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The mass expansion and racialisation of the American carceral system began in the late 1970s, took root in the 1980s, and had become a cultural fact within the American way of life by the 1990s. The 1994 Crime Bill, the largest U.S. crime bill to date, was championed by the, at the time, democratic senator Joe Biden and ultimately passed—Hillary Clinton’s now notorious comments on urban “super predators” on the senate floor was made in defence of this bill. An American turning their TV to the news in the 1990s would see images of sensationalised urban violence and overtly racialised stories—the beating of Rodney King or the OJ Simpson trial for example—within a cultural landscape housing the world’s largest incarcerated population. Alongside this, in the late 1990s Americans could choose instead to tune into new “quality” television shows differentiated by their critical approach to American subject matter.

While interferometric methods exist for classifying vortex states of light, these techniques usually require destroying the beam of interest to determine the light’s OAM. A recent two-color pump-probe experiment employed strong field ionization and beam sculpting to classify vortex beams. Here, we propose an alternative strong-field method for distinguishing OAM states of light which does not require beam sculpting and instead utilizes a noncollinear terahertz standing wave to probe ionized electrons. We then use classical trajectory Monte Carlo (CTMC) methods to simulate strong-field ionization of helium under this configuration with the terahertz field both on and off. We find that the resulting electron momenta distributions can be used to extract the OAM of the beam, as long as the vortex beam spot size does not exceed 1/4 the terahertz pulse’s wavelength.

A recent work shows how to extract the ionization site of a neutral diatomic molecule by comparing Quantum Trajectory Monte Carlo (QTMC) simulations with experimental measurements of the final electron momenta distribution. This method was applied to an experiment using a 40-femtosecond infrared pulse, finding that a downfield atom is roughly twice as likely to be ionized as an upfield atom in a neutral nitrogen molecule. However, an open question remains as to whether an assumption of the zero carrier envelope phase (CEP) used in the above work is still valid for short, few-cycle pulses where the CEP can play a large role. Given experimentalists’ limited control over the CEP and its dramatic effect on electron momenta after ionization, it is desirable to see what influence the CEP may have in determining the ionization site. In this paper, we employ QTMC techniques to simulate strong-field ionization and electron propagation from neutral N2 using an intense 6-cycle laser pulse with various CEP values. Comparing simulated electron momenta to experimental data indicates that the ratio of down-to-upfield ions remains roughly 2:1 regardless of the CEP. This confirms that the ionization site of a neutral molecule is determined predominantly by the laser frequency and intensity, as well as the ground-state molecular wavefunction, and is largely independent of the CEP.

Understanding the factors that drive the successful commercialisation of indigenous innovation in Sub-Saharan African economies is still limited. From both policy and theoretical perspectives, regulation is one factor that remains crucial for the successful commercialisation of innovation. However, the empirical evidence is still unclear regarding its effect on firm performance, urging the need for more evidence from different economies, sectors, and firms. This study, therefore, examined the effects of regulation on the performance of firms engaged in the commercialisation of indigenous innovation in the Ghanaian small-scale industry, a typical low-income economy in Sub-Sahara Africa. From the frugal innovation theoretical perspective, the study assumed that firms engaged in the commercialisation of indigenous innovation in such low-income economies operate in an environment with regulatory gaps and voids. Using a sample survey of 557, it deployed PLS-SEM to test the effects of regulation on key successful commercialisation metrics. The findings show that at a 5% statistical significance level, regulation has significant positive effects on sales, employment, and owners’ feelings of success. Regulation also positively moderates the influence of finance and organisational factors on overall firm performance. The study provides leading evidence of the effect of regulation on the commercialisation of indigenous innovation from Ghana and adds to the clarification of the impact of regulation. It suggests that in such low-income economies, the policy must consider more balanced and appropriate regulations, not less, or deregulating to promote indigenous innovation.

In melanoma, reduced ADAR1 impairs A-to-I microRNA editing. Here, the authors show that miR-378a-3p undergoes this editing in non-metastatic cells and the edited form of miR-378a-3p binds to the PARVA oncogene, inhibiting its expression and preventing melanoma progression and metastasis.

