Data from: Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback

Genetic divergence between populations is shaped by a combination of drift, migration, and selection, yielding patterns of isolation-by-distance (IBD) and isolation-by-environment (IBE). Unfortunately, IBD and IBE may be confounded when comparing divergence across habitat boundaries. For instance, parapatric lake and stream threespine stickleback (Gasterosteus aculeatus) may have diverged due to selection against migrants (IBE), or mere spatial separation (IBD). To quantitatively partition the strength of IBE and IBD, we used recently-developed population genetic software (BEDASSLE) to analyze partial genomic data from three lake-stream clines on Vancouver Island. We find support for IBD within each of three outlet streams (unlike prior studies of lake-stream stickleback). In addition, we find evidence for IBE (controlling for geographic distance): the genetic effect of habitat is equivalent to geographic separation of ∼1.9km worth of IBD. Remarkably, of our three lake-stream pairs, IBE is strongest where migration between habitats is easiest. Such microgeographic genetic divergence would require exceptionally strong divergent selection, which multiple experiments have failed to detect. Instead, we propose that non-random dispersal (e.g., habitat choice) contributes to IBE. Supporting this conclusion, we show that the few migrants between habitats are a non-random subset of the phenotype distribution of the source population.

种群间的遗传分化受遗传漂变、迁移与选择的共同塑造，形成了距离隔离（isolation-by-distance, IBD）与环境隔离（isolation-by-environment, IBE）的分布模式。遗憾的是，在比较不同生境边界间的遗传分化时，IBD与IBE的效应可能相互混淆。例如，邻域分布的湖泊与溪流三刺棘背鱼（Gasterosteus aculeatus），其遗传分化既可能源于对迁入个体的选择作用（IBE），也可能仅由单纯的空间隔离所致（IBD）。为定量拆分IBE与IBD的作用强度，我们采用新近开发的群体遗传学软件BEDASSLE，分析了温哥华岛三处湖-溪渐变群的部分基因组数据。研究发现，三处出口溪流内部均存在IBD信号——这与此前针对湖-溪棘背鱼的相关研究结论存在差异。此外，我们还检测到了IBE的证据（控制地理距离变量后）：生境差异带来的遗传效应，等效于约1.9公里空间距离所对应的IBD遗传分化水平。值得注意的是，在我们的三组湖-溪配对样本中，生境间的迁移便利性越高，IBE的强度便越强。这类微地理尺度的遗传分化需要极强的歧化选择作用才能形成，但多项相关实验均未能检测到该选择效应。据此我们提出，非随机扩散（例如生境选择）是IBE形成的潜在贡献因素。为验证这一结论，我们证实了生境间的少量迁移者并非源种群表型分布的随机子集，而是具有特定表型特征的非随机群体。