Karst systems have great ecological, cultural and economic importance, but are constantly threatened by human development. Northwestern Bexar County, Texas (USA), is an example of a region where urbanization threatens an essential karst landscape. Many studies have provided substantial contributions to the understanding and conservation of biodiversity in this area, including the delineation of Karst Fauna Regions (KFRs). However, no study has evaluated fundamentally important measures of genetic diversity, changes in population sizes, and gene flow for listed regional species. Here we used population genomic data derived from the sequence capture of ultraconserved elements (UCEs) to describe patterns of structure and connectivity among cave populations of Cicurina madla, and to estimate demographic and phylogeographic processes underlying those patterns. In addition, we evaluated if population genetic processes could have been influenced by human activities. Although there is weak phylogenomic differentiation between populations, the distribution of genetic diversity and patterns of gene flow within and between areas suggest important differences in population dynamics among KFRs. Our genomic data show that populations of C. madla in Bexar County currently carry comparatively low levels of heterozygosity and nucleotide diversity, and that these might have been influenced by human activities. Ultimately, we present genomic evidence for declining cave spider population sizes perhaps coincident with increases in an expanding human population and discuss implications of our findings for conservation.

喀斯特系统具有巨大的生态、文化和经济重要性，但不断受到人类发展的威胁。德克萨斯州西北部贝克萨尔县（美国）是城市化威胁重要喀斯特景观的地区的一个例子。许多研究为理解和保护该地区的生物多样性做出了重大贡献，包括喀斯特动物区系（KFR）的划分。然而，还没有研究评估所列区域物种的遗传多样性、种群规模变化和基因流等根本性重要指标。在这里，我们使用从超保守元件 (UCE) 序列捕获中获得的种群基因组数据来描述Cicurina madla洞穴种群之间的结构和连接模式，并估计这些模式背后的人口统计和系统发育地理过程。此外，我们还评估了群体遗传过程是否受到人类活动的影响。尽管种群之间存在微弱的系统发育差异，但区域内和区域之间遗传多样性的分布和基因流模式表明 KFR 之间的种群动态存在重要差异。我们的基因组数据显示C. madla种群贝克萨尔县目前的杂合性和核苷酸多样性水平相对较低，这些可能受到人类活动的影响。最终，我们提供了洞穴蜘蛛种群规模下降的基因组证据，这可能与人口不断扩大的同时发生，并讨论了我们的发现对保护的影响。