Early recognition of this drug-induced condition can prevent death. [ABSTRACT FROM AUTHOR]

PURPOSE: To profile adolescent Internet chat room users in terms of demographic characteristics, psychological and environmental factors, and behavioral risk factors. METHODS: The study sample was drawn from respondents to an anonymous statewide survey of 50,168 9th-grade public school students and included 40,376 students who reported Internet access at home and 19,511 who accessed chat rooms. Data were collected by the Minnesota Student Survey (MSS), a survey that has been administered triennially by the state's education department to public school students in grades 6, 9, and 12 since 1989. The MSS includes more than 117 questions (300 variables) addressing attitudinal, behavioral, and environmental issues. Data analysis consisted of comparing the odds of a particular characteristic or behavior for chat room users with that of nonusers. Analyses were run separately for boys and girls. The homogeneity of odd ratios was tested with the Breslow-Day statistic using SPSS for Windows. RESULTS: For boys and girls, use of Internet chat rooms was associated with psychological distress, a difficult living environment, and a higher likelihood of risky behaviors. Although most chat room users did not report serious problems, this group included a disproportionate number of troubled individuals. CONCLUSIONS: Because chat room use serves as an indicator of heightened vulnerability and risk-taking, parents and others need to be aware of potential dangers posed by online contact between strangers and youth. [ABSTRACT FROM AUTHOR]

A statewide treatment outcomes monitoring system included baseline interviews with 387 adolescents and 363 parents representing 37 programs. This study examined adolescent and parent predictors of treatment completion and 6-month outcomes; the adolescent follow-up rate was 83.5%. Only 21.4% of the adolescents reported abstinence for the 6 months following treatment; however, marijuana use frequency, symptom counts, illegal activities, and emotional distress declined significantly. Logistic regression analyses showed that female gender increased the likelihood of both treatment completion and posttreatment abstinence, but parent participation in treatment predicted neither. These and other results are discussed in terms of their implications for examining the current treatment system. [ABSTRACT FROM AUTHOR]

Abstract Background Parasitaemia, the percentage of infected erythrocytes, is used to measure progress of experimental Plasmodium infection in infected hosts. The most widely used technique for parasitaemia determination is manual microscopic enumeration of Giemsa-stained blood films. This process is onerous, time consuming and relies on the expertise of the experimenter giving rise to person-to-person variability. Here the development of image-analysis software, named Plasmodium AutoCount, which can automatically generate parasitaemia values from Plasmodium-infected blood smears, is reported. Methods Giemsa-stained blood smear images were captured with a camera attached to a microscope and analysed using a programme written in the Python programming language. The programme design involved foreground detection, cell and infection detection, and spurious hit filtering. A number of parameters were adjusted by a calibration process using a set of representative images. Another programme, Counting Aid, written in Visual Basic, was developed to aid manual counting when the quality of blood smear preparation is too poor for use with the automated programme. Results This programme has been validated for use in estimation of parasitemia in mouse infection by Plasmodium yoelii and used to monitor parasitaemia on a daily basis for an entire challenge infection. The parasitaemia values determined by Plasmodium AutoCount were shown to be highly correlated with the results obtained by manual counting, and the discrepancy between automated and manual counting results were comparable to those found among manual counts of different experimenters. Conclusions Plasmodium AutoCount has proven to be a useful tool for rapid and accurate determination of parasitaemia from infected mouse blood. For greater accuracy when smear quality is poor, Plasmodium AutoCount, can be used in conjunction with Counting Aid.

Abstract Pseudogenes arise from the decay of gene copies following either RNA-mediated duplication (processed pseudogenes) or DNA-mediated duplication (nonprocessed pseudogenes). Here, we show that long protein-coding genes tend to produce more nonprocessed pseudogenes than short genes, whereas the opposite is true for processed pseudogenes. Protein-coding genes longer than 3000 bp are 6 times more likely to produce nonprocessed pseudogenes than processed ones. Reviewers This article was reviewed by Dr. Dan Graur and Dr. Craig Nelson (nominated by Dr. J Peter Gogarten).

