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Agronomy
Volume 15
Issue 9
10.3390/agronomy15092139
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Transcriptome-Based Phylogenomics and Adaptive Divergence Across Environmental Gradients in Epimedium brevicornu

by
Songsong Lu
,
Jianwei Qi
,
Jun Zhao
,
Qianwen Song
,
Luna Xing
,
Weibo Du
,
Xuhu Wang
,
Xiaowei Zhang
and
Xiaolei Zhou
*
College of Forestry, Gansu Agricultural University, Lanzhou 730070, China
*
Author to whom correspondence should be addressed.
Agronomy 2025, 15(9), 2139; https://doi.org/10.3390/agronomy15092139
Submission received: 28 July 2025 / Revised: 29 August 2025 / Accepted: 4 September 2025 / Published: 5 September 2025
(This article belongs to the Special Issue Genetic Basis of Crop Selection and Evolution)
Versions Notes

Abstract

Ecology and adaptive differentiation of Epimedium are central to understanding both its taxonomic complexity and medicinal value. In this study, we integrate transcriptomic and plastid data from four natural populations of E. brevicornu (HZ, QLH, TS, WD) to reconstruct their phylogenetic relationships, estimate divergence times, and identify candidate genes associated with local adaptation. Nuclear gene-based phylogenies provide higher resolution and greater topological consistency than plastid data, underscoring the utility of nuclear data in lineages affected by hybridization and incomplete lineage sorting. Molecular dating indicated that major intraspecific divergence occurred during the mid-Quaternary (0.61–0.45 Ma), coinciding with climatic oscillations and montane isolation. Population structure showed strong correlations with temperature and precipitation gradients, suggesting environmentally driven selection. Signatures of positive selection and accelerated evolutionary rates revealed population-specific enrichment of genes involved in stress response, protein modification, signaling, and carbohydrate metabolism—key pathways linked to high-elevation adaptation. Protein–protein interaction networks further indicated a two-tier adaptation mechanism: ancestral network rewiring combined with population co-evolution of interacting genes. Together, these findings advance our understanding of alpine plant adaptation and provide candidate genes for further functional and breeding studies in Epimedium.
Keywords: Epimedium; phylogenetic reconstruction; molecular evolutionary analysis; environmental adaptation Epimedium; phylogenetic reconstruction; molecular evolutionary analysis; environmental adaptation

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MDPI and ACS Style

Lu, S.; Qi, J.; Zhao, J.; Song, Q.; Xing, L.; Du, W.; Wang, X.; Zhang, X.; Zhou, X. Transcriptome-Based Phylogenomics and Adaptive Divergence Across Environmental Gradients in Epimedium brevicornu. Agronomy 2025, 15, 2139. https://doi.org/10.3390/agronomy15092139

AMA Style

Lu S, Qi J, Zhao J, Song Q, Xing L, Du W, Wang X, Zhang X, Zhou X. Transcriptome-Based Phylogenomics and Adaptive Divergence Across Environmental Gradients in Epimedium brevicornu. Agronomy. 2025; 15(9):2139. https://doi.org/10.3390/agronomy15092139

Chicago/Turabian Style

Lu, Songsong, Jianwei Qi, Jun Zhao, Qianwen Song, Luna Xing, Weibo Du, Xuhu Wang, Xiaowei Zhang, and Xiaolei Zhou. 2025. "Transcriptome-Based Phylogenomics and Adaptive Divergence Across Environmental Gradients in Epimedium brevicornu" Agronomy 15, no. 9: 2139. https://doi.org/10.3390/agronomy15092139

APA Style

Lu, S., Qi, J., Zhao, J., Song, Q., Xing, L., Du, W., Wang, X., Zhang, X., & Zhou, X. (2025). Transcriptome-Based Phylogenomics and Adaptive Divergence Across Environmental Gradients in Epimedium brevicornu. Agronomy, 15(9), 2139. https://doi.org/10.3390/agronomy15092139

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