Monitoring ash dieback (Hymenoscyphus fraxineus) in British forests using hyperspectral remote sensing

Abstract: Large‐scale dieback of ash trees (Fraxinus spp.) caused by the fungus Hymenoscyphus fraxineus is posing an immense threat to forest health in Europe, requiring effective monitoring at large scales. In this study, a pipeline was created to find ash trees and classify dieback severity using high‐resolution hyperspectral imagery of individual tree crowns (ITCs). Hyperspectral data were collected in four forest sites near Cambridge, UK, where 422 ITCs were manually delineated and labelled using field‐measurements of species and dieback severity (for ash trees). Four algorithms, namely linear discriminant analysis (LDA), principal components analysis coupled with LDA (PCA‐LDA), partial least squares discriminant analysis (PLS‐DA) and random forest (RF), were used to build classification models for species and dieback severity classification. The effect of dark‐pixel filtering on classification accuracy was evaluated. The best performing models were then coupled with automatic ITC segmentation to map species and ash dieback distribution over 16.8 hectares of woodland. We calculated and partitioned the coefficient of variation (CV) of the reflected ash spectra to find variable wavebands associated with dieback. PLS‐DA and LDA were most accurate for classifying ITC species identifies (overall accuracy >90%), whereas RF was most accurate for classifying ash dieback severity (overall accuracy 77%). Dark pixel filtering further increased the accuracy of species classification (+6%), but not disease classification. The reflectances of narrow blue (415 nm), red‐edge (680 nm) and NIR (760 nm) bands had high CV across disease classes and should be included if multispectral imagery were to be used to monitor ash dieback. The study demonstrates the possibility of using remote sensing to forward epidemiological research by monitoring forest pathogens in landscape scales, which would allow temperate forest managers to control pathogen outbreaks, assess associated impacts and restore affected forests much more effectively

Reconciling the contribution of environmental and stochastic structuring of tropical forest diversity through the lens of imaging spectroscopy.

Both niche and stochastic dispersal processes structure the extraordinary diversity of tropical plants, but determining their relative contributions has proven challenging. We address this question using airborne imaging spectroscopy to estimate canopy β-diversity for an extensive region of a Bornean rainforest and challenge these data with models incorporating niches and dispersal. We show that remotely sensed and field-derived estimates of pairwise dissimilarity in community composition are closely matched, proving the applicability of imaging spectroscopy to provide β-diversity data for entire landscapes of over 1000 ha containing contrasting forest types. Our model reproduces the empirical data well and shows that the ecological processes maintaining tropical forest diversity are scale dependent. Patterns of β-diversity are shaped by stochastic dispersal processes acting locally whilst environmental processes act over a wider range of scales

The impact of logging on vertical canopy structure across a gradient of tropical forest degradation intensity in Borneo

Forest degradation through logging is pervasive throughout the world's tropical forests, leading to changes in the three-dimensional canopy structure that have profound consequences for wildlife, microclimate and ecosystem functioning. Quantifying these structural changes is fundamental to understanding the impact of degradation, but is challenging in dense, structurally complex forest canopies. We exploited discrete-return airborne LiDAR surveys across a gradient of logging intensity in Sabah, Malaysian Borneo, and assessed how selective logging had affected canopy structure (Plant Area Index, PAI, and its vertical distribution within the canopy). LiDAR products compared well to independent, analogue models of canopy structure produced from detailed ground-based inventories undertaken in forest plots, demonstrating the potential for airborne LiDAR to quantify the structural impacts of forest degradation at landscape scale, even in some of the world's tallest and most structurally complex tropical forests. Plant Area Index estimates across the plot network exhibited a strong linear relationship with stem basal area (R2 = 0.95). After at least 11–14 years of recovery, PAI was ~28% lower in moderately logged plots and ~52% lower in heavily logged plots than that in old-growth forest plots. These reductions in PAI were associated with near-complete lack of trees >30-m tall, which had not been fully compensated for by increasing plant area lower in the canopy. This structural change drives a marked reduction in the diversity of canopy environments, with the deep, dark understorey conditions characteristic of old-growth forests far less prevalent in logged sites. Full canopy recovery is likely to take decades. Synthesis and applications. Effective management and restoration of tropical forests requires detailed monitoring of the forest and its environment. We demonstrate that airborne LiDAR can effectively map the canopy architecture of the complex tropical forests of Borneo, capturing the three-dimensional impact of degradation on canopy structure at landscape scales, therefore facilitating efforts to restore and conserve these ecosystems

Developing hierarchical density‐structured models to study the national‐scale dynamics of an arable weed

Population dynamics can be highly variable in the face of environmental heterogeneity, and understanding this variation is central in the study of ecology. Robust management decisions require that we understand how populations respond to management at a range of scales, and under a broad suite of conditions. Population models are potentially valuable tools in addressing this challenge. However, without adequate data, models can fail to produce useful results. Populations of arable weeds are particularly problematic in this respect, as they are widespread and their dynamics are extremely variable. Owing to the inherent cost of collecting data, most studies of plant population dynamics are derived from localized experiments under a small range of environmental conditions, limiting the extent to which variance in population dynamics can be measured. Density‐structured models provide a route to rapid, large‐scale analysis of population dynamics, and can expand the scale of ecological models that are directly tied to data. Here we extend previous density‐structured models to include environmental heterogeneity, variation in management, and to account for inter‐population variation. We develop, parameterize, and test hierarchical density‐structured models for a common agricultural weed, black‐grass (Alopecurus myosuroides). We model the dynamics of this species in response to crop management, using survey data gathered over 4 yr from 364 fields across a network of 45 UK farms. We show that hierarchical density‐structured models provide a substantial improvement over their nonhierarchical counterparts. Using these models, we demonstrate that several alternative crop rotations are effective in reducing weed densities. Rotations with high wheat prevalence exhibit the most severe infestations, and diverse rotations generally have lower weed densities. However, a key outcome is that in many cases the effect of crop rotation is small compared to the high variability arising from spatiotemporal heterogeneity. This result highlights the need to monitor and model population dynamics across large spatial and temporal scales in order to account for variation in the drivers of plant dynamics. Our framework for data collection and modeling provides a means to achieve this

