Geographically proximate rare species exhibit strong population divergence while maintaining intraspecific genetic diversity in Homoranthus (Myrtaceae)

Background and Aims Species with small geographic ranges provide insights into adaptation, speciation, and genetic drift, while also presenting clear conservation challenges. Homoranthus A.Cunn. ex Schauer (Myrtaceae), an Australian genus with many narrow endemics, offers a model for understanding how ecological and spatial factors drive diversification. We examined a regional hotspot with a high number of Homoranthus narrow endemics to assess patterns of genetic diversity and inform both evolutionary understanding and conservation planning. Methods We generated genome-wide SNP data using DArTseq for 282 individuals across 13 Homoranthus species (40% of the genus), including ten narrow endemics, to assess population genetic structure and diversity. Key Results All species showed strong genetic isolation, even over a few kilometres, with populations diverging within hundreds of meters. Homoranthus lunatus includes two highly divergent, non-sister lineages, suggesting taxonomic revision. Inbreeding was common but unrelated to range size, and heterozygosity remained moderate, indicating intrinsic buffering of genetic diversity. Genome sizes were notably small relative to other angiosperms. Conclusions Ecological isolation, life-history traits, and limited dispersal drive both speciation and extinction risk in Homoranthus. Diversification and endemism are linked to habitat fragmentation, highlighting the need for conservation strategies that address ecological connectivity as well as species protection.