Mapping an invasive bryophyte species using hyperspectral remote sensing data

A new perspective on the impacts of Spartina alterniflora invasion on Chinese wetlands in the context of climate change: A case study of the Jiuduansha Shoals, Yangtze Estuary

Spartina alterniflora, an invasive plant, was introduced to the Chinese coastal zone in the early 90s. As an eco-engineering species, S. alterniflora not only alters saltmarsh species distributions, previously described as habitat degradation, but it also plays a vital role in coastal protection, especially for the development of recently emerged intertidal shoals. To provide a reference for coastal management under global change, we quantified the impact of the invasion process on provided ecological and coastal protection functions, exemplified at the emerging Jiuduansha Shoals (JDS) in the Yangtze Estuary. Results obtained by high-precision satellite monitoring and numerical modelling showed that the establishment and growth of S. alterniflora can exert considerable changes on local environment. The invasion of S. alterniflora to JDS wetland can be divided into three distinct phases, (1) establishment 1998-2003, (2) expansion 2003-2009, and (3) dominant 2009-2018 stages according to the changes in saltmarsh composition. Spatially, S. alterniflora continuously replaced Scirpus mariqueter, forcing S. mariqueter and Phragmites australis slowly to the lower and higher intertidal habitats, respectively. Notably, S. alterniflora expansion was the main driver that contributed to over 70 % of recent JDS wetland expansion even under sediment deficit conditions. Established S. alterniflora marsh (directly) dampens more waves because of aboveground stems, but it also causes more accretion and indirectly leads to higher "morphological" wave dampening. Thus, it increases coastal defense provided by the saltmarsh in the context of sea-level rise and strengthening storms. In conclusion, the role of S. alterniflora invasion to the local environment under global changes is controversial. For sustainable coastal management, we need context-dependent S. alterniflora management to maximize the benefit of coastal protection and minimize the impact on local ecology, especially in sediment-starving estuaries with expected coastline retreat.

The Spectral Species Concept in Living Color

Biodiversity monitoring is an almost inconceivable challenge at the scale of the entire Earth. The current (and soon to be flown) generation of spaceborne and airborne optical sensors (i.e., imaging spectrometers) can collect detailed information at unprecedented spatial, temporal, and spectral resolutions. These new data streams are preceded by a revolution in modeling and analytics that can utilize the richness of these datasets to measure a wide range of plant traits, community composition, and ecosystem functions. At the heart of this framework for monitoring plant biodiversity is the idea of remotely identifying species by making use of the 'spectral species' concept. In theory, the spectral species concept can be defined as a species characterized by a unique spectral signature and thus remotely detectable within pixel units of a spectral image. In reality, depending on spatial resolution, pixels may contain several species which renders species-specific assignment of spectral information more challenging. The aim of this paper is to review the spectral species concept and relate it to underlying ecological principles, while also discussing the complexities, challenges and opportunities to apply this concept given current and future scientific advances in remote sensing.

Lithological information extraction and classification in hyperspectral remote sensing data using Backpropagation Neural Network

The purposes are to solve the isomorphism encountered while processing hyperspectral remote sensing data and improve the accuracy of hyperspectral remote sensing data in extracting and classifying lithological information. Taking rocks as the research object, Backpropagation Neural Network (BPNN) is introduced. After the hyperspectral image data are normalized, the lithological spectrum and spatial information are the feature extraction targets to construct a deep learning-based lithological information extraction model. The performance of the model is analyzed using specific instance data. Results demonstrate that the overall accuracy and the Kappa coefficient of the lithological information extraction and classification model based on deep learning were 90.58% and 0.8676, respectively. This model can precisely distinguish the properties of rock masses and provide better performance compared with the state of other analysis models. After introducing deep learning, the recognition accuracy and the Kappa coefficient of the proposed BPNN model increased by 8.5% and 0.12, respectively, compared with the traditional BPNN. The proposed extraction and classification model can provide some research values and practical significances for the hyperspectral rock and mineral classification.

