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Spyridium Fenzl is a genus of ~45 species endemic to south-western and south-eastern Australia. This study provides the most comprehensive phylogenies of Spyridium to date, analysing both entire chloroplast genomes and the nuclear ribosomal array (18S–5.8S–26S). There was substantial incongruence between the chloroplast and nuclear phylogenies, creating phylogenetic uncertainty, but some clear relationships and biogeographic patterns could be established. Analyses support the monophyly of Spyridium, identifying an early east–west split at the base of the nuclear phylogeny and deep divergences of New South Wales and Tasmanian endemic clades. We also found evidence of more recent dispersal events between eastern and western Australia and between Tasmania and the mainland. Eleven taxa were found to be monophyletic in the nrDNA phylogeny and two were clearly polyphyletic (S. eriocephalum Fenzl and S. phylicoides Reissek). Although the polyphyly of S. eriocephalum correlates with the two varieties, suggesting distinct taxa, further research is required on S. phylicoides.

Eremophila R.Br. comprises at least 238 species endemic to Australia, with many more having not yet been formally described. Three putative new taxa, namely, E. sp. Hamersley Range (K. Walker KW 136), E. sp. Calvert Range (A. A. Burbidge 738) and E. sp. Rudall River (P. G. Wilson 10512), were segregated from a broadly defined E. tietkensii F.Muell. & Tate by J. Hurter at the Western Australian Herbarium in 2012. Both E. sp. Hamersley Range and E. sp. Rudall River are listed as being of conservation concern in Western Australia, the former occurring in the Pilbara region in areas of prospective interest for mining development. We sought to determine whether these phrase-named entities should be formally described as new species, using multivariate analyses of morphometric and molecular data derived from specimens in the Western Australia Herbarium. Eremophila sp. Rudall River could not be adequately separated from E. tietkensii by either morphological or molecular data, and is here included within that species. By contrast, E. sp. Hamersley Range and E. sp. Calvert Range are clearly morphologically and genetically distinct. We thus describe them here as the new species E. naaykensii A.L.Curtis & K.R.Thiele and E. hurteri A.L.Curtis & K.R.Thiele. The recognition of these taxa will help inform their conservation prioritisation and subsequent management.

Refereed/Peer-reviewed Eremophila is the largest genus in the plant tribe Myoporeae (Scrophulariaceae) and exhibits incredible morphological diversity across the Australian continent. The Australian Aboriginal Peoples recognize many Eremophila species as important sources of traditional medicine, the most frequently used plant parts being the leaves. Recent phylogenetic studies have revealed complex evolutionary relationships between Eremophila and related genera in the tribe. Unique and structurally diverse metabolites, particularly diterpenoids, are also a feature of plants in this group. To assess the full dimension of the chemical space of the tribe Myoporeae, we investigated the metabolite diversity in a chemo-evolutionary framework applying a combination of molecular phylogenetic and state-of-the-art computational metabolomics tools to build a dataset involving leaf samples from a total of 291 specimens of Eremophila and allied genera. The chemo-evolutionary relationships are expounded into a systematic context by integration of information about leaf morphology (resin and hairiness), environmental factors (pollination and geographical distribution), and medicinal properties (traditional medicinal uses and antibacterial studies), augmenting our understanding of complex interactions in biological systems.

In a cross-continental research initiative, including researchers working in Australia and Denmark, and based on joint external funding by a 3-year grant from the Novo Nordisk Foundation, we have used DNA sequencing, extensive chemical profiling and molecular networking analyses across the entire Eremophila genus to provide new knowledge on the presence of natural products and their bioactivities using polypharmocological screens. Sesquiterpenoids, diterpenoids and dimers of branched-chain fatty acids with previously unknown chemical structures were identified. The collection of plant material from the Eremophila genus was carried out according to a 'bioprospecting agreement' with the Government of Western Australia. We recognize that several Eremophila species hold immense cultural significance to Australia's First Peoples. In spite of our best intentions to ensure that new knowledge gained about the genus Eremophila and any potential future benefits are shared in an equitable manner, in accordance with the Nagoya Protocol, we encounter serious dilemmas and potential conflicts in making benefit sharing with Australia's First Peoples a reality. Refereed/Peer-reviewed