Abstract Background Transcribed pseudogenes are copies of protein-coding genes that have accumulated indicators of coding-sequence decay (such as frameshifts and premature stop codons), but nonetheless remain transcribed. Recent experimental evidence indicates that transcribed pseudogenes may regulate the expression of homologous genes, through antisense interference, or generation of small interfering RNAs (siRNAs). Here, we assessed the genomic evidence for such transcribed pseudogenes of potential functional importance, in the human genome. The most obvious indicators of such functional importance are significant evidence of conservation and selection pressure. Results A variety of pseudogene annotations from multiple sources were pooled and filtered to obtain a subset of sequences that have significant mid-sequence disablements (frameshifts and premature stop codons), and that have clear evidence of full-length mRNA transcription. We found 1750 such transcribed pseudogene annotations (TPAs) in the human genome (corresponding to ~11.5% of human pseudogene annotations). We checked for syntenic conservation of TPAs in other mammals (rhesus monkey, mouse, rat, dog and cow). About half of the human TPAs are conserved in rhesus monkey, but strikingly, very few in mouse (~3%). The TPAs conserved in rhesus monkey show evidence of selection pressure (relative to surrounding intergenic DNA) on: (i) their GC content, and (ii) their rate of nucleotide substitution. This is in spite of distributions of Ka/Ks (ratios of non-synonymous to synonymous substitution rates), congruent with a lack of protein-coding ability. Furthermore, we have identified 68 human TPAs that are syntenically conserved in at least two other mammals. Interestingly, we observe three TPA sequences conserved in dog that have intermediate character (i.e., evidence of both protein-coding ability and pseudogenicity), and discuss the implications of this. Conclusion Through evolutionary analysis, we have identified candidate sequences for functional human transcribed pseudogenes, and have pinpointed 68 strong candidates for further investigation as potentially functional transcribed pseudogenes across multiple mammal species.

Abstract Background Functional diversification of genes in mammalian genomes is engendered by a number of processes, e.g., gene duplication and alternative splicing. Gene duplication is classically discussed as leading to neofunctionalization (generation of new functions), subfunctionalization (generation of a varied function), or pseudogenization (loss of the gene and its function). Results Here, we focus on the process of pseudogenization, but specifically for individual exons from genes. It is at present unclear to what extent pseudogenization of individual exon duplications affects gene evolution, i.e., is it a random phenomenon, or is it associated with specific types of genes and encoded proteins, and positions in gene structures? We gathered genomic evidence for pseudogenic exons (ΨEs, i.e., exons disabled by frameshifts and premature stop codons), to examine for significant trends in their distribution across four mammalian genomes (specifically human, cow, mouse and rat). Across these four genomes, we observed a consistent population of ΨEs, associated with 0.4–1.0% of genes. These ΨE populations exhibit codon substitution patterns that are typical of an endemic population of decaying sequences. In human, ΨEs have significant over-representation for functional categories related to 'ion binding' and 'nucleic-acid binding', compared to duplicated exons in general. Also, ΨEs tend to be associated with some protein domains that are abundant generally, e.g., Zinc-finger and immunoglobulin protein domains, but not others, e.g., EGF-like domains. Positionally, ΨEs are also significantly associated with the 5' end of genes, but despite this, individual stop codons are positioned so that there is significant avoidance of potential targeting to nonsense-mediated decay. In human, ΨEs are often associated with alternative splicing (in 22 out of 284 genes with ΨEs in their milieu), and can have different parts of their sequence differentially spliced in alternative transcripts. Some unusual cases of ΨEs embedded within 5' and 3' non-coding exons are observed. Conclusion Our results indicate the types of genes that harbour ΨEs, and demonstrate that ΨEs have non-random distribution within gene structures. These ΨEs may function in gene regulation through generation of transcribed pseudogenes, or regulatory alternate transcripts.

Abstract Background Protein kinases and phosphatases regulate protein phosphorylation, a critical means of modulating protein function, stability and localization. The identification of functional networks for protein phosphatases has been slow due to their redundant nature and the lack of large-scale analyses. We hypothesized that a genome-scale analysis of genetic interactions using the Synthetic Genetic Array could reveal protein phosphatase functional networks. We apply this approach to the conserved type 1 protein phosphatase Glc7, which regulates numerous cellular processes in budding yeast. Results We created a novel glc7 catalytic mutant (glc7-E101Q). Phenotypic analysis indicates that this novel allele exhibits slow growth and defects in glucose metabolism but normal cell cycle progression and chromosome segregation. This suggests that glc7-E101Q is a hypomorphic glc7 mutant. Synthetic Genetic Array analysis of glc7-E101Q revealed a broad network of 245 synthetic sick/lethal interactions reflecting that many processes are required when Glc7 function is compromised such as histone modification, chromosome segregation and cytokinesis, nutrient sensing and DNA damage. In addition, mitochondrial activity and inheritance and lipid metabolism were identified as new processes involved in buffering Glc7 function. An interaction network among 95 genes genetically interacting with GLC7 was constructed by integration of genetic and physical interaction data. The obtained network has a modular architecture, and the interconnection among the modules reflects the cooperation of the processes buffering Glc7 function. Conclusion We found 245 genes required for the normal growth of the glc7-E101Q mutant. Functional grouping of these genes and analysis of their physical and genetic interaction patterns bring new information on Glc7-regulated processes.

