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

TL;DR

This study uses genetic data to uncover hidden diversity and evolutionary relationships in sandalwood species across Australia and Papua New Guinea, guiding conservation efforts.

Contribution

The study reveals novel genetic groupings and hybridization patterns in sandalwood species, suggesting new conservation strategies.

Findings

S. macgregorii in PNG is split into two distinct genetic groups.

One PNG S. macgregorii group is closely related to Australian S. lanceolatum.

Genetic divergence aligns with geography and suggests historical land bridge influences.

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.

This study explored the genetic divergence and connectivity within the Santalum genus, focusing on endangered and non‐threatened species across Australia and Papua New Guinea. Genome‐wide SNP analysis revealed significant geographic partitioning, including two distinct S. macgregorii genetic groups in PNG, with one closely related to
S. lanceolatum
from Australia's Northern Peninsula. These findings highlight the need for tailored conservation strategies and advocate for genetic rescue programs to support threatened sandalwood populations.

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