Maximizing the value of forest restoration for tropical mammals by detecting three-dimensional habitat associations

Tropical forest ecosystems are facing unprecedented levels of degradation, severely compromising habitat suitability for wildlife. Despite the fundamental role biodiversity plays in forest regeneration, identifying and prioritising degraded forests for restoration or conservation, based on their wildlife value, remains a significant challenge. Efforts to characterize habitat selection are also weakened by simple classifications of human-modified tropical forests as intact versus degraded, which ignore the influence that three-dimensional forest structure may have on species distributions. Here, we develop a framework to identify conservation and restoration opportunities across logged forests in Borneo. We couple high-resolution airborne Light Detection and Ranging (LiDAR) and camera trap data to characterize the response of a tropical mammal community to changes in three-dimensional forest structure across a degradation gradient. Mammals were most responsive to covariates that accounted explicitly for the vertical and horizontal characteristics of the forest, and actively selected structurally-complex environments comprising tall canopies, increased plant area index throughout the vertical column, and the availability of a greater diversity of niches. We show that mammals are sensitive to structural simplification through disturbance, emphasising the importance of maintaining and enhancing structurally-intact forests. By calculating occurrence thresholds of species in response to forest structural change, we identify areas of degraded forest that would provide maximum benefit for multiple high conservation value species if restored. The study demonstrates the advantages of using LiDAR to map forest structure, rather than relying on overly simplistic classifications of human-modified tropical forests, for prioritising regions for restoration

Mutations in SPATA13/ASEF2 cause primary angle closure glaucoma

Current estimates suggest 50% of glaucoma blindness worldwide is caused by primary angle-closure glaucoma (PACG) but the causative gene is not known. We used genetic linkage and whole genome sequencing to identify Spermatogenesis Associated Protein 13, SPATA13 (NM_001166271; NP_001159743, SPATA13 isoform I), also known as ASEF2 (Adenomatous polyposis coli-stimulated guanine nucleotide exchange factor 2), as the causal gene for PACG in a large seven-generation white British family showing variable expression and incomplete penetrance. The 9 bp deletion, c.1432_1440del; p.478_480del was present in all affected individuals with angle-closure disease. We show ubiquitous expression of this transcript in cell lines derived from human tissues and in iris, retina, retinal pigment and ciliary epithelia, cornea and lens. We also identified eight additional mutations in SPATA13 in a cohort of 189 unrelated PACS/PAC/PACG samples. This gene encodes a 1277 residue protein which localises to the nucleus with partial co-localisation with nuclear speckles. In cells undergoing mitosis SPATA13 isoform I becomes part of the kinetochore complex co-localising with two kinetochore markers, polo like kinase 1 (PLK-1) and centrosome-associated protein E (CENP-E). The 9 bp deletion reported in this study increases the RAC1-dependent guanine nucleotide exchange factors (GEF) activity. The increase in GEF activity was also observed in three other variants identified in this study. Taken together, our data suggest that SPATA13 is involved in the regulation of mitosis and the mutations dysregulate GEF activity affecting homeostasis in tissues where it is highly expressed, influencing PACG pathogenesis

Tn1546 is part of a larger plasmid-encoded genetic unit horizontally disseminated among clonal Enterococcus faecium lineages

o determine the genetic composition of the first VanA-type plasmid (pIP816) reported, which was isolated from a clinical Enterococcus faecium (BM4147) strain in France in 1986, and to reveal the genetic units responsible for the dissemination of the vanA gene cluster by comparisons with current, published and additionally generated vanA-spanning plasmid sequences obtained from a heterogeneous E. faecium strain collection (n = 28).Plasmid sequences were produced by shotgun sequencing using ABI dye chemistry and primer walking, and were subsequently annotated. Comparative sequence analysis of the vanA region was done with published plasmids, with a partial vanA plasmid (pVEF4) reported here and to >140 kb of sequence obtained from a collection of vanA-harbouring plasmid fragments. Bioinformatic analyses revealed that pIP816 from 1986 and contemporary vanA plasmids shared a conserved genetic fragment of 25 kb, spanning the 10.85 kb vanA cluster encoded by Tn1546, and that the larger unit is present in both clinical and animal complexes of E. faecium. A new group II intron in pVEF4 was characterized. Comparative DNA analyses suggest that Tn1546 disseminates in and between clonal complexes of E. faecium as part of a larger genetic unit, possibly as a composite transposon flanked by IS1216 elements

Historical geographies of the future: airships and the making of imperial atmospheres

