• Phylogenomics reveals reticulate evolution and ancient homoploid hybridization. • Cytonuclear discordance reflects contrasting and complex population evolutionary histories. • Strophiole traits suggest a climate-linked adaptive syndrome in xeric cliff habitats. • Floral size and colour correlates with genomic heterozygosity across lineages. The interplay between reticulate evolution and adaptive trait diversification during speciation remains a central challenge in evolutionary biology. We hypothesized that diversification in the Iberian chasmophytic genus Petrocoptis has been shaped by recurrent reticulation coupled with coordinated evolution of reproductive traits, including a strophiole-mediated seed adaptive syndrome linked to water uptake regulation in xeric cliff habitats. We analysed 63 representative populations using target enrichment of 345 nuclear loci (Angiosperms353) and 192 plastid regions. Phylogenomic relationships were inferred under concatenation and multispecies coalescent frameworks, accounting for genealogical and cytonuclear discordances, ILS and reticulate evolution. Seed and floral traits were analysed within an integrative phylogenetic comparative framework that jointly assessed evolutionary patterns, genomic variation, and climatic correlates. Cytonuclear discordance analyses and coalescent simulations rejected ILS as the unique driver of conflict. Network analyses supported at least two reticulation events, indicating ancestral hybridization. The evolution of reproductive traits displayed a framework of repeated and coordinated adaptive shifts. Floral evolution revealed multiple increases in calyx length associated with pink corollas and higher genomic heterozygosity. Seed morphology followed an ordered transition in strophiolar hair types and distinct adaptive optima: cylindrical hairs were associated with small seeds and proportionally larger strophioles, whereas claviform hairs corresponded to larger seeds with reduced relative strophioles. Strophiole traits correlated with temperature and precipitation, defining a climate-associated seed adaptive syndrome which may optimize water uptake regulation. Together, these results highlight the joint effects of reticulate genomic evolution and adaptive restructuring of reproductive traits in Petrocoptis diversification. Integrating phylogenetic networks with trait evolution provides a cohesive framework for understanding how gene flow and ecological specialization jointly drive lineage diversification in fragmented cliff systems.
Calvo-Yuste et al. (Fri,) studied this question.