Data science competition for cross-site individual tree species identification from airborne remote sensing data

Data on individual tree crowns from remote sensing have the potential to advance forest ecology by providing information about forest composition and structure with a continuous spatial coverage over large spatial extents. Classifying individual trees to their taxonomic species over large regions from remote sensing data is challenging. Methods to classify individual species are often accurate for common species, but perform poorly for less common species and when applied to new sites. We ran a data science competition to help identify effective methods for the task of classification of individual crowns to species identity. The competition included data from three sites to assess each methods' ability to generalize patterns across two sites simultaneously and apply methods to an untrained site. Three different metrics were used to assess and compare model performance. Six teams participated, representing four countries and nine individuals. The highest performing method from a previous competition in 2017 was applied and used as a baseline to understand advancements and changes in successful methods. The best species classification method was based on a two-stage fully connected neural network that significantly outperformed the baseline random forest and gradient boosting ensemble methods. All methods generalized well by showing relatively strong performance on the trained sites (accuracy = 0.46-0.55, macro F1 = 0.09-0.32, cross entropy loss = 2.4-9.2), but generally failed to transfer effectively to the untrained site (accuracy = 0.07-0.32, macro F1 = 0.02-0.18, cross entropy loss = 2.8-16.3). Classification performance was influenced by the number of samples with species labels available for training, with most methods predicting common species at the training sites well (maximum F1 score of 0.86) relative to the uncommon species where none were predicted. Classification errors were most common between species in the same genus and different species that occur in the same habitat. Most methods performed better than the baseline in detecting if a species was not in the training data by predicting an untrained mixed-species class, especially in the untrained site. This work has highlighted that data science competitions can encourage advancement of methods, particularly by bringing in new people from outside the focal discipline, and by providing an open dataset and evaluation criteria from which participants can learn.

Assessing the risk of human-to-wildlife pathogen transmission for conservation and public health

The SARS‐CoV‐2 pandemic has led to increased concern over transmission of pathogens from humans to animals, and its potential to threaten conservation and public health. To assess this threat, we reviewed published evidence of human‐to‐wildlife transmission events, with a focus on how such events could threaten animal and human health. We identified 97 verified examples, involving a wide range of pathogens; however, reported hosts were mostly non‐human primates or large, long‐lived captive animals. Relatively few documented examples resulted in morbidity and mortality, and very few led to maintenance of a human pathogen in a new reservoir or subsequent “secondary spillover” back into humans. We discuss limitations in the literature surrounding these phenomena, including strong evidence of sampling bias towards non‐human primates and human‐proximate mammals and the possibility of systematic bias against reporting human parasites in wildlife, both of which limit our ability to assess the risk of human‐to‐wildlife pathogen transmission. We outline how researchers can collect experimental and observational evidence that will expand our capacity for risk assessment for human‐to‐wildlife pathogen transmission.

Effectiveness of antifungal treatments during chytridiomycosis epizootics in populations of an endangered frog

The recently-emerged amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has had an unprecedented impact on global amphibian populations, and highlights the urgent need to develop effective mitigation strategies. We conducted in-situ antifungal treatment experiments in wild populations of the endangered mountain yellow-legged frog during or immediately after Bd-caused mass die-off events. The objective of treatments was to reduce Bd infection intensity ("load") and in doing so alter frog-Bd dynamics and increase the probability of frog population persistence despite ongoing Bd infection. Experiments included treatment of early life stages (tadpoles and subadults) with the antifungal drug itraconazole, treatment of adults with itraconazole, and augmentation of the skin microbiome of subadults with Janthinobacterium lividum, a commensal bacterium with antifungal properties. All itraconazole treatments caused immediate reductions in Bd load, and produced longer-term effects that differed between life stages. In experiments focused on early life stages, Bd load was reduced in the 2 months immediately following treatment and was associated with increased survival of subadults. However, Bd load and frog survival returned to pre-treatment levels in less than 1 year, and treatment had no effect on population persistence. In adults, treatment reduced Bd load and increased frog survival over the entire 3-year post-treatment period, consistent with frogs having developed an effective adaptive immune response against Bd. Despite this protracted period of reduced impacts of Bd on adults, recruitment into the adult population was limited and the population eventually declined to near-extirpation. In the microbiome augmentation experiment, exposure of subadults to a solution of J. lividum increased concentrations of this potentially protective bacterium on frogs. However, concentrations declined to baseline levels within 1 month and did not have a protective effect against Bd infection. Collectively, these results indicate that our mitigation efforts were ineffective in causing long-term changes in frog-Bd dynamics and increasing population persistence, due largely to the inability of early life stages to mount an effective immune response against Bd. This results in repeated recruitment failure and a low probability of population persistence in the face of ongoing Bd infection.

