Structured phylogenomic conflict and reticulate evolution shape diversification in Hedysarum

Phylogenomic studies of rapidly diversifying plant lineages often recover conflicting genomic signals, but determining whether observed discordance is compatible with expectations under the multispecies coalescent or instead suggests additional lineage-specific processes remains difficult. Hedysarum (Fabaceae), a species-rich genus distributed mainly across Eurasia, provides a suitable system for testing how incomplete lineage sorting, hybridization and historical biogeography interact during diversification. We analysed 177 plastid accessions representing 151 taxa, including 134 Hedysarum species, and 156 nuclear accessions representing 140 taxa, including 125 Hedysarum species. We integrated 115 single-copy nuclear loci with plastid coding sequences to reconstruct relationships, quantify cytonuclear discordance, evaluate incomplete lineage sorting, test reticulation and infer divergence times and ancestral ranges. Plastid analyses recovered a strongly resolved sectional framework, whereas nuclear analyses revealed extensive gene-tree heterogeneity and weaker support for deeper relationships. Cytonuclear discordance was concentrated in particular lineages, especially Hedysarum subsection Crinifera. Coalescent simulations showed that empirical discordance exceeded expectations under incomplete lineage sorting alone, although quartet-based tests indicated that multispecies-coalescent-compatible patterns were widespread. Hybridization tests detected unevenly distributed introgression signals, and phylogenetic network analyses supported limited, lineage-specific reticulation. Divergence-time and ancestral-range reconstructions placed the origin of Hedysarum in the Miocene and supported a composite ancestral range spanning Western Asia, Middle Asia and the Tibet-Himalaya region. Subsection Crinifera was consistently associated with Middle Asian diversification, whereas subsection Multicaulia retained a western Eurasian ancestral signal. Together, these results suggest that Hedysarum diversification was accompanied by extensive phylogenomic discordance, widespread incomplete lineage sorting and localized reticulation within a complex Eurasian biogeographic framework associated with Miocene environmental change.