Closing the gap between existing large-area imaging research and marine conservation needs.

Emerging technology has immense potential to increase the scale and efficiency of marine conservation. One such technology is large-area imaging (LAI), which relies on structure-from-motion photogrammetry to create composite products, including 3-dimensional (3-D) environmental models, that are larger in spatial extent than the individual images used to create them. Use of LAI has become widespread in certain fields of marine science, primarily to measure the 3D structure of benthic ecosystems and track change over time. However, the use of LAI in the field of marine conservation appears limited. We conducted a review of the coral reef literature on the use of LAI to identify research themes and regional trends in applications of this technology. We also surveyed 135 coral reef scientists and conservation practitioners to determine community familiarity with LAI, evaluate barriers practitioners face in using LAI, and identify applications of LAI believed to be most exciting or relevant to coral conservation. Adoption of LAI was limited primarily to researchers at institutions based in advanced economies and was applied infrequently to conservation, although conservation practitioners and survey respondents from emerging economies indicated they expect to use LAI in the future. Our results revealed disconnect between current LAI research topics and conservation priorities identified by practitioners, highlighting the need for more diverse, conservation-relevant research using LAI. We provide recommendations for how early adopters of LAI (typically Global North scientists from well-resourced institutions) can facilitate access to this conservation technology. These recommendations include developing training resources, creating partnerships for data storage and analysis, publishing standard operating procedures for LAI workflows, standardizing methods, developing tools for efficient data extraction from LAI products, and conducting conservation-relevant research using LAI.

Reducción de la brecha entre la investigación actual de imágenes de gran superficie y las necesidades de la conservación marina Resumen Las nuevas tecnologías tienen un enorme potencial para aumentar la escala y la eficiencia de la conservación marina. Una de ellas son las imágenes de gran superficie (IGS), que se basan en la fotogrametría de estructura a partir del movimiento para crear productos compuestos, incluidos modelos ambientales tridimensionales (3D), cuya extensión espacial es mayor que la de las imágenes individuales utilizadas para crearlos. El uso de las IGS se ha generalizado en determinados campos de las ciencias marinas, principalmente para medir la estructura tridimensional de los ecosistemas bentónicos y realizar un seguimiento de los cambios a lo largo del tiempo. Sin embargo, el uso de las IGS en el campo de la conservación marina parece limitado. Realizamos una revisión de la bibliografía sobre el uso de las IGS en los arrecifes de coral para identificar temas de investigación y tendencias regionales en las aplicaciones de esta tecnología. También encuestamos a 135 científicos de arrecifes de coral y profesionales de la conservación para determinar la familiaridad de la comunidad con las IGS, evaluar las barreras a las que se enfrentan los profesionales en el uso de las IGS e identificar sus aplicaciones consideradas como las más interesantes o relevantes para la conservación del coral. La adopción de las IGS se limitó principalmente a los investigadores de las instituciones con sede en las economías avanzadas y se aplicó con poca frecuencia a la conservación, aunque los profesionales de la conservación y los encuestados de las economías emergentes indicaron que esperan utilizar las IGS en el futuro. Nuestros resultados revelaron una desconexión entre los actuales temas de investigación de las IGS y las prioridades de conservación identificadas por los profesionales, lo que subraya la necesidad de una investigación más diversa y relevante para la conservación mediante el uso de las IGS.

Evidence of Biological Self-Organization in Spatial Patterns of a Common Tropical Alga.

AbstractTropical reef communities contain spatial patterns at multiple scales, observable from microscope and satellite alike. Many of the smaller-scale patterns are generated physiologically (e.g., skeletal structures of corals at <1-m scale), while some of the larger patterns have been attributed to scale-dependent feedbacks (e.g., spur and groove reefs at 10-100-m scales). In describing the spatial patterning of reef benthic communities at landscape levels, we uncovered unique spatial patterning among living marine algae. Populations of the calcifying green alga Halimeda were observed to form a consistent polygonal pattern at a characteristic scale of 3-4 m. The pattern showed no clear evidence of having been formed through biologically created shifts in hydrodynamical conditions or related mechanisms. In considering the specifics of Halimeda growth patterns, a model of self-organization involving separation and patterned extension is proposed, a mechanism revealed in some geological pattern formation. This observation reinforces the diversity of pathways by which striking spatial patterns can occur in ecosystems.

