Bio-acoustic tracking and localization using heterogeneous, scalable microphone arrays.

Microphone arrays are an essential tool in the field of bioacoustics as they provide a non-intrusive way to study animal vocalizations and monitor their movement and behavior. Microphone arrays can be used for passive localization and tracking of sound sources while analyzing beamforming or spatial filtering of the emitted sound. Studying free roaming animals usually requires setting up equipment over large areas and attaching a tracking device to the animal which may alter their behavior. However, monitoring vocalizing animals through arrays of microphones, spatially distributed over their habitat has the advantage that unrestricted/unmanipulated animals can be observed. Important insights have been achieved through the use of microphone arrays, such as the convergent acoustic field of view in echolocating bats or context-dependent functions of avian duets. Here we show the development and application of large flexible microphone arrays that can be used to localize and track any vocalizing animal and study their bio-acoustic behavior. In a first experiment with hunting pallid bats the acoustic data acquired from a dense array with 64 microphones revealed details of the bats' echolocation beam in previously unseen resolution. We also demonstrate the flexibility of the proposed microphone array system in a second experiment, where we used a different array architecture allowing to simultaneously localize several species of vocalizing songbirds in a radius of 75 m. Our technology makes it possible to do longer measurement campaigns over larger areas studying changing habitats and providing new insights for habitat conservation. The flexible nature of the technology also makes it possible to create dense microphone arrays that can enhance our understanding in various fields of bioacoustics and can help to tackle the analytics of complex behaviors of vocalizing animals.

Microfluidic chips provide visual access to in situ soil ecology.

Microbes govern most soil functions, but investigation of these processes at the scale of their cells has been difficult to accomplish. Here we incubate microfabricated, transparent 'soil chips' with soil, or bury them directly in the field. Both soil microbes and minerals enter the chips, which enables us to investigate diverse community interdependences, such as inter-kingdom and food-web interactions, and feedbacks between microbes and the pore space microstructures. The presence of hyphae ('fungal highways') strongly and frequently increases the dispersal range and abundance of water-dwelling organisms such as bacteria and protists across air pockets. Physical forces such as water movements, but also organisms and especially fungi form new microhabitats by altering the pore space architecture and distribution of soil minerals in the chip. We show that soil chips hold a large potential for studying in-situ microbial interactions and soil functions, and to interconnect field microbial ecology with laboratory experiments.

Out of the laboratory, into the field: perspectives on social, ethical and regulatory challenges in UK wildlife research.

Drawing on insights from qualitative social science research, this paper aims to prompt reflection on social, ethical and regulatory challenges faced by scientists undertaking invasive animal research in the field and propose ways of addressing these challenges to promote good care for animals and environments. In particular, we explore challenges relating to the management of (i) relationships with publics and stakeholders, who may be present at field sites or crucial to research success; (ii) ethical considerations not present in the laboratory, such as the impacts of research on populations and ecosystems; (iii) working under an array of regulations, which may operate in accordance with competing ethical principles or objectives; and (iv) relationships with regulators (especially vets), which may involve disagreements over ethics and expertise, especially because regulators may be more accustomed to overseeing research in the laboratory than the field. We argue that flexibility-at a personal and policy level-and respect for others' expertise emerged as two key ways of negotiating ethical challenges, fostering positive working relationships and promoting good care for individual animals and broader ecosystems. While our analysis focuses on the UK, we propose that many of these lessons are broadly applicable to international contexts. This article is part of the theme issue 'Measuring physiology in free-living animals (Part II)'.

Novel use of PDMS tubing for in-soil capture of plant natural products.

The extraction of small lipophilic molecules (SLMs) in the soil-root interface that play a role in belowground ecological interactions between plants and insect herbivores was investigated. Polydimethylsiloxane (PDMS) microtubing has been shown to absorb root SLMs selectively in low-disturbance setups, where analytes were extracted from the polymer with methanol. This technique was adapted to isolate SLMs that diffuse in the vapour phase in soil and sand and under various experimental parameters, extracting with a plug of diethyl ether pushed through the length of the silicon tubing. Moisture level had a substrate-dependent effect on the recovery rate of analytes that were applied as synthetic blends of known belowground SLM semiochemicals in the media. Higher amounts of two selected SLMs, (E)-caryophyllene and (-)-thujopsene, were extracted from sand, and increased polymer and solvent volume, as well as sampling duration, resulted in more of these two SLMs recovered by extraction. It was also shown that PDMS tubes lose no extraction capacity after repeated use. The signature compound (E)-caryophyllene was successfully isolated from the rhizosphere of maize plants infested with Diabrotica v. virgifera larvae by extracting the silicon tubing with diethyl ether. Because the tubes are preconditioned to reduce the presence of contaminants, such extracts can be directly analysed by GC and GC-MS and used in electrophysiological and behavioural assays. After further modifications, non-invasive, in situ PDMS probes can be developed that extract SLMs from plant rhizosphere for the study of belowground chemical ecology processes.