The science of the host-virus network

Better methods to predict and prevent the emergence of zoonotic viruses could support future efforts to reduce the risk of epidemics. We propose a network science framework for understanding and predicting human and animal susceptibility to viral infections. Related approaches have so far helped to identify basic biological rules that govern cross-species transmission and structure the global virome. We highlight ways to make modelling both accurate and actionable, and discuss the barriers that prevent researchers from translating viral ecology into public health policies that could prevent future pandemics.

Fusion neural networks for plant classification: learning to combine RGB, hyperspectral, and lidar data

Airborne remote sensing offers unprecedented opportunities to efficiently monitor vegetation, but methods to delineate and classify individual plant species using the collected data are still actively being developed and improved. The Integrating Data science with Trees and Remote Sensing (IDTReeS) plant identification competition openly invited scientists to create and compare individual tree mapping methods. Participants were tasked with training taxon identification algorithms based on two sites, to then transfer their methods to a third unseen site, using field-based plant observations in combination with airborne remote sensing image data products from the National Ecological Observatory Network (NEON). These data were captured by a high resolution digital camera sensitive to red, green, blue (RGB) light, hyperspectral imaging spectrometer spanning the visible to shortwave infrared wavelengths, and lidar systems to capture the spectral and structural properties of vegetation. As participants in the IDTReeS competition, we developed a two-stage deep learning approach to integrate NEON remote sensing data from all three sensors and classify individual plant species and genera. The first stage was a convolutional neural network that generates taxon probabilities from RGB images, and the second stage was a fusion neural network that “learns” how to combine these probabilities with hyperspectral and lidar data. Our two-stage approach leverages the ability of neural networks to flexibly and automatically extract descriptive features from complex image data with high dimensionality. Our method achieved an overall classification accuracy of 0.51 based on the training set, and 0.32 based on the test set which contained data from an unseen site with unknown taxa classes. Although transferability of classification algorithms to unseen sites with unknown species and genus classes proved to be a challenging task, developing methods with openly available NEON data that will be collected in a standardized format for 30 years allows for continual improvements and major gains for members of the computational ecology community. We outline promising directions related to data preparation and processing techniques for further investigation, and provide our code to contribute to open reproducible science efforts.

Risky Development: Increasing Exposure to Natural Hazards in the United States

Losses from natural hazards are escalating dramatically, with more properties and critical infrastructure affected each year. Although the magnitude, intensity, and/or frequency of certain hazards has increased, development contributes to this unsustainable trend, as disasters emerge when natural disturbances meet vulnerable assets and populations. To diagnose development patterns leading to increased exposure in the conterminous United States (CONUS), we identified earthquake, flood, hurricane, tornado, and wildfire hazard hotspots, and overlaid them with land use information from the Historical Settlement Data Compilation data set. Our results show that 57% of structures (homes, schools, hospitals, office buildings, etc.) are located in hazard hotspots, which represent only a third of CONUS area, and ∼1.5 million buildings lie in hotspots for two or more hazards. These critical levels of exposure are the legacy of decades of sustained growth and point to our inability, lack of knowledge, or unwillingness to limit development in hazardous zones. Development in these areas is still growing more rapidly than the baseline rates for the nation, portending larger future losses even if the effects of climate change are not considered.

Neural hierarchical models of ecological populations

Neural networks are increasingly being used in science to infer hidden dynamics of natural systems from noisy observations, a task typically handled by hierarchical models in ecology. This article describes a class of hierarchical models parameterised by neural networks - neural hierarchical models. The derivation of such models analogises the relationship between regression and neural networks. A case study is developed for a neural dynamic occupancy model of North American bird populations, trained on millions of detection/non-detection time series for hundreds of species, providing insights into colonisation and extinction at a continental scale. Flexible models are increasingly needed that scale to large data and represent ecological processes. Neural hierarchical models satisfy this need, providing a bridge between deep learning and ecological modelling that combines the function representation power of neural networks with the inferential capacity of hierarchical models.