Post-settlement demographics of reef building corals suggest prolonged recruitment bottlenecks.

For many organisms, early life stages experience significantly higher rates of mortality relative to adults. However, tracking early life stage individuals through time in natural settings is difficult, limiting our understanding of the duration of these 'mortality bottlenecks', and the time required for survivorship to match that of adults. Here, we track a cohort of juvenile corals (1-5 cm maximum diameter) from 12 taxa at a remote atoll in the Central Pacific from 2013 to 2017 and describe patterns of annual survivorship. Of the 537 juveniles initially detected, 219 (41%) were alive 4 years later, 163 (30%) died via complete loss of live tissue from the skeleton, and the remaining 155 (29%) died via dislodgement. The differing mortality patterns suggest that habitat characteristics, as well as species-specific features, may influence early life stage survival. Across most taxa, survival fit a logistic model, reaching > 90% annual survival within 4 years. These data suggest that mortality bottlenecks characteristic of 'recruitment' extend up to 5 years after individuals can be visually detected. Ultimately, replenishment of adult coral populations via sexual reproduction is needed to maintain both coral cover and genetic diversity. This study provides key insights into the dynamics and time scales that characterize these critical early life stages.

Re-evaluating the health of coral reef communities: baselines and evidence for human impacts across the central Pacific.

Numerous studies have documented declines in the abundance of reef-building corals over the last several decades and in some but not all cases, phase shifts to dominance by macroalgae have occurred. These assessments, however, often ignore the remainder of the benthos and thus provide limited information on the present-day structure and function of coral reef communities. Here, using an unprecedentedly large dataset collected within the last 10 years across 56 islands spanning five archipelagos in the central Pacific, we examine how benthic reef communities differ in the presence and absence of human populations. Using islands as replicates, we examine whether benthic community structure is associated with human habitation within and among archipelagos and across latitude. While there was no evidence for coral to macroalgal phase shifts across our dataset we did find that the majority of reefs on inhabited islands were dominated by fleshy non-reef-building organisms (turf algae, fleshy macroalgae and non-calcifying invertebrates). By contrast, benthic communities from uninhabited islands were more variable but in general supported more calcifiers and active reef builders (stony corals and crustose coralline algae). Our results suggest that cumulative human impacts across the central Pacific may be causing a reduction in the abundance of reef builders resulting in island scale phase shifts to dominance by fleshy organisms.

Ocean currents magnify upwelling and deliver nutritional subsidies to reef-building corals during El Niño heatwaves.

Marine heatwaves are triggering coral bleaching events and devastating coral populations globally, highlighting the need to identify processes promoting coral survival. Here, we show that acceleration of a major ocean current and shallowing of the surface mixed layer enhanced localized upwelling on a central Pacific coral reef during the three strongest El Niño-associated marine heatwaves of the past half century. These conditions mitigated regional declines in primary production and bolstered local supply of nutritional resources to corals during a bleaching event. The reefs subsequently suffered limited post-bleaching coral mortality. Our results reveal how large-scale ocean-climate interactions affect reef ecosystems thousands of kilometers away and provide a valuable framework for identifying reefs that may benefit from such biophysical linkages during future bleaching events.

Automated 2D, 2.5D, and 3D Segmentation of Coral Reef Pointclouds and Orthoprojections.

Enabled by advancing technology, coral reef researchers increasingly prefer use of image-based surveys over approaches depending solely upon in situ observations, interpretations, and recordings of divers. The images collected, and derivative products such as orthographic projections and 3D models, allow researchers to study a comprehensive digital twin of their field sites. Spatio-temporally located twins can be compared and annotated, enabling researchers to virtually return to sites long after they have left them. While these new data expand the variety and specificity of biological investigation that can be pursued, they have introduced the much-discussed Big Data Problem: research labs lack the human and computational resources required to process and analyze imagery at the rate it can be collected. The rapid development of unmanned underwater vehicles suggests researchers will soon have access to an even greater volume of imagery and other sensor measurements than can be collected by diver-piloted platforms, further exacerbating data handling limitations. Thoroughly segmenting (tracing the extent of and taxonomically identifying) organisms enables researchers to extract the information image products contain, but is very time-consuming. Analytic techniques driven by neural networks offer the possibility that the segmentation process can be greatly accelerated through automation. In this study, we examine the efficacy of automated segmentation on three different image-derived data products: 3D models, and 2D and 2.5D orthographic projections thereof; we also contrast their relative accessibility and utility to different avenues of biological inquiry. The variety of network architectures and parameters tested performed similarly, ∼80% IoU for the genus Porites, suggesting that the primary limitations to an automated workflow are 1) the current capabilities of neural network technology, and 2) consistency and quality control in image product collection and human training/testing dataset generation.