Abstract Background Efforts to gather genomic evidence for the processes of gene evolution are ongoing, and are closely coupled to improved gene annotation methods. Such annotation is complicated by the occurrence of disrupted mRNAs (dmRNAs), harbouring frameshifts and premature stop codons, which can be considered indicators of decay into pseudogenes. Results We have derived a procedure to annotate dmRNAs, and have applied it to human data. Subsequences are generated from parsing at key frame-disruption positions and are required to align significantly within any original protein homology. We find 419 high-quality human dmRNAs (3% of total). Significant dmRNA subpopulations include: zinc-finger-containing transcription factors with long disrupted exons, and antisense homologies to distal genes. We analysed the distribution of initial frame disruptions in dmRNAs with respect to positions of: (i) protein domains, (ii) alternatively-spliced exons, and (iii) regions susceptible to nonsense-mediated decay (NMD). We find significant avoidance of protein-domain disruption (indicating a selection pressure for this), and highly significant overrepresentation of disruptions in alternatively-spliced exons, and 'non-NMD' regions. We do not find any evidence for evolution of novelty in protein structures through frameshifting. Conclusion Our results indicate largely negative selection pressures related to frame disruption during gene evolution.

Abstract Background The dynamics of gene evolution are influenced by several genomic processes. One such process is retrotransposition, where an mRNA transcript is reverse-transcribed and reintegrated into the genomic DNA. Results We have surveyed eight vertebrate genomes (human, chimp, dog, cow, rat, mouse, chicken and the puffer-fish T. nigriviridis), for putatively retrotransposed copies of genes. To gain a complete picture of the role of retrotransposition, a robust strategy to identify putative retrogenes (PRs) was derived, in tandem with an adaptation of previous procedures to annotate processed pseudogenes, also called retropseudogenes (RψGs). Mammalian genomes are estimated to contain 400–800 PRs (corresponding to ~3% of genes), with fewer PRs and RψGs in the non-mammalian vertebrates. Focussing on human and mouse, we aged the PRs, analysed for evidence of transcription and selection pressures, and assigned functional categories. The PRs have significantly less transcription evidence mappable to them, are significantly less likely to arise from alternatively-spliced genes, and are statistically overrepresented for ribosomal-protein genes, when compared to the proteome in general. We find evidence for spurts of gene retrotransposition in human and mouse, since the lineage of either species split from the dog lineage, with >200 PRs formed in mouse since its divergence from rat. To examine for selection, we calculated: (i) Ka/Ks values (ratios of non-synonymous and synonymous substitutions in codons), and (ii) the significance of conservation of reading frames in PRs. We found >50 PRs in both human and mouse formed since divergence from dog, that are under pressure to maintain the integrity of their coding sequences. For different subsets of PRs formed at different stages of mammalian evolution, we find some evidence for non-neutral evolution, despite significantly less expression evidence for these sequences. Conclusion These results indicate that retrotranspositions are a significant source of novel coding sequences in mammalian gene evolution.

