RUI: Partial lizard genomes and new analytical tools provide a novel conceptual framework for understanding biogeographic patterns throughout the deserts of western North America

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The goal of many evolutionary biologists is to better understand the processes that lead to the formation of new species. In addition to providing valuable data regarding how Earth's history has shaped diversity, results can directly inform conservation and help address biodiversity loss. This study uses genetic data from lizards distributed throughout the arid regions of western North America to better understand how and why new species arise. This study also investigates the prevalence of species unknown to science, and provides formal descriptions of new species discovered. Results of this project directly inform conservation while simultaneously providing a more thorough understanding of the historical processes that led to the evolution of desert species throughout North America. Importantly, this project introduces evolutionary thinking and data analysis to historically underrepresented students enrolled in an undergraduate bioinformatics curriculum. Undergraduates are involved in all aspects of the project from study design and field work to data analysis and writing. Additional broader impacts include working with local institutions to teach genetic concepts to high school students and teachers, facilitation of an institution-wide bootcamp to enhance networking opportunities, graduate student supervision, and local research talks given to the public and to the greater academic community. Decades of research focused on the phylogeography of taxa inhabiting the arid regions of western North America has provided invaluable information regarding the propensity for cryptic lineages, while simultaneously constructing a comprehensive model describing broad biogeographic patterns observed in co-distributed taxa. However, the majority of our current knowledge comes from limited genetic information (e.g. mtDNA only) coupled with the assumption of gene tree/species tree congruence and strictly bifurcating evolutionary histories. Recent advances in genomic sequencing (e.g. RADseq, GBS) can now be combined with the multispecies coalescent (MSC) model to explicitly accommodate gene tree/species tree discordance due to incomplete lineage sorting (ILS), potentially leading to new insight regarding evolutionary relationships and biogeographic patterns. Although powerful, the MSC assumes no gene flow/introgression once species begin to diverge; an assumption that appears to be violated in a growing number of systems. To date, few empirical studies have used genomic data to explicitly quantifiy bias in parameter estimation when ignoring gene flow. This study uses multiple species of phrynosomatid lizards as models to better understand the role of gene flow during diversification throughout the North American deserts. In instances where introgression is suspected, the project quantifies the impact of ignoring gene flow on parameter estimates such as the species tree topology, divergence times and effective population sizes. This study also combines genomic data with morphological and ecological data to reassess species limits, describe new taxa, and inform conservation. The overarching goal of this study is to use newly generated genomic data from multiple species to formulate a new conceptual framework regarding the diversification and historical biogeography of taxa inhabiting the major deserts of western North America.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.