this, I carried out a comprehensive assessment of the literature to determine how the model is being used and what are the most common misconceptions. Through this I identified temporal information as the most confusing aspect. With this in mind, I provided a thorough explanation of the FBD model with a focus on how to apply it with paleontological data. In the last research chapter I explored how phylogenetics can be used when there is no fossil data available, for example as is often the case for parasitic taxa. Through cophylogenetic approaches we can reconstruct the coevolutionary history of parasites and their hosts. In this study I explored the implications of doing so using parsimony and model based approaches. Further, I show how the approach used will have an impact on any downstream interpretation of the evolution of the host-parasite system.