Abstract Background Compositionally biased (CB) regions are stretches in protein sequences made from mainly a distinct subset of amino acid residues; such regions are frequently associated with a structural role in the cell, or with protein disorder. Results We derived a procedure for the exhaustive assignment and classification of CB regions, and have applied it to thirteen metazoan proteomes. Sequences are initially scanned for the lowest-probability subsequences (LPSs) for single amino-acid types; subsequently, an exhaustive search for lowest probability subsequences (LPSs) for multiple residue types is performed iteratively until convergence, to define CB region boundaries. We analysed > 40,000 CB regions with > 20 million residues; strikingly, nine single-/double- residue biases are universally abundant, and are consistently highly ranked across both vertebrates and invertebrates. To home in subpopulations of CB regions of interest in human and D. melanogaster, we analysed CB region lengths, conservation, inferred functional categories and predicted protein disorder, and filtered for coiled coils and protein structures. In particular, we found that some of the universally abundant CB regions have significant associations to transcription and nuclear localization in Human and Drosophila, and are also predicted to be moderately or highly disordered. Focussing on Q-based biased regions, we found that these regions are typically only well conserved within mammals (appearing in 60–80% of orthologs), with shorter human transcription-related CB regions being unconserved outside of mammals; they are also preferentially linked to protein domains such as the homeodomain and glucocorticoid-receptor DNA-binding domain. In general, only ~40–50% of residues in these human and Drosophila CB regions have predicted protein disorder. Conclusion This data is of use for the further functional characterization of genes, and for structural genomics initiatives.

Biodiversity underpins the functioning of ecosystems and the diverse benefits that nature provides to people, yet is being lost at an unprecedented rate. To halt or reverse biodiversity loss, it is critical to understand the complex interdependencies between biodiversity and key drivers and sectors to inform the development of holistic policies and actions. We conducted a literature review on the interlinkages between biodiversity and climate change, food, water, energy, transport and health ("the biodiversity nexus"). Evidence extracted from 194 peer-reviewed articles was analysed to assess how biodiversity is being influenced by and is influencing the other nexus elements. Out of the 354 interlinkages between biodiversity and the other nexus elements, 53 % were negative, 29 % were positive and 18 % contained both positive and negative influences. The majority of studies provide evidence of the negative influence of other nexus elements on biodiversity, highlighting the substantial damage being inflicted on nature from human activities. The main types of negative impacts were land or water use/change, land or water degradation, climate change, and direct species fatalities through collisions with infrastructure. Alternatively, evidence of biodiversity having a negative influence on the other nexus elements was limited to the effects of invasive alien species and vector-borne diseases. Furthermore, a range of studies provided evidence of how biodiversity and the other nexus elements can have positive influences on each other through practices that promote co-benefits. These included biodiversity-friendly management in relevant sectors, protection and restoration of ecosystems and species that provide essential ecosystem services, green and blue infrastructure including nature-based solutions, and sustainable and healthy diets that mitigate climate change. The review highlighted the complexity and context-dependency of interlinkages within the biodiversity nexus, but clearly demonstrates the importance of biodiversity in underpinning resilient ecosystems and human well-being in ensuring a sustainable future for people and the planet., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Sourcing seed from local populations has been the long-standing default for native restoration plantings for numerous eco-evolutionary reasons. However, rapidly changing environments are revealing risks associated with both non-local and local provenancing. As alternative strategies gain interest, we argue to progress seed sourcing discussions towards developing risk-based decision-making that weighs the risks of changing and not changing in a changing environment, transcending historic default positions and local versus non-local debates., (© 2024 Commonwealth Scientific and Industrial Research Organisation and The Authors. Ecology Letters published by John Wiley & Sons Ltd.)

To halt further destruction of the biosphere, most people and societies around the globe need to transform their relationships with nature. The internationally agreed vision under the Convention of Biological Diversity-Living in harmony with nature-is that "By 2050, biodiversity is valued, conserved, restored and wisely used, maintaining ecosystem services, sustaining a healthy planet and delivering benefits essential for all people". In this context, there are a variety of debates between alternative perspectives on how to achieve this vision. Yet, scenarios and models that are able to explore these debates in the context of "living in harmony with nature" have not been widely developed. To address this gap, the Nature Futures Framework has been developed to catalyse the development of new scenarios and models that embrace a plurality of perspectives on desirable futures for nature and people. In this paper, members of the IPBES task force on scenarios and models provide an example of how the Nature Futures Framework can be implemented for the development of illustrative narratives representing a diversity of desirable nature futures: information that can be used to assess and develop scenarios and models whilst acknowledging the underpinning value perspectives on nature. Here, the term illustrative reflects the multiple ways in which desired nature futures can be captured by these narratives. In addition, to explore the interdependence between narratives, and therefore their potential to be translated into scenarios and models, the six narratives developed here were assessed around three areas of the transformative change debate, specifically, (1) land sparing vs. land sharing, (2) Half Earth vs. Whole Earth conservation, and (3) green growth vs. post-growth economic development. The paper concludes with an assessment of how the Nature Futures Framework could be used to assist in developing and articulating transformative pathways towards desirable nature futures., Supplementary Information: The online version contains supplementary material available at 10.1007/s11625-023-01316-1., (© The Author(s) 2023.)