Untangling the dynamics of persistence and colonization in microbial communities

A central goal of community ecology is to infer biotic interactions from observed distributions of co-occurring species. Evidence for biotic interactions, however, can be obscured by shared environmental requirements, posing a challenge for statistical inference. Here, we introduce a dynamic statistical model, based on probit regression, that quantifies the effects of spatial and temporal covariance in longitudinal co-occurrence data. We separate the fixed pairwise effects of species occurrences on persistence and colonization rates, a potential signal of direct interactions, from latent pairwise correlations in occurrence, a potential signal of shared environmental responses. We first validate our modeling framework with several simulation studies. Then, we apply the approach to a pressing epidemiological question by examining how human papillomavirus (HPV) types coexist. Our results suggest that while HPV types respond similarly to common host traits, direct interactions are sparse and weak, so that HPV type diversity depends largely on shared environmental drivers. Our modeling approach is widely applicable to microbial communities and provides valuable insights that should lead to more directed hypothesis testing and mechanistic modeling.

Spatiotemporal prediction of wildfire size extremes with Bayesian finite sample maxima

Wildfires are becoming more frequent in parts of the globe, but predicting where and when wildfires occur remains difficult. To predict wildfire extremes across the contiguous United States, we integrate a 30-yr wildfire record with meteorological and housing data in spatiotemporal Bayesian statistical models with spatially varying nonlinear effects. We compared different distributions for the number and sizes of large fires to generate a posterior predictive distribution based on finite sample maxima for extreme events (the largest fires over bounded spatiotemporal domains). A zero-inflated negative binomial model for fire counts and a lognormal model for burned areas provided the best performance. This model attains 99% interval coverage for the number of fires and 93% coverage for fire sizes over a six year withheld data set. Dryness and air temperature strongly predict extreme wildfire probabilities. Housing density has a hump-shaped relationship with fire occurrence, with more fires occurring at intermediate housing densities. Statistically, these drivers affect the chance of an extreme wildfire in two ways: by altering fire size distributions, and by altering fire frequency, which influences sampling from the tails of fire size distributions. We conclude that recent extremes should not be surprising, and that the contiguous United States may be on the verge of even larger wildfire extremes.

Quantifying climate sensitivity and climate-driven change in North American amphibian communities

Changing climate will impact species' ranges only when environmental variability directly impacts the demography of local populations. However, measurement of demographic responses to climate change has largely been limited to single species and locations. Here we show that amphibian communities are responsive to climatic variability, using >500,000 time-series observations for 81 species across 86 North American study areas. The effect of climate on local colonization and persistence probabilities varies among eco-regions and depends on local climate, species life-histories, and taxonomic classification. We found that local species richness is most sensitive to changes in water availability during breeding and changes in winter conditions. Based on the relationships we measure, recent changes in climate cannot explain why local species richness of North American amphibians has rapidly declined. However, changing climate does explain why some populations are declining faster than others. Our results provide important insights into how amphibians respond to climate and a general framework for measuring climate impacts on species richness.

Experimental investigation of alternative transmission functions: Quantitative evidence for the importance of nonlinear transmission dynamics in host-parasite systems

Understanding pathogen transmission is crucial for predicting and managing disease. Nonetheless, experimental comparisons of alternative functional forms of transmission remain rare, and those experiments that are conducted are often not designed to test the full range of possible forms.

To differentiate among 10 candidate transmission functions, we used a novel experimental design in which we independently varied four factors—duration of exposure, numbers of parasites, numbers of hosts and parasite density—in laboratory infection experiments.

We used interactions between amphibian hosts and trematode parasites as a model system and all candidate models incorporated parasite depletion. An additional manipulation involving anaesthesia addressed the effects of host behaviour on transmission form.

Across all experiments, nonlinear transmission forms involving either a power law or a negative binomial function were the best‐fitting models and consistently outperformed the linear density‐dependent and density‐independent functions. By testing previously published data for two other host–macroparasite systems, we also found support for the same nonlinear transmission forms.

Although manipulations of parasite density are common in transmission studies, the comprehensive set of variables tested in our experiments revealed that variation in density alone was least likely to differentiate among competing transmission functions. Across host–pathogen systems, nonlinear functions may often more accurately represent transmission dynamics and thus provide more realistic predictions for infection.

