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Abstract Background Drought adaptation is critical to many tree species persisting under climate change, however our knowledge of the genetic basis for trees to adapt to drought is limited. This knowledge gap impedes our fundamental understanding of drought response and application to forest production and conservation. To improve our understanding of the genomic determinants, architecture, and trait constraints, we assembled a reference genome and detected ~ 6.5 M variants in 432 phenotyped individuals for the foundational tree Corymbia calophylla. Results We found 273 genomic variants determining traits with moderate heritability (h 2 SNP = 0.26–0.64). Significant variants were predominantly in gene regulatory elements distributed among several haplotype blocks across all chromosomes. Furthermore, traits were constrained by frequent epistatic and pleiotropic interactions. Conclusions Our results on the genetic basis for drought traits in Corymbia calophylla have several implications for the ability to adapt to climate change: (1) drought related traits are controlled by complex genomic architectures with large haplotypes, epistatic, and pleiotropic interactions; (2) the most significant variants determining drought related traits occurred in regulatory regions; and (3) models incorporating epistatic interactions increase trait predictions. Our findings indicate that despite moderate heritability drought traits are likely constrained by complex genomic architecture potentially limiting trees response to climate change.

Background: Pay-it-forward is when an individual receives a gift and is offered the opportunity to donate a gift to another person. This prosocial behavior has been used to develop health interventions, including strategies to increase sexually transmitted disease (STD) testing among men who have sex with men (MSM). Although pay-it-forward has improved service uptake across several settings, the underlying mechanism is unclear. This study aims to assess the participant experience to provide a theoretical basis for how pay-it-forward works among MSM in China. Methods: MSM participants of a pay-it-forward intervention were recruited from two STD clinics in Guangzhou, China, and underwent semi-structured interviews. Responses were translated verbatim into English. Transcripts were analyzed thematically. Results: Twenty-four MSM were interviewed. Despite many men feeling detached from other MSM, pay-it-forward engendered hope and solidarity among many participants. From an emotional perspective, reading handwritten postcards from other MSM induced gratitude, warmth, and support. From the perspective of the collective, receiving a free test and donating to other MSM solidified men's connection with the MSM community, even among men not yet out. Donation gave men an opportunity to pass on their gratitude and provide for MSM in need. Conclusions: Our data suggest that upstream reciprocity and warm glow explained pay-it-forward for some men, but this pathway was often complemented by a pathway aligned with principles of mutual aid. Further qualitative and mixed-methods research is needed to understand the basis for MSM decision-making about donating to support others.

Background: Malnutrition is a common and distressing condition among pancreatic cancer patients. Fewer than a quarter of pancreatic cancer patients receive medical nutrition therapy (MNT), important for improving nutritional status, weight maintenance, quality of life and survival. System, provider, and patient level barriers limit access to MNT. We propose to examine the feasibility of a 12-week multi-level, digital health intervention designed to expand MNT access among pancreatic cancer patients. Methods: Individuals with advanced pancreatic cancer starting chemotherapy (N = 80) will be 1:1 randomized to the intervention or usual care. The Support Through Remote Observation and Nutrition Guidance (STRONG) intervention includes system-level (e.g., routine malnutrition and screening), provider-level (e.g., dietitian training and web-based dashboard), and patient-level strategies (e.g., individualized nutrition plan, self-monitoring of dietary intake via Fitbit, ongoing goal monitoring and feedback). Individuals receiving usual care will be referred to dietitians based on their oncologists’ discretion. Study assessments will be completed at baseline, 4-, 8-, 12-, and 16-weeks. Results: Primary outcomes will be feasibility (e.g., recruitment, retention, assessment completion) and acceptability. We will collect additional implementation outcomes, such as intervention adherence, perceived usability, and feedback on intervention quality via an exit interview. We will collect preliminary data on outcomes that may be associated with the intervention including malnutrition, quality of life, treatment outcomes, and survival. Conclusion: This study will advance our knowledge on the feasibility of a digital health intervention to reduce malnutrition among individuals with advanced pancreatic cancer. Trial registration: NCT05675059, registered on December 9, 2022.

AbstractConservation translocations require robust post‐release monitoring to evaluate their success, which can be challenging to implement and maintain. Monitoring techniques that can account for the dispersal and cryptic nature of translocated animals are necessary to provide critical information on persistence and distribution. In this study, we developed a highly sensitive environmental DNA (eDNA) assay specific to the critically endangered western swamp turtle (Pseudemydura umbrina), a species currently undergoing trials of assisted colonization. Actively filtering sufficient volumes of water in lentic systems is difficult due to high concentrations of clogging particulates, therefore we assessed the viability of passive sampling in a controlled environment by submerging filter membranes and directly extracting DNA. Active sampling detected P. umbrina with a 97.6% detection rate, whereas passive sampling resulted in an 8.3% detection rate. We then used a fine‐scale eDNA sampling design and radio‐tracked translocated P. umbrina at the assisted colonization wetland to investigate eDNA dispersal and spatial monitoring resolution. We detected P. umbrina at 42% (7/17) of eDNA sample sites, and the probability of a positive eDNA detection was negatively associated with the distance of P. umbrina from the sampling site, indicating limited eDNA dispersal from the source. Systems with low natural mixing and limited eDNA dispersal provide an opportunity for high‐resolution spatial and temporal monitoring via targeted eDNA approaches. This is beneficial for monitoring rare species in these systems, as such high‐resolution results can provide insights into species presence, distribution, and microhabitat use.