Agricultural and environmental policies are being fundamentally reviewed and redesigned in the UK following its exit from the European Union. The UK government and the Devolved Administrations recognise that current land use is not sustainable and that there is now an unprecedented opportunity to define a better land strategy that responds fully to the interconnected challenges of climate change, biodiversity loss and sustainable development. This paper presents evidence from three pathways (current trends, sustainable medium ambition, and sustainable high ambition) to mid-century that were co-created with UK policymakers. The pathways were applied to a national integrated food and land-use model (the FABLE calculator) to explore potential synergies and trade-offs between achieving multiple sustainability targets under limited land availability and constraints to balance food supply and demand at national and global levels. Results show that under the Current Trends pathway all unprotected open natural land would be converted to urban, agriculture and afforested land, with the consequence that from 2030 onwards tree planting targets could not be met. In contrast, the two sustainable pathways illustrate how dietary change, agricultural productivity improvements and waste reduction can free up land for nature recovery and carbon sequestration. This enables a transition to a sustainable food and land-use system that provides a net carbon sink with up to 44% of land able to support biodiversity conservation. We highlight key trade-offs and synergies, which are important to consider for designing and implementing emerging national policies. These include the strong dependence of climate, food and biodiversity targets on dietary shifts, sustainable improvements in agricultural productivity, improved land-use design for protecting and restoring nature, and rapid reductions in food loss and waste., Supplementary Information: The online version contains supplementary material available at 10.1007/s11625-022-01242-8., (© The Author(s) 2022.)

Harnessing new technologies is vital to achieve global imperatives to restore degraded ecosystems. We explored the potential of genomics as one such tool. We aimed to understand barriers hindering the uptake of genomics, and how to overcome them, via exploratory interviews with leading scholars in both restoration and its sister discipline of conservation-a discipline that has successfully leveraged genomics. We also conducted an examination of research trends to explore some insights that emerged from the interviews, including publication trends that have used genomics to address restoration and conservation questions. Our qualitative findings revealed varied perspectives on harnessing genomics. For example, scholars in restoration without genomics experience felt genomics was over-hyped. Scholars with genomics experience emphatically emphasized the need to proceed cautiously in using genomics in restoration. Both genomics-experienced and less-experienced scholars called for case studies to demonstrate the benefits of genomics in restoration. These qualitative data contrasted with our examination of research trends, which revealed 70 restoration genomics studies, particularly studies using environmental DNA as a monitoring tool. We provide a roadmap to facilitate the uptake of genomics into restoration, to help the restoration sector meet the monumental task of restoring huge areas to biodiverse and functional ecosystems. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.

With climate change impacting trees worldwide, enhancing adaptation capacity has become an important goal of provenance translocation strategies for forestry, ecological renovation, and biodiversity conservation. Given that not every species can be studied in detail, it is important to understand the extent to which climate adaptation patterns can be generalised across species, in terms of the selective agents and traits involved. We here compare patterns of genetic-based population (co)variation in leaf economic and hydraulic traits, climate-trait associations, and genomic differentiation of two widespread tree species ( Eucalyptus pauciflora and E. ovata ). We studied 2-year-old trees growing in a common-garden trial established with progeny from populations of both species, pair-sampled from 22 localities across their overlapping native distribution in Tasmania, Australia. Despite originating from the same climatic gradients, the species differed in their levels of population variance and trait covariance, patterns of population variation within each species were uncorrelated, and the species had different climate-trait associations. Further, the pattern of genomic differentiation among populations was uncorrelated between species, and population differentiation in leaf traits was mostly uncorrelated with genomic differentiation. We discuss hypotheses to explain this decoupling of patterns and propose that the choice of seed provenances for climate-based plantings needs to account for multiple dimensions of climate change unless species-specific information is available.