The Use of an Unmanned Aerial Vehicle for Tree Phenotyping Studies

A strip of 20th-century landscape woodland planted alongside a 17th to mid-18th century ancient and semi-natural woodland (ASNW) was investigated by applied aerial spectroscopy using an unmanned aerial vehicle (UAV) with a multispectral image camera (MSI). A simple classification approach of normalized difference spectral index (NDSI), derived using principal component analysis (PCA), enabled the identification of the non-native trees within the 20th-century boundary. The tree species within this boundary, classified by NDSI, were further segmented by the machine learning segmentation method of k-means clustering. This combined innovative approach has enabled the identification of multiple tree species in the 20th-century boundary. Phenotyping of trees at canopy level using the UAV with MSI, across 8052 m2, identified black pine (23%), Norway maple (19%), Scots pine (12%), and sycamore (19%) as well as native trees (oak and silver birch, 27%). This derived data was corroborated by field identification at ground-level, over an area of 6785 m2, that confirmed the presence of black pine (26%), Norway maple (30%), Scots pine (10%), and sycamore (14%) as well as other trees (oak and silver birch, 20%). The benefits of using a UAV, with an MSI camera, for monitoring tree boundaries next to a new housing development are demonstrated.

Mapping Opuntia stricta in the Arid and Semi-Arid Environment of Kenya Using Sentinel-2 Imagery and Ensemble Machine Learning Classifiers

Globally, grassland biomes form one of the largest terrestrial covers and present critical social–ecological benefits. In Kenya, Arid and Semi-arid Lands (ASAL) occupy 80% of the landscape and are critical for the livelihoods of millions of pastoralists. However, they have been invaded by Invasive Plant Species (IPS) thereby compromising their ecosystem functionality. Opuntia stricta, a well-known IPS, has invaded the ASAL in Kenya and poses a threat to pastoralism, leading to livestock mortality and land degradation. Thus, identification and detailed estimation of its cover is essential for drawing an effective management strategy. The study aimed at utilizing the Sentinel-2 multispectral sensor to detect Opuntia stricta in a heterogeneous ASAL in Laikipia County, using ensemble machine learning classifiers. To illustrate the potential of Sentinel-2, the detection of Opuntia stricta was based on only the spectral bands as well as in combination with vegetation and topographic indices using Extreme Gradient Boost (XGBoost) and Random Forest (RF) classifiers to detect the abundance. Study results showed that the overall accuracies of Sentinel 2 spectral bands were 80% and 84.4%, while that of combined spectral bands, vegetation, and topographic indices was 89.2% and 92.4% for XGBoost and RF classifiers, respectively. The inclusion of topographic indices that enhance characterization of biological processes, and vegetation indices that minimize the influence of soil and the effects of atmosphere, contributed by improving the accuracy of the classification. Qualitatively, Opuntia stricta spatially was found along river banks, flood plains, and near settlements but limited in forested areas. Our results demonstrated the potential of Sentinel-2 multispectral sensors to effectively detect and map Opuntia stricta in a complex heterogeneous ASAL, which can support conservation and rangeland management policies that aim to map and list threatened areas, and conserve the biodiversity and productivity of rangeland ecosystems.

Monitoring Invasive Plant Species Using Hyperspectral Remote Sensing Data

The species richness and biodiversity of vegetation in Hungary are increasingly threatened by invasive plant species brought in from other continents and foreign ecosystems. These invasive plant species have spread aggressively in the natural and semi-natural habitats of Europe. Common milkweed (Asclepias syriaca) is one of the species that pose the greatest ecological menace. Therefore, the primary purpose of the present study is to map and monitor the spread of common milkweed, the most common invasive plant species in Europe. Furthermore, the possibilities to detect and validate this special invasive plant by analyzing hyperspectral remote sensing data were investigated. In combination with field reference data, high-resolution hyperspectral aerial images acquired by an unmanned aerial vehicle (UAV) platform in 138 spectral bands in areas infected by common milkweed were examined. Then, support vector machine (SVM) and artificial neural network (ANN) classification algorithms were applied to the highly accurate field reference data. As a result, common milkweed individuals were distinguished in hyperspectral images, achieving an overall accuracy of 92.95% in the case of supervised SVM classification. Using the ANN model, an overall accuracy of 99.61% was achieved. To evaluate the proposed approach, two experimental tests were conducted, and in both cases, we managed to distinguish the individual specimens within the large variety of spreading invasive species in a study area of 2 ha, based on centimeter spatial resolution hyperspectral UAV imagery.

