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Phylogenomic conflict in Lycium (Solanaceae): Revealing the roles of hybridization, incomplete lineage sorting, and biogeographic history using nuclear and mitochondrial genomes
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DOI：10.1016/j.pld.2026.02.005.png)
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Abstract
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• Lycium is a globally distributed genus valued for its medicinal and edible fruits. • Phylogenetic relationships and evolutionary patterns within Lycium remain unresolved. • Our robust nuclear phylogeny of Lycium reveals a North American origin, and traces a dispersal route to South America, Africa, and finally Eurasia • Pervasive phylogenetic discordance is dissected: incomplete lineage sorting (ILS) predominantly explains intra-nuclear conflict, while historical hybridization drives cytonuclear discordance. • We assembled the complete mitochondrial genome for Lycium (L. ruthenicum) and integrated it with nuclear and plastid data, enabling a novel tripartite genomic assessment of evolutionary conflict. • Whole-genome resequencing data for 39 species provides a foundational genomic resource for future molecular breeding and germplasm studies in Lycium.
Keywords:
Phylogenomics
Reticulate evolution
Biogeography
Incomplete lineage sorting
Hybridization
Mitogenome
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