Data from: Trapped within the city: Integrating demography, time since isolation and population-specific traits to assess the genetic effects of urbanization

Urbanization is a severe form of habitat fragmentation that can cause many species to be locally extirpated and many others to become trapped and isolated within an urban matrix. The role of drift in reducing genetic diversity and increasing genetic differentiation is well recognized in urban populations. However, explicit incorporation and analysis of the demographic and temporal factors promoting drift in urban environments is poorly studied. Here, we genotyped 15 microsatellites in 320 fire salamanders from the historical city of Oviedo (Est. 8th century) to assess the effects of time since isolation, demographic history (historical effective population size; Ne) and patch size on genetic diversity, population structure and contemporary Ne. Our results indicate that urban populations of fire salamanders are highly differentiated, most likely due to the recent Ne declines, as calculated in coalescence analyses, concomitant with the urban development of Oviedo. However, urbanization only caused a small loss of genetic diversity. Regression modelling showed that patch size was positively associated with contemporary Ne, while we found only moderate support for the effects of demographic history when excluding populations with unresolved history. This highlights the interplay between different factors in determining current genetic diversity and structure. Overall, the results of our study on urban populations of fire salamanders provides some of the very first insights into the mechanisms affecting changes in genetic diversity and population differentiation via drift in urban environments, a crucial subject in a world where increasing urbanization is forecasted.城市化是一种强度极高的生境破碎化类型，可导致众多物种在局部区域灭绝，其余多数物种则被困并孤立于城市基质（urban matrix）之中。遗传漂变（genetic drift）对降低城市种群遗传多样性、提升种群遗传分化程度的作用，已在学界得到广泛认可。然而，针对城市环境中促进遗传漂变的种群统计与时间维度因素的明确纳入与系统分析，相关研究仍较为匮乏。本研究对来自始建于8世纪的历史城市奥维耶多的320只火蝾螈（fire salamanders）的15个微卫星（microsatellites）位点进行基因分型，以评估隔离时长、种群历史动态（历史有效种群大小Ne）以及生境斑块面积对遗传多样性、种群结构以及当代有效种群大小的影响。研究结果显示，火蝾螈的城市种群间存在高度遗传分化，这极有可能与奥维耶多城市发展同期通过溯祖分析（coalescence analyses）所测算出的近期Ne下降有关。但城市化仅造成了小幅的遗传多样性损失。回归建模结果表明，生境斑块面积与当代有效种群大小呈显著正相关；而在排除历史背景不明的种群后，我们仅获得了中等程度的证据支持种群历史动态的影响。这凸显了多种因素在决定当前种群遗传多样性与种群结构过程中的交互作用。总体而言，我们针对火蝾螈城市种群的研究结果，为理解城市环境中通过遗传漂变影响遗传多样性变化与种群分化的机制提供了首批关键认知之一；在全球城市化进程持续加剧的当下，这一研究主题具有至关重要的意义。