Populations of the western spadefoot (Spea hammondii) in southern California occur in one of the most urbanized and fragmented landscapes on the planet and have lost up to 80% of their native habitat. Orange County is one of the last strongholds for this pond-breeding amphibian in the region, and ongoing restoration efforts targeting S. hammondii have involved habitat protection and the construction of artificial breeding ponds. These efforts have successfully increased breeding activity, but genetic characterization of the populations, including estimates of effective population size and admixture between the gene pools of constructed artificial and natural ponds, has never been undertaken. Using thousands of genome-wide single-nucleotide polymorphisms, we characterized the population structure, genetic diversity, and genetic connectivity of spadefoots in Orange County to guide ongoing and future management efforts. We identified at least two, and possibly three major genetic clusters, with additional substructure within clusters indicating that individual ponds are often genetically distinct. Estimates of landscape resistance suggest that ponds on either side of the Los Angeles Basin were likely interconnected historically but intense urban development has rendered them essentially isolated, and the resulting risk of interruption to natural metapopulation dynamics appears to be high. Resistance surfaces show that the existing artificial ponds were well-placed and connected to natural populations by low-resistance corridors. Toad samples from all ponds (natural and artificial) returned extremely low estimates of effective population size, possibly due to a bottleneck caused by a recent multi-year drought. Management efforts should focus on maintaining gene flow among natural and artificial ponds by both assisted migration and construction of new ponds to bolster the existing pond network in the region.

中文翻译：

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在城市化的南加州受威胁的西部黑鲀的保护基因组学

加利福尼亚州南部的西部铲足 (Spea hammondii) 的种群生活在地球上城市化程度最高和支离破碎的地区之一，并且已经失去了多达 80% 的原生栖息地。奥兰治县是该地区这种池塘养殖两栖动物的最后据点之一，正在进行的针对沙门氏菌的恢复工作涉及栖息地保护和人工养殖池塘的建设。这些努力成功地增加了育种活动，但从未进行过种群的遗传表征，包括有效种群大小的估计以及人工和天然池塘基因库之间的混合物。使用数千个全基因组单核苷酸多态性，我们表征了种群结构、遗传多样性、和奥兰治县黑鲀的遗传连通性，以指导正在进行和未来的管理工作。我们确定了至少两个，可能是三个主要的遗传簇，簇内的附加子结构表明单个池塘通常在遗传上是不同的。对景观阻力的估计表明，洛杉矶盆地两侧的池塘在历史上可能是相互关联的，但密集的城市发展已使它们基本上与世隔绝，由此产生的自然复合种群动态中断的风险似乎很高。阻力面表明现有的人工池塘位置良好，并通过低阻力走廊与自然种群相连。来自所有池塘（天然和人工）的蟾蜍样本对有效种群规模的估计值极低，可能是由于最近多年干旱造成的瓶颈。管理工作应侧重于通过辅助迁移和建造新池塘来维持自然和人工池塘之间的基因流动，以加强该地区现有的池塘网络。