The generation and analysis of genome-scale data - genomics - is driving a rapid increase in plant biodiversity knowledge. However, the speed and complexity of technological advance in genomics presents challenges for the widescale use of genomics in evolutionary and conservation biology. We introduce and describe a national-scale collaboration conceived to build genomic resources and capability for understanding the Australian flora: the Genomics for Australian Plants (GAP) Framework Initiative. We outline (a) the history of the project including the collaborative framework, partners and funding; (b) GAP principles such as rigour in design, sample verification and documentation, data management and data accessibility; and (c) the structure of the consortium and the four associated activity streams (reference genomes, phylogenomics, conservation genomics and training), with the rationale and aims for each of these. We show, through discussion of successes and challenges, the value of this multi-institutional consortium approach and the enablers, such as well-curated collections and national collaborative research infrastructure, all of which have led to a substantial increase in capacity and delivery of biodiversity knowledge outcomes.

Societal Impact Statement Conservation seed banks maintain collections of many seed‐bearing plant species, providing germplasm and data to support management of wild populations. However, a proportion of plant species produce seeds that are difficult to collect, dry, store and utilise; these are known as ‘exceptional’ species. Here we tested a framework for identifying exceptional species, to document examples and provide case studies within the Australian flora. We present a workflow that may be used to identify additional exceptional species, and direct efforts to establish appropriate collection types (seeds and/or living collections, tissue culture or cryopreservation) for their ex situ conservation. Summary Seed banking is well established to contribute to the conservation of many seed‐bearing plant species ex situ for future use in restoration, translocation, agriculture and horticulture. In Australia, over 67% of currently listed threatened plants are represented in conservation seed banks. However, there are challenges to conserving the full extent of plant diversity in seed banks, with growing recognition that we need to think beyond conventional seed banking methods to conserve ‘exceptional’ plant species that are difficult to collect, store and germinate. We examine how the framework for identification of such species can be applied to the Australian flora, using examples from the recently published guidelines for ‘ Plant Germplasm Conservation in Australia ’ and case studies and data arising from the Australian Academy of Science Fenner Conference on the Environment ‘Exceptional Times, Exceptional Plants’ . We present a workflow to assist conservation decision‐makers and practitioners in identifying exceptional species and overcoming barriers to storage of germplasm, enabling appropriate ex situ collection types to be established via seeds, living collections, tissue culture, cryopreservation or a combination of these. Australia's seed conservation sector continues to expand, with increasing expertise, facilities and networks established to conserve a diversity of plant species; however, resolving the challenges relating to each exceptionality factor requires significantly more time, labour and collaboration than current capacity allows. Understanding the barriers to conservation and production of healthy plants, via germination or other methods of propagation, is a critical component of conserving species long‐term and ultimately returning plants to the landscape.

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods(1,2). A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome(3,4). Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins(5-7). However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes(8). This 15-fold increase in genus-level sampling relative to comparable nuclear studies(9) provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

Globally, there is an urgent need to improve ecological restoration despite multiple challenges, mostly related to the lack of natural and economic resources and the detrimental effects of climate change. While locally collected native seed has been the preferred seed‐sourcing strategy to achieve effective restoration outcomes, attitudes are changing. Using Australia as an example, we provide an overview of this paradigm shift toward collecting and using local seed. We found that in Australia there has been a substantial shift to combine local and non local seed for restoration across government agencies and land managers. This paradigm shift aims to improve restoration outcomes by increasing genetic diversity and to facilitate adaptation as climates rapidly change. We conclude that the increases in the frequency and intensity of extreme climate events require governments, researchers, and practitioners to adapt to the changing requirements of seed‐based restoration.

Aim: The goal of this study was to investigate the invasion history of the weed Sonchus oleraceus in Australia by comparing the population genetic structure of individuals at different locations in Australia, and in the most likely areas of origin in the native range. Location: Samples were collected in Europe and Morocco, North Africa (27 locations), and Australia (17 locations). Methods: We performed population genetic analyses using a large dataset comprising 2883 single nucleotide polymorphism markers from 547 plant samples and investigated the invasion history of S. oleraceus with Approximate Bayesian Computation and Random Forest classification algorithms. We compared single and multiple invasion scenarios considering admixture having occurred before and after introduction. Results: Our results revealed high levels of inbreeding within sampling locations in the two ranges. Analyses also showed that S. oleraceus was possibly introduced to Australia at least twice: a first introduction around 1000years ago before British settlement and a more recent introduction (similar to 65 years ago) from Europe and North Africa. We also found evidence of post-introduction admixture and a potential reintroduction of S. oleraceus from Australia back to its native range. Main conclusions: We conclude that the invasion history of S. oleraceus into Australia is probably historic (i.e. prior to British settlements) and complex showing recent evidence of post-introduction admixture. The complex invasion history of S. oleraceus in Australia poses challenges for the search of potential biological control agents.

