Conservation and restoration of genetic diversity in Tuart (Eucalyptus gomphocephala DC.): using novel genomic tools to understand local adaption

[Truncated abstract] The science and practice of ecological restoration is a growing phenomenon worldwide in response to unprecedented rates of habitat destruction. New genomic technologies and analysis techniques (e.g. population and landscape genomics) can provide novel avenues for the investigation of functional and adaptive genetic diversity in natural populations of conservation significance, allowing a transition to a new paradigm of restoration genomics. In this thesis, I apply genomic tools to better understand patterns of adaptation at the molecular level in natural populations of the iconic but declining Tuart tree (Eucalyptus gomphocephala DC.) in southwest Western Australia, incorporating this information with traditional measures of neutral genetic diversity and assessments of inbreeding, and applied in the context of seed sourcing for ecological restoration. To develop gene-linked molecular markers, I identified microsatellite repeat motifs within Eucalyptus expressed sequence tag (EST) databases, and designed 133 new ESTderived microsatellite primers (EST-SSRs) for Eucalyptus. Sequences with homology to annotated coding genes of putative ecological significance were targeted, such as Lea14 involved in desiccation tolerance and CONSTANS involved in flowering time. A subset of these markers were optimised for variation within E. gomphocephala, and up to 94% amplified DNA in three other eucalypt species from diverse subgenera (E. marginata, E. camaldulensis, E. victrix), illustrating the utility of this novel, gene-linked primer resource for studies of eucalypt conservation and restoration. To identify the presence and extent of inbreeding in natural populations of Tuart, I used microsatellite markers to quantify mating system parameters among six key seed source populations that are currently or potentially used for ecological restoration, some of which are highly disturbed.