State Herbarium of South Australia

Abstract The classification of the legume family proposed here addresses the long‐known non‐monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near‐complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well‐supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community‐endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or clade‐based classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

Evolution occurs rapidly and is an ongoing process in our environments. Evolutionary principles need to be built into conservation efforts, particularly given the stressful conditions organisms are increasingly likely to experience because of climate change and ongoing habitat fragmentation. The concept of evolutionary resilience is a way of emphasizing evolutionary processes in conservation and landscape planning. From an evolutionary perspective, landscapes need to allow in situ selection and capture high levels of genetic variation essential for responding to the direct and indirect effects of climate change. We summarize ideas that need to be considered in planning for evolutionary resilience and suggest how they might be incorporated into policy and management to ensure that resilience is maintained in the face of environmental degradation.

Abstract. Tropical tree height-diameter (H:D) relationships may vary by forest type and region making large-scale estimates of above-ground biomass subject to bias if they ignore these differences in stem allometry. We have therefore developed a new global tropical forest database consisting of 39 955 concurrent H and D measurements encompassing 283 sites in 22 tropical countries. Utilising this database, our objectives were: 1. to determine if H:D relationships differ by geographic region and forest type (wet to dry forests, including zones of tension where forest and savanna overlap). 2. to ascertain if the H:D relationship is modulated by climate and/or forest structural characteristics (e.g. stand-level basal area, A). 3. to develop H:D allometric equations and evaluate biases to reduce error in future local-to-global estimates of tropical forest biomass. Annual precipitation coefficient of variation (PV), dry season length (SD), and mean annual air temperature (TA) emerged as key drivers of variation in H:D relationships at the pantropical and region scales. Vegetation structure also played a role with trees in forests of a high A being, on average, taller at any given D. After the effects of environment and forest structure are taken into account, two main regional groups can be identified. Forests in Asia, Africa and the Guyana Shield all have, on average, similar H:D relationships, but with trees in the forests of much of the Amazon Basin and tropical Australia typically being shorter at any given D than their counterparts elsewhere. The region-environment-structure model with the lowest Akaike's information criterion and lowest deviation estimated stand-level H across all plots to within amedian −2.7 to 0.9% of the true value. Some of the plot-to-plot variability in H:D relationships not accounted for by this model could be attributed to variations in soil physical conditions. Other things being equal, trees tend to be more slender in the absence of soil physical constraints, especially at smaller D. Pantropical and continental-level models provided less robust estimates of H, especially when the roles of climate and stand structure in modulating H:D allometry were not simultaneously taken into account.

Abstract Long‐term ecological studies are critical for providing key insights in ecology, environmental change, natural resource management and biodiversity conservation. In this paper, we briefly discuss five key values of such studies. These are: (1) quantifying ecological responses to drivers of ecosystem change; (2) understanding complex ecosystem processes that occur over prolonged periods; (3) providing core ecological data that may be used to develop theoretical ecological models and to parameterize and validate simulation models; (4) acting as platforms for collaborative studies, thus promoting multidisciplinary research; and (5) providing data and understanding at scales relevant to management, and hence critically supporting evidence‐based policy, decision making and the management of ecosystems. We suggest that the ecological research community needs to put higher priority on communicating the benefits of long‐term ecological studies to resource managers, policy makers and the general public. Long‐term research will be especially important for tackling large‐scale emerging problems confronting humanity such as resource management for a rapidly increasing human population, mass species extinction, and climate change detection, mitigation and adaptation. While some ecologically relevant, long‐term data sets are now becoming more generally available, these are exceptions. This deficiency occurs because ecological studies can be difficult to maintain for long periods as they exceed the length of government administrations and funding cycles. We argue that the ecological research community will need to coordinate ongoing efforts in an open and collaborative way, to ensure that discoverable long‐term ecological studies do not become a long‐term deficiency. It is important to maintain publishing outlets for empirical field‐based ecology, while simultaneously developing new systems of recognition that reward ecologists for the use and collaborative sharing of their long‐term data sets. Funding schemes must be re‐crafted to emphasize collaborative partnerships between field‐based ecologists, theoreticians and modellers, and to provide financial support that is committed over commensurate time frames.

