Inferring the history of divergence between species in a framework that permits the presence of gene flow has been crucial for characterizing the "gray zone" of speciation, which is the period of time where lineages have diverged but have not yet achieved strict reproductive isolation. However, estimates of both divergence times and rates of gene flow often ignore spatial information, for example when considering the location and width of hybrid zones with respect to changes in environment between lineages. To connect phylogeographic estimates of lineage structure, migration, historical demography, and timing of divergence with hybrid zone dynamics, we used population genomic data from the North American ratsnake complex (Pantherophis obsoletus). We examined the spatial context of diversification by linking migration and timing of divergence to the location and widths of hybrid zones. Artificial neural network approaches were applied to understand how landscape features and past climate have influenced population genetic structure among these lineages. We found that rates of migration between lineages were associated with the overall width of hybrid zones. Timing of divergence was not related to migration rate or hybrid zone width across species pairs but may be related to the number of alleles weakly introgressing through hybrid zones. This research underscores how incomplete reproductive isolation can be better understood by considering differential allelic introgression and the effects of historical and contemporary landscape features on the formation of lineages as well as overall genomic estimates of migration rates through time. This article is protected by copyright. All rights reserved.

中文翻译：

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在北美鼠蛇（Pantherophis obsoletus complex）物种形成灰色地带的背景下解决杂交的空间复杂性

在允许基因流动的框架中推断物种之间的分化历史对于表征物种形成的“灰色地带”至关重要，这是谱系已经分化但尚未实现严格生殖隔离的时期。然而，对基因流的发散时间和速率的估计通常会忽略空间信息，例如在考虑与谱系之间环境变化相关的杂交区的位置和宽度时。为了将谱系结构、迁移、历史人口统计学和分化时间的系统地理学估计与混合区动态联系起来，我们使用了来自北美鼠蛇复合体 (Pantherophis obsoletus) 的种群基因组数据。我们通过将迁移和分化时间与混合区的位置和宽度联系起来，研究了多样化的空间背景。应用人工神经网络方法来了解景观特征和过去的气候如何影响这些谱系中的种群遗传结构。我们发现谱系之间的迁移率与杂交区的整体宽度有关。发散的时间与跨物种对的迁移率或杂交区宽度无关，但可能与通过杂交区弱渗入的等位基因数量有关。这项研究强调了如何通过考虑差异等位基因渗入以及历史和当代景观特征对谱系形成的影响以及随时间推移对迁移率的整体基因组估计来更好地理解不完全生殖隔离。本文受版权保护。版权所有。