The Phylogenomics and Macroevolutionary Dynamics of Australasian Diplodactyloid Geckos

Our planet supports a staggering array of biodiversity. A firm understanding of the species with which we share this planet requires researchers to develop a solid basis on which pertinent questions about biodiversity can addressed. My dissertation uses one group of speciose and ecologically diverse geckos to ask questions regarding evolutionary relationships, macroevolutionary patterns, adaptive radiation, and processes at the species level responsible for generating this diversity. I implement a number of cutting edge molecular and computational methods to demonstrate the importance of taking an integrative approach by incorporating both molecules and morphology./nChapter 1: Molecular data has vast applications in exploring the evolutionary histories of organisms. Some groups, however, continually confound attempts at elucidating their relationships with conventional molecular methods. The advent of genomic sequencing has allowed researchers to gather vast amounts of sequence data to tackle troublesome phylogenetic questions. The diplodactyloid geckos endemic to Australasia are an extremely diverse of clade squamates with an array of ecologies and phenotypes. However, there exist a number of poorly resolved relationships and some studies recover well-supported groups which disagree across datasets. Here, we implement 4,268 ultraconserved element loci (UCEs) to address the phylogeny of the diplodactyloids. In comparison to previous studies, the UCEs resolved nearly every node, the exceptions being some at the base of the New Caledonian and core Australian diplodactylid clades. Our concatenated and coalescent phylogenies directly conflict with those from four previous studies, sometimes by as much as 45% of nodes, and received much higher support. Divergence time estimates were largely congruent previous estimates, though slightly older for some deeper nodes. Our findings demonstrate the importance of incorporating numerous independent loci in phylogenetic estimates./nChapter 2: Adaptive radiations are notoriously difficult to define, particularly across broad taxonomic and temporal scales. However, most examples can be characterized by ecological differentiation. The diplodactyloid geckos exhibit a staggering array of ecologies accompanied by a morphological diversity that vastly exceeds that seen elsewhere in Gekkota. Using ecological data and ecomorphological measurements, we address how ecological differentiation has progressed in this clade as well as the prevalence of convergent evolution due to similar selective pressures. Ancestral trait reconstruction methods find that diplodactyloids were ancestrally rupicolous. Hansen models find that arboreal forms have higher rates body size evolution than all other ecological categories. We also find that convergence is widespread within the diplodactyloids, though intraclade convergence was more common that interclade convergence. Furthermore, tests of phenotypic convergence reveal that convergence is most widespread in the insular diplodactylids. The phenomenon of adaptive radiation has been most well documented in groups like Anolis lizards and cichlid fishes, but diplodactyloids likely represent another example of exceptional morphological diversification in novel habitats./nChapter 3: The generation of biodiversity has fascinated researchers for decades, particularly in the case of putative adaptive radiations. Speciation and extinction rates are subject to both biotic and abiotic forces, and both are notoriously difficult to estimate from molecular data without fossils. However, many methods have limited power to inform us of diversification trajectories. The diplodactyloids represent a unique opportunity to investigate rates of diversification and trait evolution. Examination of branch lengths and divergence times indicated that the insular forms, which were recent arrivals, had experienced bursts of diversification over the background rate for the whole clade. We used likelihood and Bayesian-based methods to infer diversification trajectories of diplodactyloids, implementing a phylogenomic estimate of more the 4,200 independent loci. Remarkably, most methods find that there is no rate heterogeneity in the diplodactyloid tree, but that the background rate of speciation is relatively high. In contrast to previous studies that have suggested a mass extinction event around the Eocene-Oligocene boundary (EOb), we find very little support for any such event. The weak signature of mass extinction we find vastly predates the EOb, dating back to the Campanian. Diplodactyloids demonstrate a complex pattern of trait evolution, with signatures of modularity in the rate of phenotypic diversification. Using Bayesian methods, we found that not all traits are evolving at the same rate for all clades. Rather, certain traits, namely those tied to substrate and diet experienced higher rates of diversification than others. While the insular clades possessed similar net diversification patterns to the rest of the diplodactyloids, they exhibited higher rates of trait evolution. A similar pattern is evident in clades that have transitioned to new substrates. These findings suggest that high rates of background diversification coupled with dispersal and environmental instability have facilitated phenotypic and ecological diversification in this clade./nChapter 4: Australia has acted as an engine of biodiversity for a number of disparate clades, producing a wide diversity of species and ecologies seen nowhere else in the world. While the continent is typified by arid environs, a major epicenter of biodiversity is located in the ancient monsoonal tropics of the north. In this study, we investigate the phylogeographic patterns of the marbled velvet gecko (Oedura marmorata) in the Top End. Using mitochondrial (mtDNA) data and 4,268 UCEs, we find that there are eight well supported clades in this species complex. However, the UCEs vastly outperform the mtDNA in resolving the phylogenetic relationships between them as well provide context as to the geographic features that led to this diversity. Furthermore, we find signatures of potential hybrid speciation and Dobzhansky-Muller incompatibilities. From clustering analyses, it appears that several major rivers have played a large role in isolating lineages in the Top End. In conjunction with ancient formations such as the Arnhem Plateau and Carpentarian Gap, these rivers have allowed for the formation and maintenance of these lineages.

Advisor: McGuire, Jimmy A