Leech blood-meal invertebrate-derived DNA reveals differences in Bornean mammal diversity across habitats

The application of metabarcoding to environmental and invertebrate-derived DNA (eDNA and iDNA) is a new and increasingly applied method for monitoring biodiversity across a diverse range of habitats. This approach is particularly promising for sampling in the biodiverse humid tropics, where rapid land-use change for agriculture means there is a growing need to understand the conservation value of the remaining mosaic and degraded landscapes. Here we use iDNA from blood-feeding leeches (Haemadipsa picta) to assess differences in mammalian diversity across a gradient of forest degradation in Sabah, Malaysian Borneo. We screened 557 individual leeches for mammal DNA by targeting fragments of the 16S rRNA gene and detected 14 mammalian genera. We recorded lower mammal diversity in the most heavily degraded forest compared to higher quality twice logged forest. Although the accumulation curves of diversity estimates were comparable across these habitat types, diversity was higher in twice logged forest, with more taxa of conservation concern. In addition, our analysis revealed differences between the community recorded in the heavily logged forest and that of the twice logged forest. By revealing differences in mammal diversity across a human-modified tropical landscape, our study demonstrates the value of iDNA as a noninvasive biomonitoring approach in conservation assessments. © 2020 The Authors. Molecular Ecology published by John Wiley & Sons Lt

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

Polygenic basis and biomedical consequences of telomere length variation

Telomeres, the end fragments of chromosomes, play key roles in cellular proliferation and senescence. Here we characterize the genetic architecture of naturally occurring variation in leukocyte telomere length (LTL) and identify causal links between LTL and biomedical phenotypes in 472,174 well-characterized UK Biobank participants. We identified 197 independent sentinel variants associated with LTL at 138 genomic loci (108 new). Genetically determined differences in LTL were associated with multiple biological traits, ranging from height to bone marrow function, as well as several diseases spanning neoplastic, vascular and inflammatory pathologies. Finally, we estimated that, at the age of 40 years, people with an LTL >1 s.d. shorter than the population mean had a 2.5-year-lower life expectancy compared with the group with ≥1 s.d. longer LDL. Overall, we furnish new insights into the genetic regulation of LTL, reveal wide-ranging influences of LTL on physiological traits, diseases and longevity, and provide a powerful resource available to the global research community

Leech blood-meal invertebrate-derived DNA reveals differences in Bornean mammal diversity across habitats.

The application of metabarcoding to environmental and invertebrate-derived DNA (eDNA and iDNA) is a new and increasingly applied method for monitoring biodiversity across a diverse range of habitats. This approach is particularly promising for sampling in the biodiverse humid tropics, where rapid land-use change for agriculture means there is a growing need to understand the conservation value of the remaining mosaic and degraded landscapes. Here we use iDNA from blood-feeding leeches (Haemadipsa picta) to assess differences in mammalian diversity across a gradient of forest degradation in Sabah, Malaysian Borneo. We screened 557 individual leeches for mammal DNA by targeting fragments of the 16S rRNA gene and detected 14 mammalian genera. We recorded lower mammal diversity in the most heavily degraded forest compared to higher quality twice logged forest. Although the accumulation curves of diversity estimates were comparable across these habitat types, diversity was higher in twice logged forest, with more taxa of conservation concern. In addition, our analysis revealed differences between the community recorded in the heavily logged forest and that of the twice logged forest. By revealing differences in mammal diversity across a human-modified tropical landscape, our study demonstrates the value of iDNA as a noninvasive biomonitoring approach in conservation assessments

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

Consequences of changing rainfall for fungal pathogen-induced mortality in tropical tree seedlings.

Most general circulation models predict that most tropical forests will experience lower and less frequent rainfall in future as a result of climate change, which may reduce the capacity of fungal pathogens to drive density-dependent tree mortality. This is potentially significant because fungal pathogens are thought to play a key role in promoting and structuring plant diversity in tropical forests through the Janzen-Connell mechanism. Therefore, we hypothesize that the drying of tropical forests will negatively impact species coexistence. To test one prediction of this hypothesis, we imposed experimental watering regimes on the seedlings of a tropical tree, Pleradenophora longicuspis, and measured mortality induced by fungal pathogens under shade house conditions. The frequency of watering had a strong impact on survival. Seedlings watered daily experienced significantly higher mortality than those watered every three or every six days, while increasing the volume of water applied also led to increased mortality, although this relationship was less pronounced. These results suggest that the capacity of fungal pathogens to drive density-dependent mortality may be reduced in drier climates and when rainfall is less frequent, with potential implications for the diversity enhancing Janzen-Connell mechanism