Technological advances in field studies of pollinator ecology and the future of e-ecology.

Our review looks at recent advances in technologies applied to studying pollinators in the field. These include RFID, radar and lidar for detecting and tracking pollinators; wireless sensor networks (e.g. 'smart' hives); automated visual and audio monitoring systems including vision motion software for monitoring fine-scale pollinator behaviours over extended periods; and automated species identification systems based on machine learning that can vastly reduce the bottleneck in (big) data analysis. An improved e-ecology platform that leverages these tools is needed for ecologists to acquire and understand large spatiotemporal datasets, and thus inform knowledge gaps in environmental policy-making. Developing the next generation of e-ecology tools will require synergistic partnerships between academia and industry and significant investment in a cross-disciplinary scientific consortia.

3D printed objects do not impact the behavior of a coral-associated damselfish or survival of a settling stony coral.

3D printing technology offers significant advantages in the development of objects and tools across an array of fields and has been implemented in an increasing number of ecological studies. As rates of degradation or chemical leaching of 3D printed models has not been well documented under environmental conditions, it is essential to examine if these objects will alter the behavior or impact the survivorship of the focal species prior to widespread implementation. Here, we explored the efficacy of using 3D printed models in coral reef behavioral research, an area of study where this form of additive manufacturing could offer significant advantages. Coral-associated blue-green chromis (Chromis viridis) individuals were exposed to natural and 3D printed coral habitats, and larval mustard hill coral (Porites astreoides) were offered 3D printed substrate as a settlement surface. Habitat association and behavioral analyses indicated that C. viridis did not discriminate or display modified behaviors between 3D printed and natural coral skeletons or between 3D printed materials. P. astreoides displayed significantly higher settlement when provided with 3D printed settlement surfaces than when provided with no settlement surface and settled at similar rates between 3D printed surfaces of differing materials. Additionally, growth and mortality of P. astreoides settled on different 3D printed surfaces did not significantly differ. Our results suggest that the 3D printed models used in this study are not inherently harmful to a coral reef fish or species of brooding coral, supporting further exploration of the benefits that these objects and others produced with additive manufacturing may offer as ecological research tools.

Optimized Pitfall Trap Design for Collecting Terrestrial Insects (Arthropoda: Insecta) in Biodiversity Studies.

Pitfall traps are commonly used for the collection of terrestrial insects in ecology and biology studies; they are relatively straightforward to manufacture and there is a large variety of models described in the literature. However, they present a few drawbacks: (i) the removal and transport of the collected material are not practical; (ii) they have low resistance and durability; (iii) they fail to correctly protect the attractive bait against adverse weather conditions and scavengers, and (iv) evaporation of the liquid used inside the trap. We proposed an optimized pitfall trap design for terrestrial insect collection made from cheap and easily accessible materials. The new design allows the transfer of the collected material to the lab by removing only that part of the trap where the insects have been captured; the other part remains in its original place. Thus, the proposed trap allows easier operation since there is no need to transport water to replenish the traps after each transfer; in addition, there is less volume and weight to be carried. The trap can remain in the field for months because of the durability of its material. Furthermore, the collected material is better protected against adverse weather conditions and scavengers. Currently, an efficient and rapid sampling strategy in the field is of global interest to understand mechanisms that can contribute to the monitor changes in phenology, succession, and biodiversity.

Geolocator deployment reduces return rate, alters selection, and impacts demography in a small songbird.

In the past few years, miniature light-level geolocators have been developed for tracking wild bird species that were previously too small to track during their full annual cycle. Geolocators offer an exciting opportunity to study the full annual cycle for many species. However, the potential detrimental effects of carrying geolocators are still poorly understood, especially for small-bodied birds. Here, we deployed light-level geolocators on common yellowthroat warblers (Geothlypis trichas). Over two years, we monitored return rates and neighborhood demography for 40 warblers carrying a geolocator and 20 reference birds that did not carry a geolocator. We compared the two groups with long-term data from 108 unmanipulated birds breeding at the same location in previous and subsequent years. Overall, we found that individuals carrying a geolocator were less likely to return to the study site in the following year (21% to 33% returned, depending on inclusion criteria) than either contemporaneous controls (55%) or long-term controls (55%). Among birds marked with geolocators, we also detected viability selection for greater wing length, whereas this pattern was not present in control birds. Finally, in each year after geolocator deployment, inexperienced breeders colonized vacant territories and this demographic effect persisted for two years after deployment. Sexual selection and ornamentation are strongly age-dependent in this system, and behavioral data collected after geolocator deployment is likely to differ systematically from natural conditions. Clearly geolocators will continue to be useful tools, but we suggest that future studies should carefully consider the potential for biased returns and the ecological validity of behavioral data collected from geolocator marked populations.