Abstract Climate change is shifting temperatures from historical patterns, globally impacting forest composition and resilience. Seed germination is temperature‐sensitive, making the persistence of populations and colonization of available habitats vulnerable to warming. This study assessed germination response to temperature in foundation trees in south‐western Australia's Mediterranean‐type climate forests (Eucalyptus marginata (jarrah) and Corymbia calophylla (marri)) to estimate the thermal niche and vulnerability among populations. Seeds from the species' entire distribution were collected from 12 co‐occurring populations. Germination thermal niche was investigated using a thermal gradient plate (5–40°C). Five constant temperatures between 9 and 33°C were used to test how the germination niche (1) differs between species, (2) varies among populations, and (3) relates to the climate of origin. Germination response differed among species; jarrah had a lower optimal temperature and thermal limit than marri (To 15.3°C, 21.2°C; ED50 23.4°C, 31°C, respectively). The thermal limit for germination differed among populations within both species, yet only marri showed evidence for adaptation to thermal origins. While marri has the capacity for germination at higher thermal temperatures, jarrah is more vulnerable to global warming exceeding safety margins. This discrepancy is predicted to alter species distributions and forest composition in the future.

Understanding population connectivity and its effect on patterns of adaptation and plasticity is important for development of climate adaptation strategies to manage species under a changing climate. Local adaptation is a balance between selection pressure and gene flow and provides species with fitness benefits under current conditions. Management strategies to respond to predicted shifts in climate may be able to leverage local adaptation to assist with species persistence. In this study we examine the genomic diversity, gene flow and associations between genomic and environmental variation in Taxandria linearifolia across its distribution in the Warren River Catchment. Gene flow was restricted between populations in the drier hotter upper catchment compared to those residing in the cooler wetter regions of the catchment, potentially limiting the flow of genes adapted to predicted future climates. Using two separate methods to search for candidate loci, we found the highest number of correlations between loci and the environmental variable of mean moisture content of the coldest quarter, supporting the hypothesis that floodplain species are linked with water availability. These research findings indicate that species restricted to wet environments and having traits facilitating high gene flow, can show signals of adaptation when gene flow is disrupted, and populations are isolated. This development of adaptation in isolated populations makes assisted migration of dry adapted genotypes to other populations an effective strategy for facilitating long term persistence under changing climates.

Abstract Parasitism is a pervasive phenomenon in nature with the relationship between species driving evolution in both parasite and host. Due to their host‐dependent lifestyle, parasites may adapt to the abiotic environment in ways that differ from their hosts or from free‐living relatives; yet rarely has this been assessed. Here, we test two competing hypotheses related to whether putatively adaptive genetic variation in a specialist mistletoe associates with the same, or different, climatic variables as its host species. We sampled 11 populations of the specialist mistletoe Amyema gibberula var. tatei (n = 154) and 10 populations of its associated host Hakea recurva subsp. recurva (n = 160). Reduced‐representation sequencing was used to obtain genome‐wide markers and putatively adaptive variation detected using genome scan methods. Climate associations were identified using generalized dissimilarity modelling, and these were mapped geographically to visualize the spatial patterns of genetic composition. Our results supported the hypothesis of parasites and host species responding differently to climatic variables. Temperature was relatively more important in predicting allelic turnover in the specialist mistletoe while precipitation was more important for the host. This suggests that parasitic plants and host species may respond differently to selective pressures, potentially as a result of differing nutrient acquisition strategies. Specifically, mistletoes acquire water from hosts (rather than the abiotic environment), which may provide a buffer to precipitation as a selective pressure. This work deepens and complements the physiological and other ecological studies of adaptation and provides a window into the evolutionary processes that underlie previously observed phenomena. Applying these methods to a comparative study in a host–parasite system has also highlighted factors that affect the study of selection pressure on nonmodel organisms, such as differing adaptation rates and lack of reference genomes.

The bat fauna of Australia comprises some 25% of all terrestrial species, yet we know very little of the demography, dispersal, and movement dynamics of most bat species. The Pilbara leaf-nosed bat (Rhinonicteris aurantia Pilbara form) is a threatened microbat that roosts exclusively in caves that occur in mineral rich deposits in the Pilbara region. Due to their specific roost microclimate requirements these bats cannot survive for long without a suitable roost and are sensitive to roost disturbance. Understanding the connectivity of roosts throughout the Pilbara is crucial for informed decisions to mitigate potential impacts to persistence of this species in areas under economic development. Along with mitochondrial DNA (mtDNA) markers, we used reduced representation genomic sequencing of over 150 individuals from eight roost sites throughout the Pilbara and tested for landscape-scale population differentiation associated with the two major subregions — the Hamersley and Chichester, as well as finer-scale among roost variation. We found evidence of high rates of dispersal and low population structure within the Pilbara, indicating one panmictic population, with mtDNA results suggesting evidence of some female philopatry. Our results highlight the ongoing need for detailed genetic studies to provide critical insight to species dispersal, particularly in multi-use landscapes. We discuss the importance of identifying and retaining connectivity of key habitat to maintain genetic diversity and gene flow throughout panmictic populations.