Savannas are defined based on vegetation structure, the central concept being a discontinuous tree cover in a continuous grass understorey. However, at the high-rainfall end of the tropical savanna biome, where heavily wooded mesic savannas begin to structurally resemble forests, or where tropical forests are degraded such that they open out to structurally resemble savannas, vegetation structure alone may be inadequate to distinguish mesic savanna from forest. Additional knowledge of the functional differences between these ecosystems which contrast sharply in their evolutionary and ecological history is required. Specifically, we suggest that tropical mesic savannas are predominantly mixed tree–C4 grass systems defined by fire tolerance and shade intolerance of their species, while forests, from which C4 grasses are largely absent, have species that are mostly fire intolerant and shade tolerant. Using this framework, we identify a suite of morphological, physiological and life-history traits that are likely to differ between tropical mesic savanna and forest species. We suggest that these traits can be used to distinguish between these ecosystems and thereby aid their appropriate management and conservation. We also suggest that many areas in South Asia classified as tropical dry forests, but characterized by fire-resistant tree species in a C4 grass-dominated understorey, would be better classified as mesic savannas requiring fire and light to maintain the unique mix of species that characterize them.

Abstract 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.

Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.

Abstract Aim Comparative analyses of fire regimes at large geographical scales can potentially identify ecological and climatic controls of fire. Here we describe A ustralia's broad fire regimes, and explore interrelationships and trade‐offs between fire regime components. We postulate that fire regime patterns will be governed by trade‐offs between moisture, productivity, fire frequency and fire intensity. Location Australia. Methods We reclassified a vegetation map of A ustralia, defining classes based on typical fuel and fire types. Classes were intersected with a climate classification to derive a map of ‘fire regime niches’. Using expert elicitation and a literature search, we validated each niche and characterized typical and extreme fire intensities and return intervals. Satellite‐derived active fire detections were used to determine seasonal patterns of fire activity. Results Fire regime characteristics are closely related to the latitudinal gradient in summer monsoon activity. Frequent low‐intensity fires occur in the monsoonal north, and infrequent, high‐intensity fires in the temperate south, demonstrating a trade‐off between frequency and intensity: that is, very high‐intensity fires are only associated with very low‐frequency fire regimes in the high biomass eucalypt forests of southern A ustralia. While these forests occasionally experience extremely intense fires (> 50,000 kW m −1 ), such regimes are exceptional, with most of the continent dominated by grass fuels, typically burning with lower intensity (< 5000 kW m −1 ). Main conclusions Australia's fire regimes exhibit a coherent pattern of frequent, grass‐fuelled fires in many differing vegetation types. While eucalypts are a quintessential A ustralian entity, their contribution as a dominant driver of high‐intensity fire regimes, via their litter and bark fuels, is restricted to the forests of the continent's southern and eastern extremities. Our analysis suggests that the foremost driver of fire regimes at the continental scale is not productivity, as postulated conceptually, but the latitudinal gradient in summer monsoon rainfall activity.

Next generation sequencing is revolutionizing molecular ecology by simplifying the development of molecular genetic markers, including microsatellites. Here, we summarize the results of the large-scale development of microsatellites for 54 nonmodel species using next generation sequencing and show that there are clear differences amongst plants, invertebrates and vertebrates for the number and proportion of motif types recovered that are able to be utilized as markers. We highlight that the heterogeneity within each group is very large. Despite this variation, we provide an indication of what number of sequences and consequent proportion of a 454 run are required for the development of 40 designable, unique microsatellite loci for a typical molecular ecological study. Finally, to address the challenges of choosing loci from the vast array of microsatellite loci typically available from partial genome runs (average for this study, 2341 loci), we provide a microsatellite development flowchart as a procedural guide for application once the results of a partial genome run are obtained.

