29Phylogeographic divergence and population genetic diversity within species reflect 30 the impacts of habitat connectivity, demographics, and landscape level processes in both 31 the recent and distant past. Characterizing patterns of differentiation across the geographic 32 range of a species provides insight on the roles of organismal and environmental traits, on 33 evolutionary divergence, and future population persistence. This is particularly true of 34 habitat specialists where habitat availability and resource dependence may result in 35 pronounced genetic structure as well as increased population vulnerability. We use DNA 36 sequence data as well as microsatellite genotypes to estimate range-wide phylogeographic 37 divergence, historical population connectivity, and historical demographics in an endemic 38 habitat specialist, the dunes sagebrush lizard (Sceloporus arenicolus). This species is found 39 exclusively in dune blowouts and patches of open sand within the shinnery oak-sand dune 40 ecosystem of southeastern New Mexico and adjacent Texas. We find evidence of 41 phylogeographic structure consistent with breaks and constrictions in suitable habitat at 42 the range-wide scale. In addition, we find support for a dynamic and variable evolutionary 43 history across the range of S. arenicolus. Populations in the Monahans Sandhills have 44 deeply divergent lineages consistent with long-term demographic stability. In contrast, 45 populations in the Mescalero Sands are not highly differentiated, though we do find 46 evidence of demographic expansion in some regions and relative demographic stability in 47 others. Phylogeographic history and population genetic differentiation in this species has 48 been shaped by the configuration of habitat patches within a geologically complex and 49 historically dynamic landscape. Our findings identify regions as genetically distinctive 50 4 conservation units as well as underscore the genetic and demographic history of different 51 lineages of S. arenicolus. 52 53 Introduction 54 Patterns of population genetic diversity within species are shaped by both 55 evolutionary and contemporary history (Rissler, 2016). Though anthropogenic changes to 56 landscapes alter patterns of connectivity that can result in the divergence or coalescence of 57 populations, these processes take place on a background of evolutionary history 58 determined by chance, species' life history, and also geologic and climatic changes. 59 Characterizing this evolutionary history, and identifying the role that organismal traits, 60 evolutionary processes, and ecological conditions have on patterns of phylogeographic 61 divergence adds to our understanding of evolution, and is also fundamental to conserving 62 evolutionary potential in the face of anthropogenic disturbance and climate change 63 (Olivieri et al., 2015). 64 The phylogeographic history of species can reflect the roles that habitat 65 connectivity, gene flow, and population stability have played in a species' evolutionary 66 persistence....