Abstract Widespread plant species are expected to maintain genetic diversity and gene flow via pollen and seed dispersal. Stature is a key life history trait that affects seed and potentially pollen dispersal, with limited stature associated with limited dispersal and greater genetic differentiation. We sampled Hill’s tabletop wattle (Acacia hilliana) and curry wattle (Acacia spondylophylla), two co‐distributed, widespread, Acacia shrubs of low stature, across the arid Pilbara region of north‐western Australia. Using chloroplast sequence and nuclear microsatellite data we evaluated patterns of population genetic and phylogeographic diversity and structure, demographic signals, ratios of pollen to seed dispersal, evidence for historical refugia, and association between elevation and diversity. Results showed strong phylogeographic (chloroplast, GST = 0.831 and 0.898 for A. hilliana and A. spondylophylla, respectively) and contemporary (nuclear, FST = 0.260 and 0.349 for A. hilliana and A. spondylophylla, respectively) genetic structure in both species. This indicates limited genetic connectivity via seed and pollen dispersal associated with Acacia species of small stature compared to taller tree and shrub acacias across the Pilbara bioregion. This effect of stature on genetic structure is superimposed on moderate levels of genetic diversity that were expected based on widespread ranges (haplotype diversity h = 25 and 12; nuclear diversity He = 0.60 and 0.47 for A. hilliana and A. spondylophylla, respectively). Contemporary genetic structure was congruent at the greater landscape scale, especially in terms of strong genetic differentiation among geographically disjunct populations in less elevated areas. Measures of diversity and connectivity were associated with traits of greater geographic population proximity, population density, population size, and greater individual longevity, and some evidence for range expansion in A. hilliana. Results illustrate that low stature is associated with limited dispersal and greater patterns of genetic differentiation for congenerics in a common landscape and highlight the complex influence of taxon‐specific life history and ecological traits to seed and pollen dispersal.

Abstract Genetic studies are increasingly detecting cryptic taxa that likely represent a significant component of global biodiversity. However, cryptic taxa are often criticized because they are typically detected serendipitously and may not receive the follow‐up study required to verify their geographic or evolutionary limits. Here, we follow‐up a study of Eucalyptus salubris that unexpectedly detected two divergent lineages but was not sampled sufficiently to make clear interpretations. We undertook comprehensive sampling for an independent genomic analysis (3,605 SNPs) to investigate whether the two purported lineages remain discrete genetic entities or if they intergrade throughout the species’ range. We also assessed morphological and ecological traits, and sequenced chloroplast DNA. SNP results showed strong genome‐wide divergence (FST = 0.252) between two discrete lineages: one dominated the north and one the southern regions of the species’ range. Within lineages, gene flow was high, with low differentiation (mean FST = 0.056) spanning hundreds of kilometers. In the central region, the lineages were interspersed but maintained their genomic distinctiveness: an indirect demonstration of reproductive isolation. Populations of the southern lineage exhibited significantly lower specific leaf area and occurred on soils with lower phosphorus relative to the northern lineage. Finally, two major chloroplast haplotypes were associated with each lineage but were shared between lineages in the central distribution. Together, these results suggest that these lineages have non‐contemporary origins and that ecotypic adaptive processes strengthened their divergence more recently. We conclude that these lineages warrant taxonomic recognition as separate species and provide fascinating insight into eucalypt speciation.

Abstract The impact of Quaternary glaciation on the development of phylogeographic structure in plant species is well documented. In unglaciated landscapes, phylogeographic patterns tend to reflect processes relating to persistence and stochasticity, yet other factors, associated with the palaeogeographical history of the landscape, including geomorphological events, can also have a significant influence. The unglaciated landscape of south‐western Western Australia is an ideal location to observe these ancient drivers of lineage diversification, with tectonic activity associated with the Darling Fault in the late Pliocene attributed to patterns of deep phylogeographic divergence in a widespread tree from this region. Interestingly, other species within this region have not shown this pattern and this palaeogeographical boundary therefore presents an opportunity to examine age and historical distribution of plant species endemic to this region. In this study, we assess patterns of genetic diversity and structure across 28 populations of the widespread shrub Banksia sessilis using three cpDNA markers and nine nuclear microsatellite markers. Sixteen cpDNA haplotypes were identified, comprising two major chloroplast DNA lineages that are estimated to have diverged in the Pliocene, approximately 3.3 million years ago. This timing coincides with major geomorphological processes in the landscape, including the separation of the Darling Plateau from the adjacent Swan Coastal Plain, as well as eustatic changes on the Swan Coastal Plain that are likely to have resulted in the physical isolation of historical plant lineages. Chloroplast lineages were broadly aligned with populations associated with older lateritic soils of the Darling Plateau and Geraldton sandplains or the younger sandy soils associated with the Swan Coastal Plain and Southern Coastline. This structural pattern of lateritic versus non‐lateritic division was not observed in the nuclear microsatellite data that identified three genetic clades that roughly corresponded to populations in the North, South, and Central portions of the distributions.