The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.

Prescribed burning is a commonly applied management tool, and there has been considerable debate over the efficacy of its application. We review data relating to the effectiveness of prescribed burning in Australia. Specifically, we address two questions: (1) to what extent can fuel reduction burning reduce the risk of loss of human life and economic assets posed from wildfires? (2) To what extent can prescribed burning be used to reduce the risk of biodiversity loss? Data suggest that prescribed burning can achieve a reduction in the extent of wildfires; however, at such levels, the result is an overall increase in the total area of the landscape burnt. Simulation modelling indicates that fuel reduction has less influence than weather on the extent of unplanned fire. The need to incorporate ecological values into prescribed burning programmes is becoming increasingly important. Insufficient data are available to determine if existing programs have been successful. There are numerous factors that prevent the implementation of better prescribed burning practices; most relate to a lack of clearly defined, measurable objectives. An adaptive risk management framework combined with enhanced partnerships between scientists and fire-management agencies is necessary to ensure that ecological and fuel reduction objectives are achieved.

Summary Leaf area (LA), mass per area (LMA), nitrogen per unit area (N area ) and the leaf‐internal to ambient CO 2 ratio (χ) are fundamental traits for plant functional ecology and vegetation modelling. Here we aimed to assess how their variation, within and between species, tracks environmental gradients. Measurements were made on 705 species from 116 sites within a broad north–south transect from tropical to temperate Australia. Trait responses to environment were quantified using multiple regression; within‐ and between‐species responses were compared using analysis of covariance and trait‐gradient analysis. Leaf area, the leaf economics spectrum (indexed by LMA and N area ) and χ (from stable carbon isotope ratios) varied almost independently among species. Across sites, however, χ and LA increased with mean growing‐season temperature (mGDD 0 ) and decreased with vapour pressure deficit (mVPD 0 ) and soil pH. LMA and N area showed the reverse pattern. Climate responses agreed with expectations based on optimality principles. Within‐species variability contributed < 10% to geographical variation in LA but > 90% for χ, with LMA and N area intermediate. These findings support the hypothesis that acclimation within individuals, adaptation within species and selection among species combine to create predictable relationships between traits and environment. However, the contribution of acclimation/adaptation vs species selection differs among traits.

In coastal areas around the world, the dominant primary producers are benthic macrophytes, including seagrasses and macroalgae, that provide habitat structure and food for diverse and abundant populations and communities, and drive ecosystem processes. Seagrass meadows and macroalgal forests are economically central to coastal human communities, particularly in the developing world, contributing to fisheries yield, storm protection, blue carbon storage, and important cultural values. These services are threatened worldwide by human activities, with substantial areas of seagrass and kelp forests lost over the last half-century. Tracking status and trends in marine macrophyte cover and quality is an emerging priority for ocean and coastal management, but doing so has been challenged by limited coordination across the numerous efforts to monitor macrophytes, which vary widely in goals, methodologies, scales, capacity, governance approaches, and data availability. Here, we present a consensus assessment and recommendations on the current state of and opportunities for advancing global marine macrophyte observations, integrating contributions from a community of researchers with broad geographic and disciplinary expertise. The time is ripe to harmonize marine macrophyte observations by building on existing networks and identifying a core set of common metrics and approaches in sampling design, field measurements, taxonomy, governance, capacity building, and data management. A global macrophyte observation community would then be facilitated by ensuring rigorous documentation, archiving and open-access sharing of protocols and resources at all stages of workflow, from field surveys to data management, and provision of open-access data. Realizing these recommendations will produce more effective, efficient, and responsive observing, a more accurate global picture of change in macrophyte systems, and stronger international capacity for sustaining observations.

