Genomic data inform conservation of rare tree species: clonality, diversity and hybridity in Eucalyptus series in a global biodiversity hotspot

Rare species are key targets of biodiversity conservation worldwide, but assessments of genetic diversity and conservation priority can be impeded by limited sample size. Reduced-representation genome sequencing improves resolution of analysis in this context, enabling applications in conservation genomics. The tree genus Eucalyptus contains many rare taxa, but clarity on conservation actions can be confounded in this group due to taxonomic complexity, unrecognised clonality and hybridisation. Using SNPs, we address key questions surrounding taxonomy, clonality and genetic diversity in two rare species, Eucalyptus virginea and a putative hybrid E. × phylacis, to inform conservation. We confirm that a highly disjunct population belongs to E. virginea despite sharing a multi-stemmed short-statured (‘mallee’) growth form and geographic proximity with a closely-related species, indicating that growth form was unrelated to phylogenetic distance. Clonality was confirmed in the disjunct population but the number of discrete clumps vs unique genets was not equal, reflecting the importance of genetic assessments of population size. The small, clonal, disjunct population had the lowest allelic richness and highest differentiation, as expected. However, heterozygosity excess suggested that clonality may prevent the loss of heterozygosity in mallee eucalypts by facilitating long-term persistence, contrary to expectations that small, isolated populations face increased conservation genetic threat. Analyses also confirmed that the Critically Endangered E. × phylacis is an F1 hybrid of E. decipiens and E. virginea, therefore its conservation listing should be revised. Our data highlight the usefulness of genomic analysis in applied conservation of non-model taxa.