The Evolutionary History of Cryptoblepharus Lizards: Recent Diversification across Continents and Oceans

Understanding the evolutionary processes that generate and maintain biodiversity is a fundamental objective in ecology and evolution. In this dissertation, I characterize phylogenetic patterns in a recent radiation of Australian skinks, discuss the ecological context of diversification and how this has translated into macroevolutionary change across the continent. By also reconstructing the evolutionary history of all Cryptoblepharus species globally, I shed further light on the evolutionary and biogeographic processes that have shaped the diversity of the genus. This dissertation project has generated an empirical framework for future studies into the continuous nature between micro- and macroevolutionary change. To infer the phylogeny of Australian Cryptoblepharus, I generated an exon- capture dataset and designed a bioinformatic pipeline to generate quality filtered sequence alignments (Appendix A). Multi-locus datasets are required to confidently infer species trees for rapidly speciating clades due to a high prevalence of gene tree incongruence among loci. In Chapter I, I use the Cryptoblepharus radiation as an empirical example and describe how to account for differences in gene tree resolution when employing summary-coalescent methods for species tree inference. Our study highlights the importance of phylogenetically informative loci but simultaneously demonstrates that the addition of non-informative loci does not introduce phylogenetic noise. In Chapter II, I then use comparative methods and morphological measurements for over 800 individuals, to examine the ecological context of diversification in Australian Cryptoblepharus. Specifically, I focus on whether habitat specialisation can explain current patterns of variation in ecologically relevant traits. I observed significant differences in morphology between species that occur in distinct environments (rock, arboreal and littoral) and species that occur within the same habitat are often cryptic. These findings suggest that isolated analogous habitats have provided ecological opportunity and repeatedly promoted adaptive diversification, while speciation within habitat has accrued without ecomorphological change. In contrast to well known adaptive radiations in insular environments, continental radiations are likely driven by alternative diversification processes that jointly stimulate species proliferation. In Chapter III, I explore patterns of introgression between phylogenetically divergent species. I combine population and phylogenetic tools, to quantify the extent of introgression between ecomorphologically distinct and similar taxa. I describe the frequent occurrence of mitochondrial haplotype sharing across species boundaries and the complete replacement of the mitochondrial genome in one species. Furthermore, non-sister species often share more nuclear variants than as expected under a model of incomplete lineage sorting only, suggesting substantial historical introgression. Finally, Cryptoblepharus skinks are renowned for their widespread distribution, across continents and many island archipelagoes, while they have only emerged and diversified recently (i.e. since late Miocene/early Pliocene). In Chapter IV, I reconstruct the global phylogeny and discuss the importance of trait-based dispersal. Large scale range expansions across the Indian and Pacific Ocean have only occurred relatively recently, after an ancestor adapted to a more littoral habitat, and many extralimital taxa still only occur in close vicinity to coastal areas (Appendix B). These lizards therefore exemplify how ecological traits can increase the propensity of dispersal and that disjunct geographic distributions are not solely explained by a vicariance model