Ben G. Weinstein

MotionMeerkat: integrating motion video detection and ecological monitoring

Summary Human observation is expensive and limits the breadth of data collection. For this reason, remotely placed video cameras are increasingly used to monitor animals. One drawback of field-based video recordings is extensive review time. Computer vision can mitigate this cost and enhance data collection by extracting biological information from images with minimal time investment. MotionMeerkat is a new standalone program that identifies motion events from a video stream. After running a video, the user reviews a folder of candidate motion frames for the target organism. This tool reduces the time needed to review videos and accommodates a variety of inputs. I tested MotionMeerkat using hummingbird–plant videos recorded in a tropical montane forest. To validate the optimal parameter set for finding motion events, I counted hummingbirds observed from direct video review compared to events found in images returned from MotionMeerkat. To show the generality of the approach, MotionMeerkat was tested on a set of terrestrial and underwater videos. To assess the performance of the background subtraction for further image analysis, I hand counted the number of frames with target organisms and compared them to the MotionMeerkat output. MotionMeerkat was highly successful in finding motion events and often reduced the number of frames needed to capture hummingbird visitation by over 90%. Both background approaches effectively found a variety of organisms in ecological videos. I provide general recommendations for parameter settings and extending this approach in the future.

Taxonomic, phylogenetic, and trait Beta diversity in South American hummingbirds.

Comparison of the taxonomic, phylogenetic, and trait dimensions of beta diversity may uncover the mechanisms that generate and maintain biodiversity, such as geographic isolation, environmental filtering, and convergent adaptation. We developed an approach to predict the relationship between environmental and geographic distance and the dimensions of beta diversity. We tested these predictions using hummingbird assemblages in the northern Andes. We expected taxonomic beta diversity to result from recent geographic barriers limiting dispersal, and we found that cost distance, which includes barriers, was a better predictor than Euclidean distance. We expected phylogenetic beta diversity to result from historical connectivity and found that differences in elevation were the best predictors of phylogenetic beta diversity. We expected high trait beta diversity to result from local adaptation to differing environments and found that differences in elevation were correlated with trait beta diversity. When combining beta diversity dimensions, we observe that high beta diversity in all dimensions results from adaption to different environments between isolated assemblages. Comparisons with high taxonomic, low phylogenetic, and low trait beta diversity occurred among lowland assemblages separated by the Andes, suggesting that geographic barriers have recently isolated lineages in similar environments. We provide insight into mechanisms governing hummingbird biodiversity patterns and provide a framework that is broadly applicable to other taxonomic groups.

Process-Based Species Pools Reveal the Hidden Signature of Biotic Interactions Amid the Influence of Temperature Filtering

A persistent challenge in ecology is to tease apart the influence of multiple processes acting simultaneously and interacting in complex ways to shape the structure of species assemblages. We implement a heuristic approach that relies on explicitly defining species pools and permits assessment of the relative influence of the main processes thought to shape assemblage structure: environmental filtering, dispersal limitations, and biotic interactions. We illustrate our approach using data on the assemblage composition and geographic distribution of hummingbirds, a comprehensive phylogeny and morphological traits. The implementation of several process-based species pool definitions in null models suggests that temperature—but not precipitation or dispersal limitation—acts as the main regional filter of assemblage structure. Incorporating this environmental filter directly into the definition of assemblage-specific species pools revealed an otherwise hidden pattern of phylogenetic evenness, indicating that biotic interactions might further influence hummingbird assemblage structure. Such hidden patterns of assemblage structure call for a reexamination of a multitude of phylogenetic- and trait-based studies that did not explicitly consider potentially important processes in their definition of the species pool. Our heuristic approach provides a transparent way to explore patterns and refine interpretations of the underlying causes of assemblage structure.

Persistent bill and corolla matching despite shifting temporal resources in tropical hummingbird‐plant interactions

By specialising on specific resources, species evolve advantageous morphologies to increase the efficiency of nutrient acquisition. However, many specialists face variation in resource availability and composition. Whether specialists respond to these changes depends on the composition of the resource pulses, the cost of foraging on poorly matched resources, and the strength of interspecific competition. We studied hummingbird bill and plant corolla matching during seasonal variation in flower availability and morphology. Using a hierarchical Bayesian model, we accounted for the detectability and spatial overlap of hummingbird-plant interactions. We found that despite seasonal pulses of flowers with short-corollas, hummingbirds consistently foraged on well-matched flowers, leading to low niche overlap. This behaviour suggests that the costs of searching for rare and more specialised resources are lower than the benefit of switching to super-abundant resources. Our results highlight the trade-off between foraging efficiency and interspecific competition, and underline niche partitioning in maintaining tropical diversity.

A computer vision for animal ecology

A central goal of animal ecology is to observe species in the natural world. The cost and challenge of data collection often limit the breadth and scope of ecological study. Ecologists often use image capture to bolster data collection in time and space. However, the ability to process these images remains a bottleneck. Computer vision can greatly increase the efficiency, repeatability and accuracy of image review. Computer vision uses image features, such as colour, shape and texture to infer image content. I provide a brief primer on ecological computer vision to outline its goals, tools and applications to animal ecology. I reviewed 187 existing applications of computer vision and divided articles into ecological description, counting and identity tasks. I discuss recommendations for enhancing the collaboration between ecologists and computer scientists and highlight areas for future growth of automated image analysis.