Space-filling and benthic competition on coral reefs.

Reef-building corals are ecosystem engineers that compete with other benthic organisms for space and resources. Corals harvest energy through their surface by photosynthesis and heterotrophic feeding, and they divert part of this energy to defend their outer colony perimeter against competitors. Here, we hypothesized that corals with a larger space-filling surface and smaller perimeters increase energy gain while reducing the exposure to competitors. This predicted an association between these two geometric properties of corals and the competitive outcome against other benthic organisms. To test the prediction, fifty coral colonies from the Caribbean island of Curaçao were rendered using digital 3D and 2D reconstructions. The surface areas, perimeters, box-counting dimensions (as a proxy of surface and perimeter space-filling), and other geometric properties were extracted and analyzed with respect to the percentage of the perimeter losing or winning against competitors based on the coral tissue apparent growth or damage. The increase in surface space-filling dimension was the only significant single indicator of coral winning outcomes, but the combination of surface space-filling dimension with perimeter length increased the statistical prediction of coral competition outcomes. Corals with larger surface space-filling dimensions (Ds > 2) and smaller perimeters displayed more winning outcomes, confirming the initial hypothesis. We propose that the space-filling property of coral surfaces complemented with other proxies of coral competitiveness, such as life history traits, will provide a more accurate quantitative characterization of coral competition outcomes on coral reefs. This framework also applies to other organisms or ecological systems that rely on complex surfaces to obtain energy for competition.

Modelling the linkage between coral assemblage structure and pattern of environmental forcing.

Geographical comparisons suggest that coral reef communities can vary as a function of their environmental context, differing not just in terms of total coral cover but also in terms of relative abundance (or coverage) of coral taxa. While much work has considered how shifts in benthic reef dynamics can shift dominance of stony corals relative to algal and other benthic competitors, the relative performance of coral types under differing patterns of environmental disturbance has received less attention. We construct an empirically-grounded numerical model to simulate coral assemblage dynamics under a spectrum of disturbance regimes, contrasting hydrodynamic disturbances (which cause morphology-specific, whole-colony mortality) with disturbances that cause mortality independently of colony morphology. We demonstrate that the relative representation of morphological types within a coral assemblage shows limited connection to the intensity, and essentially no connection to the frequency, of hydrodynamic disturbances. Morphological types of corals that are more vulnerable to mortality owing to hydrodynamic disturbance tend to grow faster, with rates sufficiently high to recover benthic coverage during inter-disturbance intervals. By contrast, we show that factors causing mortality without linkage to morphology, including those that cause only partial colony loss, more dramatically shift coral assemblage structure, disproportionately favouring fast-growing tabular morphologies. Furthermore, when intensity and likelihood of such disturbances increases, assemblages do not adapt smoothly and instead reveal a heightened level of temporal variance, beyond which reefs demonstrate drastically reduced coral coverage. Our findings highlight that adaptation of coral reef benthic assemblages depends on the nature of disturbances, with hydrodynamic disturbances having little to no effect on the capacity of reef coral communities to resist and recover with sustained coral dominance.

Future sea-level rise drives rocky intertidal habitat loss and benthic community change.

