The resolution offered by genomic data sets coupled with recently developed spatially informed analyses are allowing researchers to quantify population structure at increasingly fine temporal and spatial scales. However, both empirical research and conservation measures have been limited by questions regarding the impacts of data set size, data quality thresholds and the timescale at which barriers to gene flow become detectable. Here, we used restriction site associated DNA sequencing to generate a 2,140 single nucleotide polymorphism (SNP) data set for the copperhead snake (Agkistrodon contortrix) and address the population genomic impacts of recent and widespread landscape modification across an ~1,000-km2 region of eastern Kentucky, USA. Nonspatial population-based assignment and clustering methods supported little to no population structure. However, using individual-based spatial autocorrelation approaches we found evidence for genetic structuring which closely follows the path of a historically important highway which experienced high traffic volumes from c. 1920 to 1970 before losing most traffic to a newly constructed alternative route. We found no similar spatial genomic signatures associated with more recently constructed highways or surface mining activity, although a time lag effect may be responsible for the lack of any emergent spatial genetic patterns. Subsampling of our SNP data set suggested that similar results could be obtained with as few as 250 SNPs, and a range of thresholds for missing data exhibited limited impacts on the spatial patterns we detected. While we were not able to estimate relative effects of land uses or precise time lags, our findings highlight the importance of temporal factors in landscape genetics approaches, and suggest the potential advantages of genomic data sets and fine-scale, spatially informed approaches for quantifying subtle genetic patterns in temporally complex landscapes.

中文翻译：

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空间基因组学方法可以在迅速破碎的阿巴拉契亚景观中识别时间流逝和基因流动的历史障碍。

基因组数据集提供的分辨率与最近开发的空间信息分析相结合，使研究人员能够在日益精细的时空尺度上量化种群结构。然而，实证研究和保护措施都受到有关数据集大小，数据质量阈值和可检测到基因流障碍的时间尺度的影响的问题的限制。在这里，我们使用限制性酶切位点相关的DNA测序，为铜头蛇（Agkistrodon contortrix）生成了2,140个单核苷酸多态性（SNP）数据集，并解决了东部约1,000平方公里区域近期和广泛的景观改造对种群基因组的影响美国肯塔基州。基于非空间人口的分配和聚类方法几乎没有支持人口结构​​。但是，使用基于个体的空间自相关方法，我们发现了遗传结构的证据，该结构紧密遵循一条历史悠久的重要公路的路径，该公路经历了来自c的高交通量。1920年至1970年，之后大部分流量都流向了新建的替代路线。我们发现没有类似的空间基因组特征与最近修建的高速公路或露天采矿活动有关，尽管时滞效应可能是缺乏任何新兴的空间遗传模式的原因。对我们的SNP数据集进行二次采样表明，使用少至250个SNP即可获得相似的结果，并且缺失数据的一系列阈值对我们检测到的空间模式的影响有限。尽管我们无法估算土地使用或相对精确的时滞的相对影响，