Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletus complex)

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 gene flow often ignore spatial information, for example the formation and shape of hybrid zones. Using population genomic data from the eastern ratsnake complex (Pantherophis obsoletus), we infer phylogeographic groups, gene flow, changes in demography, the timing of divergence, and hybrid zone widths. We examine the spatial context of diversification by linking migration and timing of divergence to the location and widths of hybrid zones. Artificial neural network approaches are applied to understand how landscape features and past climate have influenced population genetic structure among these lineages prior to hybridization. Rates of migration between lineages are associated with the width and shape of hybrid zones. Timing of divergence is not related to migration rate across species pairs and is therefore a poor proxy for inferring position in the gray zone. However, timing of divergence is related to the number of loci weakly introgressing through hybrid zones.