UC Davis

The flat-tailed horned lizard (Phrynosoma mcallii) is a Colorado Desert endemic species with a long history of conservation and active management. Ongoing monitoring has relied on traditional mark-recapture data to inform management action. I used reduced representation genotype-by-sequencing techniques to generate a large single nucleotide polymorphism data set to assess fine-scale P. mcallii population structure, dispersal, landscape barriers to gene flow, and genetic diversity in California’s Imperial Valley with the overall goal to inform ongoing management and monitoring of the species.In my first chapter, over 500 individual P. mcallii DNA samples were genotyped to assess fine-scale population structure across the Imperial Valley. Using sparse non-negative matrix factorization paired with geographic capture data and discriminant analysis of principal components, I detected population structure across the east-west axis of the Imperial Valley, which had been described using mitochondrial DNA markers. I observed less pronounced but significant population structure between West Mesa and Yuha Basin populations which may indicate contemporary barriers to migration. I detailed estimates of contemporary genetic diversity, finding generally lower than expected heterozygosity, low inbreeding, and little variation in nucleotide diversity. These results indicate management-relevant population structure that aligns with existing management units.In my second chapter I developed genetic pedigrees to identify sex-biased patterns of dispersal, isolation-by-distance and landscape barriers to gene flow. I calculated pairwise relatedness between individuals and measured the decay of relatedness by distance to investigate sex-biased dispersal; with these methods we detected evidence of male-biased dispersal. I also used this data to build pedigrees that revealed the first documented instance of multiple paternity in P. mcallii. I tested for isolation-by-distance using the inverse proportion of shared alleles and found patterns that indicate high gene flow, and little effect of isolation-by-distance. We used Estimated Effective Migration Surfaces to identify barriers to gene flow associated with CA-98 and I-8 as well as Superstition Mountain and two BLM OHV areas. These contemporary barriers seem to reduce gene flow, but it is unclear to what extent. We recommend further landscape analyses to understand how landscape arrangement and abiotic factors may influence gene flow in the Western Imperial Valley.In my third chapter I used samples collected from ongoing P. mcallii long-term monitoring plots to estimate baseline measures of genetic diversity for three management areas, estimate effective population size on each demographic monitoring plot, and test for heterozygosity fitness correlations. I found no evidence of inbreeding through estimation of genetic diversity or heterozygosity fitness correlations. Effective population sizes differed by plot but were limited in their applicability beyond the scale of sampling. I estimated an effective population size of 1,048 individuals across the western Imperial Valley. I then synthesized the results of these chapters into recommendations for ongoing management of the species. I recommend the integration of genetic monitoring into ongoing monitoring efforts including decadal reassessments of genetic diversity and effective population sizes, with additional recommendations to assemble a high-quality P. mcallii reference genome, to research genetic variation near range edges, to research climate change adaptation, and to investigate hybrid zone dynamics with P. platyrhinos and P. goodei.