Aim Recent unprecedented efforts to digitise and mobilise biodiversity data have resulted in the generation of 'biodiversity big data', enabling ecological research at scales previously not possible. However, gaps, biases and uncertainties in these data influence analytical outcomes and the validity of scientific research and conservation actions. Here, we estimated tree species inventory completeness globally and identified where future surveys should focus to maximise regional inventories. LocationGlobal. Methods We analysed spatial patterns in sampling effort of tree species occurrence records from the Global Biodiversity and Information Facility (GBIF) and estimated global tree species inventory completeness for 100 x 100 km grid cells (sampling units) and ecoregions. We also identified forested areas for future botanical exploration, by examining the spatial overlap between inventory completeness, remaining natural habitat and protected areas and degrees of forest modification by anthropogenic pressure (forest integrity). Results Spatial patterns in sampling effort and tree species inventory completeness were unevenly distributed around the world. Only 35% of ecoregions and 18% of sampling units can be considered well surveyed, most of which were concentrated in the Global North, including Europe, North America and Australia. Large areas in species-rich tropical regions, especially in Southeast Asia, remained poorly documented. Moreover, our results showed that many areas with low inventory completeness overlapped with ecoregions retaining less than 50% of natural habitat and protected land area, as well as sampling units with low forest integrity. Main Conclusions Due to limitations in biodiversity data, simply sampling more will not necessarily lead to increasing knowledge. We illustrated how gaps in these data can be used to improve existing knowledge by identifying priority areas for future surveys. With ongoing anthropogenic impacts and escalating rates of biodiversity loss, limited resources should be allocated to strategically survey regions likely to yield new knowledge and improve biodiversity representativeness.

Human domination of landscapes is a key driver of biodiversity loss, with the fingerprint of climate change becoming increasingly pronounced. Frameworks and tools for identifying threats to biodiversity are required to meet Post-2020 Global Biodiversity Framework targets for 2030 that call for, among other things, reducing or halting species extinction rates ( 1 ). Hence, we compiled a phylogenetic tree for terrestrial tetrapods, mapped hotspots of geographically restricted and evolutionarily distinct lineages, and identified which hotspots may simultaneously face the highest magnitudes of land use impacts and climate change. Across a quarter of Earth’s surface, hotspots contain the entire ranges of 45% of tetrapods, representing 39% of terrestrial tetrapod evolutionary heritage. By 2070, we estimate 8–13% of this heritage to occur entirely within hotspots highly exposed to climate change, with 13–29% of hotspots projected to experience high exposure to both stressors simultaneously. Most hotspots at highest risk occur in countries least able to take action. Our analysis highlights the need for global ambition and coordination to avoid catastrophic loss of tetrapod evolutionary heritage.

Abstract Premise Understanding evolutionary history and classifying discrete units of organisms remain overwhelming tasks, and lags in this workload concomitantly impede an accurate documentation of biodiversity and conservation management. Rapid advances and improved accessibility of sensitive high‐throughput sequencing tools are fortunately quickening the resolution of morphological complexes and thereby improving the estimation of species diversity. The recently described and critically endangered Banksia vincentia is morphologically similar to the hairpin banksia complex (B. spinulosa s.l.), a group of eastern Australian flowering shrubs whose continuum of morphological diversity has been responsible for taxonomic controversy and possibly questionable conservation initiatives. Methods To assist conservation while testing the current taxonomy of this group, we used high‐throughput sequencing to infer a population‐scale evolutionary scenario for a sample set that is comprehensive in its representation of morphological diversity and a 2500‐km distribution. Results Banksia spinulosa s.l. represents two clades, each with an internal genetic structure shaped through historical separation by biogeographic barriers. This structure conflicts with the existing taxonomy for the group. Corroboration between phylogeny and population statistics aligns with the hypothesis that B. collina, B. neoanglica, and B. vincentia should not be classified as species. Conclusions The pattern here supports how morphological diversity can be indicative of a locally expressed suite of traits rather than relationship. Oversplitting in the hairpin banksias is atypical since genomic analyses often reveal that species diversity is underestimated. However, we show that erring on overestimation can yield negative consequences, such as the disproportionate prioritization of a geographically anomalous population.