Dynamic foraging of a top predator in a seasonal polar marine environment

The seasonal movement of animals at broad spatial scales provides insight into life-history, ecology and conservation. By combining high-resolution satellite-tagged data with hierarchical Bayesian movement models, we can associate spatial patterns of movement with marine animal behavior. We used a multi-state mixture model to describe humpback whale traveling and area-restricted search states as they forage along the West Antarctic Peninsula. We estimated the change in the geography, composition and characteristics of these behavioral states through time. We show that whales later in the austral fall spent more time in movements associated with foraging, traveled at lower speeds between foraging areas, and shifted their distribution northward and inshore. Seasonal changes in movement are likely due to a combination of sea ice advance and regional shifts in the primary prey source. Our study is a step towards dynamic movement models in the marine environment at broad scales.

Cultural Diversity in the Amazon Borderlands: Implications for Conservation and Development

Abstract The Amazon basin, one of the worlds core areas for biocultural diversity, includes or borders on nine South American states. The remote and biodiverse Amazon borderlands shared by these states contain over 12,000 kilometers of international boundaries and are increasingly threatened by transboundary infrastructure initiatives. This paper combines geographic information systems (GIS), field observations, and document research to investigate the relationship between cultural diversity and the Amazon borderlands: (1) Are the borderlands more culturally diverse than the Amazonian countries and Amazonian lowland rainforest biome? (2) If so, what characterizes this diversity? Results introduce the unique characteristics of the Amazon borderlands and underscore the argument for an alternative means of Amazon integration based on standing forest and biocultural diversity.

Global mammal beta diversity shows parallel assemblage structure in similar but isolated environments.

The taxonomic, phylogenetic and trait dimensions of beta diversity each provide us unique insights into the importance of historical isolation and environmental conditions in shaping global diversity. These three dimensions should, in general, be positively correlated. However, if similar environmental conditions filter species with similar trait values, then assemblages located in similar environmental conditions, but separated by large dispersal barriers, may show high taxonomic, high phylogenetic, but low trait beta diversity. Conversely, we expect lower phylogenetic diversity, but higher trait biodiversity among assemblages that are connected but are in differing environmental conditions. We calculated all pairwise comparisons of approximately 110 × 110 km grid cells across the globe for more than 5000 mammal species (approx. 70 million comparisons). We considered realms as units representing geographical distance and historical isolation and biomes as units with similar environmental conditions. While beta diversity dimensions were generally correlated, we highlight geographical regions of decoupling among beta diversity dimensions. Our analysis shows that assemblages from tropical forests in different realms had low trait dissimilarity while phylogenetic beta diversity was significantly higher than expected, suggesting potential convergent evolution. Low trait beta diversity was surprisingly not found between isolated deserts, despite harsh environmental conditions. Overall, our results provide evidence for parallel assemblage structure of mammal assemblages driven by environmental conditions at a global scale.

The role of environment, dispersal and competition in explaining reduced co-occurrence among related species

The composition of ecological assemblages depends on a variety of factors including environmental filtering, biotic interactions and dispersal limitation. By evaluating the phylogenetic pattern of assemblages, we gain insight into the relative contribution of these mechanisms to generating observed assemblages. We address some limitations in the field of community phylogenetics by using simulations, biologically relevant null models, and cost distance analysis to evaluate simultaneous mechanisms leading to observed patterns of co-occurrence. Building from past studies of phylogenetic community structure, we applied our approach to hummingbird assemblages in the Northern Andes. We compared the relationship between relatedness and co-occurrence among predicted assemblages, based on estimates of suitable habitat and dispersal limitation, and observed assemblages. Hummingbird co-occurrence peaked at intermediate relatedness and decreased when a closely-related species was present. This result was most similar to simulations that included simultaneous effects of phylogenetic conservatism and repulsion. In addition, we found older sister taxa were only weakly more separated by geographic barriers, suggesting that time since dispersal is unlikely to be the sole factor influencing co-occurrence of closely related species. Our analysis highlights the role of multiple mechanisms acting simultaneously, and provides a hypothesis for the potential importance of competition at regional scales.

Capturing foraging and resting behavior using nested multivariate Markov models in an air-breathing marine vertebrate

BackgroundMatching animal movement with the behaviors that shape life history requires a rigorous connection between the observed patterns of space use and inferred behavioral states. As animal-borne dataloggers capture a greater diversity and frequency of three dimensional movements, we can increase the complexity of movement models describing animal behavior. One challenge in combining data streams is the different spatial and temporal frequency of observations. Nested movement models provide a flexible framework for gleaning data from long-duration, but temporally sparse, data sources.ResultsUsing a two-layer nested model, we combined geographic and vertical movement to infer traveling, foraging and resting behaviors of Humpback whales off the West Antarctic Peninsula. This approach refined previous work using only geographic data to delineate coarser behavioral states. Our results showed increased intensity in foraging activity in late season animals as the whales prepared to migrate north to tropical calving grounds. Our model also suggests strong diel variation in movement states, likely linked to daily changes in prey distribution.ConclusionsUsing a combination of two-dimensional and three-dimensional movement data, we highlight the connection between whale movement and krill availability, as well as the complex spatial pattern of whale foraging in productive polar waters.