Semi-automated detection of eagle nests: an application of very high-resolution image data and advanced image analyses to wildlife surveys

Very high-resolution (VHR) image data, including from unmanned aerial vehicle (UAV) platforms, are increasingly acquired for wildlife surveys. Animals or structures they build (e.g. nests) can be photointerpreted from these images, however, automated detection is required for more efficient surveys. We developed semi-automated analyses to map white-bellied sea eagle (Haliaeetus leucogaster) nests in VHR aerial photographs of the Houtman Abrolhos Islands, Western Australia, an important breeding site for many seabird species. Nest detection is complicated by high environmental heterogeneity at the scale of nests (~1–2 m), the presence of many features that resemble nests and the variability of nest size, shape and context. Finally, the rarity of nests limits the availability of training data. These challenges are not unique to wildlife surveys and we show how they can be overcome by an innovative integration of object-based image analyses (OBIA) and the powerful machine learning one-class classifier Maxent. Maxent classifications using features characterizing object texture, geometry and neighborhood, along with limited object color information, successfully identified over 90% of high quality nests (most weathered and unusually shaped nests were also detected, but at a slightly lower rate) and labeled <2% of objects as candidate nests. Although this overestimates the occurrence of nests, the results can be visually screened to rule out all but the most likely nests in a process that is simpler and more efficient than manual photointerpretation of the full image. Our study shows that semi-automated image analyses for wildlife surveys are achievable. Furthermore, the developed strategies have broad relevance to image processing applications that seek to detect rare features differing only subtly from a heterogeneous background, including remote sensing of archeological remains. We also highlight solutions to maximize the use of imperfect or uncalibrated image data, such as some UAV-based imagery and the growing body of VHR imagery available in Google Earth and other virtual globes

Contemporary remotely sensed data products refine invasive plants risk mapping in data poor regions

Invasive weeds are a serious problem worldwide, threatening biodiversity and damaging economies. Modeling potential distributions of invasive weeds can prioritize locations for monitoring and control efforts, increasing management efficiency. Forecasts of invasion risk at regional to continental scales are enabled by readily available downscaled climate surfaces together with an increasing number of digitized and georeferenced species occurrence records and species distribution modeling techniques. However, predictions at a finer scale and in landscapes with less topographic variation may require predictors that capture biotic processes and local abiotic conditions. Contemporary remote sensing (RS) data can enhance predictions by providing a range of spatial environmental data products at fine scale beyond climatic variables only. In this study, we used the Global Biodiversity Information Facility (GBIF) and empirical maximum entropy (MaxEnt) models to model the potential distributions of 14 invasive plant species across Southeast Asia (SEA), selected from regional and Vietnam’s lists of priority weeds. Spatial environmental variables used to map invasion risk included bioclimatic layers and recent representations of global land cover, vegetation productivity (GPP), and soil properties developed from Earth observation data. Results showed that combining climate and RS data reduced predicted areas of suitable habitat compared with models using climate or RS data only, with no loss in model accuracy. However, contributions of RS variables were relatively limited, in part due to uncertainties in the land cover data. We strongly encourage greater adoption of quantitative remotely sensed estimates of ecosystem structure and function for habitat suitability modeling. Through comprehensive maps of overall predicted area and diversity of invasive species, we found that among lifeforms (herb, shrub, and vine), shrub species have higher potential invasion risk in SEA. Native invasive species, which are often overlooked in weed risk assessment, may be as serious a problem as non-native invasive species. Awareness of invasive weeds and their environmental impacts is still nascent in SEA and information is scarce. Freely available global spatial datasets, not least those provided by Earth observation programs, and the results of studies such as this one provide critical information that enables strategic management of environmental threats such as invasive species

Tephra isochrons and chronologies of colonisation

This paper demonstrates the use of tephrochronology in dating the earliest archaeological evidence for the settlement of Iceland. This island was one of the last places on Earth settled by people and there are conflicting ideas about the pace and scale of initial colonisation. Three tephra layers, the Landnám (‘land-taking’) tephra layer (A.D. 877 ± 1), the Eldgjá tephra (A.D. 939) and the recently dated V-Sv tephra (A.D. 938 ± 6) can be found at 58% of 253 securely-dated early settlement sites across the country. The presence of the tephras permits both a countrywide comparison, and a classification of these settlement sites into pre-Landnám, Landnám and post-Landnám. The data summarised here for the first time indicate that it will be possible to reconstruct the tempo and development of the colonisation process in decadal resolution by more systematically utilising the dating potential of tephrochronology

Coupling of fog and marine microbial content in the near-shore coastal environment