The expansions and contractions of a species' range in response to temporal changes in selective filters leave genetic signatures that can inform a more accurate reconstruction of their evolutionary history across the landscape. After a long period of continental decline, Australian rainforests settled into localized patterns of contraction or expansion during the climatic fluctuations of the Quaternary. The environmental impacts of recurring glacial and interglacial periods also intensified the arrival of new lineages from the Sunda shelf, and it can be expected that immigrant versus locally persistent taxa responded to environmental challenges in quantifiably different manner. To investigate how such differences impact on species' distribution, we contrast landscape genomic patterns and changes in habitat availability between a species with a long continental history on Doryphora sassafras and a Sunda-derived species (Toona ciliata), across a distributional overlap. Extensive landscape-level homogeneity across chloroplast and nuclear genomes for the Sunda-derived T. ciliata, characterize the genetic signature of a very recent invasion and a rapid southern "exploratory" expansion that had not been previously recorded in the Australian flora (i.e., of Gondwanan origin or Sahul-derived). In contrast, D. sassafras is consistent with other Sahul-derived species characterized by strong geographical divergence and regional differentiation. Interestingly, our findings suggest that admixture between genetically divergent populations during expansion events might be a contributing factor to the successful colonization of novel habitats. Overall, this study identifies some of the mechanisms regulating the rearrangements in species distributions and assemblage composition that follow major environmental shifts, and reminds us how a species' current range might not necessarily define species' habitat preference, with the consequence that estimates of past or future range might not always be reliable.

Niche models are now widely used in many branches of the biological sciences and are often used to contrast the distribution of favourable environments between regions or under changes in environmental conditions such as climate change. Evaluating model performance and selecting optimal models is now accepted as best-practice, and a number of methods are available assist this process. One aspect of ENM application which has not received as much attention is developing methods to communicate the degree and nature of changes between model outputs (typically as raster maps). The method described in this paper, Binned Relative Environmental Change Index (BRECI), seeks to address this shortfall in communicating model results. ### Competing Interest Statement The authors have declared no competing interest.

Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia purpureopetala, a beautiful sprawling shrub with mauve flowers, restricted to a few disjunct populations in far north Queensland, Australia. Seed production is poor and germination sporadic, but the species occurs in abundance at some field sites. While several thousands of SNP markers were recovered, comparable to other Acacia species, very low levels of heterozygosity and allelic variation suggested inbreeding. Limited dispersal most likely contributed towards the high levels of divergence amongst field sites and, using a generalised dissimilarity modelling framework amongst environmental, spatial and floristic data, spatial distance was found to be the strongest factor explaining the current distribution of genetic diversity. We illustrate how population genomic data can be utilised to design a collecting strategy for a germplasm conservation collection that optimises genetic diversity. For this species, inclusion of all field sites will capture maximum genetic diversity for both in situ and ex situ conservation. Assisted cross pollination, within and between field sites and genetically structured groups, is recommended to enhance heterozygosity particularly at the most disjunct sites and further fragmentation should be discouraged to avoid loss of genetic connectivity.

The effectiveness and predictability of 2 different oral appliance (OA) designs to reduce the respiratory event index (REI) in moderate and severe obstructive sleep apnea (OSA) patients requires elucidation. The primary aim of the trial was to determine if 2 widely used midline-traction and bilateral-thrust OA designs differ in effectiveness to reduce the REI within a single test population categorized by OSA severity. Moderate and severe adult OSA patients, who were previously prescribed continuous positive airway pressure therapy (CPAP) but were dissatisfied with it (n= 56), were studied by home-polygraphy in a randomized crossover trial using either midline-traction with restricted mouth opening (MR) or bilateral thrust with opening permitted (BP) design OAs. OAs were used nightly for 4 wk (T2) followed by a 1-wk washout period, then 4 wk (T4) using the alternate OA. REI and oxygen saturation (SaO(2)) were primary outcomes, while predictability and efficacy comparison of the 2 OAs were secondary outcomes. Thirty-six participants had used MR and BP OAs during both 4-wk study legs. Twenty (55.6%) MR OA-using participants, 25 (69.4%) BP OA-using participants, and 16 (44.4%) participants using both OAs had significant REI reductions. Overall baseline (T0) median REI (interquartile range) of 33.7 (20.7-54.9) was reduced to 18.0 (8.5-19.4) at T2 and to 12.5 (8.2-15.9) at T4 (P< 0.001). Comparison of the 2 sequence groups' (MR-BP and BP-MR) REI showed the median differences between T0 and T2 and T4 were highly significant (P< 0.001). Regression analysis predicted about half of all users will have REIs between 8 and 16 after 2 mo. Baseline overjet measures >2.9 mm predicted greater OA advancement at T4. Mean and minimum SaO(2)did not change significantly from T0 to T2 or T4. MR and BP OA designs similarly attenuated REI in moderate and severe OSA individuals who completed the 8-wk study protocol with greater REI reduction in those with severe OSA (ClinicalTrials.gov NCT03219034).

