Genetic diversity in a clade of Cape endemic grasses is related to both environment and species traits

Population genetic diversity (PGD) underpins the adaptive capacity of species, shaping resilience to environmental change and long-term persistence. Yet the drivers of PGD variation remain difficult to disentangle because they act across multiple scales and reflect both ecological context and evolutionary history. Here, we investigate PGD in the <i>Ehrharta setacea</i> Clade (Poaceae), an ecologically and morphologically diverse lineage endemic to the Cape Floristic Region of South Africa. Using genotyping-by-sequencing data, we test the relative influence of species traits, climate gradients, and metapopulation connectivity on spatial patterns of PGD. Our analyses reveal a strong species effect, indicating that evolutionary history and niche-defining traits, particularly habitat preference and reproductive investment, are fundamental determinants of PGD. Wet-habitat species consistently maintain higher PGD than dry-habitat species, while spikelet length emerges as an important predictor of genetic diversity across both habitat types. Regional climate variation also plays a role, with PGD positively associated with mean annual precipitation and negatively associated with interannual variability. Population isolation is linked to reduced PGD, with outlier populations exhibiting especially low diversity. Together, these findings highlight how species biology, regional climate, and metapopulation processes interact to structure PGD and emphasise the southwestern CFR as a critical hotspot for its conservation.