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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. 

Climate and ecosystem dynamics vary across timescales, but research into climate-driven vegetation dynamics usually focuses on singular timescales. We developed a spectral analysis–based approach that provides detailed estimates of the timescales at which vegetation tracks climate change, from 10¹to 10⁵years. We report dynamic similarity of vegetation and climate even at centennial frequencies (149⁻¹to 18,012⁻¹year⁻¹, that is, one cycle per 149 to 18,012 years). A breakpoint in vegetation turnover (797⁻¹year⁻¹) matches a breakpoint between stochastic and autocorrelated climate processes, suggesting that ecological dynamics are governed by climate across these frequencies. Heightened vegetation turnover at millennial frequencies (4650⁻¹year⁻¹) highlights the risk of abrupt responses to climate change, whereas vegetation-climate decoupling at frequencies >149⁻¹year⁻¹may indicate long-lasting consequences of anthropogenic climate change for ecosystem function and biodiversity. 

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 While human activities are known to elicit rapid turnover in species composition through time, the properties of the species that increase or decrease their spatial occupancy underlying this turnover are less clear. Here, we used an extensive dataset of 238 metacommunity time series of multiple taxa spread across the globe to evaluate whether species that are more widespread (large-ranged species) differed in how they changed their site occupancy over the 10–90 years the metacommunities were monitored relative to species that are more narrowly distributed (small-ranged species). We found that on average, large-ranged species tended to increase in occupancy through time, whereas small-ranged species tended to decrease. These relationships were stronger in marine than in terrestrial and freshwater realms. However, in terrestrial regions, the directional changes in occupancy were less extreme in protected areas. Our findings provide evidence for systematic decreases in occupancy of small-ranged species, and that habitat protection could mitigate these losses in the face of environmental change. 

Estimating biodiversity change across the planet in the context of widespread human modification is a critical challenge. Here, we review how biodiversity has changed in recent decades across scales and taxonomic groups, focusing on four diversity metrics: species richness, temporal turnover, spatial beta-diversity and abundance. At local scales, change across all metrics includes many examples of both increases and declines and tends to be centred around zero, but with higher prevalence of declining trends in beta-diversity (increasing similarity in composition across space or biotic homogenization) and abundance. The exception to this pattern is temporal turnover, with changes in species composition through time observed in most local assemblages. Less is known about change at regional scales, although several studies suggest that increases in richness are more prevalent than declines. Change at the global scale is the hardest to estimate accurately, but most studies suggest extinction rates are probably outpacing speciation rates, although both are elevated. Recognizing this variability is essential to accurately portray how biodiversity change is unfolding, and highlights how much remains unknown about the magnitude and direction of multiple biodiversity metrics at different scales. Reducing these blind spots is essential to allow appropriate management actions to be deployed. This article is part of the theme issue ‘Detecting and attributing the causes of biodiversity change: needs, gaps and solutions’. 

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 Biodiversity metrics often integrate data on the presence and abundance of multiple species. Yet our understanding of covariation between changes to the numbers of individuals, the evenness of species relative abundances, and the total number of species remains limited. Using individual‐based rarefaction curves, we show how expected positive relationships among changes in abundance, evenness and richness arise, and how they can break down. We then examined interdependencies between changes in abundance, evenness and richness in more than 1100 assemblages sampled either through time or across space. As predicted, richness changes were greatest when abundance and evenness changed in the same direction, and countervailing changes in abundance and evenness acted to constrain the magnitude of changes in species richness. Site‐to‐site differences in abundance, evenness, and richness were often decoupled, and pairwise relationships between these components across assemblages were weak. In contrast, changes in species richness and relative abundance were strongly correlated for assemblages varying through time. Temporal changes in local biodiversity showed greater inertia and stronger relationships between the component changes when compared to site‐to‐site variation. Overall, local variation in assemblage diversity was rarely due to repeated passive samples from an approximately static species abundance distribution. Instead, changing species relative abundances often dominated local variation in diversity. Moreover, how changing relative abundances combined with changes to total abundance frequently determined the magnitude of richness changes. Embracing the interdependencies between changing abundance, evenness and richness can provide new information to better understand biodiversity change in the Anthropocene. 

ABSTRACT BackgroundHuman pressures are driving the emergence of unprecedented, ‘novel’, ecological and environmental systems. The concept of novel (eco)systems is well accepted by the scientific community, but the use and measurement of novelty has outgrown initial definitions and critiques. There are still unresolved methodological and conceptual differences in quantifying novelty that prevent a unified research approach. FrameworkHere we present a conceptual framework and guidelines to unify past and future measurement of ecological novelty. Under this framework, novelty is a property of an ecological or environmental entity of interest. Novelty is quantified as the comparison between the target entity and a reference set, measured as the summary of degrees of difference across one or more dimensions. Choices in these components, particularly the reference set, can change resulting novelty measurements and inferences. ShowcaseWe provide a case‐study to showcase our framework, measuring pre‐ and post‐European novelty in 99 pollen assemblages in Midwest USA forests. We paired this quantitative exploration with a five‐step process designed to improve the utility and outcomes of novelty analyses. ConclusionsQuantitative novelty has immense value in studies of abrupt ecological change, linking climatic and ecological change, biotic interactions and invasions, species range shifts and fundamental theories. Our framework offers a unified overview and is also primed for integration into management and restoration workflows, providing consistent and robust measurements of novelty to support decision making, priority setting and resource allocation.