Abstract Reptile populations are in decline globally, with total reptile abundance halving in the past half century, and approximately a fifth of species currently threatened with extinction. Research on reptile distributions, population trends, and trophic interactions can greatly improve the accuracy of conservation listings and planning for species recovery, but data deficiency is an impediment for many species. Environmental DNA (eDNA) can detect species and measure community diversity at diverse spatio‐temporal scales, and is especially useful for detection of elusive, cryptic, or rare species, making it potentially very valuable in herpetology. We aim to summarize the utility of eDNA as a tool for informing reptile conservation and management and discuss the benefits and limitations of this approach. A literature review was conducted to collect all studies that used eDNA and focus on reptile ecology, conservation, or management. Results of the literature search are summarized into key discussion points, and the review also draws on eDNA studies from other taxa to highlight methodological challenges and to identify future research directions. eDNA has had limited application to reptiles, relative to other vertebrate groups, and little use in regions with high species richness. eDNA techniques have been more successfully applied to aquatic reptiles than to terrestrial reptiles, and most (64%) of studies focused on aquatic habitats. Two of the four reptilian orders dominate the existing eDNA studies (56% Testudines, 49% Squamata, 5% Crocodilia, 0% Rhynchocephalia). Our review provides direction for the application of eDNA as an emerging tool in reptile ecology and conservation, especially when it can be paired with traditional monitoring approaches. Technologies associated with eDNA are rapidly advancing, and as techniques become more sensitive and accessible, we expect eDNA will be increasingly valuable for addressing key knowledge gaps for reptiles.

Topographically heterogeneous areas are likely to act as refugia for species because they facilitate survival during regional climatic stress due to availability of a range of microenvironments. The Stirling Ranges are a topographically complex area in the generally subdued and ancient landscape of south-western Australia. We investigated the influence of these landscape features on the evolutionary history of the rare woody shrub, Banksia brownii through a combined approach using phylogeographic analysis of sequence data from three chloroplast sequences, the trnV–ndhC, trnQ–rps16, and rpl32–ndhF intergenic spacer regions, and species distribution modeling. The Stirling Ranges showed high genetic diversity and differentiation among populations consistent with localized persistence and maintenance of large populations in an area that species distribution modeling identified as providing habitat stability at the Last Glacial Maximum as well as under warmer conditions. In contrast, populations in the adjacent subdued lowlands showed signals of low diversity, suggesting contraction, and subsequent expansion from localized refugia in the west. Cool summers are an important climatic variable for the species and species distribution modeling showed suitable habitat identified at the LGM suggesting expansion at this time following likely contraction during earlier warmer climatic oscillations. The isolated, coastal population at Vancouver Peninsula showed low diversity but no differentiation and it may have been established in more recent historical times, possibly through Aboriginal movement of seed. Our analysis of B. brownii highlights the complex evolutionary history of the species and the influence of topographic complexity and habitat heterogeneity in this global biodiversity hotspot.

Abstract Background Herbaria are valuable sources of extensive curated plant material that are now accessible to genetic studies because of advances in high-throughput, next-generation sequencing methods. As an applied assessment of large-scale recovery of plastid and ribosomal genome sequences from herbarium material for plant identification and phylogenomics, we sequenced 672 samples covering 21 families, 142 genera and 530 named and proposed named species. We explored the impact of parameters such as sample age, DNA concentration and quality, read depth and fragment length on plastid assembly error. We also tested the efficacy of DNA sequence information for identifying plant samples using 45 specimens recently collected in the Pilbara. Results Genome skimming was effective at producing genomic information at large scale. Substantial sequence information on the chloroplast genome was obtained from 96.1% of samples, and complete or near-complete sequences of the nuclear ribosomal RNA gene repeat were obtained from 93.3% of samples. We were able to extract sequences for the core DNA barcode regions rbcL and matK from 96 to 93.3% of samples, respectively. Read quality and DNA fragment length had significant effects on sequencing outcomes and error correction of reads proved essential. Assembly problems were specific to certain taxa with low GC and high repeat content (Goodenia, Scaevola, Cyperus, Bulbostylis, Fimbristylis) suggesting biological rather than technical explanations. The structure of related genomes was needed to guide the assembly of repeats that exceeded the read length. DNA-based matching proved highly effective and showed that the efficacy for species identification declined in the order cpDNA >> rDNA > matK >> rbcL. Conclusions We showed that a large-scale approach to genome sequencing using herbarium specimens produces high-quality complete cpDNA and rDNA sequences as a source of data for DNA barcoding and phylogenomics.

Abstract Climate change is testing the resilience of forests worldwide pushing physiological tolerance to climatic extremes. Plant functional traits have been shown to be adapted to climate and have evolved patterns of trait correlations (similar patterns of distribution) and coordinations (mechanistic trade‐off). We predicted that traits would differentiate between populations associated with climatic gradients, suggestive of adaptive variation, and correlated traits would adapt to future climate scenarios in similar ways. We measured genetically determined trait variation and described patterns of correlation for seven traits: photochemical reflectance index (PRI), normalized difference vegetation index (NDVI), leaf size (LS), specific leaf area (SLA), δ13C (integrated water‐use efficiency, WUE), nitrogen concentration (NCONC), and wood density (WD). All measures were conducted in an experimental plantation on 960 trees sourced from 12 populations of a key forest canopy species in southwestern Australia. Significant differences were found between populations for all traits. Narrow‐sense heritability was significant for five traits (0.15–0.21), indicating that natural selection can drive differentiation; however, SLA (0.08) and PRI (0.11) were not significantly heritable. Generalized additive models predicted trait values across the landscape for current and future climatic conditions (>90% variance). The percent change differed markedly among traits between current and future predictions (differing as little as 1.5% (δ13C) or as much as 30% (PRI)). Some trait correlations were predicted to break down in the future (SLA:NCONC, δ13C:PRI, and NCONC:WD). Synthesis: Our results suggest that traits have contrasting genotypic patterns and will be subjected to different climate selection pressures, which may lower the working optimum for functional traits. Further, traits are independently associated with different climate factors, indicating that some trait correlations may be disrupted in the future. Genetic constraints and trait correlations may limit the ability for functional traits to adapt to climate change.