Aquatic plants share a range of convergent reproductive strategies, such as the ability to reproduce both sexually and asexually through vegetative growth. In dryland river systems, floodplain inundation is infrequent and irregular, and wetlands consist of discrete and unstable habitat patches. In these systems life-history strategies such as long-distance dispersal, seed longevity, self-fertilisation, and reproduction from vegetative propagules are important strategies which allow plants to persist. Using two aquatic plants Marsilea drummondii and Eleocharis acuta , we investigated the proportions of sexual and asexual reproduction and self-fertilisation employing next generation sequencing approaches and used this information to understand population genetic structure in a large inland floodplain, in western New South Wales (NSW) Australia. Asexual vegetative reproduction and self-fertilisation was more common in M. drummondii , but both species used sexual reproduction as the main mode of reproduction. This resulted in highly differentiated genetic structure between wetlands and similar genetic structure within wetlands. The similarity in genetic structure was influenced by the wetland in the two species highlighting the influence of the floodplain landscape and hydrology in structuring population genetic structure. The high levels of genetic variation among wetlands and low variation within wetlands suggests that dispersal and pollination occur within close proximity and that gene flow is restricted. This suggests a reliance on locally sourced (persistent) seed, rather than asexual (clonal) reproduction or recolonisation via dispersal, for population maintenance in plants in dryland rivers. This highlights the importance of floodplain inundation to promote seed germination, establishment and reproduction in dryland regions.

Allocasuarina verticillata (Lam.) L.A.S. Johnson is a widespread species in south-eastern Australia providing vegetation cover, protecting fragile soils and providing food for birds. Understanding the effects of gene flow on the recruitment patterns, genetic differentiation and structure of fragmented populations provides fundamental guidelines to underpin plant conservation strategies and activities. In this study, four spatially disjunct populations of A. verticillata were sampled to explore the effects of population size, reproductive patterns and pollen and seed dispersal on among-population genetic diversity, genetic differentiation and structure, using field survey and microsatellite marker techniques. It was found that stands of A. verticillata were predominantly sexually reproductive, but asexual reproduction through root suckering was an additional mode of reproduction. The reproductive success of A. verticillata is positively correlated with the effective population size rather than actual population size. The reduction in effective population size and increment of spatial isolation resulted in lower genetic diversity and higher inbreeding coefficient of progenies. Moderate pairwise genetic differentiation and weak genetic structure were identified. The results suggest that exogenous, wind-mediated pollen flow provides some maintenance of genetic diversity in the isolated stands. Seed dispersal appears mainly to be over short distances (i.e., within populations), but the infrequent transport of seeds between disjunct locations cannot be ruled out as another factor that may help maintain genetic diversity.

Seed production areas (SPAs) are critical infrastructure for ecological restoration, particularly in fragmented landscapes where wildland seed crops are unavailable or wildland harvest is unsustainable. SPAs are useful for a wide range of species that are amenable to cultivation. Despite increasing research on SPAs, their value for biodiversity conservation has yet to be comprehensively described. Here, we highlight the key benefits of SPAs to biodiversity conservation. First, SPAs allow restoration to be conducted on a much greater scale than could be accomplished with wildland-harvested seed, thus protecting key biodiversity assets from harvest pressures. Second, the native seed production industry adds to the base of stakeholders who are invested in restoring and enhancing biodiversity. Third, SPAs provide novel opportunities for research and public exposure to native biodiversity. We also describe how cultivation can alter plant fitness compared to wildland plants, which acts as a multiplier to their conservation implications. SPAs could lead to two interrelated negative consequences that generate risks for taxonomic and genetic diversity at multiple scales: (1) SPAs can cause and multiply negative genetic legacies as a result of cultivation practices, and (2) SPA progenies can numerically and genetically dominate wildland plant populations. Nevertheless, SPA cultivation offers an opportunity to genetically diversify SPA-derived populations for success in restoration and enlarge the pool of species available for restoration, thus mitigating or solving some of these risks. Targeted government policies toward SPAs, additional research, and sound SPA management are necessary to minimize genetic risks and taxonomic redundancy, and also to maximize the conservation benefits of SPAs.

