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How can we objectively delimit species and identify biodiversity hotspots, thereby addressing consequential problems in conservation biology? How has the dynamic geological and climatic history of western North America shaped the diversification and distribution of the endemic marine and terrestrial fauna? These are the fundamental questions that have inspired my research program. I am using a variety of next-generation sequencing and bioinformatics approaches to address these questions in several systems. Looking to the future, I am searching for opportunities to make synergistic contributions to global sustainability and human health using genomic tools.

Conservation Genomics

My research career started with fringe-toed lizards (Uma), arguably the most specialized lizards in North America, restricted and adapted to sand dune habitats. Due to the fragmented nature of dune systems, they occur in insular populations scattered across the southwestern deserts. My master's thesis (Gottscho 2010, Gottscho et al. 2014) focused on the Mojave Desert fringe-toed lizard (Uma scoparia), a California Species of Special Concern in southern California and western Arizona. By analyzing multiple nuclear loci in a coalescent framework, we found that U. scoparia speciated in the Pleistocene and has very low levels of genetic diversity, with important conservation implications. The second chapter of my Ph.D. dissertation (Gottscho 2015) focused on the population genomics of the U. notata species complex, including the endangered Coachella Valley fringe-toed lizard (U. inornata) in southern California, and was just published as an 'Editor's Choice' article in Molecular Phylogenetics and Evolution (Gottscho et al. 2016). Scaling up to the NGS era, we analyzed restriction-associated DNA sequencing (RADseq) data collected using the Illumina HiSeq 2500 platform with coalescent models to delimit the numbers and boundaries of species within this complex. We found a broad hybrid zone to the east of the Colorado River delta in Sonora, Mexico, and confirmed the existence of an undescribed, highly divergent yet cryptic species from the Mohawk Dunes in southwestern Arizona. This work was funded by sources including the U.S. Army Research Office, the Community Foundation, the Joshua Tree National Park Association, the University of California Institute for Mexico and the United States (UC MEXUS), and the Anza-Borrego Foundation.

The debate over renewable energy in the deserts of southern California is a difficult challenge where trade-offs between competing global vs. local sustainability goals are unavoidable. How might managers plan renewable energy developments to reduce the impact on population connectivity and genetic diversity of sensitive species? One way to address this question is to compile large genetic or genomic databases for co-distributed species and then search for 'evolutionary hotspots' (areas with high genetic diversity within species or high divergence among populations) that provide the raw material for adaptation and evolution. My collaborators at the U.S. Geological Survey and I combined datasets for 17 animal species, including data from my master's thesis, across the Mojave Desert (Vandergast et al. 2013). We located ten regions of high genetic diversity and divergence among species, and found that while 30-40% of the total hotspot area fell within protected areas such as national parks or wilderness areas, up to 17% overlapped with project footprints or transmission corridors.

Working with Dr. Rob Lovich (U.S. Navy) and Dr. Dan Mulcahy (Smithsonian Institution), I am leading a new project on the flat-tailed horned lizard (Phrynosoma mcallii), a California Species of Special Concern that has been evaluated for both federal and state endangered status. The goal is to develop a genomic model of gene flow across the Colorado Desert landscape, eventually to be integrated with a population viability analysis led by the Arizona Department of Game and Fish, that can be used to aid land managers in siting renewable energy and military developments to reduce the impact on this sensitive species. I currently have a Memorandum of Understanding with the California Department of Fish and Wildlife, and am working with multiple agencies including the U.S. Navy, U.S. Air Force, California State Parks, San Diego Natural History Museum, and the El Pinacate Biosphere Reserve (Mexico), to obtain tissue samples. This work is funded by the U.S. Department of Defense Legacy Program. I am also working with Nicole Angeli, a Ph.D. candidate at Texas A&M university, on the conservation genomics of the endangered St. Croix Ground Lizard (Ameiva polops) and the rest of the A. exsul complex in the Caribbean.

Uma cowlesi, Sonora, Mexico

Sand dune habitat, Mohawk Dunes, Arizona

Genetic diversity heatmap (Vandergast et al. 2013)

Phrynosoma mcallii, Ocotillo Wells, CA

Ameiva exsul, Anegada Island

The Baja California Peninsula

Callisaurus draconoides

Petrosaurus thalassinus

Urosaurus nigricaudus

Sceloporus orcutti
Comparative Phylogeography of the San Andreas Fault System

Rugged, arid, and remote, the Baja California Peninsula (BCP) is one of North America's last biological frontiers. Over the past six million years, the BCP rifted away from mainland Mexico along the San Andreas Fault system, forming the Gulf of California and its islands, now home to many endemic reptiles. Pleistocene glacial cycles further impacted the regional herpetofauna, causing dramatic fluctuations in sea level and climate. Due to this complex tectonic and climatic history, the BCP and its offshore islands offer herpetologists a plethora of natural experiments to study speciation. However, the biogeographic patterns observed in this region, particularly in the Vizcaino Desert, where numerous lineages demonstrate spatially concordant genetic breaks, have been the source of controversy. The leading hypothesis to explain the Vizcaino break, a trans-peninsular seaway, has been debunked based on the available geological evidence, but a satisfactory alternative hypothesis has eluded naturalists for decades. For the first chapter of my dissertation, now published in Biological Reviews (Gottscho 2016), I shed light on this problem by reviewing the zoogeographic and geological literature pertaining to the San Andreas Fault system. I called attention to a major Pacific fracture zone that was aligned with the Vizcaino Desert, and proposed an ultimate tectonic hypothesis for the historical biogeography of the region.

For the third chapter of my dissertation, I took a comparative approach to testing this hypothesis by studying a clade of lizards (Phrynosomatidae, including Callisaurus, Petrosaurus, Urosaurus, and Sceloporus) that are widely distributed throughout the BCP using RADseq data. The results indicate that several taxa share spatially concordant phylogeographic boundaries, especially in the Vizcaino Desert, but molecular clock analyses support the hypothesis that multiple waves of divergence likely occurred, thus different lineages must have dispersed across the landscape in idiosyncratic ways. I am currently analyzing a phylogenomic dataset for a subset of these lizards collected using target enrichment of ultra-conserved elements (UCEs) and protein-coding genes and sequenced on the new Illumina NextSeq platform (paired end 150 bp reads). My goal is to better calibrate the molecular clock with fossil data and to use approximate Bayesian computation (ABC) coalescent approaches to better test the simultaneous divergence hypothesis. This research was funded by UC MEXUS, the National Science Foundation (Doctoral Dissertation Improvement Grant), and the American Philosophical Society (Lewis and Clark Grant for Exploration and Field Research). This research would not have been possible without the collaboration of Dr. Brad Hollingsworth (San Diego Natural History Museum) and Dr. Julio Lemos-Espinal (UNAM).

For my postdoctoral research at the Smithsonian Institution with Dr. Kevin de Queiroz and Dr. Michael Braun, I am expanding the dataset for one of my focal groups, zebra-tailed lizards (Callisaurus draconoides complex), which have an enormous distribution in the deserts of North America. Eleven (sub)species have been described between 1835 and 1942, but the genus is currently considered to be monotypic despite extensive geographic variation. The primary goal of this project is to use population genomic data to test biogeographic hypotheses and delimit populations/species across the North American aridlands, including seven islands in the Gulf of California.

Copyright 2016 Andrew Gottscho. Last updated Dec 12 2016.