MAcroecological Framework for Invasive Aliens (MAFIA): disentangling large-scale context dependence in biological invasions

Macroecology is the study of patterns, and the processes that determine those patterns, in the distribution and abundance of organisms at large scales, whether they be spatial (from hundreds of kilometres to global), temporal (from decades to centuries), and organismal (numbers of species or higher taxa). In the context of invasion ecology, macroecological studies include, for example, analyses of the richness, diversity, distribution, and abundance of alien species in regional floras and faunas, spatio-temporal dynamics of alien species across regions, and cross-taxonomic analyses of species traits among comparable native and alien species pools. However, macroecological studies aiming to explain and predict plant and animal naturalisations and invasions, and the resulting impacts, have, to date, rarely considered the joint effects of species traits, environment, and socioeconomic characteristics. To address this, we present the MAcroecological Framework for Invasive Aliens (MAFIA). The MAFIA explains the invasion phenomenon using three interacting classes of factors – alien species traits, location characteristics, and factors related to introduction events – and explicitly maps these interactions onto the invasion sequence from transport to naturalisation to invasion. The framework therefore helps both to identify how anthropogenic effects interact with species traits and environmental characteristics to determine observed patterns in alien distribution, abundance, and richness; and to clarify why neglecting anthropogenic effects can generate spurious conclusions. Event-related factors include propagule pressure, colonisation pressure, and residence time that are important for mediating the outcome of invasion processes. However, because of context dependence, they can bias analyses, for example those that seek to elucidate the role of alien species traits. In the same vein, failure to recognise and explicitly incorporate interactions among the main factors impedes our understanding of which macroecological invasion patterns are shaped by the environment, and of the importance of interactions between the species and their environment. The MAFIA is based largely on insights from studies of plants and birds, but we believe it can be applied to all taxa, and hope that it will stimulate comparative research on other groups and environments. By making the biases in macroecological analyses of biological invasions explicit, the MAFIA offers an opportunity to guide assessments of the context dependence of invasions at broad geographical scales.

Employing Machine Learning for Detection of Invasive Species using Sentinel-2 and AVIRIS Data: The Case of Kudzu in the United States

Invasive plants are causing massive economic and environmental troubles for our societies worldwide. The aim of this study is to employ a set of machine learning classifiers for detecting invasive plant species using remote sensing data. The target species is Kudzu vine, which mostly grows in the south-eastern states of the US and quickly outcompetes other plants, making it a relevant and threatening species to consider. Our study area is Atlanta, Georgia and the surrounding area. Five different algorithms: Boosted Logistic Regression (BLR), Naive Bayes (NB), Neural Network (NN), Random Forest (RF) and Support Vector Machine (SVM) were tested with the aim of testing their performance and identifying the most optimal one. Furthermore, the influence of temporal, spectral and spatial resolution in detecting Kudzu was also tested and reviewed. Our finding shows that random forest, neural network and support vector machine classifiers outperformed. While the achieved internal accuracies were about 97%, an external validation conducted over an expanded area of interest resulted in 79.5% accuracy. Furthermore, the study indicates that high accuracy classification can be achieved using multispectral Sentinel-2 imagery and can be improved while integrating with airborne visible/infrared imaging spectrometer (AVIRIS) hyperspectral data. Finally, this study indicates that dimensionality reduction methods such as principal component analysis (PCA) should be applied cautiously to the hyperspectral AVIRIS data to preserve its utility. The applied approach and the utilized set of methods can be of interest for detecting other kinds of invasive species as part of fulfilling UN sustainable development goals, particularly number 12: responsible consumption and production, 13: climate action, and 15: life on land.

Comparison of Support Vector Machine and Random Forest Algorithms for Invasive and Expansive Species Classification Using Airborne Hyperspectral Data

