Islands and Integrals: Processes of Diversification in an Island Archipelago and Bayesian Methods of Comparative Phylogeographical Model Choice

Understanding the processes that generate, maintain, and regulate the assembly of biodiversity is a major goal of evolutionary biology. An important component of this goal is understanding how large-scale processes cause diversification across entire communities of species. These processes include geological and climatic mechanisms that alter the landscape and environment across which populations of organisms are distributed. Given the dynamic nature of our planet, such large-scale historical processes are likely common across most ecosystems, making them potential key drivers of diversification and community assembly. By simultaneously affecting entire communities of species, large-scale geological and climatic events are expected to generate patterns of divergences that are temporally clustered across affected groups of species. Such pulses of speciation are expected to leave a signature in the genetic variation within and among these lineages. This signal provides us with an opportunity to understand how past regional and global biogeographical processes have affected diversification by estimating the temporal patterns of divergence across present-day co-distributed species. The primary goal of this work is to (1) better understand processes of diversification within the Philippine Islands using DNA sequence data from a diverse set of vertebrate species, and (2) advance statistical methods of comparative phylogeographical model choice in order to improve the estimation of diversification models from genetic data. The Philippine Islands are a particularly interesting system in which to address questions of diversification processes. Over the past few million years, the Islands of the Philippines have been repeatedly joined and fragmented due to oscillations in sea levels associated with iv glacial cycles. It has been hypothesized that inter-glacial rises in sea level caused bouts of speciation across the islands due to the fragmentation of populations distributed across adjacent islands. In the first chapter of this dissertation, we test this hypothesis by applying a popular approximate-Bayesian method of phylogeographical model choice to infer the distribution of divergence times across a diverse set of 22-vertebrate taxa distributed across the Philippine Islands. Consistent with the sea-level driven model of diversification, the results strongly support recent and highly clustered divergences shared across the 22 population pairs. However, we also perform a suite of simulation-based analyses to assess the behavior of the method and find it to be biased toward supporting models with less parameter space and thus small numbers of divergence events shared across taxa. In response to our findings in Chapter 1, a modification of the model-choice method was proposed as a means of circumventing the biases we reported. In Chapter 2, we used empirical and simulation-based analyses to investigate the behavior of this proposed method. We find the approach is still biased toward models with less parameter space, which can manifest in a strong tendency to sample predominantly from models that exclude the true values of the model’s parameters. We also find that the bias toward small models still causes the method to prefer overly clustered models of divergence. In Chapter 3, we introduce a new approximate-Bayesian model for comparative phylogeographical model-choice that estimates the temporal distribution of divergences across taxa from multi-locus DNA sequence data. By reparameterizing the model used in Chapter 1, and using more flexible priors on divergence models and nuisance parameters, we improve the robustness, accuracy, and power of the method for estimating the posterior probabilities of models of divergence across taxa. Our results demonstrate that the bias of the original model toward inferring models of clustered divergences is caused by a combination of (1) uniform priors on nuisance parameters reducing the marginal likelihoods of models with more divergence time parameters, and (2) a prior on divergence models that disfavors models with intermediate numbers of divergence time parameters. v In Chapter 4, we explore broad-scale temporal patterns of colonization and diversification of vertebrate groups in the Philippines. We mine the literature for estimates, and data to obtain estimates, of clade ages for a diverse set of vertebrate groups within the islands. We test whether time of colonization explains vertebrate species diversity in the islands (i.e., a time-for-diversification effect). Furthermore, we establish general patterns of colonization times and diversity across major vertebrate groups and discuss their implications in the formation of the archipelago’s impressive biodiversity.