Managing pest vertebrate species in Australia is a significant challenge for government, industry, research sectors and land-managers. Innovative tools such as genetic biocontrol offers decision-makers a potentially effective means of reducing the impact of pest species incursions. To determine the conditions for investment in genetic biocontrol, we applied qualitative engagement methodologies to identify and integrate existing knowledge of pest species research and management in Australia. Two facilitated workshops were held to determine key topics related to genetic biocontrol technologies for selected pest species. The topics explored during workshop discussions included: identifying existing knowledge gaps; risk perceptions; social and ethical considerations and; industry and business considerations. The workshops' aim was to assess the potential, the priorities and the risk parameters among expert stakeholders and decision-makers for using genetic biocontrol approaches to reduce the impacts of key pest species in Australia. This paper reports on the design, process and outcomes of each workshop to inform the creation of a decision framework. Stakeholders were cautiously optimistic of pursuing continued research and development for vertebrate pest management in Australia. However, employing an appropriate, transparent process for incorporating diverse stakeholder perspectives on genetic biocontrol technologies is essential to ensure their development and use remains supported. This outcome will require meaningful investment in both social science investigations and well-considered engagement processes concurrent with biotechnology development globally.

Genomic analysis can be a valuable tool to assistmanagement of non-native invasive species, through determining source and number of introductions as well as clarifying phylogenetic relationships. Here, we used whole chloroplast sequencing to investigate the introduction history of Passiflora foetida sensu lato in Australia and clarify its relationship with other Passiflora species present. Phylogenetic analysis of chloroplast genome data identified three separate genetic lineages of P. foetida s. l. present in Australia, indicating multiple introductions. These lineages had affinities to samples from three separate areas within the native range in Central and South America that represented phylogenetically distinct lineages. These results provide a basis for a targeted search of the native range of P. foetida s. l. for candidate biological control agents that have co-evolved with this species and are thus better adapted to the lineages that are present in Australia. Results also indicated that the Passiflora species native to Australia are in a separate clade to that of P. foetida s. l. and other introduced Passiflora species cultivated in Australia. This knowledge is important to assess the likelihood of finding biological control agents for P. foetida s. l. that will be sufficiently host-specific for introduction in Australia. As P. foetida s. l. is a widespread non-native invasive species across many regions of the world, outcomes from this work highlight the importance of first evaluating the specific entities present in a country before the initiation of a biological control program.

Abstract Fragmentation of natural vegetation is currently one of the largest threats to plant populations and their interactions with pollinators. Plant reproductive susceptibility to habitat fragmentation has been investigated in many species; however, the response of wild mass‐flowering species is poorly known, with research limited to mainly boreal plant species. Here, we studied twelve remnant populations of the threatened mass‐flowering shrub Conospermum undulatum in the southwest Australian biodiversity hotspot, each presenting different population size, level of isolation, and floral display. We assessed the impact of fragmentation on (a) fruit and seed production; and (b) seed germination. To gain a deeper understanding of factors influencing the reproductive success of C. undulatum, we performed pollinator exclusion and self‐pollination treatments to experimentally assess the mating system of this threatened shrub. We found C. undulatum to be strictly self‐incompatible and totally reliant on pollinators visiting with an outcrossed pollen load to complete the reproductive cycle. Further, we found that fruit production dropped from 35% to

Abstract Determining patterns of plant diversity on granite inselbergs is an important task for conservation biogeography due to mounting threats. However, beyond the tropics there are relatively few quantitative studies of floristic diversity, or consideration of these patterns and their environmental, biogeographic, and historical correlates for conservation. We sought to contribute broader understanding of global patterns of species diversity on granite inselbergs and inform biodiversity conservation in the globally significant Southwest Australian Floristic Region (SWAFR). We surveyed floristics from 16 inselbergs (478 plots) across the climate gradient of the SWAFR stratified into three major habitats on each outcrop. We recorded 1,060 species from 92 families. At the plot level, local soil and topographic variables affecting aridity were correlated with species richness in herbaceous (HO) and woody vegetation (WO) of soil‐filled depressions, but not in woody vegetation on deeper soils at the base of outcrops (WOB). At the outcrop level, bioclimatic variables affecting aridity were correlated with species richness in two habitats (WO and WOB) but, contrary to predictions from island biogeography, were not correlated with inselberg area and isolation in any of the three habitats. Species turnover in each of the three habitats was also influenced by aridity, being correlated with bioclimatic variables and with interplot geographic distance, and for HO and WO habitats with local site variables. At the outcrop level, species replacement was the dominant component of species turnover in each of the three habitats, consistent with expectations for long‐term stable landscapes. Our results therefore highlight high species diversity and turnover associated with granite outcrop flora. Hence, effective conservation strategies will need to focus on protecting multiple inselbergs across the entire climate gradient of the region.

