Divergence, hybridization, and diversification in an eastern North American willow syngameon

Summary Present‐day patterns of genetic diversity and phylogeography are influenced by various factors, with hybridization and historical climate changes often pivotal. The Salix genus presents an ideal case study for these dynamics because of the large numbers of hybridizing species. This study investigates the intricate hybridization dynamics within a quadra‐species hybrid syngameon that includes Salix nigra and three closely related species: S. amygdaloides , S. gooddingii , and S. caroliniana . Employing sequence capture techniques, we analyzed 6646 975 single nucleotide polymorphisms (SNPs) across 265 individuals from 18 populations to investigate population structure, genetic diversity, phylogenetic relationships, demography, and hybridization patterns. Significant hybridization was observed between S. nigra and its close relatives. Hybridization can account for up to 31% of the genome in hybrid‐zone populations of S. nigra ; nucleotide diversity is up to 56% higher than in allopatric populations, thereby strongly shaping population structure and genetic diversity. Demographic analyses suggest a model of ongoing gene flow throughout the speciation process. Species distribution modeling indicated that currently allopatric species likely had overlapping distributions in the past, which allowed past hybridization. This study illuminates how historical glaciation in North America influences the timing and location of hybridization and, in turn, shapes contemporary geographic patterns of genetic diversity.