Validation of a Noninvasive Hair Trapping Method for Extractive-Foraging Primates.

Hair is a useful source of biological information. For example, the bulb can be a source of high-quality genetic material, whereas the shaft can be useful for measuring heavy metals and some hormones, such as cortisol. The stable isotope composition of hair is another valuable source of biological information. Consequently, noninvasive methods of hair sampling have become important research tools. Several hair-trapping methods have been developed for use on mammals, but these are rarely deployed on primates in part because their travel patterns can be difficult to predict and because many species are averse to novel objects in their environments. Yet if a species has a natural propensity to envision, manipulate, and withdraw extractable food resources, then a baited receptacle lined with double-sided tape may prove successful as a hair trap. Recently, researchers demonstrated the success of such a contraption with tufted capuchins, a Neotropical monkey species with a high degree of somatosensory intelligence and a proclivity for extractive foraging. Here, we replicate this method in a population of tool-using long-tailed macaques (Macaca fascicularis). Our trials validate the effectiveness of the method, suggesting that it is suitable for long-tailed macaques and other extractive-foraging primates.

Benefits and limitations of three-dimensional printing technology for ecological research.

BACKGROUND: Ecological research often involves sampling and manipulating non-model organisms that reside in heterogeneous environments. As such, ecologists often adapt techniques and ideas from industry and other scientific fields to design and build equipment, tools, and experimental contraptions custom-made for the ecological systems under study. Three-dimensional (3D) printing provides a way to rapidly produce identical and novel objects that could be used in ecological studies, yet ecologists have been slow to adopt this new technology. Here, we provide ecologists with an introduction to 3D printing. RESULTS: First, we give an overview of the ecological research areas in which 3D printing is predicted to be the most impactful and review current studies that have already used 3D printed objects. We then outline a methodological workflow for integrating 3D printing into an ecological research program and give a detailed example of a successful implementation of our 3D printing workflow for 3D printed models of the brown anole, Anolis sagrei, for a field predation study. After testing two print media in the field, we show that the models printed from the less expensive and more sustainable material (blend of 70% plastic and 30% recycled wood fiber) were just as durable and had equal predator attack rates as the more expensive material (100% virgin plastic). CONCLUSIONS: Overall, 3D printing can provide time and cost savings to ecologists, and with recent advances in less toxic, biodegradable, and recyclable print materials, ecologists can choose to minimize social and environmental impacts associated with 3D printing. The main hurdles for implementing 3D printing-availability of resources like printers, scanners, and software, as well as reaching proficiency in using 3D image software-may be easier to overcome at institutions with digital imaging centers run by knowledgeable staff. As with any new technology, the benefits of 3D printing are specific to a particular project, and ecologists must consider the investments of developing usable 3D materials for research versus other methods of generating those materials.

Re-wilding Collective Behaviour: An Ecological Perspective.

The earliest studies of collective animal behaviour were inspired by and conducted in the wild. Over the past decades much of the research in this field has shifted to the laboratory, combining high-resolution tracking of individuals with mathematical simulations or agent-based models. Today we are beginning to see a 're-wilding' of collective behaviour thanks to technological advances, providing researchers with the opportunity to quantify and model the heterogeneity that exists within the social groupings they study and within the environments in which these groups live. The perspective we present here aims to inspire and steer this research toward answering fundamental and outstanding behavioural and ecological questions, while also tackling pertinent conservation challenges.

Collective movement in ecology: from emerging technologies to conservation and management.

Recent advances in technology and quantitative methods have led to the emergence of a new field of study that stands to link insights of researchers from two closely related, but often disconnected disciplines: movement ecology and collective animal behaviour. To date, the field of movement ecology has focused on elucidating the internal and external drivers of animal movement and the influence of movement on broader ecological processes. Typically, tracking and/or remote sensing technology is employed to study individual animals in natural conditions. By contrast, the field of collective behaviour has quantified the significant role social interactions play in the decision-making of animals within groups and, to date, has predominantly relied on controlled laboratory-based studies and theoretical models owing to the constraints of studying interacting animals in the field. This themed issue is intended to formalize the burgeoning field of collective movement ecology which integrates research from both movement ecology and collective behaviour. In this introductory paper, we set the stage for the issue by briefly examining the approaches and current status of research in these areas. Next, we outline the structure of the theme issue and describe the obstacles collective movement researchers face, from data acquisition in the field to analysis and problems of scale, and highlight the key contributions of the assembled papers. We finish by presenting research that links individual and broad-scale ecological and evolutionary processes to collective movement, and finally relate these concepts to emerging challenges for the management and conservation of animals on the move in a world that is increasingly impacted by human activity.This article is part of the theme issue 'Collective movement ecology'.