Aim: If we are able to determine the geographic origin of an invasion, as well as its known area of introduction, we can better appreciate the innate environmental tolerance of a species and the strength of selection for adaptation that colonizing populations have undergone. It also enables us to maximize the success of searches for effective biological control agents. We determined the number of successful colonization events that have occurred throughout the world for two Cakile species and compared the climates from which they originated, in which they established and then spread. Location: Worldwide. Taxon: Sea-Rockets (Cakile spp.), Brassicaceae. Methods: We used a high-throughput sequencing and a genome skimming approach combined with Bayesian Inference phylogenetics to examine variation in entire chloroplast genomes and regions of nuclear ribosomal DNA within native and introduced areas. Databases were used to compare climates between native ranges and introduced regions for multiple clades within each species. Results: At least seven clades have invaded different regions of the world. In most cases we were able to identify their source regions and climates. The environmental bottlenecks differed in intensity: while some clades colonized into climates that were similar to climates in their native range, other clades had a very broad innate environmental tolerance such that new invasions succeeded beyond the climate range of native populations. We found clear evidence of hybridization—specifically, chloroplast capture—between two species in Australia. Conclusions: Results here show that these species are sometimes capable of colonizing in climates that are beyond the climate range of native populations. Whether successful colonization beyond native climate niches requires de novo adaptation, or whether it represents an innate broad fundamental niche requires further investigation. Cakile species provide an excellent opportunity to study replicated climate adaptation trajectories.

Aim To infer relationships between populations of the semi‐arid, mallee eucalypt, Eucalyptus behriana, to build hypotheses regarding evolution of major disjunctions in the species' distribution and to expand understanding of the biogeographical history of southeastern Australia. Location Southeastern Australia. Taxon Eucalyptus behriana (Myrtaceae, Angiospermae). Methods We developed a large dataset of anonymous genomic loci for 97 samples from 11 populations of E. behriana using double digest restriction site‐associated DNA sequencing (ddRAD‐seq), to determine genetic relationships between the populations. These relationships, along with species distribution models, were used to construct hypotheses regarding environmental processes that have driven fragmentation of the species’ distribution. Results Greatest genetic divergence was between populations on either side of the Lower Murray Basin. Populations west of the Basin showed greater genetic divergence between one another than the eastern populations. The most genetically distinct population in the east (Long Forest) was separated from others by the Great Dividing Range. A close relationship was found between the outlying northernmost population (near West Wyalong) and those in the Victorian Goldfields despite a large disjunction between them. Conclusions Patterns of genetic variation are consistent with a history of vicariant differentiation of disjunct populations. We infer that an early disjunction to develop in the species distribution was that across the Lower Murray Basin, an important biogeographical barrier separating many dry sclerophyll plant taxa in southeastern Australia. Additionally, our results suggest that the western populations fragmented earlier than the eastern ones. Fragmentation, both west and east of the Murray Basin, is likely tied to climatic changes associated with glacial‐interglacial cycles although it remains possible that major geological events including uplift of the Mount Lofty Ranges and basalt flows in the Newer Volcanics Province also played a role.

We aimed to test the extent to which plastid DNA gives incongruent phylogeographic patterns to nuclear DNA in a species of eucalypt, Eucalyptus behriana, a taxonomic group where chloroplast capture is a well-established phenomenon. Furthermore, we aimed to test the degree of influence chloroplast capture has on the observed patterns by broadly sampling co-occurring, related species. A genome skimming approach was used to sequence and assemble chloroplast genomes from population-level sampling of E. behriana, as well as samples of twenty-one other Eucalyptus section Adnataria species which co-occur with it. Phylogenetic analyses were first undertaken on just E. behriana to allow direct comparison to previously reported phylogeographic patterns based upon nuclear markers. A subsequent analysis including the related taxa was undertaken to investigate the degree of chloroplast capture and how this may be influencing the observed phylogeographic patterns. We found strong geographic structuring of plastid DNA relationships across the geographic range of E. behriana, with a basal divergence between the most northerly isolated population at West Wyalong and all other populations which does not match phylogeographic patterns based on nuclear markers. When outgroups were included, we found that E. behriana is highly polyphyletic with respect to all other species, starkly contrasting with the species well-supported monophylly based upon nuclear markers, and that chloroplast capture is so widespread that geographic patterns of the plastid genomes are consistent across species boundaries.