Invasive and expansive plant species are considered a threat to natural biodiversity because of their high adaptability and low habitat requirements. Species investigated in this research, including Solidago spp., Calamagrostis epigejos, and Rubus spp., are successfully displacing native vegetation and claiming new areas, which in turn severely decreases natural ecosystem richness, as they rapidly encroach on protected areas (e.g., Natura 2000 habitats). Because of the damage caused, the European Union (EU) has committed all its member countries to monitor biodiversity. In this paper we compared two machine learning algorithms, Support Vector Machine (SVM) and Random Forest (RF), to identify Solidago spp., Calamagrostis epigejos, and Rubus spp. on HySpex hyperspectral aerial images. SVM and RF are reliable and well-known classifiers that achieve satisfactory results in the literature. Data sets containing 30, 50, 100, 200, and 300 pixels per class in the training data set were used to train SVM and RF classifiers. The classifications were performed on 430-spectral bands and on the most informative 30 bands extracted using the Minimum Noise Fraction (MNF) transformation. As a result, maps of the spatial distribution of analyzed species were achieved; high accuracies were observed for all data sets and classifiers (an average F1 score above 0.78). The highest accuracies were obtained using 30 MNF bands and 300 sample pixels per class in the training data set (average F1 score > 0.9). Lower training data set sample sizes resulted in decreased average F1 scores, up to 13 percentage points in the case of 30-pixel samples per class.

Early Detection of Invasive Exotic Trees Using UAV and Manned Aircraft Multispectral and LiDAR Data

Exotic conifers can provide significant ecosystem services, but in some environments, they have become invasive and threaten indigenous ecosystems. In New Zealand, this phenomenon is of considerable concern as the area occupied by invasive exotic trees is large and increasing rapidly. Remote sensing methods offer a potential means of identifying and monitoring land infested by these trees, enabling managers to efficiently allocate resources for their control. In this study, we sought to develop methods for remote detection of exotic invasive trees, namely Pinus sylvestris and P. ponderosa. Critically, the study aimed to detect these species prior to the onset of maturity and coning as this is important for preventing further spread. In the study environment in New Zealand’s South Island, these species reach maturity and begin bearing cones at a young age. As such, detection of these smaller individuals requires specialist methods and very high-resolution remote sensing data. We examined the efficacy of classifiers developed using two machine learning algorithms with multispectral and laser scanning data collected from two platforms—manned aircraft and unmanned aerial vehicles (UAV). The study focused on a localized conifer invasion originating from a multi-species pine shelter belt in a grassland environment. This environment provided a useful means of defining the detection thresholds of the methods and technologies employed. An extensive field dataset including over 17,000 trees (height range = 1 cm to 476 cm) was used as an independent validation dataset for the detection methods developed. We found that data from both platforms and using both logistic regression and random forests for classification provided highly accurate (kappa < 0.996 ) detection of invasive conifers. Our analysis showed that the data from both UAV and manned aircraft was useful for detecting trees down to 1 m in height and therefore shorter than 99.3% of the coning individuals in the study dataset. We also explored the relative contribution of both multispectral and airborne laser scanning (ALS) data in the detection of invasive trees through fitting classification models with different combinations of predictors and found that the most useful models included data from both sensors. However, the combination of ALS and multispectral data did not significantly improve classification accuracy. We believe that this was due to the simplistic vegetation and terrain structure in the study site that resulted in uncomplicated separability of invasive conifers from other vegetation. This study provides valuable new knowledge of the efficacy of detecting invasive conifers prior to the onset of coning using high-resolution data from UAV and manned aircraft. This will be an important tool in managing the spread of these important invasive plants.

Multispectral Approach for Identifying Invasive Plant Species Based on Flowering Phenology Characteristics

Invasive plant species (IPS) are the second biggest threat to biodiversity after habitat loss. Since the spatial extent of IPS is essential for managing the invaded ecosystem, the current study aims at identifying and mapping the aggressive IPS of Acacia salicina and Acacia saligna, to understand better the key factors influencing their distribution in the coastal plain of Israel. This goal was achieved by integrating airborne-derived hyperspectral imaging and multispectral earth observation for creating species distribution maps. Hyperspectral data, in conjunction with high spatial resolution species distribution maps, were used to train the multispectral images at the species level. We incorporated a series of statistical models to classify the IPS location and to recognize their distribution and density. We took advantage of the phenological flowering stages of Acacia trees, as obtained by the multispectral images, for the support vector machine classification procedure. The classification yielded an overall Kappa coefficient accuracy of 0.89. We studied the effect of various environmental and human factors on IPS density by using a random forest machine learning model, to understand the mechanisms underlying successful invasions, and to assess where IPS have a higher likelihood of occurring. This algorithm revealed that the high density of Acacia most closely related to elevation, temperature pattern, and distances from rivers, settlements, and roads. Our results demonstrate how the integration of remote-sensing data with different data sources can assist in determining IPS proliferation and provide detailed geographic information for conservation and management efforts to prevent their future spread.

