In the large genus Eucalyptus, which dominates most of Australia's open forests and woodlands, genetic studies commonly show signs of introgression between closely related, co-occurring species. Here we assessed genetic variation in two sister species with geographically overlapping distributions in northern Australia. One species, Eucalyptus tetrodonta, is a dominant species in many lowland savannas. It is found on gravelly red-lateritic to sandy soils, with a large distribution spanning over 2000 km east-to-west and 1000 km north-to-south, from the Kimberley region of Western Australia to northern Queensland. The other, E. megasapala, was taxonomically separated from E. tetrodonta in 2006 on the basis of its larger sepals, prominently ribbed buds and operculum, and fruit and peduncle shape. It typically occurs on rocky substrates in northeast Queensland, within the range of E. tetrodonta, where the two species can form stands within a few hundred metres of one another. Contrary to expectations, DArTseq genotyping showed strong differentiation between the two species (F ST: 0.28) and little evidence of genetic admixture. Analyses of data from the Australasian Virtual Herbarium showed significant differences in flowering times between the two species. SNP outlier analyses identified multiple loci potentially under selection that are associated with differences between the two species, including the gene FT-interacting protein 7 (FTIP7), which is known to modulate flowering time in plants. Based on current data, it is unclear whether differentiation of these species is the product of parapatric/sympatric speciation or if it was allopatric with secondary geographic overlap. Within E. tetrodonta, genetic variation showed a strong signal of isolation-by-distance, with an east-west trend in the pattern of genetic relatedness. The most substantial genetic break in E. tetrodonta was associated with the Carpentarian Gap, a region of seasonally arid, alluvial plains on the southern margin of the Gulf of Carpentaria known as a biogeographic barrier for other Australian biota.

Generalized guidance such as “local is best” has prevailed regarding seed sourcing strategies for ecological restoration in the past. A shift is currently underway in this guidance, moving toward using pre‐adapted material in the face of human induced climate change and species‐specific strategies to maximize the success and self‐sustainability of restoration plantings. Meanwhile, population‐level genetic data is proving an increasingly valuable tool to achieve this, providing restoration biologists insights into evolutionary history and processes that impact restoration practices. Combining these factors is a major step toward the development and implementation of species‐specific, evolutionarily informed seed sourcing strategies. We seek to establish a balanced approach that bridges the gap between broad generalizations, which lack the nuance needed for successful restoration of individual species, and the highly intensive and costly bespoke single‐species studies sometimes undertaken. To this end, we present a workflow and decision‐making process to develop species‐specific seed sourcing strategies using Single Nucleotide Polymorphism (SNP) data and test its implementation on 10 common and abundant woodland species frequently used in ecological restoration in Australia. The workflow we have developed highlights factors that need to be considered when undertaking ecological restoration including taxonomic uncertainties, hybridization, and range extensions resulting from human activities. It also helps to develop insights into species' reproductive biology and biogeography to enable informed seed movement across the landscape. Thus, it establishes a framework for undertaking restoration genomics studies to facilitate the development of evolutionarily informed seed sourcing. This in turn will help ensure the successful establishment of self‐sustaining restored populations.

The relationship between intra-specific and inter-specific patterns and processes over evolutionary time is key to ecological investigations. We examine this relationship taking an approach of focussing on the association between vegetation and floristic classifications, summaries of inter-specific processes, and intra-specific genetic structuring. Applying an innovative, multispecies, and standardised population genomic approach, we test the relationship between vegetation mapping schemes and structuring of genetic variation across a large, environmentally heterogenous region in eastern Australia. We show that intra-specific genetic variation shows limited correspondence to vegetation and floristic classifications and is better explained by distance between sampled populations and the location of biogeographical features which limit gene flow. Mapping schemes with contiguous mapping classes, particularly larger ones, were more predictive of genetic lineages, whether based on environmental factors or not, than geographically non-contiguous schemes. We conclude that vegetation and floristic classifications are not closely correlated with intra-specific genetic patterns, showing that intra-specific processes are not recapitulated by inter-specific floristic assembly processes. This study showcases the need to implement landscape level evolutionary patterns, based on species specific datasets, in restoration and conservation activities.

