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 are 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 provide 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.城市化是一种极具破坏性的生境破碎化类型，可致使诸多物种在局部区域灭绝，另有大量物种被困并孤立于城市基质（urban matrix）之中。遗传漂变（drift）在降低城市种群遗传多样性、加剧种群遗传分化方面的作用已得到广泛认可，但针对城市化环境下促进遗传漂变的人口统计学与时间相关因素的明确纳入与分析，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（历史有效种群大小（Ne））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。研究结果表明，火蝾螈的城市种群具有高度的遗传分化，这极有可能与奥维耶多城市发展同期发生的近期有效种群规模下降有关——该结果由溯祖分析（coalescence analyses）计算得出。不过城市化仅造成了少量的遗传多样性损失。回归模型分析显示，生境斑块面积与当代有效种群大小呈正相关；而在排除历史背景不明的种群后，仅能为种群历史因素的影响提供中等强度的支持证据。这凸显了诸多因素在决定当前种群遗传多样性与结构过程中的相互作用。总体而言，本针对火蝾螈城市种群的研究结果，为探究城市化环境下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相关见解之一，而在全球城市化进程持续加剧的当下，该主题具有至关重要的研究价值。