Genomic insights unlocked: adaptive divergence of Capsella bursa-pastoris across altitudinal gradients

Date: May 7, 2026

Guangzhou, China: A research team from the South China Botanical Garden, Chinese Academy of Sciences, has revealed the genomic basis of altitudinal adaptation in the widespread annual herb Capsella bursa-pastoris (L.) Medik. (shepherd’s purse), a close relative of model plant Arabidopsis thaliana. The findings, published in Biological Diversity, improve understanding of how ecological selection drives population differentiation and local adaptation in widely distributed polyploid plants under changing climates.

The researchers sampled 40 individuals from 14 Capsella bursa-pastoris populations across eastern low-altitude and western high-altitude regions in China and performed whole-genome resequencing. Population genomic analyses including population structure, PCA, and phylogenetic reconstruction consistently identified two distinct genetic lineages corresponding to low- and high-altitude habitats.

Genome-wide scans for selective sweeps using F_ST and XP-CLR detected 54 candidate genes under positive selection related to energy metabolism, photosynthesis, signal transduction, growth regulation, and membrane transport. Notably, subgenome CbpB was enriched with adaptive loci, suggesting asymmetric subgenomic evolution contributes to altitudinal divergence.

Genotype–environment association and partial redundancy analysis (pRDA) showed that climatic factors independently explained 12.7% of genetic variation—far exceeding the effects of geography and population structure—highlighting temperature seasonality and precipitation as key drivers of adaptive divergence. Environment-associated loci were mainly linked to light, temperature, and water-related responses.

The study demonstrates that ecological selection is a major driver of population genomic divergence in Capsella bursa-pastoris. The results provide a robust framework for understanding local adaptation in widely distributed weeds and polyploid plants, with implications for predicting species resilience under climate change.

Corresponding author Hui-Run Huang stated that the research highlights the importance of integrating population genomics and landscape ecology to uncover adaptive mechanisms in heterogeneous environments.

Original Source

Liu, Lu, Jia Li, Xin Liu, Xue-Jun Ge, and Hui-Run Huang. 2026. “Adaptive Genomic Divergence Across Altitudes in Capsella bursa-pastoris,” Biological Diversity: 1–11. 

https://onlinelibrary.wiley.com/doi/10.1002/bod2.70025

Keywords

Capsella bursa-pastoris, ecological adaptation, genetic divergence, population genomics, selection

About the Author

Lu Liu (First Author), Postdoctoral Fellow at the South China Botanical Garden, Chinese Academy of Sciences. Her research focuses on conservation genetics. She has published a series of high-quality papers as first author in renowned journals including New Phytologist and Ecology and Evolution.

Hui-Run Huang (Corresponding Author), Associate Professor and Master’s Supervisor at the South China Botanical Garden, Chinese Academy of Sciences. Her research interests include genome assembly, adaptive evolution, and plant resource utilization. She has published extensively as first author or corresponding author in prestigious journals such as New Phytologist, Horticulture Research, and Journal of Systematics and Evolution. 

About the Journal

Biological Diversity (ISSN: 2994-4139) is a new open-access, high-impact, English-language journal, devoted to advancing biodiversity conservation, enhancing ecosystem services, and promoting the sustainable use of resources under global change. It features innovative research addressing the global biodiversity crisis.