Eremophilais the largest genus in the plant tribe Myoporeae (Scrophulariaceae) and exhibits incredible morphological diversity across the Australian continent. The Australian Aboriginal Peoples recognize manyEremophilaspecies as important sources of traditional medicine, the most frequently used plant parts being the leaves. Recent phylogenetic studies have revealed complex evolutionary relationships betweenEremophilaand related genera in the tribe. Unique and structurally diverse metabolites, particularly diterpenoids, are also a feature of plants in this group. To assess the full dimension of the chemical space of the tribe Myoporeae, we investigated the metabolite diversity in a chemo-evolutionary framework applying a combination of molecular phylogenetic and state-of-the-art computational metabolomics tools to build a dataset involving leaf samples from a total of 291 specimens ofEremophilaand allied genera. The chemo-evolutionary relationships are expounded into a systematic context by integration of information about leaf morphology (resin and hairiness), environmental factors (pollination and geographical distribution) and medicinal properties (traditional medicinal uses and antibacterial studies) augmenting our understanding of complex interactions in biological systems.

Aim To infer relationships between populations of the semi‐arid, mallee eucalypt, Eucalyptus behriana, to build hypotheses regarding evolution of major disjunctions in the species' distribution and to expand understanding of the biogeographical history of southeastern Australia. Location Southeastern Australia. Taxon Eucalyptus behriana (Myrtaceae, Angiospermae). Methods We developed a large dataset of anonymous genomic loci for 97 samples from 11 populations of E. behriana using double digest restriction site‐associated DNA sequencing (ddRAD‐seq), to determine genetic relationships between the populations. These relationships, along with species distribution models, were used to construct hypotheses regarding environmental processes that have driven fragmentation of the species’ distribution. Results Greatest genetic divergence was between populations on either side of the Lower Murray Basin. Populations west of the Basin showed greater genetic divergence between one another than the eastern populations. The most genetically distinct population in the east (Long Forest) was separated from others by the Great Dividing Range. A close relationship was found between the outlying northernmost population (near West Wyalong) and those in the Victorian Goldfields despite a large disjunction between them. Conclusions Patterns of genetic variation are consistent with a history of vicariant differentiation of disjunct populations. We infer that an early disjunction to develop in the species distribution was that across the Lower Murray Basin, an important biogeographical barrier separating many dry sclerophyll plant taxa in southeastern Australia. Additionally, our results suggest that the western populations fragmented earlier than the eastern ones. Fragmentation, both west and east of the Murray Basin, is likely tied to climatic changes associated with glacial‐interglacial cycles although it remains possible that major geological events including uplift of the Mount Lofty Ranges and basalt flows in the Newer Volcanics Province also played a role., In this study, we investigate the phylogeography and biogeographic history of the southeast Australian mallee eucalypt, Eucalyptus behriana, which has a distribution divided by several major biogeographical barriers. By reconstructing the relationships between isolated populations and building species distribution models to investigate potential environmental factors influencing the species distribution, we build hypotheses regarding how the species scattered distribution comes about. Both climatic and edaphic changes are shown to likely have influenced the species distribution, with current isolated populations representing refugia where the species has survived as intervening populations have become extinct.

