Genomic Discoveries Reveal How Wild Plants Survive Extreme Altitude Shifts

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.