Field and laboratory studies of 19 diclinous species endemic to Australia help to clarify the nature and evolution of andromonoecy, androdioecy, and dioecy in the genus Solanum. Ten species are andromonoecious; typically these species bear inflorescences with a single, large basal hermaphroditic flower and 12-60 distal, smaller staminate flowers. We suggest that the andromonoecious condition was derived from hermaphroditic-flowered ancestors in part by hemisterilization of flowers but largely by addition of staminate flowers. The resultant larger inflorescences are hypothesized to serve both to attract and to entrain pollinators, yielding more or higher-quality seed set in hermaphroditic flowers and/or greater dispersion of pollen from staminate flowers. We suggest that andromonoecy may also serve to reduce selling. Nine other species are morphologically androdioecious but functionally dioecious. In these species, staminate flowers, like those of the andromonoecious species, bear anthers with copious tricolporate pollen and a highly reduced gynoecium. The morphologically hermaphroditic flowers are functionally pistillate and borne singly in inflorescences, and they bear anthers with inaperturate pollen. The inaperturate pollen, although viable, never germinates and is hypothesized to be retained in pistillate flowers as a reward to pollinators in the nectarless Solanum flowers. All other species of Solanum studied with pollen dimorphism in which one pollen morph is inaperturate are also best treated as functionally dioecious. We conclude that there is no evidence for androdioecy in Solanum. A review of other families suggests that there is little support for this unusual breeding system in any other angiosperm group either. Preliminary analyses suggest that andromonoecy and dioecy are polyphyletic in Solanum. Furthermore, dioecy is as likely to have arisen from hermaphroditic as from andromonoecious ancestors.

Accurate ground-based estimation of the carbon stored in terrestrial ecosystems is critical to quantifying the global carbon budget. Allometric models provide cost-effective methods for biomass prediction. But do such models vary with ecoregion or plant functional type? We compiled 15 054 measurements of individual tree or shrub biomass from across Australia to examine the generality of allometric models for above-ground biomass prediction. This provided a robust case study because Australia includes ecoregions ranging from arid shrublands to tropical rainforests, and has a rich history of biomass research, particularly in planted forests. Regardless of ecoregion, for five broad categories of plant functional type (shrubs; multistemmed trees; trees of the genus Eucalyptus and closely related genera; other trees of high wood density; and other trees of low wood density), relationships between biomass and stem diameter were generic. Simple power-law models explained 84-95% of the variation in biomass, with little improvement in model performance when other plant variables (height, bole wood density), or site characteristics (climate, age, management) were included. Predictions of stand-based biomass from allometric models of varying levels of generalization (species-specific, plant functional type) were validated using whole-plot harvest data from 17 contrasting stands (range: 9-356 Mg ha(-1) ). Losses in efficiency of prediction were <1% if generalized models were used in place of species-specific models. Furthermore, application of generalized multispecies models did not introduce significant bias in biomass prediction in 92% of the 53 species tested. Further, overall efficiency of stand-level biomass prediction was 99%, with a mean absolute prediction error of only 13%. Hence, for cost-effective prediction of biomass across a wide range of stands, we recommend use of generic allometric models based on plant functional types. Development of new species-specific models is only warranted when gains in accuracy of stand-based predictions are relatively high (e.g. high-value monocultures).

Wood density is often considered to be a key plant functional trait. But it is not clear what actually wood density is? We rigorously quantified anatomical underpinnings of wood density variation. We found that density was mainly driven by properties of mechanical tissue such as fibre wall fraction and fibre lumen fraction. However, there was also a substantial anatomical variation independent of density. This variation suggests that different plant ecological strategies may be available to woods with the same density. Our results imply that density is a complex characteristic of wood rather than a straightforward indicator of plant ecological strategies.