Aim Exchange of plant lineages between Australia and Southeast Asia has had a substantial impact on the evolution of Australia's northern, tropical flora, with important ramifications for its conservation and biosecurity. Despite this, floristic exchange tracks between northern Australia and Southeast Asia remain poorly understood. To address this, we conducted a molecular phylogeographic case study to identify exchange tracks between Australia and Southeast Asia. Location India, Southeast Asia, Australia and Pacific islands. Taxon The widespread tropical monsoonal tree species Aglaia elaeagnoidea (Meliaceae). Methods We conducted a DArTseq phylogeographic study of 141 herbarium and silica-dried samples sourced from across the range of A. elaeagnoidea. We analysed 176,331 single nucleotide polymorphisms (SNPs) across 90,456 loci using multivariate, admixture, genetic differentiation and coalescent methods to characterise phylogeographic and phylogenetic patterns. These analyses were considered in the context of an environmental niche model for the last glacial maximum. Results Two exchange tracks were identified: one from New Guinea to Cape York Peninsula in north-east Australia, and a second from Timor-Leste to the Kimberley Plateau of north-west Australia. The Cape York Peninsula track is contemporary, characterised by ongoing genetic exchange, whereas the Kimberley Plateau track is historic, facilitated by multiple past exposures of the Arafura Shelf during the Pleistocene. Overall, we suggest that phylogeographic patterns of A. elaeagnoidea have resulted from a combination of repeated range expansion and contraction cycles concurrent with Quaternary climate fluctuations and stochastic dispersal events. Main conclusions This study provides the first molecular phylogeographic evidence for two floristic exchange tracks between northern Australia and Southeast Asia. It also highlights the influence of Quaternary climate fluctuations on the complex biogeography of the region, and supports the idea that the Kimberley Plateau and Cape York Peninsula in northern Australia have separate biogeographic histories.

Ecological restoration requires balancing levels of genetic diversity to achieve present-day establishment as well as long-term sustainability. Assumptions based on distributional, taxonomic or functional generalizations are often made when deciding how to source plant material for restoration. We investigate this assumption and ask whether species-specific data is required to optimize provenancing strategies. We use population genetic and environmental data from five congeneric and largely co-distributed species of Acacia to specifically ask how different species-specific genetic provenancing strategies are based on empirical data and how well a simple, standardized collection strategy would work when applied to the same species. We find substantial variability in terms of patterns of genetic diversity and differentiation across the landscape among these five co-distributed Acacia species. This variation translates into substantial differences in genetic provenancing recommendations among species (ranging from 100% to less than 1% of observed genetic variation across species) that could not have been accurately predicted a priori based on simple observation or overall distributional patterns. Furthermore, when a common provenancing strategy was applied to each species, the recommended collection areas and the evolutionary representativeness of such artificially standardized areas were substantially different (smaller) from those identified based on environmental and genetic data. We recommend the implementation of the increasingly accessible array of evolutionary-based methodologies and information to optimize restoration efforts.

