Genomic footprints of (pre) colonialism: Population declines in urban and forest túngara frogs coincident with historical human activity

Urbanisation is rapidly altering ecosystems, leading to profound biodiversity loss. To mitigate these effects, we need a better understanding of how urbanisation impacts dispersal and reproduction. Two contrasting population demographic models have been proposed that predict that urbanisation either promotes (facilitation model) or constrains (fragmentation model) gene flow and genetic diversity. Which of these models prevails likely depends on the strength of selection on specific phenotypic traits that influence dispersal, survival, or reproduction. Here, we a priori examined the genomic impact of urbanisation on the Neotropical túngara frog (Engystomops pustulosus), a species known to adapt its reproductive traits to urban selective pressures. Using whole-genome resequencing for multiple urban and forest populations we examined genomic diversity, population connectivity and demographic history. Contrary to both the fragmentation and facilitation models, urban populations did not exhibit substantial changes in genomic diversity or differentiation compared to forest populations, and genomic variation was best explained by geographic distance rather than environmental factors. Adopting an a posteriori approach, we additionally found both urban and forest populations to have undergone population declines. The timing of these declines appears to coincide with extensive human activity around the Panama Canal during the last few centuries rather than recent urbanisation. Our study highlights the long-lasting legacy of past anthropogenic disturbances in the genome and the importance of considering the historical context in urban evolution studies as anthropogenic effects may be extensive and impact non-urban areas on both recent and older timescales. 

Methods
Full Methods description provided in manuscript: Moran et al., 2023

Genomic data: Whole genome resequencing data used in this study is available from the European Nucleotide Archive (ENA) (PRJEB60348).

Environmental data: The collection of light (in Lux), noise (in dB SPL, fast, max, A-weighted) and canopy cover data (percentage canopy cover estimated from pictures) data was previously described and published in Halfwerk et al., 2019. The level of urbanisation (Urban_score) was calculated based on the type of landscape-cover for each sampling location using ‘Urbanisation Score’ software (Lipovits et al., 2015; Seress et al., 2014). This program accesses satellite images via GoogleMaps and applies a semi-automated approach to quantify the relative abundance of vegetation and impervious surfaces within a 1 km2 area around each sampling location. These values were then combined using principal component analysis (PCA) and an urbanisation score retained (PC1) for each location.

城市化正快速改变生态系统，引发严重的生物多样性丧失。为缓解这些影响，我们需要更深入理解城市化如何影响扩散与繁殖。目前已提出两种截然相反的种群人口统计模型，分别预测城市化会促进（促进模型）或限制（片段化模型）基因流与遗传多样性。哪种模型更占优势，大概率取决于对影响扩散、存活或繁殖的特定表型性状的选择强度。
本研究先验地（a priori）考察了城市化对新热带界泡蟾（Engystomops pustulosus）的基因组影响——该物种已知可根据城市化带来的选择压力调整其繁殖性状。我们对多个城市种群与森林种群开展全基因组重测序，以此分析基因组多样性、种群连通性与种群历史动态。
与片段化模型和促进模型的预测均相悖的是，相较于森林种群，城市种群的基因组多样性或遗传分化程度未出现显著变化；且基因组变异最适合用地理距离而非环境因素解释。采用后验（a posteriori）分析方法后，我们还发现城市与森林种群均经历了种群衰退。这些种群衰退的时间节点，似乎与近几个世纪巴拿马运河周边的大规模人类活动相吻合，而非近期的城市化进程。本研究强调了过去人为扰动在基因组中留下的长期遗留效应，以及在城市演化研究中纳入历史背景的重要性——因为人为影响可能波及范围广泛，且在近期与较久的时间尺度上均会对非城市区域造成冲击。

方法
完整的方法描述见论文：Moran等人，2023年
基因组数据：本研究使用的全基因组重测序数据可从欧洲核苷酸档案馆（European Nucleotide Archive, ENA）获取（登录号：PRJEB60348）。
环境数据：光照数据（单位：勒克斯）、噪声数据（单位：dB SPL，快时最大A计权）以及冠层覆盖数据（由图像估算的冠层覆盖百分比）的采集流程已在Halfwerk等人2019年的研究中详细描述并发表。城市化水平（Urban_score）基于每个采样点的景观覆盖类型，通过"Urbanisation Score"软件计算得到（Lipovits等人，2015；Seress等人，2014）。该程序通过谷歌地图（GoogleMaps）获取卫星图像，并采用半自动化方法量化每个采样点周边1平方千米区域内的植被与不透水面相对丰度。随后通过主成分分析（Principal Component Analysis, PCA）整合这些数值，保留每个采样点的城市化得分（PC1主成分）。