This dataset includes molecular data and associated metadata supporting the analysis of Prostanthera volucris (Lamiaceae) as a new, distinct species in the Central Tablelands. Samples of 3 taxa for this study were collected from across New South Wales, Australia.

Analysis code can be found at https://github.com/rpodonnell/ASB_PEC

Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses. Here, we re-analyse genomic data from thousands of individuals from 25 plant species as diverged as lodgepole pine and Arabidopsis (~300Myr). We test for genetic repeatability based on within-species associations between allele frequencies in genes and variation in 21 climate variables. Our results demonstrate signifcant statistical evidence for genetic repeatability across deep time that is not expected under randomness, identifying a suite of 108 gene families (orthogroups) and gene functions that repeatedly drive local adaptation to climate. This set includes many orthogroups with well-known functions in abiotic stress response. Using gene co-expression networks to quantify pleiotropy, we find that orthogroups with stronger evidence for repeatability exhibit greater network centrality and broader expression across tissues (higher pleiotropy), contrary to the 'cost of complexity' theory. These gene families may be important in helping wild and crop species cope with future climate change, representing important candidates for future study.

The Australian and New Guinean everlasting paper daisy genus Xerochrysum, widely grown around the world as Strawflower, Everlasting or Immortelle, was recently revised. The first and type species, Xerochrysum bracteatum, was described in 1803 as Xeranthemum bracteatum from a plant cultivated in the Empress Joséphine's garden at Malmaison. During our project, we learned that Xerochrysum was naturalised in St. Helena, the place of Napoleón Bonaparte's last exile, and is presumed to have been introduced by him. We conducted genetic analyses to test the derivation of the St. Helena plants. Comparisons with some colourful hybrid cultivars and naturally occurring populations in Australia found the St. Helena plants to be most similar to Xerochrysum bracteatum s. str. of the Sydney Basin. The St. Helena plants were without admixture of another species as would be expected if they were more recently escaped ornamental cultivars. Our results support the conclusion that the St. Helena Xerochrysum were introduced during Napoleón's exile, likely as a reminder of his wife's garden.

Two narrowly endemic, endangered species of Melichrus R.Br. from north-eastern New South Wales currently bearing phrase names are formally named and described. Melichrus hirsutus J.B.Williams ex H.T.Kenn. & I.Telford is validly published more than 50 years after the first herbarium specimens were collected. Melichrus gibberagee J.B.Williams ex H.T.Kenn. & J.J.Bruhl is also described as new. Notes are provided on the distribution, habitat and conservation status of both species. An updated key to the species of Melichrus in New South Wales is provided.

A taxonomic classification that captures both the evolutionary history and the morphological diversity of a group of organisms lays an essential foundation for studies on their biology, and for better management and conservation of the named species. The urgent importance of science-informed conservation management cannot be overstated amidst the global species extinction crisis, especially in Australia, which is both megadiverse and losing that diversity through species extinctions at a high rate. A comprehensive, integrative taxonomic revision of understudied groups, such as Melichrus R.Br. is a potent means of assuring species are discovered, described, named and ultimately conserved.

Melichrus R.Br. (Ericaceae: Epacridoideae) is a genus of shrubs endemic to Australia, with a widespread distribution in mainland eastern Australia (four species) and a more geographically constrained presence in south-western Western Australia (three phrase-named taxa). Prior to this study, Melichrus had received very little taxonomic study, and its few treating authors largely disagreed on species delimitation. The eastern Australian clade of Melichrus was last revised in 1958.

This thesis investigated species boundaries in the eastern Australian Melichrus (Chapter 3) and the phylogenetic relationships amongst all species of Melichrus (Chapter 4), leading to a new revised taxonomy based on in-depth morphological and molecular evidence (Chapters 2 & 5).