The charge given to the members of the economic section was to look critically at economic aspects of stored and processed products, which need to be examined in assessing the potential of products developed from root crops. While recognizing that foreign exchange problems or national defense needs can override economic considerations and cause government to deliberately influence supply and consumption, the chapter focuses on the more normal situation where economic considerations are paramount. The purely economic function of agricultural marketing is the allocation of scarce products over time, space, and form and among consumers. For the economists the major concern when evaluating root crop products is their competitiveness. Among the root crops taro and yams sometimes partake of the characteristic of super foods but there may be strong local preference for sweet potato and cassava. Consumer tastes and preferences affect the demand for a root crop product. Frequently special processing of tropical root crops is required to remove toxic principles.

Here we present “Restore and Renew,” a replicable framework for gathering and interpreting evolutionary, ecological, and genomic data in support of restoration practices. In an era of rapid climatic change and continuous widespread clearing, revegetation projects need to focus on producing resilient and long‐term self‐sustaining populations. Restore and Renew expands current knowledge of genetic provenance via genome‐scan data, environmental niche modeling (ENM), and site‐specific climate information. The sampling strategy is to obtain leaf tissue representing the distributions of over 100 species commonly used in restoration. We apply generalized dissimilarity modeling to genome‐wide single nucleotide polymorphism datasets from hundreds of samples. Species‐specific local provenances are obtained using a model that represents observed patterns of genetic variation across the landscape. Climate modeling is implemented to interpret genetic provenance boundaries in the context of current and future climatic conditions at the specified site. Results are presented in an easy‐to‐use webtool ( www.restore‐and‐renew.org.au ), where the user simply selects their site of interest and a target species to obtain the size and distribution of local genetic provenance. Although Restore and Renew is not prescriptive, it allows restoration practitioners to make informed decisions on where to source material from, to fulfill their restoration scenario of choice. Two examples, Westringia fruticosa and Acacia suaveolens , are presented to demonstrate how the analytical pipeline responds to different ecological and evolutionary patterns. The webtool has multiple applications for biodiversity management and will continue to evolve with new species and analytical/interpretative outputs.

Climate refugia—areas that remain suitable for species during periods of climate disruption—have played an important role in species persistence over time. Identifying and protecting these refugia is a key climate change adaptation approach for conservation planning. To identify climate refugia for Australian tropical/sub-tropical rainforest flora, from the Last Glacial Maximum to 2070. Habitat suitability models were calibrated for 30 species using Maxent, and projected onto climate data for: Last Glacial Maximum (LGM, ~ 22,000 ybp); mid-Holocene (MH, ~ 6000 ybp); current period; and 2070. The intersection of suitable habitat over consecutive periods was assessed, identifying: current refugia (LGM–MH–Current); future refugia (Current–Future); and High Value Refugia (HVR, suitable over all four periods). Refugial hotspots (regions suitable for at least 15 species) were also identified. Suitable habitat was generally projected to span the greatest area in the current period. Four current refugial hotspots were identified: Wet Tropics, Central Mackay Coast, South Eastern Queensland, and North Coast (New South Wales). While suitable habitat for most species may decline in the future, HVRs will likely be retained for all species to at least 2070, although restricted in size. Future refugia was also projected in areas beyond species’ dispersal ranges. HVRs are highly important for the conservation of these rainforest species, given their generation times, limited dispersal capabilities and additional anthropogenic barriers to movement. This study assists in understanding long-term spatial shifts in rainforest flora in response to climate change and in designing future conservation strategies.

Niche partitioning can lead to differences in the range dynamics of plant species through its impacts on habitat availability, dispersal, or selection for traits that affect colonization and persistence. We investigated whether niche partitioning into upland and riparian habitats differentiates the range dynamics of two closely related and sympatric eastern Australian trees: the mountain water gum (Tristaniopsis collina) and the water gum (T. laurina). Using genomic data from SNP genotyping of 480 samples, we assessed the impact of biogeographic barriers and tested for signals of range expansion. Circuit theory was used to model isolation-by-resistance across three palaeo-environment scenarios: the Last Glacial Maximum, the Holocene Climate Optimum and present-day (1950-2014). Both trees showed similar genetic structure across historically dry barriers, despite evidence of significant environmental niche differentiation and different post-glacial habitat shifts. Tristaniopsis collina exhibits the signature of serial founder effects consistent with recent or rapid range expansion, whilst T. laurina has genetic patterns consistent with long-term persistence in geographically isolated populations despite occupying a broader bioclimatic niche. We found the minor influence of isolation-by-resistance on both species, though other unknown factors appear to shape genetic variation. We postulate that specialized recruitment traits (adapted to flood-disturbance regimes) rather than habitat availability limited post-glacial range expansion in T. laurina. Our findings indicate that niche breadth does not always facilitate range expansion through colonization and migration across barriers, though it can promote long-term persistence in situ.