Habitat heterogeneity drives the host-diversity-begets-parasite-diversity relationship: evidence from experimental and field studies

Despite a century of research into the factors that generate and maintain biodiversity, we know remarkably little about the drivers of parasite diversity. To identify the mechanisms governing parasite diversity, we combined surveys of 8100 amphibian hosts with an outdoor experiment that tested theory developed for free-living species. Our analyses revealed that parasite diversity increased consistently with host diversity due to habitat (i.e. host) heterogeneity, with secondary contributions from parasite colonisation and host abundance. Results of the experiment, in which host diversity was manipulated while parasite colonisation and host abundance were fixed, further reinforced this conclusion. Finally, the coefficient of host diversity on parasite diversity increased with spatial grain, which was driven by differences in their species-area curves: while host richness quickly saturated, parasite richness continued to increase with neighbourhood size. These results offer mechanistic insights into drivers of parasite diversity and provide a hierarchical framework for multi-scale disease research.

"One Health" or Three? Publication Silos Among the One Health Disciplines

The One Health initiative is a global effort fostering interdisciplinary collaborations to address challenges in human, animal, and environmental health. While One Health has received considerable press, its benefits remain unclear because its effects have not been quantitatively described. We systematically surveyed the published literature and used social network analysis to measure interdisciplinarity in One Health studies constructing dynamic pathogen transmission models. The number of publications fulfilling our search criteria increased by 14.6% per year, which is faster than growth rates for life sciences as a whole and for most biology subdisciplines. Surveyed publications clustered into three communities: one used by ecologists, one used by veterinarians, and a third diverse-authorship community used by population biologists, mathematicians, epidemiologists, and experts in human health. Overlap between these communities increased through time in terms of author number, diversity of co-author affiliations, and diversity of citations. However, communities continue to differ in the systems studied, questions asked, and methods employed. While the infectious disease research community has made significant progress toward integrating its participating disciplines, some segregation--especially along the veterinary/ecological research interface--remains.

Integrating occupancy models and structural equation models to understand species occurrence

Understanding the drivers of species occrrece s a fundamenal goal in basic and applied ecology. Occupancy models have emerged as a popular approach for inferring species occurrence because they account for problems associated with imperfect detection in field surveys. Current models, however, are limited because they assume covariates are independent (i.e., indirect effects do not occur). Here, we combined structural equation and occupancy models to investigate complex influences on species occurrence while accounting for imperfect detection. These two methods are inherently compatible because they both provide means to make inference on latent or unobserved quantities based on observed data. Our models evaluated the direct and indirect roles of cattle grazing, water chemistry, vegetation, nonnative fishes, and pond permanence on the occurrence of six pond-breeding amphibians, two of which are threatened: the California tiger salamander (Ambysloma californiense) and the California red-legged frog (Rana draytonil). While cattle had strong effects on pond vegetation and water chemistry, their overall effects on amphibian occurrence were small compared to the consistently negative effects of nonnative fish. Fish strongly reduced occurrence probabilities for four of five native amphibians, including both species of conservation concern. These results could help to identify drivers of amphibian declines and to prioritize strategies for amphibian conservation. More generally, this approach facilitates a more mechanistic representation of ideas about the causes of species distributions in space and time. As shown here, occupancy modeling and structural equation modeling are readily combined, and bring rich sets of techniques that may provide unique theoretical and applied insights into basic ecological questions.

Endohelminths in Bird Hosts from Northern California and an Analysis of the Role of Life History Traits on Parasite Richness

The life history characteristics of hosts often influence patterns of parasite infection either by affecting the likelihood of parasite exposure or the probability of infection after exposure. In birds, migratory behavior has been suggested to affect both the composition and abundance of parasites within a host, although whether migratory birds have more or fewer parasites is unclear. To help address these knowledge gaps, we collaborated with airports, animal rescue/rehabilitation centers, and hunter check stations in the San Francisco Bay Area of California to collect 57 raptors, egrets, herons, ducks, and other waterfowl for parasitological analysis. After dissections of the gastrointestinal tract of each host, we identified 64 taxa of parasites: 5 acanthocephalans, 24 nematodes, 8 cestodes, and 27 trematodes. We then used a generalized linear mixed model to determine how life history traits influenced parasite richness among bird hosts, while controlling for host phylogeny. Parasite richness was greater in birds that were migratory with larger clutch sizes and lower in birds that were herbivorous. The effects of clutch size and diet are consistent with previous studies and have been linked to immune function and parasite exposure, respectively, whereas the effect of migration supports the hypothesis of "migratory exposure" rather than that of "migratory escape."