Forest vulnerability to drought is expected to increase under anthropogenic climate change, and drought-induced mortality and community dynamics following drought have major ecological and societal impacts. Here, we show that tree mortality concomitant with drought has led to short-term (mean 5 y, range 1 to 23 y after mortality) vegetation-type conversion in multiple biomes across the world (131 sites). Self-replacement of the dominant tree species was only prevalent in 21% of the examined cases and forests and woodlands shifted to nonwoody vegetation in 10% of them. The ultimate temporal persistence of such changes remains unknown but, given the key role of biological legacies in long-term ecological succession, this emerging picture of postdrought ecological trajectories highlights the potential for major ecosystem reorganization in the coming decades. Community changes were less pronounced under wetter postmortality conditions. Replacement was also influenced by management intensity, and postdrought shrub dominance was higher when pathogens acted as codrivers of tree mortality. Early change in community composition indicates that forests dominated by mesic species generally shifted toward more xeric communities, with replacing tree and shrub species exhibiting drier bioclimatic optima and distribution ranges. However, shifts toward more mesic communities also occurred and multiple pathways of forest replacement were observed for some species. Drought characteristics, species-specific environmental preferences, plant traits, and ecosystem legacies govern postdrought species turnover and subsequent ecological trajectories, with potential far-reaching implications for forest biodiversity and ecosystem services.

We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.

Seagrasses are important marine ecosystems situated throughout the world’s coastlines. They are facing declines around the world due to global and local threats such as rising ocean temperatures, coastal development and pollution from sewage outfalls and agriculture. Efforts have been made to reduce seagrass loss through reducing local and regional stressors, and through active restoration. Seagrass restoration is rapidly maturing but improved restoration practices are needed to enhance the success of future programs. Major gaps in knowledge remain, especially our understanding of how to restore tropical species in Australia. Prior research efforts have provided valuable insights into factors influencing the outcomes of restoration and there are now several examples of successful large-scale restoration programs. A variety of tools and techniques have recently been developed that will improve the efficiency, cost effectiveness, and scalability of restoration programs. This review describes emerging techniques for restoration, key considerations for future programs, and highlights the benefits of increased collaboration, Traditional Owner (First Nation) and stakeholder engagement. Combined, these lessons and emerging approaches show that seagrass restoration is possible and efforts should be directed at upscaling seagrass restoration into the future. This is critical for the future conservation of this important ecosystem and the ecological and coastal communities they support.

Abstract Aim Understanding the relative importance of climatic and non‐climatic distribution drivers for co‐occurring, functionally similar species is required to assess potential consequences of climate change. This understanding is, however, lacking for most ecosystems. We address this knowledge gap and forecast changes in distribution for habitat‐forming seaweeds in one of the world's most species‐rich temperate reef ecosystems. Location The Great Southern Reef. The full extent of Australia's temperate coastline. Methods We assessed relationships between climatic and non‐climatic environmental data known to influence seaweed, and the presence of 15 habitat‐forming seaweeds. Distributional data (herbarium records) were analysed with MAXENT and generalized linear and additive models, to construct species distribution models at 0.2° spatial resolution, and project possible distribution shifts under the RCP 6.0 (medium) and 2.6 (conservative) emissions scenarios of ocean warming for 2100. Results Summer temperatures, and to a lesser extent winter temperatures, were the strongest distribution predictors for temperate habitat‐forming seaweeds in Australia. Projections for 2100 predicted major poleward shifts for 13 of the 15 species, on average losing 78% (range: 36%–100%) of their current distributions under RCP 6.0 and 62% (range: 27%–100%) under RCP 2.6. The giant kelp ( Macrocystis pyrifera) and three prominent fucoids ( Durvillaea potatorum, Xiphophora chondrophylla and Phyllospora comosa ) were predicted to become extinct from Australia under RCP 6.0. Many species currently distributed up the west and east coasts, including the dominant kelp Ecklonia radiata (71% and 49% estimated loss for RPC 6.0 and 2.6, respectively), were predicted to become restricted to the south coast. Main conclusions In close accordance with emerging observations in Australia and globally, our study predicted major range contractions of temperate seaweeds in coming decades. These changes will likely have significant impacts on marine biodiversity and ecosystem functioning because large seaweeds are foundation species for 100s of habitat‐associated plants and animals, many of which are socio‐economically important and endemic to southern Australia.