Spyridium parvifolium is a widespread and morphologically variable shrub from south-eastern Australia. Several varieties have been recognised, and there is disagreement on the accepted taxonomy between Australian states. This study investigated the phylogeography of the species and assessed genetic distinctiveness of its morphological variants. Nuclear ribosomal DNA and complete chloroplast genomes from seventy-two samples of S. parvifolium and seven samples from closely related species were sequenced and analysed using both Bayesian and maximum likelihood phylogenetic methods. The results showed incongruence in the placement of several associated taxa ( S. cinereum , S. obcordatum and S. daltonii ), plausibly due to long branch attraction, introgression or incomplete lineage sorting. Spyridium parvifolium was resolved as paraphyletic in both phylogenies, with accessions from west of the Murray Darling Depression divergent from those east of the Depression. We found evidence of isolation within S. parvifolium on the inland side of the Great Dividing Range and recent gene flow across Bass Strait. The variants of S. parvifolium were not supported as genetically distinct, and with the prevalence of several variants at single sites and morphological intergrades between variants, we conclude that the taxon is a single, morphologically variable species and that no infraspecific classification is warranted.

Eucalypts are a large and ecologically important group of plants on the Australian continent, and understanding their evolution is important in understanding evolution of the unique Australian flora. Previous phylogenies using plastome DNA, nuclear-ribosomal DNA, or random genome-wide SNPs, have been confounded by limited genetic sampling or by idiosyncratic biological features of the eucalypts, including widespread plastome introgression. Here we present phylogenetic analyses of Eucalyptus subgenus Eudesmia (22 species from western, northern, central and eastern Australia), in the first study to apply a target-capture sequencing approach using custom, eucalypt-specific baits (of 568 genes) to a lineage of Eucalyptus. Multiple accessions of all species were included, and target-capture data were supplemented by separate analyses of plastome genes (average of 63 genes per sample). Analyses revealed a complex evolutionary history likely shaped by incomplete lineage sorting and hybridization. Gene tree discordance generally increased with phylogenetic depth. Species, or groups of species, toward the tips of the tree are mostly supported, and three major clades are identified, but the branching order of these clades cannot be confirmed with confidence. Multiple approaches to filtering the nuclear dataset, by removing genes or samples, could not reduce gene tree conflict or resolve these relationships. Despite inherent complexities in eucalypt evolution, the custom bait kit devised for this research will be a powerful tool for investigating the evolutionary history of eucalypts more broadly.

The relationship between intra-specific and inter-specific patterns and processes over evolutionary time is key to ecological investigations. We examine this relationship from a novel perspective, focussing on the association between floristic classifications, a summary of inter-specific processes, and intra-specific genetic structuring. Applying an innovative, multispecies, and standardised population genomic approach we test the relationship between vegetation mapping schemes and landscape-level estimates of gene flow across a large, environmentally heterogenous region. We show that intra-specific genetic variation shows limited correspondence to vegetation classifications and is better explained by distance between sampled populations and the location of biogeographical features which limit gene flow. However, vegetation classification schemes with contiguous mapping classes were more predictive of genetic lineages than geographically non-contiguous schemes. The size of mapping units was found to be important, as most local vegetation types contained only single intra-specific genetic lineages, while these genetic lineages spanned hundreds of km’s across multiple vegetation types. We conclude that floristic classifications are not closely correlated with intra-specific genetic patterns, showing that intra-specific genetic processes are independent of inter-specific floristic assembly processes. This study also showcases the depth of understanding that can be developed using large, multispecies genetic datasets.

Context. Given the effort and resources that go into collecting and maintaining seed collections, it is crucial that we maximise their usefulness. Conservation, restoration and research rely heavily on good quality collections in order to establish new populations, create habitat, minimise extinction and address scientific questions.Aims. Although seed viability, excellent metadata and genetic representativeness make for good quality collections, we provide 10 detailed reasons why the maintenance of separate maternal lines further increases the quality and usefulness of seed collections.Key results. Maternal line seed collections can accommodate new information, this is especially important given the increasing longevity of seed collections. For example, maintaining separate maternal lines facilitates accommodation of taxonomic changes, minimises the impact of erroneous plant identifications, and facilitates separation of polyploid races, hybrids and inappropriate lineages. Separate maternal line collections also facilitate better estimates of the genetic diversity captured, and consequently better inform conservation translocations and the establishment of conservation gardens and seed orchards. Separate maternal line collections can also expedite breeding for specific traits, such as disease resistance or other selective challenges that impact on biodiversity conservation. New seed microbiome data show how only some maternal lines contain pathogenic fungi, reminding seed collectors and collections managers that contamination can be better contained by keeping each maternal line separate.Conclusions and implications. Maintaining separate maternal lines is a simple and effective way to increase the value of seed collections for multiple applications.

