Award Date


Degree Type


Degree Name

Doctor of Philosophy (PhD)


Biological Science

First Committee Member

Brett R. Riddle

Second Committee Member

Brian I. Crother

Third Committee Member

Javier A. Rodríguez

Fourth Committee Member

Daniel B. Thompson

Fifth Committee Member

Matthew S. Lachniet

Number of Pages



As a fundamental component of the developing discipline of conservation biogeography, broadscale analyses of biotic assembly and disassembly across multiple temporal and spatial scales provide an enhanced understanding of how geologic transformations and climate oscillations have shaped extant patterns of biodiversity. As with any scientific field, there are limitations in the case of biogeographic historical reconstructions. Historical reconstructions are only as robust as the theoretical underpinnings of the methods of reconstruction (including data collection, quality, analysis, and interpretation). Nevertheless, historical reconstructions of species distributions can help inform our understanding of how species respond to environmental change.

My dissertation takes a critical look at the current state of biotic-level biogeographic analyses across an array of spatio-temporal scales and I use the North American warm deserts as a model system to both develop and test biogeographic methods. In particular, I address the biogeographic issue of pseudo-congruence (similar biogeographic patterns produced by historically dissimilar events) and develop potential approaches to reduce the issue of pseudo-congruence in biotic-level analyses. I review potential confounding issues that could produce pseudo-congruence in climate change-based biogeographic analyses and I incorporate temporal components into complex biogeographic theories and methods to reduce pseudo-congruence in biogeographic analysis. My dissertation goals and approaches are described in Chapter 1, which serves as an introduction.

In Chapter 2, I provide a summary of paleoclimatic patterns and processes in the North American deserts. A refined understanding of paleoclimatic pattern and process can facilitate the generation of enhanced hypotheses about how biotas are altered by climate change events, particularly in cases where climate change events occurring at different times and scales could produce pseudo-congruent biogeographic patterns.

In Chapter 3, I propose a modification to the Phylogenetic Analysis for Comparing Trees (PACT) multi-clade biogeographic analysis, in order to facilitate a modern, integrative biotic-level analysis. I developed a modified PACT (mPACT) protocol that incorporates a temporal component (to reduce pseudo-congruence) and facilitates likelihood-based phylogenetic ancestral area reconstruction. To test the performance of my modification, I conducted modified and standard PACT (mPACT and PACT, respectively) analyses on data previously generated for the North American warm deserts and compared these results to those of a prior analysis that uses Secondary Brooks Parsimony Analysis (Secondary BPA), which is a binary-coded pre-cursor method to PACT. This analysis showed that results from mPACT revealed more diversification compared to Secondary BPA and PACT analyses and that pseudo-congruent patterns were rampant in this dataset.

Finally, in Chapter 4, I developed and tested a novel operational approach to exploring evolutionary dynamics of areas of endemism (areas thought by some biogeographers to generate and maintain unique lineages through time). My procedure implements mPACT analyses as well as paleoclimatic and geologic information and I tested my analysis by conducting an analysis on the North American warm deserts. The results of my analysis were congruent with the pre-existing biogeographic hypotheses of the North American warm deserts but also showed that there were more pseudo-congruent events than previously recognized, which may alter the understanding of areas of endemism on a temporal scale. Moreover, I provide novel insights into the potential for areas of endemism to act as both areas of persistence (or stability) as well as areas of transition (ephemeral areas) for biodiversity and I address the issue that diagnosed areas of endemism may not all be equal with respect to biodiversity production and stability through time.


Analysis; Biodiversity; Biogeography; Biogeography – Climatic factors; Climatic changes; Community; Deserts; Ecology; Evolution; Evolution (Biology); North America


Biodiversity | Climate | Desert Ecology | Ecology and Evolutionary Biology | Geography | Zoology