This article explores the elemental encounters and imaginative geographies of empire to develop a new means of engaging with the historical geographies of the future. Futures have recently become an important topic of historical and cultural inquiry, and historical geographers have an important role to play in understanding the place of the future in the past and in interrogating the role of posited futures in shaping action in historical presents. Drawing on literature from science and technology studies, a framework is developed for engaging with the material and imaginative geographies that coalesce around practices of imagination, expectation, and prediction. This framework is then used to reconstruct efforts to develop airship travel in the British Empire in the 1920s and 1930s. At a moment of imperial anxiety, airships were hoped to tie the empire together by conveying bodies, capital, and military capacity between its furthest points. Confident projections of the colonization of global airspace were nonetheless undermined by material encounters with a vibrant, often unpredictable atmospheric environment. The article aims to spur renewed work on the historical geographies of the future, while also contributing to debates on the cultural and political geographies of the atmosphere and of atmospheric knowledge making. Key Words: atmosphere, empire, future, mobility, technology

Thresholds for adding degraded tropical forest to the conservation estate

Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems1 that provide refugia for large amounts of biodiversity2,3, so we cannot afford to underestimate their conservation value4. Here we present empirically defined thresholds for categorizing the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation-relevant thresholds. First, lightly logged forests (68%) of their biomass removed, and these are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable5, but they also reinforce the message that logged forests retain considerable conservation value that should not be overlooked

Research data supporting “Recommendations to enhance breeding bird diversity in managed plantation forests determined using LiDAR”

This dataset contains habitat and bird diversity data collected in Thetford Forest. The data were derived from Breeding Bird Surveys, LiDAR structural information and management databases. Further details of the method and statistics are available in Tew et al “Recommendations to enhance breeding bird diversity in managed plantation forests determined using LiDAR” (Ecological Applications). Each row contains data for a management/age class group. Columns ‘Management type’, ‘Age class’ and ‘(Log) total area’ were derived from forest management databases. Columns ‘Horizontal heterogeneity, ‘Gap fraction’, ‘Top canopy height’, ‘Vertical heterogeneity’, ‘Shrub density’ and ‘Canopy density’ were derived from high-resolution remote sensing LiDAR data. ‘Horizontal heterogeneity’, ‘Gap fraction’ and ‘Top canopy height’ are summarised at four different resolutions: 0.5 m, 2 m, 5 m, 10 m. Bird diversity data were derived from bird surveys.NER

Recommendations to enhance breeding bird diversity in managed plantation forests determined using LiDAR.

Funder: Arcadia Fund; Id: http://dx.doi.org/10.13039/100012088Funder: University of Cambridge; Id: http://dx.doi.org/10.13039/501100000735Funder: Forestry EnglandWidespread afforestation is a crucial component of climate mitigation strategies worldwide. This presents a significant opportunity for biodiversity conservation if forests are appropriately managed. Within forests, structural and habitat diversity are known to be critical for biodiversity but pragmatic management recommendations are lacking. We make a comprehensive assessment of the effects of habitat variables on bird populations using data from over 4000 ha of forested landscape. We combine high-resolution remote sensing data with comprehensive management databases to classify habitat attributes and measure the response of six taxonomic and functional diversity metrics: species richness, Shannon diversity, functional richness, functional evenness, functional divergence, and functional dispersion. We use a novel approach that combines hierarchical partitioning analysis with linear models to determine the relative importance of different habitat variables for each bird diversity metric. The age class of forest stands was consistently the most important variable across all bird diversity metrics, outperforming other structural measures such as horizontal and vertical heterogeneity and canopy density. Shrub density and gap fraction were each significantly associated with one bird diversity metric. In contrast, variables describing within-stand structural heterogeneity (vertical and horizontal) were generally less important while tree species identity (e.g., conifer or broadleaved) was not significant for any bird diversity metric. Each of the six bird diversity metrics had different patterns of independent variable importance and significance, emphasizing the need to consider multiple diversity metrics in biodiversity assessments. Similarly, the optimal resolution for remote sensing metrics varied between structural variables and bird diversity metrics, suggesting that the use of remote sensing data in biodiversity studies could be greatly improved by first exploring different resolutions and data aggregations. Based on the results from this comprehensive study, we recommend that managers focus on creating habitat diversity at the between-, rather than exclusively within-stand scale, such as by creating a matrix of different age classes, to maximize bird diversity. This recommendation for forest managers is powerful yet pragmatic in its simplicity

Biodiversity credits: learning lessons from other approaches to incentivize conservation

Biodiversity credits are an emerging vehicle for pro-environmental financing. Here we define and delimit biodiversity credits and explore the pathways through which credits can be issued. We scrutinize early evidence from pilots and suggest lessons from other market-based incentives for conservation and climate mitigation, including biodiversity offsets and forest carbon credits that have attracted large private funding flows, but have been questioned regarding their additionality, permanence, and leakage. All these issues apply to biodiversity credits, but they face yet another challenge: rendering biodiversity commensurable. While new monitoring technologies can help quantify biodiversity, tradeoffs exist between simple metrics that enable liquid markets, and costly ones that more adequately represent biodiversity. To avoid carbon and offset market mistakes, biodiversity credit design, implementation, and impact evaluation requires more robust crediting baselines, standards, and governance. Quality credits will be more expensive than those cutting integrity corners, which may dampen the expected biodiversity credit boom