Background and Aims: Hybridization is increasingly recognized as an integral part of the dynamics of species range expansion and contraction. Thus, it is important to understand the reproductive barriers between co-occurring species. Extending previous studies that argued that the rare Eucalyptus risdonii was expanding into the range of the surrounding E. amygdalina by both seed and pollen dispersal, we here investigate the long-term fitness of both species and their hybrids and whether expansion is continuing., Methods: We assessed the survival of phenotypes representing a continuum between the two pure species in a natural hybrid swarm after 29 years, along with seedling recruitment. The performance of pure species as well as of artificial and natural hybrids was also assessed over 28 years in a common garden trial., Key Results: In the hybrid zone, E. amygdalina adults showed greater mortality than E. risdonii, and the current seedling cohort is still dominated by E. risdonii phenotypes. Morphologically intermediate individuals appeared to be the least fit. Similar results were observed after growing artificial first-generation and natural hybrids alongside pure species families in a common garden trial. Here, the survival, reproduction, health and growth of the intermediate hybrids were significantly less than those of either pure species, consistent with hybrid inferiority, although this did not manifest until later reproductive ages. Among the variable progeny of natural intermediate hybrids, the most E. risdonii-like phenotypes were the most fit., Conclusions: This study contributes to the increasing number of reports of hybrid inferiority in Eucalyptus, suggesting that post-zygotic barriers contribute to the maintenance of species integrity even between closely related species. However, with fitness rapidly recovered following backcrossing, it is argued that hybridization can still be an important evolutionary process, in the present case appearing to contribute to the range expansion of the rare E. risdonii in response to climate change., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Restoration of degraded drylands is urgently needed to mitigate climate change, reverse desertification and secure livelihoods for the two billion people who live in these areas. Bold global targets have been set for dryland restoration to restore millions of hectares of degraded land. These targets have been questioned as overly ambitious, but without a global evaluation of successes and failures it is impossible to gauge feasibility. Here we examine restoration seeding outcomes across 174 sites on six continents, encompassing 594,065 observations of 671 plant species. Our findings suggest reasons for optimism. Seeding had a positive impact on species presence: in almost a third of all treatments, 100% of species seeded were growing at first monitoring. However, dryland restoration is risky: 17% of projects failed, with no establishment of any seeded species, and consistent declines were found in seeded species as projects matured. Across projects, higher seeding rates and larger seed sizes resulted in a greater probability of recruitment, with further influences on species success including site aridity, taxonomic identity and species life form. Our findings suggest that investigations examining these predictive factors will yield more effective and informed restoration decision-making., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

Genotype-environment association (GEA) methods have become part of the standard landscape genomics toolkit, yet, we know little about how to best filter genotype-by-sequencing data to provide robust inferences for environmental adaptation. In many cases, default filtering thresholds for minor allele frequency and missing data are applied regardless of sample size, having unknown impacts on the results, negatively affecting management strategies. Here, we investigate the effects of filtering on GEA results and the potential implications for assessment of adaptation to environment. We use empirical and simulated data sets derived from two widespread tree species to assess the effects of filtering on GEA outputs. Critically, we find that the level of filtering of missing data and minor allele frequency affect the identification of true positives. Even slight adjustments to these thresholds can change the rate of true positive detection. Using conservative thresholds for missing data and minor allele frequency substantially reduces the size of the data set, lessening the power to detect adaptive variants (i.e., simulated true positives) with strong and weak strengths of selection. Regardless, strength of selection was a good predictor for GEA detection, but even some SNPs under strong selection went undetected. False positive rates varied depending on the species and GEA method, and filtering significantly impacted the predictions of adaptive capacity in downstream analyses. We make several recommendations regarding filtering for GEA methods. Ultimately, there is no filtering panacea, but some choices are better than others, depending on the study system, availability of genomic resources, and desired objectives., (© 2021 John Wiley & Sons Ltd.)

Climate and socio-economic change impacts are likely to cross traditional sectoral and regional boundaries with cascading indirect, and potentially far-reaching, repercussions. This is particularly important for the food-water-land-ecosystems (FWLE) nexus, which is fundamental for the achievement of at least six of the seventeen Sustainable Development Goals (SDGs). A holistic understanding of the FWLE nexus interactions and how and to what extent various exogenous drivers of change affect them is therefore central to cross-sectoral adaptation planning. Here, we present such an integrated assessment for Europe applying a regional Integrated Assessment Platform (IAP). The study explores a wide range of future climate and socio-economic scenarios using more than 900 model simulations. The results show that food production is likely to be the main driver of Europe's future landscape change dynamics (with or without climate change). Agriculture and land use allocation is often driven by complex cross-sectoral interactions with cascading effects on other sectors such as forestry, biodiversity, and water under the various scenarios. The modelling also highlighted that while sustaining current levels of food production at the European level could be achievable under most climate and socio-economic scenarios, there are significant regional differences with winners and losers. The analysis raises the question of whether current production and consumption policies are sustainable in the long-term. Such systematic integrated model-based analysis plays a crucial role in informing development of cross-sectoral policies that maximise synergies and minimise trade-offs across nexus sectors, regions, and scenarios. This is essential to achieve the SDGs., Competing Interests: Declaration of competing interest No conflict of interest., (Copyright © 2021 Elsevier B.V. All rights reserved.)

