Genomic Comparisons in an Austral–Pacific Sandalwood (Santalaceae) Complex Highlights Novel Clades, Divergent Groups, and the Conservation Dynamics of Critically Endangered and Non‐Threatened Lineages

Understanding the genetic processes underlying divergence and connectivity among species is crucial for identifying evolutionary histories and informing conservation strategies. The <i>Santalum</i> 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 <i>Santalum lanceolatum</i>, <i>S. leptocladum</i>, and <i>S. macgregorii</i>. Our findings revealed significant geographic partitioning and genetic divergence mostly aligned with current taxonomic classifications. However, notably, we showed <i>S. macgregorii</i> 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 <i>S. lanceolatum</i> 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 <i>S. lanceolatum</i>; the <i>S. macgregorii</i> 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 <i>S. lanceolatum</i> to enhance reproductive success in threatened sandalwood populations, offering crucial guidance for conservation and management efforts in Australasia.