Phylogenomics reveal incomplete lineage sorting as the primary source of phylogenetic discordance in East African Zanthoxylum L. and Vepris Comm. ex A. Juss. (Rutaceae)

Evolutionary relationships in Zanthoxylum L. and Vepris Comm. ex A. Juss. remain poorly resolved due to limited genomic resources and conflicting signals from individual markers, hindering efforts to understand their diversification and adaptation across tropical environments. In this study, we generated Angiosperms353 target‐capture data for 187 individuals representing 51 Zanthoxylum and Vepris species from East Africa. Using concatenated and multispecies coalescent analyses combined with concordance‐factor approaches, we recovered Zanthoxylum and Vepris as monophyletic clades. However, species‐level relationships within each genus exhibited substantial phylogenetic discordance. Concordance factor analysis revealed moderate genome‐wide site concordance (mean sCF = 46.64%) but markedly lower gene concordance (mean gCF = 28.76%), indicating widespread gene‐tree heterogeneity. Both sCF and gCF exhibited strong positive correlations with branch lengths; r = 0.698 and r = 0.687, respectively. Discordance patterns showed an almost perfect balance between alternative topologies (sDF1 = 24.9%, sDF2 = 24.8%), minimal mean asymmetry (3.5%–5.1%), and a high proportion of polyphyly (gDFP = 59.7%), all consistent with incomplete lineage sorting (ILS) as the primary source of phylogenomic conflict. A small fraction of branches (1.9%–4.7%) displayed significant asymmetry, which signals only limited evidence for processes beyond ILS and should be interpreted with caution pending explicit tests of introgression. Generally, our findings offer a comprehensive phylogenomic framework for East African Zanthoxylum and Vepris and demonstrate that ILS has played a major role in shaping genomic variation and phylogenetic discordance within these genera. Further analyses are required to investigate the extent to which hybridization or other reticulate processes have contributed to their evolutionary history.