We present a phylogeographic study of the tree species Eucalyptus baueriana Schauer, which occurs in disjunct areas on the near coastal plains and ranges of the south-east Australian mainland. DArTseq data are used to build a phylogeny including E. baueriana and closely related taxa to test its monophyly, test the genetic distinctness of the three subspecies of E. baueriana, and investigate relationships between its disjunct populations. Additionally, we use population structure analysis to investigate the genetic distinctness of populations, and MaxEnt to investigate the environmental factors potentially influencing the species' distribution. We show E. baueriana is monophyletic and most closely related to three other Blue Box eucalypt species: E. conica H.Deane & Maiden, E. dalveenica T.L.Collins, R.L.Andrew & J.J.Bruhl and E. magnificata L.A.S.Johnson & K.D.Hill, with some evidence for genetic introgression between these taxa. Within E. baueriana, the deepest genetic breaks do not correspond with the subspecies classification as the two geographically restricted subspecies, together with samples of the more widespread E. baueriana subsp. baueriana from west of the Gippsland lowlands, form a south-western clade with that is sister to other populations of subsp. baueriana. The oldest genetic break in the species occurs in far eastern Gippsland (Victoria), corresponding to one of the shortest geographic disjunctions in the species' distribution. Genetic breaks in other species have been observed in this region which is broadly referred to as the southern transition zone. Both total annual rainfall and the seasonality of this rainfall are hypothesised to affect the species' distribution; gaps in its distribution are in areas of higher rainfall that support closed forest and in regions with more winter dominated rainfall.

ABSTRACT To investigate the relationships among species in the taxonomically problematic Eucalyptus odorata species complex, we generated molecular data using double-digest restriction site-associated DNA sequencing (ddRADseq) and Diversity Arrays Technology sequencing (DArTseq). These data were analysed utilising principal-component analysis (PCA), phylogenetic networks, phylogeny reconstruction and hybridisation tests. Twelve species that are variously recognised in the complex were sampled from across their ranges, along with co-occurring members of E. section Adnataria, to allow for patterns of hybridisation and gene flow to be identified. Despite the large genetic datasets generated, many relationships within the E. odorata complex were poorly resolved, and few species were monophyletic, likely owing to both biological factors including recent speciation and extensive hybridisation and introgression, and potential over-splitting of taxa. We show that multiple taxa with limited distributions are the result of reticulate evolutionary events and that typical Eucalyptus viridis R.T.Baker and the possibly con-specific E. aenea K.D.Hill are sister to the rest of the complex. The remaining species appeared to represent a discontinuous crescent-shaped cline running from the Flinders Ranges to the south-western slopes region of New South Wales, with limited support for an east–west split in this cline across the Murray River Basin. Eucalytpus viridis var. latiuscula Blakely, which is not closely related to the typical variety of this species in our data, may represent a northern extension to this cline.

To investigate the relationships among species in the taxonomically problematic Eucalyptus odorata species complex, we generated molecular data using double-digest restriction site-associated DNA sequencing (ddRADseq) and Diversity Arrays Technology sequencing (DArTseq). These data were analysed utilising principal-component analysis (PCA), phylogenetic networks, phylogeny reconstruction and hybridisation tests. Twelve species that are variously recognised in the complex were sampled from across their ranges, along with co-occurring members of E. section Adnataria, to allow for patterns of hybridisation and gene flow to be identified. Despite the large genetic datasets generated, many relationships within the E. odorata complex were poorly resolved, and few species were monophyletic, likely owing to both biological factors including recent speciation and extensive hybridisation and introgression, and potential over-splitting of taxa. We show that multiple taxa with limited distributions are the result of reticulate evolutionary events and that typical Eucalyptus viridis R.T.Baker and the possibly con-specific E. aenea K.D.Hill are sister to the rest of the complex. The remaining species appeared to represent a discontinuous crescent-shaped cline running from the Flinders Ranges to the south-western slopes region of New South Wales, with limited support for an east–west split in this cline across the Murray River Basin. Eucalytpus viridis var. latiuscula Blakely, which is not closely related to the typical variety of this species in our data, may represent a northern extension to this cline.

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.

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.

Abstract 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.

The artesian springs of inland Australia are a unique habitat in what is otherwise an arid environment. They support a rich collection of endemic flora and fauna. Here, morphological and molecular data are employed to describe a new species, Chloris circumfontinalis Fahey & Fensham, endemic to artesian spring systems in central Queensland. A morphological ordination failed to distinguish this species from other Australian native flora, but the shape of the florets distinguishes it from the species with which it co-occurs. Phylogenies estimated from molecular data showed that the species represents a distinct lineage that may be sister to species of Chloris from outside Australia. Chloris circumfontinalis occurs only in the saline scalds that form around the springs, and population surveys at the two sites where it occurs indicated a threat status of Endangered under the IUCN Red List criteria.

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).