LAUSR

ABSTRACT Understanding the genetic processes underlying divergence and connectivity among species is crucial for identifying evolutionary histories and informing conservation strategies. The Santalum genus exhibits distinct genetic variations across the complex geographic regions of Australia, Asia, and the Pacific Islands. This study leveraged genome‐wide SNP markers to explore the genetic relationships within critically endangered and non‐threatened species in an Austral‐Pacific sandalwood complex, including Santalum lanceolatum, S. leptocladum , and S. macgregorii. Our findings revealed significant geographic partitioning and genetic divergence mostly aligned with current taxonomic classifications. However, notably, we showed S. macgregorii populations in Papua New Guinea (PNG) were divided into two distinct genetic groups: one in the Central and Gulf provinces and another in the Western Province, which shows a closer genetic relationship with S. lanceolatum from Australia's Northern Peninsula Area (NPA). This genetic connection suggests a history of secondary contact and potential hybridisation, influenced by historical land bridges and geological events. Our study highlighted that the sandalwood trees from the Western Province may represent a divergent lineage of S. lanceolatum ; the S. macgregorii populations in the Central and Gulf provinces display vicariant divergence due to geographic isolation. These insights underscore the evolutionary complexity of sandalwoods and emphasise the need for tailored conservation strategies. Our results advocate for genetic rescue programs involving NPA S. lanceolatum to enhance reproductive success in threatened sandalwood populations, offering crucial guidance for conservation and management efforts in Australasia.