New prospects in the detection and comparative analysis of hybridization in the tree of life

Assessing the relative importance of the various pathways to diversification is a central goal of biodiversity researchers. For plant biologists, and increasingly across the spectrum of biological sciences, among these pathways of interest is hybridization. New methodological developments are moving the field away from questions of whether natural hybridization occurs or hybrids can persist and toward more direct assessments of the long-term impact of hybridization on diversification and genome organization. Advances in theory and new data, especially phylogenomic data, have changed the face of this field, revealing extensive occurrences of hybridization at both shallow and deep levels, but lacking is a synthesis of these advancements. Here we provide an overview of methods that have been proposed for detecting hybridization with molecular data and advocate a time-extended, comparative view of reticulate evolution. In particular, we pose three overarching questions, newly placed within reach, that are critical for advancing our understanding of hybridization pattern and process: (1) How often is introgression biased toward certain genomes and loci, and is this bias selectively neutral? (2) What are the relative rates of formation of hybrid species and introgressants, and how does this compare to their subsequent fates? (3) Has the frequency of hybridization increased under historical periods of greater dynamism in climate and geographic range, such as the Pleistocene?