As the pressure to take action against global warming is growing in urgency, scenarios that incorporate multiple social, economic and environmental drivers become increasingly critical to support governments and other stakeholders in planning climate change mitigation or adaptation actions. This has led to the recent explosion of future scenario analyses at multiple scales, further accelerated since the development of the Intergovernmental Panel on Climate Change (IPCC) research community Shared Socioeconomic Pathways (SSPs) and Representative Concentration Pathways (RCPs). While RCPs have been widely applied to climate models to produce climate scenarios at multiple scales for investigating climate change impacts, adaptation and vulnerabilities (CCIAV), SSPs are only recently being scaled for different geographical and sectoral applications. This is seen in the UK where significant investment has produced the RCP-based UK Climate Projections (UKCP18), but no equivalent UK version of the SSPs exists. We address this need by developing a set of multi-driver qualitative and quantitative UK-SSPs, following a state-of-the-art scenario methodology that integrates national stakeholder knowledge on locally-relevant drivers and indicators with higher level information from European and global SSPs. This was achieved through an intensive participatory process that facilitated the combination of bottom-up and top-down approaches to develop a set of UK-specific SSPs that are locally comprehensive, yet consistent with the global and European SSPs. The resulting scenarios balance the importance of consistency and legitimacy, demonstrating that divergence is not necessarily the result of inconsistency, nor comes as a choice to contextualise narratives at the appropriate scale., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 The Author(s). Published by Elsevier B.V. All rights reserved.)

The evolutionary response to selection depends on the distribution of genetic variation in traits under selection within populations, as defined by the additive genetic variance-covariance matrix ( G ). The structure and evolutionary stability of G will thus influence the course of phenotypic evolution. However, there are few studies assessing the stability of G and its relationship with population divergence within foundation tree species. We compared the G -matrices of Mainland and Island population groups of the forest tree Eucalyptus globulus , and determined the extent to which population divergence aligned with within-population genetic (co)variation. Four key wood property traits exhibiting signals of divergent selection were studied-wood density, extractive content, and lignin content and composition. The comparison of G -matrices of the mainland and island populations indicated that the G -eigenstructure was relatively well preserved at an intra-specific level. Population divergence tended to occur along a major direction of genetic variation in G . The observed conservatism of G , the moderate evolutionary timescale, and close relationship between genetic architecture and population trajectories suggest that genetic constraints may have influenced the evolution and diversification of the E. globulus populations for the traits studied. However, alternative scenarios, including selection aligning genetic architecture and population divergence, are discussed.

Drought is a major stress impacting forest ecosystems worldwide. We utilized quantitative trait loci (QTL) analysis to study the genetic basis of variation in (a) drought resistance and recovery and (b) candidate traits that may be associated with this variation in the forest tree Eucalyptus globulus. QTL analysis was performed using a large outcrossed F 2 mapping population from which 300 trees were phenotyped based on the mean performance of their open-pollinated F 3 progeny. Progenies were grown in a glasshouse in a randomized complete block design. A subset of seedlings was subjected to a drought treatment after which they were rewatered and scored for damage and growth postdrought. Nondroughted seedlings were assessed for growth traits as well as lignotuber size and resprouting following severe damage to the main stem. QTL were detected for most traits. Importantly, independent QTL were detected for (a) drought damage and plant size, (b) drought damage and growth recovery, and (c) lignotuber size and resprouting capacity. Such independence argues that trade-offs are unlikely to be a major limitation to the response to selection and at the early life history stage studied; there are opportunities to improve resilience to drought without adverse effects on productivity., (© 2019 John Wiley & Sons Ltd.)