Bile acid imbalance causes progressive familial intrahepatic cholestasis type 2 (PFIC2) or type 3 (PFIC3), severe liver diseases associated with genetic defects in the biliary bile acid transporter bile salt export pump (BSEP; ABCB11) or phosphatidylcholine transporter multidrug resistance protein 3 (MDR3; ABCB4), respectively. Mdr2(-/-) mice (a PFIC3 model) develop progressive cholangitis, ductular proliferation, periportal fibrosis, and hepatocellular carcinoma (HCC) because the nonmicelle-bound bile acids in the bile of these mice are toxic. We asked whether the highly hydrophilic bile acids generated by Bsep(-/-) mice could protect Mdr2(-/-) mice from progressive liver damage. We generated double-KO (DKO: Bsep(-/-) and Mdr2(-/-)) mice. Their bile acid composition resembles that of Bsep(-/-) mice, with increased hydrophilic muricholic acids, tetrahydroxylated bile acids (THBAs), and reduced hydrophobic cholic acid. These mice lack the liver pathology of their Mdr2(-/-) littermates. The livers of DKO mice have gene expression profiles very similar to Bsep(-/-) mice, with 4,410 of 6,134 gene expression changes associated with the Mdr2(-/-) mutation being suppressed. Feeding with THBAs partially alleviates liver damage in the Mdr2(-/-) mice. Hydrophilic changes to biliary bile acid composition, including introduction of THBA, can prevent the progressive liver pathology associated with the Mdr2(-/-) (PFIC3) mutation.

Objectives: Mycobacterium chimaera infection following cardiac surgery, due to contaminated cardiopulmonary bypass heater-cooler units, has been reported worldwide. However, the spectrum of clinical disease remains poorly understood. To address this, we report the clinical and laboratory features, treatment and outcome of the first 30 UK cases. Methods: Case note review was performed for cases identified retrospectively through outbreak investigations and prospectively through ongoing surveillance. Case definition was Mycobacterium chimaera detected in any clinical specimen, history of cardiothoracic surgery with cardiopulmonary bypass, and compatible clinical presentation. Results: Thirty patients were identified (28 with prosthetic material) exhibiting a spectrum of disease including prosthetic valve endocarditis (14/30), sternal wound infection (2/30), aortic graft infection (4/30) and disseminated (non-cardiac) disease (10/30). Patients presented a median of 14 months post surgery (maximum 5 years) most commonly complaining of fever and weight loss. Investigations frequently revealed lymphopenia, thrombocytopenia, liver cholestasis and non-necrotizing granulomatous inflammation. Diagnostic sensitivity for a single mycobacterial blood culture was 68% but increased if multiple samples were sent. In all, 27 patients started macrolide-based combination treatment and 14 had further surgery. To date, 18 patients have died (60%) a median of 30 months (interquartile range 20-39 months) after initial surgery. Survival analysis identified younger age, mitral valve surgery, mechanical valve replacement, higher serum sodium concentration and lower C-reactive protein as factors associated with better survival. Conclusions: Mycobacterium chimaera infection following cardiac surgery is associated with a wide spectrum of disease. The diagnosis should be considered in all patients who develop an unexplained illness following cardiac surgery. (C) 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

