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To understand how various patterns of biodiversity evolve, we must understand not only how various factors influence these patterns, but also the effects of evolutionary history on these patterns. A continuing discussion in biology is the relationship among various levels and forms of diversity. Most studies that focus on past, current, or predicted future changes in diversity use a phylogenetic context, yet lack a phylogenetic framework. Closing that conceptual gap can help to produce a more coherent understanding of diversity patterns and can be more useful when integrated with new dimensions (i.e., time). Here I focus on how extinction and origination rates affect measures of taxonomic (taxic), phylogenetic (sensu Faithâs diversity), and morphological diversity.In chapter 1, I analyze the relationship between taxonomic and phylogenetic diversity in canids and varanids using time calibrated phylogenies. To understand how phylogenetic diversity and taxonomic diversity compare temporally, analyses were run on whole trees as well as trees modified to represent designated time bins. All statistical analyses showed that although taxonomic and phylogenetic diversity can be strongly correlated in certain instances, they also often diverge. This divergence indicates a significant shift in tree geometry (overall assembly of branches across the tree within and across time bins), especially during the extinction of evolutionarily deep, and thus vital, lineages.In chapter 2, I use 2D geometric morphometric analysis of the skulls of extant monitors and some fossil relatives to quantify and compare morphological diversity. I then test the robustness of these patterns using a phylogenetic framework alongside taxonomic and phylogenetic diversity on a molecular tree both temporally and spatially. Monitor lizards are a good model for these shape analyses because they are morphologically conservative, but regionally variable in diversity. Fossil varanoids fall well within the range of extant morphological variation, but the region of lowest taxonomic but relatively high phylogenetic diversity relates to a large amount of shape disparity. Phylomorphospace and phylogenetic signal analyses also showed that evolutionary history is a strong influence on size and shape patterns, but the influence of allometry on shape patterns decreases when accounting for evolutionary history. In chapter 3, I analyze disparity through time (sensu Slater) on a time calibrated molecular varanid tree using size and cranial geometric morphometric data (from chapter 2) to compare with taxonomic diversity. Disparity starts high and falls through time because the nestedness of originations increases across the phylogeny. Size disparity often falls below the expected measures of disparity whereas shape disparity rises above expected. Although considered morphologically conservative, ecological variation within Varanus is portrayed in aspects of size and cranial shape disparity, and the originations of certain groups (e.g., largest and smallest taxa) are correlated with certain patterns of disparity through time. These results also corroborate inferences made in studies of Varanus fossil material that size variation in Varanus (which influences shape variation) may have been higher in the past. These results suggest that in order to understand the evolutionary consequences and causes of diversity shifts, we cannot just look at diversity today or one metric alone. Origination and extinction rates can have disparate effects on morphological and phylogenetic diversity, and integrating evolutionary history into these studies can result in different inferences about underlying processes. As a consequence, trying to understand extant and past diversity using the power of a phylogenetic framework may provide a wealth of information on the effects of origination and extinctions on evolutionary depth.