This study presents an analysis of plastomes to assess relationships among the seven genera of tribe Myoporeae (Scrophulariaceae). Sampling included individuals from type species for all seven genera included in Myoporeae (Bontia, Calamphoreus, Diocirea, Eremophila, Glycocystis, Myoporum, Pentacoelium), one additional species of the large genus Eremophila, one representative of the sister tribe Leucophylleae (Leucophyllum), and the previously published plastome of Scrophularia takesimensis as an outgroup. Phylogenetic analyses were performed using maximum parsimony and Bayesian inference analyses based on > 7000 variable nucleotide positions. Maximum parsimony analysis produced a single tree with the same topology as the Bayesian consensus tree, and all nodes were fully resolved with 100% bootstrap support and 1.0 Bayesian posterior probability. Tribe Myoporeae was supported as monophyletic and sister to Leucophylleae. Two lineages are identified within Myoporeae; one containing the Australian endemic genera Calamphoreus, Diocirea, Glycocystis and the type species of Eremophila (E. oppositifolia), the second containing species with distributions outside of Australia (Bontia, Myoporum, Pentacoelium) and a species of Eremophila (E. gibbifolia). Eremophila is thus supported as polyphyletic. The application of genome skimming and assembly of plastomes has resolved generic relationships in tribe Myoporeae and revealed variable regions of the genome that will be useful in further genetic study of the group.

We sequenced and assembled the whole chloroplast genome of the Australian-endemic shrub Platylobium obtusangulum. The total size of the genome is 150,090 base pairs (bp), including two inverted repeat regions of 25,511 bp each, one large single copy region of 80,567 bp and a small single copy region of 18,501 bp. The genome has a GC content of 36.7% and includes 127 annotated genes (83 protein coding, 36 tRNA genes and eight rRNA genes). Phylogenetic analysis of chloroplast genomes placed the Platylobium obtusangulum genome in the expected position of the Mirbelioid clade in the legume family (Leguminosae: Papilionoideae).

Previous molecular phylogenetic analyses have resolved the Australian bloodwood eucalypt genus Corymbia (~100 species) as either monophyletic or paraphyletic with respect to Angophora (9-10 species). Here we assess relationships of Corymbia and Angophora using a large dataset of chloroplast DNA sequences (121,016 base pairs; from 90 accessions representing 55 Corymbia and 8 Angophora species, plus 33 accessions of related genera), skimmed from high throughput sequencing of genomic DNA, and compare results with new analyses of nuclear ITS sequences (119 accessions) from previous studies. Maximum likelihood and maximum parsimony analyses of cpDNA resolve well supported trees with most nodes having >95% bootstrap support. These trees strongly reject monophyly of Corymbia, its two subgenera (Corymbia and Blakella), most taxonomic sections (Abbreviatae, Maculatae, Naviculares, Septentrionales), and several species. ITS trees weakly indicate paraphyly of Corymbia (bootstrap support

The Kimberley region of Western Australia is recognised for its high biodiversity and many endemic species, including the charismatic boab tree, Adansonia gregorii F.Muell. (Malvaceae: Bombacoideae). In order to assess the effects of biogeographic barriers on A. gregorii, we examined the genetic diversity and population structure of the tree species across its range in the Kimberley and adjacent areas to the east. Genetic variation at six microsatellite loci in 220 individuals from the entire species range was examined. Five weakly divergent populations, separated by west–east and coast–inland divides, were distinguished using spatial principal components analysis. However, the predominant pattern was low geographic structure and high gene flow. Coalescent analysis detected a population bottleneck and significant gene flow across these inferred biogeographic divides. Climate cycles and coastline changes following the last glacial maximum are implicated in decreases in ancient A. gregorii population size. Of all the potential gene flow vectors, various macropod species and humans are the most likely.

Although the Australasian grass genus Austrostipa is species rich, abundant and ecologically significant, the subgeneric classification of its 62 species has not been comprehensively tested with molecular data. We used three molecular markers from 51 species to determine a phylogeny of the genus and found strong support for the following seven of the existing subgenera: Falcatae, Austrostipa, Aulax, Lobatae, Bambusina, Lancea and Longiaristatae. The molecular data do not support Tuberculatae and Eremophilae, which could be combined with subgenus Austrostipa. The data are equivocal or insufficient regarding monophyly of Ceres, Arbuscula, Petaurista and Lanterna. Data from the nuclear internal transcribed spacer region appear to be suitable for phylogenetic analysis of this group, and the degree of sequence variability resolves species-level relationships with good levels of support. In contrast, chloroplast sequence data from the matK and rbcL genes do not resolve most relationships at the species level, and the inferred phylogeny hints at gene duplication, chloroplast capture, or deep coalescence in the evolutionary history of Austrostipa.