Implementation of a UAV–Hyperspectral Pushbroom Imager for Ecological Monitoring

Hyperspectral remote sensing provides a wealth of data essential for vegetation studies encompassing a wide range of applications (e.g., species diversity, ecosystem monitoring, etc.). The development and implementation of UAV-based hyperspectral systems have gained popularity over the last few years with novel efforts to demonstrate their operability. Here we describe the design, implementation, testing, and early results of the UAV-μCASI system, which showcases a relatively new hyperspectral sensor suitable for ecological studies. The μCASI (288 spectral bands) was integrated with a custom IMU-GNSS data recorder built in-house and mounted on a commercially available hexacopter platform with a gimbal to maximize system stability and minimize image distortion. We deployed the UAV-μCASI at three sites with different ecological characteristics across Canada: The Mer Bleue peatland, an abandoned agricultural field on Ile Grosbois, and the Cowichan Garry Oak Preserve meadow. We examined the attitude data from the flight controller to better understand airframe motion and the effectiveness of the integrated Differential Real Time Kinematic (RTK) GNSS. We describe important aspects of mission planning and show the effectiveness of a bundling adjustment to reduce boresight errors as well as the integration of a digital surface model for image geocorrection to account for parallax effects at the Mer Bleue test site. Finally, we assessed the quality of the radiometrically and atmospherically corrected imagery from the UAV-μCASI and found a close agreement (<2%) between the image derived reflectance and in-situ measurements. Overall, we found that a flight speed of 2.7 m/s, careful mission planning, and the integration of the bundling adjustment were important system characteristics for optimizing the image quality at an ultra-high spatial resolution (3–5 cm). Furthermore, environmental considerations such as wind speed (<5 m/s) and solar illumination also play a critical role in determining image quality. With the growing popularity of “turnkey” UAV-hyperspectral systems on the market, we demonstrate the basic requirements and technical challenges for these systems to be fully operational.

Modelling the distribution of the vector Aedes aegypti in a central Argentine city

Aedes aegypti (Diptera: Culicidae) is an urban mosquito involved in the transmission of numerous viruses, including dengue, chikungunya and Zika. In Argentina, Ae. aegypti is the main vector of dengue virus and has been involved in several outbreaks in regions ranging from northern to central Argentina since 2009. In order to evaluate areas of potential vector-borne disease transmission in the city of Córdoba, Argentina, the present study aimed to identify the environmental, socioeconomic and demographic factors driving the distribution of Ae. aegypti larvae through spatial analysis in the form of species distribution models (SDMs). These models elucidate relationships between known occurrences of a species and environmental data in order to identify areas with suitable habitats for that species and the consequent risk for disease transmission. The maximum entropy species distribution model was able to fit the training data well, with an average area under the receiver operating characteristic curve (AUC) of > 0.8, and produced models with fair extrapolation capacity (average test AUC: > 0.75). Human population density, distance to vegetation and water channels were the main variables predictive of the vector suitability of an area. The results of this work will be used to target surveillance and prevention measures, as well as in mosquito management.

The DIARS toolbox: a spatially explicit approach to monitor alien plant invasions through remote sensing

The synergies between remote sensing technologies and ecological research have opened new avenues for the study of alien plant invasions worldwide. Such scientific advances have greatly improved our capacity to issue warnings, develop early-response systems and assess the impacts of alien plant invasions on biodiversity and ecosystem functioning. Hitherto, practical applications of remote sensing approaches to support nature conservation actions are lagging far behind scientific advances. Yet, for some of these technologies, knowledge transfer is difficult due to the complexity of the different data handling procedures and the huge amounts of data it involves per spatial unit.

In this context, the next logical step is to develop clear guidelines for the application of remote sensing data to monitor and assess the impacts of alien plant invasions, that enable scientists, landscape managers and policy makers to fully exploit the tools which are currently available. It is desirable to have such guidelines accompanied by freely available remote sensing data and generated in a free and open source environment that increases the availability and affordability of these new technologies.

Here we present a toolbox that provides an easy-to-use, flexible, transparent and open source set of tools to sample, map, model and assess the impact of alien plant invasions using two high-resolution remote sensing products (hyperspectral and LiDAR images). This online toolbox includes a real case dataset designed to facilitate testing and training in any computer system and processing capacity.