One of the major uncertainties of 21st century climate change is the potential for shifts to the intensity and frequency of the El Nino Southern Oscillation (ENSO) cycle. Although this phenomenon is known to have dramatic impacts on ecosystems regionally and globally, the biological consequences of climate change-driven shifts in future ENSO events have been unexplored. Here, we investigate the potential impacts that a persistent El Nino, La Nina, or Neutral' phase may have on species distributions. Using MaxEnt, we model the distribution of climatically suitable habitat for three northeast Australian butterfly subspecies (Doleschallia bisaltide australis, Hypolimnas alimena lamina, and Mycalesis terminus terminus) across the three ENSO phases. We find that the spatial extent and quality of habitat are lowest under conditions that would characterize a persistent El Nino (hot/dry). In contrast, suitable habitat is broadest under the warm/wet conditions associated with La Nina. Statistical analyses of the difference between pair-wise combinations of suitability maps using Hellinger distance showed that projections for each subspecies and ENSO phase combination were significantly different from other combinations. The resilience of these, and other, butterfly (sub)species to changes in ENSO will be influenced by fluctuations in the strength of these events, availability of refugia, and life-history characteristics. However, the population dynamics of wet- and dry-season phenotypes of M. t. terminus and physiological limitations to high temperatures suggest that this subspecies, in particular, may have limited resilience should the strength and frequency of El Nino events increase.

Background Prehistoric human activities have contributed to the dispersal of many culturally important plants. The study of these traditional interactions can alter the way we perceive the natural distribution and dynamics of species and communities. Comprehensive research on native crops combining evolutionary and anthropological data is revealing how ancient human populations influenced their distribution. Although traditional diets also included a suite of non-cultivated plants that in some cases necessitated the development of culturally important technical advances such as the treatment of toxic seed, empirical evidence for their deliberate dispersal by prehistoric peoples remains limited. Here we integrate historic and biocultural research involving Aboriginal people, with chloroplast and nuclear genomic data to demonstrate Aboriginal-mediated dispersal of a non-cultivated rainforest tree. Results We assembled new anthropological evidence of use and deliberate dispersal of Castanospermum australe (Fabaceae), a non-cultivated culturally important riparian tree that produces toxic but highly nutritious water-dispersed seed. We validated cultural evidence of recent human-mediated dispersal by revealing genomic homogeneity across extensively dissected habitat, multiple catchments and uneven topography in the southern range of this species. We excluded the potential contribution of other dispersal mechanisms based on the absence of suitable vectors and current distributional patterns at higher elevations and away from water courses, and by analyzing a comparative sample from northern Australia. Conclusions Innovative studies integrating evolutionary and anthropological data will continue to reveal the unexpected impact that prehistoric people have had on current vegetation patterns. A better understanding of how traditional practices shaped species’ distribution and assembly will directly inform cultural heritage management strategies, challenge “natural” species distribution assumptions, and provide innovative baseline data for pro-active biodiversity management.

Species distribution models (SDMs) frequently project substantial declines in the spatial extent of climatically suitable habitat in response to scenarios of future climate change. Such projections are highly disconcerting. Yet, considerable variation can occur in the direction and magnitude of range changes projected by different SDM methods, even when predictive performance is similar. In this study, we assessed whether particular methods have a tendency to predict substantial loss or gain of suitable habitat. In particular, we asked, "are 14 SDM methods equally likely to predict extreme changes to the future extent of suitable habitat for 220 Australian mammal species?". We defined five non-mutually exclusive categories of 'extreme' change, based on stability or loss of current habitat, or the dislocation of current and future habitat: a) no future habitat (range extinction); b) low stability of current habitat (<= 10% remains); c) no gain of habitat in new locations; d) all future habitat is in new locations (i.e. completely displaced from current habitat); and e) substantial increase in size of habitat (future habitat is >= 100% larger than current). We found that some SDM methods were significantly more likely than others to predict extreme changes. In particular, distance-based models were significantly less likely than other methods to predict substantial increases in habitat size; Random Forest models and Surface Range Envelopes were significantly more likely to predict a complete loss of current habitat, and future range extinction. Generalised Additive Models and Generalised Linear Models rarely predicted range extinction; future habitat completely disjunct from current habitat was predicted more frequently than expected by Classification Tree Analysis and less frequently by Maxent. Random Forest generally predicted extreme range changes more frequently than other SDM methods. Our results identify trends among different methods with respect to tendency to predict extreme range changes. These are of significance for climate-impact assessments, with implications for transferability of models to novel environments. Our findings emphasise the need to explore and justify the use of different models and their parameterisations, and to develop approaches to assist with optimisation of models. (C) 2016 Elsevier B.V. All rights reserved.