Abstract Natural ecosystems are under pressure from increasing abiotic and biotic stressors, including climate change and novel pathogens, which are putting species at risk of local extinction, and altering community structure, composition and function. Here, we aim to assess adaptive variation in growth and fungal disease resistance within a foundation tree, Corymbia calophylla to determine local adaptation, trait heritability and genetic constraints in adapting to future environments. Two experimental planting sites were established in regions of contrasting rainfall with seed families from 18 populations capturing a wide range of climate origins (~4,000 individuals at each site). Every individual was measured in 2015 and 2016 for growth (height, basal diameter) and disease resistance to a recently introduced leaf blight pathogen (Quambalaria pitereka). Narrow‐sense heritability was estimated along with trait covariation. Trait variation was regressed against climate‐of‐origin, and multivariate models were used to develop predictive maps of growth and disease resistance. Growth and blight resistance traits differed significantly among populations, and these differences were consistent between experimental sites and sampling years. Growth and blight resistance were heritable, and comparisons between trait differentiation (QST) and genetic differentiation (FST) revealed that population differences in height and blight resistance traits are due to divergent natural selection. Traits were significantly correlated with climate‐of‐origin, with cool and wet populations showing the highest levels of growth and blight resistance. These results provide evidence that plants have adaptive growth strategies and pathogen defence strategies. Indeed, the presence of standing genetic variation and trait heritability of growth and blight resistance provide capacity to respond to novel, external pressures. The integration of genetic variation into adaptive management strategies, such as assisted gene migration and seed sourcing, may be used to provide greater resilience for natural ecosystems to both biotic and abiotic stressors.

The Southwest Australian Floristic Region (SWAFR) is a global biodiversity hotspot with high plant diversity and endemism and a broad range of threatening processes. An outcome of this is a high proportion of rare and threatened plant species. Ongoing discovery and taxonomic description of new species, many of which are rare, increases the challenges for recovery of threatened species and prioritisation of conservation actions. Current conservation of this diverse flora is based on integrated and scientific evidence-based management. Here we present an overview of current approaches to the conservation of threatened flora in the SWAFR with a focus on active management through recovery and restoration that is integrated with targeted research. Key threats include disease, fragmentation, invasive weeds, altered fire regimes, grazing, altered hydro-ecology and climate change. We highlight the integrated approach to management of threats and recovery of species with four case studies of threatened flora recovery projects that illustrate the breadth of interventions ranging from In situ management to conservation reintroductions and restoration of threatened species habitats. Our review and case studies emphasise that despite the scale of the challenge, a scientific understanding of threats and their impacts enables effective conservation actions to arrest decline and enhance recovery of threatened species and habitats. Keywords: Threatened species, Threatening processes, Conservation, Recovery, Restoration, Biodiversity hotspot

The Southwest Australian Floristic Region (SWAFR) supports an exceptional number of threatened and data-deficient flora. In this study, we: (i) collated statistics on the number, listing criteria and tenure of occurrence of threatened and data-deficient flora; (ii) conducted spatial and biogeographic analyses to address questions concerning patterns of diversity of threatened and data-deficient flora relative to the whole flora and evolutionary and threat drivers; and (iii) examined whether threatened and data-deficient flora richness is evenly distributed across plant lineages. We found that although threatened and data-deficient flora occurred across the breadth of the SWAFR, high richness was concentrated in a limited number of locations, which were not always strongly aligned with areas of higher land transformation. Data-deficient flora demonstrated different spatial patterns of occurrence to threatened flora. Approximately 70% of the populations of threatened and data-deficient flora occurred outside of lands managed primarily for conservation. Both evolutionary history and contemporary threats contribute to the current status and distribution of diversity of the threatened and data-deficient flora, with evolutionary history playing a significant role in predisposing a portion of the flora to having population traits that result in those flora meeting IUCN Red List criteria, along with ecological traits that predispose some to specific novel threats. An understanding of the distribution of species and threats, flora traits, and how these traits mediate susceptibility to threats, offers one potential way forward for an initial assessment of which of the 1819 data-deficient flora may be most at risk of extinction.

Globally, species and ecosystems continue to decline, and the impact on threatened species is increasing [...]

Subspecies are traditionally defined using phenotypic differences associated with different geographical areas. Yet patterns of morphological and genetic variation may not coincide and thereby fail to reflect species’ evolutionary history. The division of the shrub Banksia nivea Labill. into one widespread (B. nivea subsp. nivea) and two geographically localized subspecies (B. nivea subsp. uliginosa (A.S. George) A.R. Mast & K.R. Thiele and B. nivea subsp. Morangup (M. Pieroni 94/2)) in south-west Australia has been based mainly on variation in leaf shape and pistil length, although flowering time and habitat differences are also evident, and subsp. uliginosa occurs on a different substrate. To assess the genetic divergence of B. nivea subspecies, we genotyped representatives from each subspecies for nuclear microsatellite and non-coding chloroplast sequence variation. We used distance and parsimony-based methods to assess genetic relatedness. Patterns were consistent with the existing taxonomy of subsp. nivea and uliginosa but not subsp. Morangup. Phylogenetic analyses revealed evidence for a more recent divergence of subsp. uliginosa associated with expansion from dryer sandy soils into the winter-wet ironstone soils in the southwest of Western Australia, consistent with progressive long-term climatic drying. Nuclear microsatellites showed low to moderate diversity, high population differentiation overall, and genetic structuring of subspecies in different biogeographical areas. We propose this pattern reflects the predicted impact of a patchy distribution, small populations, and restrictions to gene flow driven by both distance and biogeographic differences in subspecies’ habitats.