A thorough morphological dataset was constructed (90 individuals from 68 populations, for 26 characters) for analysis by NMDS ordination with Bayesian Inference cluster modelling (Mclust) and UPGMA hierarchical clustering to identify morphological discontinuities in the genus that could indicate species boundaries. Discontinuities in the morphological analyses were compared to those apparent in ordination and clustering (Principal Component Analysis, SplitsTree Neighbour-Net, STRUCTURE and ConStruct) and statistical analyses (H_E, H_O, F_ISand F_ST) of a DArTseq SNP dataset of 548 samples from 110 populations of Melichrus. This new evidence was interpreted to provide detailed recommendations for a revised species taxonomy of Melichrus (Chapter 3, Table 5).

The first species-level phylogenetic trees for Melichrus were inferred from two independent genomic datasets: a DArTseq SNP dataset of 557 samples and 4,100 high quality SNP markers and a target capture dataset of 34 samples of Melichrus based on the Angiosperms353 bait set. The phylogenetic trees inferred from these complementary datasets were used to test the sister relationship between the eastern and western groups of Melichrus, the monophyly of species limits proposed in Chapter 3, and to gain a deeper understanding of the evolutionary relationships among species of Melichrus. HybPhaser was used to identify the parental lineages of a putative hybrid Melichrus sp. Mareeba (Chapter 4).

I considered all available evidence to revise Melichrus, which included the description of eleven new species, clarification of the boundaries of previously described species, and the rectification of a longstanding nomenclatural misapplication (Chapters 2 & 5). In Chapter 2, two long-standing, APC accepted, phrase-named species were formally named and described as, Melichrus hirsutus J.B.Williams ex H.T.Kenn. & I.Telford and Melichrus gibberagee J.B.Williams ex H.T.Kenn. & J.J.Bruhl. Both species are gazetted as Endangered at the State and Federal levels and were therefore prioritised for description early in this study. Chapter 5 brings together the morphological and molecular evidence produced in Chapters 3 and 4 to describe nine new species. Melichrus urceolatus R.Br. was recircumscribed so that it is no longer paraphyletic and is reliably recognisable by its morphology. The long-standing misapplication of the name Melichrus adpressus A. Cunn. ex DC. was rectified. A dichotomous key to species is included in Chapter 5 with additional resources for identification, including an online key and curated photographs that will be deployed in the Flora of Australia (see Appendix 1).

A revised taxonomic classification for Melichrus is produced in this study on the basis of strong new evidence, rectifying many of the long-standing taxonomic and nomenclatural problems inherent in the status quo taxonomy. The improved understanding of species limits and their phylogenetic relationships establishes a strong foundation for future biological research, including further systematics studies. Through the development of identification aids, the results of this research are now accessible and usable for a wide range of stakeholders, in turn facilitating better conservation outcomes for species of Melichrus in eastern Australia.

Dodonaea crucifolia I.Telford & J.J.Bruhl (Sapindaceae, Dodonaeoideae), endemic to north-eastern New South Wales, Australia, and previously confused with D. hirsuta (Maiden & Betche) Maiden & Betche, is described as new. Dodonaea hirsuta is recircumscribed with the D. crucifolia components removed and with male flowers described for the first time. The distribution, habitat, and conservation status of both species are discussed and a table is provided comparing selected morphological attributes. Images of the new species and D. hirsuta are provided. The identification keys in Flora of Australia and NSW FloraOnline are modified to include the new species.

Over two centuries of taxonomic studies on the species rich genus Phyllanthus have culminated in a broad and complicated classification with many subgenera and (sub)sections. Past taxonomic work has only focused on local revisions, mostly because of the size of the genus. In this study we aim to summarize most of the taxonomic work in a list containing the infrageneric delimitations of Phyllanthus. This work will serve as a reference, placing most currently recognized species in subgenera and if possible, in sections for further study. Here we recognize 880 species of Phyllanthus, classified in 18 subgenera, 70 sections and 14 subsections. A few taxonomic changes are necessary to reconcile published phylogenetic data with the current classification. Subsections Callidisci and Odontadenii are raised to sectional rank, while section Eleutherogynium and section Physoglochidion are reduced to subsections and P. oxycarpus is transferred to the genus Glochidion. A provisional key for the subgeneric classification of Phyllanthus is provided.