Multimodal signalling in the North American barn swallow: a phenotype network approach

Complex signals, involving multiple components within and across modalities, are common in animal communication. However, decomposing complex signals into traits and their interactions remains a fundamental challenge for studies of phenotype evolution. We apply a novel phenotype network approach for studying complex signal evolution in the North American barn swallow (Hirundo rustica erythrogaster). We integrate model testing with correlation-based phenotype networks to infer the contributions of female mate choice and male-male competition to the evolution of barn swallow communication. Overall, the best predictors of mate choice were distinct from those for competition, while moderate functional overlap suggests males and females use some of the same traits to assess potential mates and rivals. We interpret model results in the context of a network of traits, and suggest this approach allows researchers a more nuanced view of trait clustering patterns that informs new hypotheses about the evolution of communication systems.

The scaling of host density with richness affects the direction, shape, and detectability of diversity-disease relationships

Pathogen transmission responds differently to host richness and abundance, two unique components of host diversity. However, the heated debate around whether biodiversity generally increases or decreases disease has not considered the relationships between host richness and abundance that may exist in natural systems. Here we use a multi-species model to study how the scaling of total host community abundance with species richness mediates diversity-disease relationships. For pathogens with density-dependent transmission, non-monotonic trends emerge between pathogen transmission and host richness when host community abundance saturates with richness. Further, host species identity drives high variability in pathogen transmission in depauperate communities, but this effect diminishes as host richness accumulates. Using simulation we show that high variability in low richness communities and the non-monotonic relationship observed with host community saturation may reduce the detectability of trends in empirical data. Our study emphasizes that understanding the patterns and predictability of host community composition and pathogen transmission mode will be crucial for predicting where and when specific diversity-disease relationships should occur in natural systems.

Does life history mediate changing disease risk when communities disassemble?

Biodiversity loss sometimes increases disease risk or parasite transmission in humans, wildlife and plants. Some have suggested that this pattern can emerge when host species that persist throughout community disassembly show high host competence - the ability to acquire and transmit infections. Here, we briefly assess the current empirical evidence for covariance between host competence and extirpation risk, and evaluate the consequences for disease dynamics in host communities undergoing disassembly. We find evidence for such covariance, but the mechanisms for and variability around this relationship have received limited consideration. This deficit could lead to spurious assumptions about how and why disease dynamics respond to community disassembly. Using a stochastic simulation model, we demonstrate that weak covariance between competence and extirpation risk may account for inconsistent effects of host diversity on disease risk that have been observed empirically. This model highlights the predictive utility of understanding the degree to which host competence relates to extirpation risk, and the need for a better understanding of the mechanisms underlying such relationships.

Taming wildlife disease: bridging the gap between science and management

Parasites and pathogens of wildlife can threaten biodiversity, infect humans and domestic animals, and cause significant economic losses, providing incentives to manage wildlife diseases. Recent insights from disease ecology have helped transform our understanding of infectious disease dynamics and yielded new strategies to better manage wildlife diseases. Simultaneously, wildlife disease management (WDM) presents opportunities for large‐scale empirical tests of disease ecology theory in diverse natural systems.

To assess whether the potential complementarity between WDM and disease ecology theory has been realized, we evaluate the extent to which specific concepts in disease ecology theory have been explicitly applied in peer‐reviewed WDM literature.

While only half of WDM articles published in the past decade incorporated disease ecology theory, theory has been incorporated with increasing frequency over the past 40 years. Contrary to expectations, articles authored by academics were no more likely to apply disease ecology theory, but articles that explain unsuccessful management often do so in terms of theory.

Some theoretical concepts such as density‐dependent transmission have been commonly applied, whereas emerging concepts such as pathogen evolutionary responses to management, biodiversity–disease relationships and within‐host parasite interactions have not yet been fully integrated as management considerations.

Synthesis and applications. Theory‐based disease management can meet the needs of both academics and managers by testing disease ecology theory and improving disease interventions. Theoretical concepts that have received limited attention to date in wildlife disease management could provide a basis for improving management and advancing disease ecology in the future.

Theory‐based disease management can meet the needs of both academics and managers by testing disease ecology theory and improving disease interventions. Theoretical concepts that have received limited attention to date in wildlife disease management could provide a basis for improving management and advancing disease ecology in the future.