Geographic isolation and holocene climatic oscillations drive north–south genetic divergence in the recretohalophyte Limonium sinense

Abstract Background Limonium sinense is a recretohalophyte with both ecological and economic value inhabiting China’s coastal saline-alkali zones, and it can play an important role in saline-alkali soil amelioration and coastal vegetation restoration. Impacted by coastal development and habitat fragmentation, the size of its wild populations has declined sharply in recent years; thus, elucidating its population genetic and evolutionary characteristics is urgently needed to inform conservation strategy development. Results This study employed whole-genome resequencing technology to analyze 170 individuals from 17 wild populations covering the complete natural distribution range of this species, yielding a total of 2, 558.79 Gb of high-quality clean sequencing reads and detecting 126, 690, 413 SNP loci. Analysis revealed north–south divergence in genetic diversity: southern populations exhibited higher genetic diversity (mean Ho = 0.330, He = 0.296) with heterozygote excess, whereas northern populations displayed lower genetic diversity (mean Ho = 0.221, He = 0.258) and potential inbreeding depression risk. Population genetic structure analysis confirmed that the 17 populations could be delineated into two major genetic lineages, northern and southern, with a clear demarcation between them; southern populations exhibited a relatively complex ancestral composition, whereas northern populations remained comparatively homogeneous. Inter-population genetic differentiation analysis combined with the isolation-by-distance model revealed that contemporary gene flow among northern populations is restricted, whereas southern populations experience relatively weak differentiation and more frequent gene exchange. Treemix historical gene flow model detected no large-scale cross-regional gene flow events; only intra-lineage gene flow events were identified: a high-intensity historical gene flow event occurred within the northern lineage, reflecting past connectivity, while only weak genetic introgression was detected within the southern lineage. Demographic history reconstruction, together with genome-wide neutrality tests (Tajima’s D and Fu’s Fs) and folded site frequency spectrum (SFS), consistently supported that all populations experienced a phased trajectory of prolonged stability, Holocene climatic oscillation-driven bottleneck contraction, and synchronous rapid recovery, with southern populations exhibiting a greater recovery magnitude than northern populations. Genome-wide runs of homozygosity (ROH) further confirmed divergent inbreeding patterns between northern and southern lineages. Conclusion Our results indicate that populations of this species can be classified into two major genetic lineages: northern and southern. Geographic isolation is the core factor driving genetic divergence; the current patterns of genetic diversity, genetic structure, and lineage distribution are shaped primarily by the combined effects of geographic isolation, climatic oscillations, and anthropogenic disturbance together with habitat fragmentation. Based on these findings, this study proposes region-specific targeted conservation strategies, providing a theoretical basis for the germplasm conservation and sustainable utilization of this species, as well as a representative case study for research on adaptive evolution in coastal halophytes.