Hybrid zone analysis using coalescent-based estimates of introgression and migration

Hybrid zones can serve as natural experiments allowing us to investigate the evolutionary consequences of introgression between distinct populations with divergent genomic backgrounds. Modeling hybrid zones using a coalescent framework can provide critical insights into the historical demography of populations, including population divergence times, population sizes, introgression proportions, migration rates, and the timing of hybrid zone formation. We used coalescent analyses to test whether a hybrid zone between Plateau Fence Lizard (Sceloporus tristichus) populations in Arizona formed recently because of human-induced landscape alterations or originated during Pleistocene climatic shifts. Introgression analysis places the divergence time between the parental populations at approximately 140 kya and their secondary contact and hybridization at approximately 10 kya at the end of the Pleistocene. Introgression proportions for hybrid populations are correlated with their geographic distance from the parental populations, a pattern that is repeated with admixture proportions and hybrid index values. The multispecies coalescent with migration model supports asymmetric migration rates with a bias for gene flow moving towards the northern end of the hybrid zone. The direction of this asymmetry is consistent with spatial cline analyses that suggest a slow but steady northward shift of the center of the hybrid zone. When analyzing hybrid populations sampled along a linear transect, coalescent methods can provide novel insights into the evolutionary history of hybrid zone formation that complement existing spatial and genomic methods.