Phylogenetics, conservation and taxonomy of threatened Australian rainforest plant species of the Fontainea genus
Creators: name: Brunton, Aaron
Publisher: name: University of the Sunshine Coast, Queensland
Year: 2023
Subjects: subject: conservation genetics
subject: phylogeography
subject: single-nucleotide polymorphism
subject: Gondwana rainforest
subject: plant ecology
subject: biodiversity
subject: Genetics
subject: FOS: Biological sciences
subject: Ecological applications

description: Fontainea Heckel (Euphorbiaceae) comprises a group of nine, dioecious rainforest shrub species distributed in small, isolated populations in eastern Australia, Papua New Guinea and some Western Pacific Islands including New Caledonia and Vanuatu. Eight of the species are listed as threatened including two Critically Endangered species. In addition, a Fontainea species endemic to the Atherton Tablelands region of northern Australia is cultivated commercially as the source of a cancer therapeutic. Despite the ecological and medicinal importance of this genus, the phylogenetic, taxonomic, and biogeographic traits of Fontainea are not well understood. This thesis presents a comprehensive analysis of Fontainea species, centring on the phylogeny, ecology, and morphometrics and bringing attention to the conservation implications associated with this scientifically important genus.
description: This research began (Chapter 2) by reconstructing the phylogenetic and evolutionary relationships of the Fontainea genus using reduced-representation SNPs (single nucleotide polymorphisms) and chloroplast sequences to infer the biogeographic history of Fontainea. Phylogenetic reconstructions showed that Fontainea contained three major lineages that mostly supported the current taxonomical nomenclature for the genus. Additionally, phylogenetic analyses suggested Fontainea originated in Australia in the late Oligocene-Miocene, and subsequently dispersed throughout the continent, indicating a trans-oceanic dispersal scenario to some Pacific Islands (New Caledonia and Vanuatu). Within some lineages, this research identified several subclades that reflect the geographic and evolutionary relationships among the species. Importantly, this chapter showed that the Vulnerable F. australis and Critically Endangered F. oraria shared plastid genotypes and that additional genetic, ecological and morphological data was needed to better understand the relationship between these two species., Resolving the complex, evolutionary relationship between F. australis and F. oraria will have important consequences for their conservation and was a key focus in the following chapters.
description: Chapter 3 explored the spatiotemporal dynamics of F. australis and F. oraria, with a focus on predicting the potential range of suitable habitat for the two species, and highlighted areas that could contain novel Fontainea populations. Using distribution models that combined climate and topographic variables, this study predicted the proportion of suitable habitat under current conditions that exists within protected areas. To understand how these two species could respond under future environmental conditions, models were projected into two emission scenarios (low and high) up to the end of this century (2081-2100). Model projections indicated suitable habitat could expand under future climate settings, however projected areas were in regions where large-scale clearing has occurred and the potential for dispersal into these sites is low. In addition, the current location of F. oraria was projected to lose suitable habitat under a high-emission scenario. This emphasised serious conservation concern for F. oraria and resulted in a recommendation to translocate representative material into areas of suitable habitat that could be crucial for long-term survival of this species.
description: In Chapter 4, I examined the evolutionary forces that influence spatial patterns of genetic variation between F. australis and F. oraria. These two threatened Fontainea species are restricted to a narrow, but complex geographic and ecological region, and thus subject to spatially explicit conditions that limit genetic exchange and drive genetic differentiation between population localities. With a large set (10, 000) of reduced-representation SNP markers, and a range-wide sampling approach, reciprocal admixture was detected among F. oraria and geographic neighbouring populations of F. australis to provide renewed evidence of the close genetic affinities among these taxa. Genotype-by-environmental analysis showed there was a pattern of divergent selection at the local-habitat scale, driven by dispersal limitation and environmental heterogeneity. This result suggested that while the two species are genetically close, there are signals of adaptive divergence among some populations that harbour putatively, stress-tolerant SNPs that could be crucial for the persistence of both taxa under future climate projections.
description: The final research chapter (chapter 5) of the thesis used a unifying species concept to investigate the species limits of F. australis, F. oraria and the recently discovered F. sp. Coffs Harbour. Using a combination of molecular (SNPs) and morphological data from leaf characters, we were able to indicate the species boundaries of these three, cryptic Fontainea species. This research provided clear evidence of genetic and morphometric limits of F. sp. Coffs Harbour as a putative, independent lineage and indicated there are genetically and geographically distinct F. australis clusters with some merging of taxonomically distinct groups. Also of major note, this research supported the recognition of a new subspecies rank within F. australis, with the proposed name of F. australis subsp. Mooball. Based on results from this study, a taxonomic revision of this central, eastern Australia Fontainea complex was suggested that covers the geographic, genetic and morphometric range of F. australis, as well as the inclusion of reproductive material to clearly recover the species relationships for these three, threatened taxa.
description: In conclusion, using a multidisciplinary approach, this research has made considerable progress to understanding the genetic characteristics and evolutionary potential of Fontainea that is critical to improving the conservation focus for a number of closely related species. Utilising genetics-based methods alongside ecological and phenotypic modelling, the findings from this research form the basis for a series of future recommendations that can be applied to conservation planning to reduce the risk of extirpation. Some key priorities for the conservation include increasing formal protection for areas of suitable habitat and stresses the value of preserving populations that have the capacity to adapt to environmental change. Finally, this comprehensive study showed the ongoing challenge in defining species boundaries and revealed that a renewed taxonomic revision could benefit a number of closely related taxa (i.e., F. australis and F. oraria) among within this unique genus.