Identifying species from the air: UAVs and the very high resolution challenge for plant conservation.

The Pacific Equatorial dry forest of Northern Peru is recognised for its unique endemic biodiversity. Although highly threatened the forest provides livelihoods and ecosystem services to local communities. As agro-industrial expansion and climatic variation transform the region, close ecosystem monitoring is essential for viable adaptation strategies. UAVs offer an affordable alternative to satellites in obtaining both colour and near infrared imagery to meet the specific requirements of spatial and temporal resolution of a monitoring system. Combining this with their capacity to produce three dimensional models of the environment provides an invaluable tool for species level monitoring. Here we demonstrate that object-based image analysis of very high resolution UAV images can identify and quantify keystone tree species and their health across wide heterogeneous landscapes. The analysis exposes the state of the vegetation and serves as a baseline for monitoring and adaptive implementation of community based conservation and restoration in the area.

Maize Cropping Systems Mapping Using RapidEye Observations in Agro-Ecological Landscapes in Kenya.

Cropping systems information on explicit scales is an important but rarely available variable in many crops modeling routines and of utmost importance for understanding pests and disease propagation mechanisms in agro-ecological landscapes. In this study, high spatial and temporal resolution RapidEye bio-temporal data were utilized within a novel 2-step hierarchical random forest (RF) classification approach to map areas of mono- and mixed maize cropping systems. A small-scale maize farming site in Machakos County, Kenya was used as a study site. Within the study site, field data was collected during the satellite acquisition period on general land use/land cover (LULC) and the two cropping systems. Firstly, non-cropland areas were masked out from other land use/land cover using the LULC mapping result. Subsequently an optimized RF model was applied to the cropland layer to map the two cropping systems (2nd classification step). An overall accuracy of 93% was attained for the LULC classification, while the class accuracies (PA: producer's accuracy and UA: user's accuracy) for the two cropping systems were consistently above 85%. We concluded that explicit mapping of different cropping systems is feasible in complex and highly fragmented agro-ecological landscapes if high resolution and multi-temporal satellite data such as 5 m RapidEye data is employed. Further research is needed on the feasibility of using freely available 10-20 m Sentinel-2 data for wide-area assessment of cropping systems as an important variable in numerous crop productivity models.

Forest cover mapping in post-Soviet Central Asia using multi-resolution remote sensing imagery.

Despite rapid advances and large-scale initiatives in forest mapping, reliable cross-border information about the status of forest resources in Central Asian countries is lacking. We produced consistent Central Asia forest cover (CAFC) maps based on a cost-efficient approach using multi-resolution satellite imagery from Landsat and MODIS during 2009-2011. The spectral-temporal metrics derived from 2009-2011 Landsat imagery (overall accuracy of 0.83) was used to predict sub-pixel forest cover on the MODIS scale for 2010. Accuracy assessment confirmed the validity of MODIS-based forest cover map with a normalized root-mean-square error of 0.63. A general paucity of forest resources in post-Soviet Central Asia was indicated, with 1.24% of the region covered by forest. In comparison to the CAFC map, a regional map derived from MODIS Vegetation Continuous Fields tended to underestimate forest cover, while the Global Forest Change product matched well. The Global Forest Resources Assessments, based on individual country reports, overestimated forest cover by 1.5 to 147 times, particularly in the more arid countries of Turkmenistan and Uzbekistan. Multi-resolution imagery contributes to regionalized assessment of forest cover in the world's drylands while developed CAFC maps (available at https://data.zef.de/ ) aim to facilitate decisions on biodiversity conservation and reforestation programs in Central Asia.

Actogram analysis of free-flying migratory birds: new perspectives based on acceleration logging.

The use of accelerometers has become an important part of biologging techniques for large-sized birds with accelerometer data providing information about flight mode, wing-beat pattern, behaviour and energy expenditure. Such data show that birds using much energy-saving soaring/gliding flight like frigatebirds and swifts can stay airborne without landing for several months. Successful accelerometer studies have recently been conducted also for free-flying small songbirds during their entire annual cycle. Here we review the principles and possibilities for accelerometer studies in bird migration. We use the first annual actograms (for red-backed shrike Lanius collurio) to explore new analyses and insights that become possible with accelerometer data. Actogram data allow precise estimates of numbers of flights, flight durations as well as departure/landing times during the annual cycle. Annual and diurnal rhythms of migratory flights, as well as prolonged nocturnal flights across desert barriers are illustrated. The shifting balance between flight, rest and different intensities of activity throughout the year as revealed by actogram data can be used to analyse exertion levels during different phases of the life cycle. Accelerometer recording of the annual activity patterns of individual birds will open up a new dimension in bird migration research.