Australia’s 2019–2020 ‘Black Summer’ bushfires burnt more than 8 million hectares of vegetation across the south-east of the continent, an event unprecedented in the last 200 years. Here we report the impacts of these fires on vascular plant species and communities. Using a map of the fires generated from remotely sensed hotspot data we show that, across 11 Australian bioregions, 17 major native vegetation groups were severely burnt, and up to 67–83% of globally significant rainforests and eucalypt forests and woodlands. Based on geocoded species occurrence data we estimate that >50% of known populations or ranges of 816 native vascular plant species were burnt during the fires, including more than 100 species with geographic ranges more than 500 km across. Habitat and fire response data show that most affected species are resilient to fire. However, the massive biogeographic, demographic and taxonomic breadth of impacts of the 2019–2020 fires may leave some ecosystems, particularly relictual Gondwanan rainforests, susceptible to regeneration failure and landscape-scale decline.

Landscape degradation is a major threat to global biodiversity that is being further exacerbated by climate change. Halting or reversing biodiversity decline using seed-based restoration requires tons of seed, most of which is sourced from wild populations. However, in regions where restoration is most urgent, wild seed sources are often fragmented, declining and producing seed with low genetic diversity. Seed production areas (SPAs) can help to reduce the burden of collecting native seed from remnant vegetation, improve genetic diversity in managed seed crops and contribute to species conservation. Banksia marginata (Proteaceae) is a key restoration species in south-eastern Australia but is highly fragmented and declining across much of its range. We evaluated genetic diversity, population genetic structure and relatedness in two B. marginata SPAs and the wild populations from which the SPA germplasm was sourced. We found high levels of relatedness within most remnants and that the population genetic structure was best described by three groups of trees. We suggest that SPAs are likely to be important to meet future native seed demand but that best practice protocols are required to assist land managers design and manage these resources including genetic analyses to guide the selection of germplasm.

The Australian Native Seed Sector survey was conducted in 2016–2017 under the auspices of the Australian Network for Plant Conservation. Respondents self‐selected into a seed supply (Seed Collector, Seed Production Area Grower) or seed demand (Seed Purchaser, Other User) group category. Issue statements facing the sector with respect to limiting opportunities for ecological restoration were presented to survey respondents who ranked them in order of importance. Findings revealed that the order of statement importance varied depending on the primary role (Group) of the respondent in the sector. When combined across groups, the issues of most importance were: future seed demand will be difficult to meet from wild harvest; the seed market is unwilling to pay for the true cost of seed collection/seed production; there is a lack of available seed from a broad range of species; and demand for seed is inconsistent and/or unpredictable. The survey also revealed that the native seed sector is underpinned by a remarkably small and underresourced workforce, composed primarily of sole or small operators, which presents a clear concern to all users of native seed, not only in terms of current capacity for ecological restoration, but also to meet any large and rapid increases in future demand.

The Australian native seed sector is critical for undertaking ecological restoration but faces serious challenges from interacting factors, including native vegetation loss and habitat fragmentation, low funding levels, and climate change impacts. The Australian Native Seed Survey was conducted in 2016–2017 to better understand sector structure, practitioner perceptions, and practice. It found that most native seed is collected from small and fragmented tenures and from geographic ranges that greatly exceed “local provenance”; that the diversity of species available for restoration is typically low; that native seed is seldom quality tested; and that most annual seed collections (wild or production) are small in volume suggesting overall seed yields are modest in quantity and not sufficient to support large‐scale restoration. Together, survey findings raise serious concerns about the ability of the sector, as currently constituted and resourced, to meet projected future increases in the demand for seed or for achieving the effectiveness and efficiency required to meet UN‐Decade type ecological restoration outcomes. Central to recommendations for sector improvement are the following focus areas: maturing the native seed sector; sustainability; seed production; licensing; seed testing and tracking; and research.