Premise Recent habitat fragmentation is posing a risk to the wavy‐leaved smokebush, Conospermum undulatum (Proteaceae), a rare plant species endemic to southwestern Western Australia. Microsatellite markers are required to characterize the genetic diversity and structure of the species for conservation purposes and to facilitate ecological studies. Methods and Results Illumina MiSeq high‐throughput sequencing was used to develop 20 novel microsatellite markers for C. undulatum. Polymorphism at each locus was assessed using 72 individuals from three natural populations. Nineteen markers were polymorphic, with the number of alleles per locus ranging from two to 21, and observed and expected heterozygosity ranging from 0.000 to 1.000 and 0.117 to 0.919, respectively. All markers successfully amplified in three congeneric species (C. stoechadis, C. canaliculatum and C. triplinervium). Conclusions The microsatellite markers will be useful for revealing patterns of genetic diversity, dispersal dynamics, and hybridization events for C. undulatum to inform future conservation efforts.

The taxonomy of Australian Isoodon bandicoots has changed continuously over the last 20 years, with recent genetic studies indicating discordance of phylogeographic units with current taxonomic boundaries. Uncertainty over species relationships within southern and western Isoodon, encompassing I. obesulus, I. auratus, and I. fusciventer, has been ongoing and hampered by limited sampling in studies to date. Identification of taxonomic units remains a high priority, as all are threatened to varying extents by ongoing habitat loss and feral predation. To aid diagnosis of conservation units, we increased representative sampling of I. auratus and I. fusciventer from Western Australia (WA) and investigated genetic relationships of these with I. obesulus from South Australia (SA) and Victoria (Vic) using microsatellite markers and mitochondrial DNA. mtDNA analysis identified three major clades concordant with I. obesulus (Vic), I. auratus, and I. fusciventer; however, I. obesulus from SA was polyphyletic to WA taxa, complicating taxonomic inference. Microsatellite data aided identification of evolutionarily significant units consistent with existing taxonomy, with the exception of SA I. obesulus. Further, analyses indicated SA and Vic I. obesulus have low diversity, and these populations may require more conservation efforts than others to reduce further loss of genetic diversity.

Current approaches to biodiversity conservation are largely based on geographic areas, ecosystems, ecological communities, and species, with less attention on genetic diversity and the evolutionary continuum from populations to species. Conservation management generally rests on discrete categories, such as identified species, and, for threated taxa, intraspecific units. Species, in particular, provide a common measure of biodiversity yet in both theory and nature, speciation is typically a protracted process progressing from connected populations to unambiguous species with variable rates of phenotypic, ecological and genetic divergence. Thus, most recognized species are not genetically uniform and are sometimes highly structured into historically isolated populations worthy of consideration as intraspecific units that represent unique genetic diversity for conservation. Genome screens offer unprecedented resolution of structure across taxonomic boundaries in species complexes, and have the potential to oversplit species if not interpreted conservatively. This highlights the blurred line between populations and species, and can confound simple dichotomies of “species” vs. “not species.” At the same time, like plants, there is increasing evidence that even distantly related animal species can hybridize and exchange genes. A review of conservation legislation reveals that legal definitions of “species” are quite flexible and can accommodate a range of infra-specifictaxa and divergent populations, as well as taxonomically recognized species. For example, the legislative definition of a species around the world can include: species, subspecies, varieties, and geographically and/or genetically distinct populations. In principle, this flexibility allows for protection of genetic diversity and maintenance of evolutionary processes at a broad range of infra-specific levels. However, evolutionary biologists often fail to adequately justify and then translate their evidence for genetically defined units into categories suited to assessment under local legislation. We recommend that (i) genomic data should be interpreted conservatively when formally naming species, (ii) concomitantly, there should be stronger impetus and a more uniform approach to identifying clearly justified intraspecific units, (iii) guidelines be developed for recognizing and labeling intraspecific data that align with best scientific practice, and (iv) that the more nuanced view of species and speciation emerging from genomic analyses is communicated more effectively by scientists to decision makers.