The impacts of sea-level rise (SLR) are likely to be the greatest for ecosystems that exist at the land-sea interface, where small changes in sea-level could result in drastic changes in habitat availability. Rocky intertidal ecosystems possess a number of characteristics which make them highly vulnerable to changes in sea-level, yet our understanding of potential community-scale responses to future SLR scenarios is limited. Combining remote-sensing with in-situ large-area imaging, we quantified habitat extent and characterized the biological community at two rocky intertidal study locations in California, USA. We then used a model-based approach to estimate how a range of SLR scenarios would affect total habitat area, areal extent of dominant benthic space occupiers, and numerical abundance of invertebrates. Our results suggest that SLR will reduce total available rocky intertidal habitat area at our study locations, leading to an overall decrease in areal extent of dominant benthic space occupiers, and a reduction in invertebrate abundances. As large-scale environmental changes, such as SLR, accelerate in the next century, more extensive spatially explicit monitoring at ecologically relevant scales will be needed to visualize and quantify their impacts to biological systems.

Considering the rates of growth in two taxa of coral across Pacific islands.

Reef-building coral taxa demonstrate considerable flexibility and diversity in reproduction and growth mechanisms. Corals take advantage of this flexibility to increase or decrease size through clonal expansion and loss of live tissue area (i.e. via reproduction and mortality of constituent polyps). The biological lability of reef-building corals may be expected to map onto varying patterns of demography across environmental contexts which can contribute to geographic variation in population dynamics. Here we explore the patterns of growth of two common coral taxa, corymbose Pocillopora and massive Porites, across seven islands in the central and south Pacific. The islands span a natural gradient of environmental conditions, including a range of pelagic primary production, a metric linked to the relative availability of inorganic nutrients and heterotrophic resources for mixotrophic corals, and sea surface temperature and thermal histories. Over a multi-year sampling interval, most coral colonies experienced positive growth (greater planar area of live tissue in second relative to first time point), though the distributions of growth varied across islands. Island-level median growth did not relate simply to estimated pelagic primary productivity or temperature. However, at locations that experienced an extreme warm-water event during the sampling interval, most Porites colonies experienced net losses of live tissue and nearly all Pocillopora colonies experienced complete mortality. While descriptive statistics of demographics offer valuable insights into trends and variability in colony change through time, simplified models predicting growth patterns based on summarized oceanographic metrics appear inadequate for robust demographic prediction. We propose that the complexity of life history strategies among colonial reef-building corals introduces unique demographic flexibility for colonies to respond to a wide breadth of environmental conditions.

Insights into coral reef benthic dynamics from nonlinear spatial forecasting.

Nonlinear time-series forecasting, or empirical dynamic modelling, has been used extensively in the past two decades as a tool for distinguishing between random temporal behaviour and nonlinear deterministic dynamics. Previous authors have extended nonlinear time-series forecasting to continuous spatial data. Here, we adjust spatial forecasting to handle discrete data and apply the technique to explore the ubiquity of nonlinear determinism in irregular spatial configurations of coral and algal taxa from Palmyra Atoll, a relatively pristine reef in the central Pacific Ocean. We find that the spatial distributions of coral and algal taxa show signs of nonlinear determinism in some locations and that these signals can change through time. We introduce the hypothesis that nonlinear spatial determinism may be a signal of systems in intermediate developmental (i.e. successional) stages, with spatial randomness characterizing early (i.e. recruitment dominated) and late-successional (i.e. 'climax' or attractor) phases. Common state-based metrics that sum community response to environmental forcing lack resolution to detect dynamics of (potential) recovery phases; incorporating signal of spatial patterning among sessile taxa holds unique promise to elucidate dynamical characters of complex ecological systems, thereby enhancing study and response efforts.

Free-space optical communication through a forest canopy.

We model the effects of the leaves of mature broadleaf (deciduous) trees on air-to-ground free-space optical communication systems operating through the leaf canopy. The concept of leaf area index (LAI) is reviewed and related to a probabilistic model of foliage consisting of obscuring leaves randomly distributed throughout a treetop layer. Individual leaves are opaque. The expected fractional unobscured area statistic is derived as well as the variance around the expected value. Monte Carlo simulation results confirm the predictions of this probabilistic model. To verify the predictions of the statistical model experimentally, a passive optical technique has been used to make measurements of observed sky illumination in a mature broadleaf environment. The results of the measurements, as a function of zenith angle, provide strong evidence for the applicability of the model, and a single parameter fit to the data reinforces a natural connection to LAI. Specific simulations of signal-to-noise ratio degradation as a function of zenith angle in a specific ground-to-unmanned aerial vehicle communication situation have demonstrated the effect of obscuration on performance.