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Abstract Technological advances in three imaging techniques have opened the door to advanced morphological analyses and habitat mapping for biologists and ecologists.At the same time, the challenge of translating complex 3D data into meaningful metrics that can be used in conjunction with biological data currently hinders progress and accessibility.We introducehabtools, an R package that provides R functions to efficiently calculate complexity and shape metrics from DEMs, 3D meshes and 2D shapes as well as some helper functions to facilitate workflow.We expect the functionality ofhabtoolsto continue to expand as new metrics and faster methods become available, and we welcome new contributions and ideas. 

Abstract Life‐history traits are promising tools to predict species commonness and rarity because they influence a population's fitness in a given environment. Yet, species with similar traits can have vastly different abundances, challenging the prospect of robust trait‐based predictions. Using long‐term demographic monitoring, we show that coral populations with similar morphological and life‐history traits show persistent (decade‐long) differences in abundance. Morphological groups predicted species positions along two, well known life‐history axes (the fast‐slow continuum and size‐specific fecundity). However, integral projection models revealed that density‐independent population growth (λ) was more variable within morphological groups, and was consistently higher in dominant species relative to rare species. Within‐group λ differences projected large abundance differences among similar species in short timeframes, and were generated by small but compounding variation in growth, survival, and reproduction. Our study shows that easily measured morphological traits predict demographic strategies, yet small life‐history differences can accumulate into large differences in λ and abundance among similar species. Quantifying the net effects of multiple traits on population dynamics is therefore essential to anticipate species commonness and rarity. 

Abstract Insights into assemblages that can persist in extreme environments are still emerging. Ocean warming and acidification select against species with low physiological tolerance (trait‐based ‘filtering’). However, intraspecific trait variation can promote species adaptation and persistence, with potentially large effects on assemblage structure. By sampling nine coral traits (four morphological, four tissue and one skeletal) along an offshore–inshore gradient in temperature and pH, we show that distantly related coral species undergo consistent intraspecific changes as they cross into warm, acidic environments. Intraspecific variation and species turnover each favoured colonies with greater tissue biomass, higher symbiont densities and reduced skeletal investments, indicating strong filtering on colony physiology within and across species. Physiological tissue traits were highly variable within species and were independent of morphology, enabling morphologically diverse species to cross into sites of elevated temperature and acidity. Widespread intraspecific change can therefore counter the loss of biodiversity and morphological structure across a steep environmental gradient. 

Coral bleaching and mortality can show significant spatial and taxonomic heterogeneity at local scales, highlighting the need to understand the fine-scale drivers and impacts of thermal stress. In this study, we used structure-from-motion photogrammetry to track coral bleaching, mortality, and changes in community composition during the 2019 marine heatwave in Kāneʻohe Bay, Hawaiʻi. We surveyed 30 shallow reef patches every 3 weeks for the duration of the bleaching event (August-December) and one year after, resulting in a total of 210 large-area, high-resolution photomosaics that enabled us to follow the fate of thousands of coral colonies through time. We also measured environmental variables such as temperature, sedimentation, depth, and wave velocity at each of these sites, and extracted estimates of habitat complexity (rugosity R and fractal dimension D) from digital elevation models to better understand their effects on patterns of bleaching and mortality. We found that up to 80% of corals experienced moderate to severe bleaching in this period, with peak bleaching occurring in October when heat stress (Degree Heating Weeks) reached its maximum. Mortality continued to accumulate as bleaching levels dropped, driving large declines in more heat-susceptible species (77% loss of Pocillopora cover) and moderate declines in heat-tolerant species (19% and 23% for Porites compressa and Montipora capitata , respectively). Declines in live coral were accompanied by a rapid increase in algal cover across the survey sites. Spatial differences in bleaching were significantly linked to habitat complexity and coral species composition, with reefs that were dominated by Pocillopora experiencing the most severe bleaching. Mortality was also influenced by species composition, fractal dimension, and site-level differences in thermal stress. Our results show that spatial heterogeneity in the impacts of bleaching are driven by a mix of environmental variation, habitat complexity, and differences in assemblage composition. 

Abstract As on land, oceans exhibit high temporal and spatial temperature variation. This “ocean weather” contributes to the physiological and ecological processes that ultimately determine the patterns of species distribution and abundance, yet is often unrecognized, especially in tropical oceans. Here, we tested the paradigm of temperature stability in shallow waters (<12.5 m) across different zones of latitude. We collated hundreds of in situ, high temporal-frequency ocean temperature time series globally to produce an intuitive measure of temperature variability, ranging in scale from quarter-diurnal to annual time spans. To estimate organismal sensitivity of ectotherms (i.e. microbes, algae, and animals whose body temperatures depend upon ocean temperature), we computed the corresponding range of biological rates (such as metabolic rate or photosynthesis) for each time span, assuming an exponential relationship. We found that subtropical regions had the broadest temperature ranges at time spans equal to or shorter than a month, while temperate and tropical systems both exhibited narrow (i.e. stable) short-term temperature range estimates. However, temperature-dependent biological rates in tropical regions displayed greater ranges than in temperate systems. Hence, our results suggest that tropical ectotherms may be relatively more sensitive to short-term thermal variability. We also highlight previously unexplained macroecological patterns that may be underpinned by short-term temperature variability. 

Abstract AimHabitat complexity plays an important role in the structure and function of ecosystems worldwide. On coral reefs, habitat complexity influences ecosystem services such as harvestable fish biomass and attenuation of wave energy. Here, we test how three descriptors of surface complexity—rugosity, fractal dimension, and height range—trend with the geological age of reefs (0.2–5.1 million years old), depth (1–25 m), wave exposure (1–306 kW/m), coral cover (0–80%), and three habitat types (aggregated reef, rock and boulder, and pavement). LocationWe surveyed across 234 sites and 4 degrees of latitude in the eight main Hawaiian Islands. Time PeriodApril 2019 – July 2019. Major Taxa StudiedReef building corals. MethodsWe estimate three surface descriptors (rugosity, fractal dimension and height range) using structure‐from‐motion photogrammetry. We evaluate hypothesized relationships between these descriptors and geological reef age, depth, wave exposure, coral cover and reef habitat type using generalized linear models that account for survey design. ResultsThe rugosity of reef habitats decreased with geological reef age; fractal dimension (and coral cover) decreased with wave exposure; and height range decreased with depth. Variations in these patterns were explained by the different habitat types and the way they are formed over time. Nonetheless, the three surface descriptors were geometrically constrained across all habitat types, and so habitats occupied distinctly different regions of habitat complexity space. Main ConclusionsThis study showed how broad environmental characteristics influence the structural complexity of habitats, and therefore geodiversity, which is an important first step toward understanding the communities supported by these habitats and their ecosystem services.