Microbes in the atmosphere (microbial aerosols) play an important role in climate and provide an ecological and biogeochemical connection between oceanic, atmospheric, and terrestrial environments. However, the sources and environmental factors controlling the concentration, diversity, transport, and viability of microbial aerosols are poorly understood. This study examined culturable microbial aerosols from a coastal environment in Maine (USA) and determined the effect of onshore wind speed and fog presence on deposition rate, source, and community composition. During fog events with low onshore winds (<2 m s−1) the near-shore deposition of microbial aerosols (microbial fallout) decreased with increasing wind speeds, whereas microbial fallout rates under clear conditions and comparable low wind speeds showed no wind speed dependence. Mean aerosol particle size also increased with onshore wind speed when fog was present, indicating increased shoreward transport of larger aerosol particles. 16S rRNA sequencing of culturable ocean surface bacteria and microbial aerosols deposited onshore resulted in the detection of 31 bacterial genera, with 5 dominant genera (Vibrio, Bacillus, Pseudoalteromonas, Psychrobacter, Salinibacterium) making up 66 % of all sequences. The sequence library from microbial aerosol isolates, as with libraries found in other coastal/marine aerosol studies, was dominated at the phylum level by Proteobacteria, with additional representation from Firmicutes, Actinobacteria and Bacteroidetes. Seventy-five percent of the culturable microbial aerosols falling out under foggy conditions were most similar to GenBank-published sequences detected in marine environments. Using a 97 % similarity cut-off, sequence libraries from ocean surface and fog isolates shared eight operational taxonomic units (OTU's) in total, three of which were the most dominant OTU's in the library, representing large fractions of the ocean (28 %) and fog (21 %) libraries. The fog and ocean surface libraries were significantly more similar in microbial community composition than clear (non-foggy) and ocean surface libraries, according to both Jaccard and Sorenson indices. These findings provide the first evidence of a difference in community composition and microbial culturability of aerosols associated with fog compared to clear conditions. The data support a dual role for fog in enhancing the fallout of viable microbial aerosols via increased gravitational settling rates and decreased aerosolization stress on the organisms, which may include relief from UV inactivation, desiccation, and oligotrophic microconditions. This study provides a strong case for ocean to terrestrial transport of microbes and a potential connection between water quality and air quality at coastal sites

Hepatic effects of tartrazine (E 102) after systemic exposure are independent of oestrogen receptor interactions in the mouse

Tartrazine is a food colour that activates the transcriptional function of the human oestrogen receptor alpha in an in vitro cell model. Since oestrogens are cholestatic, we hypothesised tartrazine will cause periportal injury to the liver in vivo. To test this hypothesis, tartrazine was initially administered systemically to mice resulting in a periportal recruitment of inflammatory cells, increased serum alkaline phosphatase activity and mild periportal fibrosis. To determine whether an oestrogenic effect may be a key event in this response, tartrazine, sulphonated metabolites and a food additive contaminant were screened for their ability to interact with murine oestrogen receptors. In all cases, there were no interactions as agonists or antagonists and further, no oestrogenicity was observed with tartrazine in an in vivo uterine growth assay. To examine the relevance of the hepatic effects of tartrazine to its use as a food additive, tartrazine was orally administered to transgenic NF-κB-Luc mice. Pre- and concurrent oral treatment with alcohol was incorporated given its potential to promote gut permeability and hepatic inflammation. Tartrazine alone induced NF- κB activities in the colon and liver but there was no periportal recruitment of inflammatory cells or fibrosis. Tartrazine, its sulphonated metabolites and the contaminant inhibited sulphotransferase activities in murine hepatic S9 extracts. Given the role of sulfotransferases in bile acid excretion, the initiating event giving rise to periportal inflammation and subsequent hepatic pathology through systemic tartrazine exposure is therefore potentially associated an inhibition of bile acid sulphation and excretion and not on oestrogen receptor-mediated transcriptional function. However, these effects were restricted to systemic exposures to tartrazine and did not occur to any significant effect after oral exposure

Modelling the habitat of the endangered Carpentarian Grasswren (Amytornis dorotheae): The importance of spatio-temporal habitat availability in a fire prone landscape

