INTRODUCTION: Genetic diversity is considered as a crucial aspect in assessment and conservation of rare and endangered species. Brachystachyum densiflorum is a species endemic to eastern China. In recent years, with rapid economic development, accelerated urbanization, and escalating pollutant emissions, the habitat of B. densiflorum has been continuously degraded, habitat fragmentation has intensified, and its populations have shown a tendency to decline.

RATIONALE: Genetic diversity endows species with abundant genetic resources and plays a pivotal role in shaping their capacity to adapt to new environments. To elucidate the genetic diversity of B. densiflorum and evaluate the influence of climate change on its genetic variation, reduced-representation genome sequencing technology was employed to obtain single nucleotide polymorphisms (SNPs), and subsequently population genetics and landscape genetics together with species distribution modelling were analyzed.

RESULTS: B. densiflorum had a moderate level of genetic diversity. Six populations were divided into two groups, and there was moderate differentiation (F_ST=0.102) and high gene flow (Nm=2.442) between them. Genotype-environment association analysis indicated that the two groups were diverged attributable to local adaptation to the climate. Temperature differences and low-temperature regimes interacting together with precipitation gave rise to genetic variation of this species. In total, 544 adaptive loci were identified, which displayed significant correlations with temperature difference, low-temperature factors (Bio2, Bio6, Bio11, and Bio7), and precipitation factors (Bio19). B. densiflorum migrated evidently northward from the Last Glacial Maximum to the current, with its distribution area increased by 89.5%. However, during the period from 2061 to 2080, the extent of the suitable area for this species will be contracted, and there will be partial degradation and fragmentation occurring in highly suitable areas within Anhui Province.

CONCLUSION: B. densiflorum showed a moderate level of genetic diversity and a moderate degree of genetic differentiation. Local adaptation drove the formation of the current genetic pattern of B. densiflorum, and temperature differences, low-temperature, and precipitation led to genetic variation. B. densiflorum has evidently migrated northward from the Last Glacial Maximum to the current with increase of distribution area. However, niche modelling indicated that during the period from 2061 to 2080, the suitable habitat area of B. densiflorum would be contracted, with partial degradation and fragmentation occurring in highly suitable areas within Anhui Province. These results provide the basis for conservation and utilization of B. densiflorum.

Population genetic structure analysis of Brachystachyum densiflorum