Building DNA barcode databases for plants has historically been ad hoc, and often with a relatively narrow taxonomic focus. To realize the full potential of DNA barcoding for plants, and particularly its application to metabarcoding for mixed-species environmental samples, systematic sequencing of reference collections is required using an augmented set of DNA barcode loci, applied according to agreed data generation and analysis standards. The largest and most complete reference collections of plants are held in herbaria. Australia has a globally significant flora that is well sampled and expertly curated by its herbaria, coordinated through the Council of Heads of Australasian Herbaria. There exists a tremendous opportunity to provide a comprehensive and taxonomically robust reference database for plant DNA barcoding applications by undertaking coordinated and systematic sequencing of the entire flora of Australia utilizing existing herbarium material. In this paper, we review the development of DNA barcoding and metabarcoding and consider the requirements for a robust and comprehensive system. We analyzed the current availability of DNA barcode reference data for Australian plants, recommend priority taxa for database inclusion, and highlight future applications of a comprehensive metabarcoding system. We urge that large-scale and coordinated analysis of herbarium collections be undertaken to realize the promise of DNA barcoding and metabarcoding, and propose that the generation and curation of reference data should become a national investment priority.

Failing to test multiple or non-standard variables in studies that investigate the effects of habitat fragmentation on plant populations may limit the detection of unexpected causative relationships. Here, we investigated the impacts of habitat fragmentation on the pollination, reproduction, mating system and progeny performance of Eucalyptus wandoo, a foundation tree that is bird and insect pollinated with a mixed-mating system. We explored a range of possible causative mechanisms, including soil properties that are likely to be altered in the agricultural matrix of a landscape that has naturally nutrient-poor soils and secondary soil salinization caused by the removal of native vegetation. We found very strong negative relationships between soil salinity and fruit production, thus providing some of the first evidence for the effects of salinity on reproduction in remnant plant populations. Additionally, we found unexpectedly higher rates of seedling survival in linear populations, most likely driven by increased soil P content from adjacent cereal cropping. Higher rates of seed germination in small populations were related to both higher pollen immigration and greater nutrient availability. Trees in small populations had unexpectedly much higher levels of pollination than in large populations, but they produced fewer seeds per fruit and outcrossing rates did not vary consistently with fragmentation. These results are consistent with small populations having much higher insect abundances but also increased rates of self-pollination, combined with seed abortion mechanisms that are common in the Myrtaceae. This study highlights the need to better understand and mitigate sub-lethal effects of secondary soil salinity in plants growing in agricultural remnants, and indicates that soil properties may play an important role in influencing seed quality.

As species face rapid environmental change, we can build resilient populations through restoration projects that incorporate predicted future climates into seed sourcing decisions. Eucalyptus melliodora is a foundation species of a critically endangered community in Australia that is a target for restoration. We examined genomic and phenotypic variation to make empirical based recommendations for seed sourcing. We examined isolation by distance and isolation by environment, determining high levels of gene flow extending for 500 km and correlations with climate and soil variables. Growth experiments revealed extensive phenotypic variation both within and among sampling sites, but no site-specific differentiation in phenotypic plasticity. Model predictions suggest that seed can be sourced broadly across the landscape, providing ample diversity for adaptation to environmental change. Application of our landscape genomic model to E. melliodora restoration projects can identify genomic variation suitable for predicted future climates, thereby increasing the long term probability of successful restoration.

Invasive animals have been linked to the extinctions of native wildlife, and to significant agricultural financial losses or impacts. Current approaches to control invasive species require ongoing resources and management over large geographic scales, and often result in the short-term suppression of populations. New and innovative approaches are warranted. Recently, the RNA guided gene drive system based on CRISPR/Cas9 is being proposed as a potential gene editing tool that could be used by wildlife managers as a non-lethal addition or alternative to help reduce pest animal populations. While regulatory control and social acceptance are crucial issues that must be addressed, there is an opportunity now to identify the knowledge and research gaps that exist for some important invasive species. Here we systematically determine the knowledge gaps for pest species for which gene drives could potentially be applied. We apply a conceptual ecological risk framework within the gene drive context within an Australian environment to identify key requirements for undertaking work on seven exemplar invasive species in Australia. This framework allows an evaluation of the potential research on an invasive species of interest and within a gene drive and risk context. We consider the currently available biological, genetic and ecological information for the house mouse, European red fox, feral cat, European rabbit, cane toad, black rat and European starling to evaluate knowledge gaps and identify candidate species for future research. We discuss these findings in the context of future thematic areas of research worth pursuing in preparation for a more formal assessment of the use of gene drives as a novel strategy for the control of these and other invasive species. Keywords: Invasive species, Gene drive, CRISPR, Pest management, Islands

There is increasing awareness that the long-term success of ecological restoration efforts can be compromised if projected climate change is not effectively incorporated in restoration planning. We propose an approach that aims to support the decision-making process for seed provenance selection in ecological restoration when clear genetic-based guidelines for seed transfer are not available. The approach takes advantage of the increasing availability and refinement of user-friendly web-based GIS interfaces that allow non-experts to directly access biodiversity and environmental data, and build species distribution models. It offers an easily accessible desktop method that land managers and practitioners can use to gain insight: (1) on the overall spatial implications of projected climate change to their restoration project; (2) whether assisted gene flow through climate-adjusted provenance may be appropriate for a given species at a given restoration site; and (3) how far away and in which direction from the restoration site seeds should be collected from. This approach should be used in the early stages of the restoration project to help frame the decision-making process in a climate change context, and can also be used as a platform where other lines of evidence are integrated. We advocate that, in the context of rapid climate change, the climate-adjusted provenance is a promising approach to seed sourcing in ecological restoration, and we suggest its refinement in a way that hedges against uncertainty in climatic projections.