Species distribution modelling (SDM), a tool increasingly adopted to quantify geographic range size, often predicts species’ distributions as static. However, habitat availability may exhibit spatial and temporal variation when dynamic processes, such as fire, determine suitability. Static SDM approaches may not satisfactorily represent this dynamic process. We investigated the potential use of SDM to quantify dynamic habitat availability by applying the MaxEnt SDM technique to model the habitat of the Carpentarian Grasswren (Amytornis dorotheae), an endangered Australian passerine dependent on long unburnt vegetation in a fire prone system. By adjusting a typical SDM approach to incorporate the dynamic nature of fire, we modelled the spatio-temporal variation of suitable habitat over 12 years and compared it to a static modelling approach. Incorporating fire as a dynamic process increased the importance of the fire variable to models (from 35% permutation importance) and improved model performance, as evaluated by the AUC using cross-validation. Our dynamic model revealed sizeable temporal variation in the area and spatial arrangement of suitable habitat that was not apparent in the static model. This result may partly solve the mystery of why the species occurs as widely separated populations despite the presence of seemingly suitable intervening habitat. In areas where the species is no longer found, habitat availability was less consistent due to frequent fire, and fire refugia was more limited and isolated, when compared to sites with recent records. These results demonstrate that, when compared to a static approach, a dynamic SDM approach can lead to improved understanding of dynamic ecological processes, and their impact on a species

Potential contributions of remote sensing to ecosystem service assessments

Ecological and conservation research has provided a strong scientific underpinning to the modeling of ecosystem services (ESs) over space and time, by identifying the ecological processes and components of biodiversity (ecosystem service providers, functional traits) that drive ES supply. Despite this knowledge, efforts to map the distribution of ESs often rely on simple spatial surrogates that provide incomplete and non-mechanistic representations of the biophysical variables they are intended to proxy. However, alternative data sets are available that allow for more direct, spatially nuanced inputs to ES mapping efforts. Many spatially explicit, quantitative estimates of biophysical parameters are currently supported by remote sensing, with great relevance to ES mapping. Additional parameters that are not amenable to direct detection by remote sensing may be indirectly modeled with spatial environmental data layers. We review the capabilities of modern remote sensing for describing biodiversity, plant traits, vegetation condition, ecological processes, soil properties, and hydrological variables and highlight how these products may contribute to ES assessments. Because these products often provide more direct estimates of the ecological properties controlling ESs than the spatial proxies currently in use, they can support greater mechanistic realism in models of ESs. By drawing on the increasing range of remote sensing instruments and measurements, data sets appropriate to the estimation of a given ES can be selected or developed. In so doing, we anticipate rapid progress to the spatial characterization of ecosystem services, in turn supporting ecological conservation, management, and integrated land use planning

Increasing phenological asynchrony between spring green-up and arrival of migratory birds

Consistent with a warming climate, birds are shifting the timing of their migrations, but it remains unclear to what extent these shifts have kept pace with the changing environment. Because bird migration is primarily cued by annually consistent physiological responses to photoperiod, but conditions at their breeding grounds depend on annually variable climate, bird arrival and climate-driven spring events would diverge. We combined satellite and citizen science data to estimate rates of change in phenological interval between spring green-up and migratory arrival for 48 breeding passerine species across North America. Both arrival and green-up changed over time, usually in the same direction (earlier or later). Although birds adjusted their arrival dates, 9 of 48 species did not keep pace with rapidly changing green-up and across all species the interval between arrival and green-up increased by over half a day per year. As green-up became earlier in the east, arrival of eastern breeding species increasingly lagged behind green-up, whereas in the west—where green-up typically became later—birds arrived increasingly earlier relative to green-up. Our results highlight that phenologies of species and trophic levels can shift at different rates, potentially leading to phenological mismatches with negative fitness consequences

Classifying white rot decay resistance of some hardwoods from Sarawak and Peninsular Malaysia and correlations with their tropical in-ground durability

White rot wood decay under Malaysian (humid tropical) terrestrial conditions pose more serious threats to the in-ground service life of hardwoods than other common fungal decay types. A study is made on decay resistance variation for a total combined list of 30 Peninsular Malaysian and Sarawak timber species (plus 6 exotic reference temperate commercial woods for comparison) using the laboratory soilblock decay test method of ASTM D 2017, challenged with a representative virulent Malaysian white rot Basidiomycete Pycnoporus sanguineus. Results showed that Hevea brasiliensis (rubberwood) suffered the most severe wood decay with average percentage mass loss of 43.9%, and regarded as non-durable. On the other scale, there was expectedly negligible decay of the most durable species Eusideroxylon zwageri (belian) heartwood with mean mass loss of only 0.7 %. The remaining species varies between non-durability and high decay durability, but mainly moderately durable on the American ASTM 2017 and European EN350-1 decay resistance classification scales. The decay test findings were weakly correlated with recent Malaysian stake test results. Comparative variation of the white rot decay resistance among the timber species will augment the existing pool of information on wood quality classifications of some tropical timbers that are currently sought by the international timber trade, as well as detecting promising relatively decay resistant lesser-utilised species, that the international forest products trade may also be inclined to utilize in addition to the traditional commercial Malaysian species that are now in limited supplies