Beyond species trees: pervasive gene flow limits phylogenomic resolution in the diversification of Juniperus from the Qinghai-Tibet Plateau.

Yujiao Zhang; Jialiang Li; Dayu Wu; Heng Yang; Zhitong Han; Kangshan Mao

doi:10.1016/j.ympev.2026.108717

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Beyond species trees: pervasive gene flow limits phylogenomic resolution in the diversification of Juniperus from the Qinghai-Tibet Plateau.

Yujiao Zhang·Jialiang Li·Dayu Wu·Heng Yang·Zhitong Han·Kangshan Mao

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Abstract

Understanding how lineages diversify despite persistent ancestral polymorphism and recurrent gene flow remains a central challenge in evolutionary biology. Juniperus distributed across the Qinghai-Tibet Plateau provide an ideal system for addressing this question because repeated geological uplift and climatic oscillations have likely promoted cycles of lineage divergence, range shifts, and secondary contact. Here, we combined approximately 1.08 million genome-wide SNPs from 164 individuals representing thirteen Juniperus lineages with phylogenomic datasets comprising 3,381 nuclear single-copy genes and nearly complete plastomes. We detected extensive phylogenomic discordance and cytonuclear incongruence across genomic datasets. Topology weighting, coalescent simulations, quartet-based tests, and analyses of gene flow and reticulation collectively support the interpretation that these patterns were shaped by the combined effects of prolonged incomplete lineage sorting and gene flow during lineage diversification. Ecological niche analyses further provide a spatial and climatic context in which environmentally similar lineages may have had greater opportunities for secondary contact during historical range shifts. Collectively, our results reveal that the evolutionary history of Qinghai-Tibet Plateau Juniperus is characterized by reticulate diversification rather than strictly bifurcating evolution, and demonstrate how genome-wide discordance can provide biological insights into the evolutionary processes underlying lineage diversification.

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Gene Flow Phylogeny Juniperus Tibet Polymorphism, Single Nucleotide Evolution, Molecular Sequence Analysis, DNA Models, Genetic Cell Nucleus Gene flow Incomplete lineage sorting Introgression Phylogenetic discordance Reticulate evolution Journal Article

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Yujiao Zhang, Jialiang Li, Dayu Wu, Heng Yang, Zhitong Han, Kangshan Mao. 2026-08-14. Beyond species trees: pervasive gene flow limits phylogenomic resolution in the diversification of Juniperus from the Qinghai-Tibet Plateau.. https://doi.org/10.1016/j.ympev.2026.108717

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Journal Article resource Cell Nucleus subject Evolution, Molecular subject Gene Flow subject Introgression subject Journal Article subject Models, Genetic subject

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