Scripts and files for "Small-scale population divergence is driven by local larval environment in a temperate amphibian"

Genomic variation within and among populations is shaped by the interplay between natural selection and the effects of genetic drift and gene flow. Adaptive divergence can be found in small scale natural systems even when population sizes are small and the potential for gene flow is high, suggesting that local environments exert selection pressures strong enough to counteract the opposing effects of drift and gene flow. Here, we investigated genomic differentiation in nine moor frog (Rana arvalis) populations in a small-scale network of local wetlands using 16 707 ddRAD-seq SNPs, relating levels of differentiation with local environments as well as with properties of the surrounding landscape. We characterized population structure and differentiation, and partitioned the effects of geographic distance, local larval environment and landscape features on total genomic variation. We also conducted gene-environment association studies using univariate and multivariate approaches. We found small-scale population structure corresponding to 6-8 clusters. Local larval environment was the most influential component explaining 2.3% of the total genetic variation followed by landscape features (1.8%) and geographic distance (0.8%), indicative of isolation-by-environment, -by-landscape and -by-distance, respectively. We identified 1000 potential candidate SNPs putatively under divergent selection mediated by the local larval environment. The candidate SNPs were involved in, among other biological functions, immune system function and development. Our results suggest that small scale environmental differences can exert selection pressures strong enough to counteract homogenizing effects of gene flow and drift in this small-scale system leading to observable population differentiation.

种群内部与种群间的基因组变异，由自然选择与遗传漂变、基因流的效应之间的相互作用共同塑造。即便在种群规模较小、基因流潜力较高的小型自然系统中，亦可观测到适应性分化现象，这表明当地环境施加的选择压力足够强大，足以抵消遗传漂变与基因流的反向作用。本研究依托16707个ddRAD-seq单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记，对一处小型本地湿地网络中的9个林蛙（Rana arvalis）种群开展基因组分化分析，将种群分化水平与当地环境及周边景观属性进行关联研究。我们解析了种群结构与分化模式，并对地理距离、本地幼体环境以及景观特征对总基因组变异的效应贡献进行了拆分。此外，我们还采用单变量与多变量方法开展了基因-环境关联分析。研究结果显示，该系统存在对应6-8个聚类群的小型种群结构。本地幼体环境是最具影响力的解释因子，可解释总遗传变异的2.3%，其次为景观特征（1.8%）与地理距离（0.8%），分别对应环境隔离、景观隔离与距离隔离模式。我们共鉴定出1000个潜在候选SNPs，推测其处于由当地幼体环境介导的歧化选择作用下。这些候选SNPs所涉及的生物学功能涵盖免疫系统功能与发育过程等多个方面。本研究结果表明，在该小型系统中，小规模的环境差异所施加的选择压力足以抵消基因流与遗传漂变的同质化效应，进而催生可观测的种群分化。