Biology subjects

Pandolfi, J. M.

Publications and source records attributed to Pandolfi, J. M..

5 recordsLinked to original sources

bioRxiv2026

Anomaly detection uncovers emerging novelty in coral assemblages of the Great Barrier Reef

Earth's biosphere is being altered by human actions, with all ecosystems, especially coral reefs, rapidly transforming in response to climate change and local stressors. As these changes manifest, ecology needs tools to measure change from past states, termed "ecological novelty", within complex multidimensional data such as taxa-abundance time series. Here we use an anomaly detection method new to ecology, Local Outlier Factor (LOF), to measure ecological novelty via neighborhood density in compositional space. We estimated novelty using LOF within 106 coral time series, spanning 29 years, from a long-term monitoring program on the Great Barrier Reef (GBR). We tested whether reef assemblages were becoming more novel over time and whether novelty correlated with common ecological indicators: coral cover, diversity and assemblage turnover. We found novelty correlated with low coral cover, low diversity and high turnover. Even after accounting for these correlations, we found reefs became more novel over time, with novelty across the GBR increasing by 15% between 1998 and 2021. We conclude that GBR coral assemblages are systematically shifting away from past compositional states, a detectable trend on a decadal scale that is increasing across all GBR regions. Our results indicate that anomaly detection methods can contribute to both ecological research and management by providing a new way to quantify ecological novelty under climate change and anthropogenic pressures. Novelty can be estimated from compositional data without needing to establish reference baselines, providing a unique, non-equilibrium perspective that can advance ecological research aims and incorporate into conservation and restoration decision-making frameworks across different taxa and ecosystems. For reef assemblages, the widespread and consistent increase in novelty we identified echo warnings of a global ecological crisis. While a novel species assemblage does not necessarily translate into altered reef functionality or loss of resilience, our findings point to a new for reef management to account for the increasing gap between past reef states and emerging states of the future.

ecology↗

bioRxiv2025

Beyond Coral Cover: A framework for assessing the condition of coral reef habitats and informing conservation targets

The goal of ecosystem management is to maintain healthy and resilient ecosystems over time. These attributes can be summarised under a general term widely used in management plans: ecosystem condition, defined as the overall quality of an ecosystem relative to a desired or reference state. However, measuring and monitoring ecosystem condition remains a challenge. Monitoring ecosystem condition requires a suite of ecological indicators that simultaneously capture the complexity and variability of ecological processes, while being informative and usable in management and decision-making contexts. Such indicators need to be holistic, measurable, sensitive and scalable. Here we outline a resilience-based monitoring framework for coral reefs that consolidates monitoring data and research insights into a relevant, integrated format. The framework includes indicators of ecosystem state (coral cover) and key processes (represented by recovery performance, macroalgae prevalence, community composition, and coral juvenile density). Indicators are generated and scaled from monitoring data by applying explicit, reef-specific thresholds, providing a simple but comprehensive set of ecosystem condition values. Using cases from the Great Barrier Reef, we demonstrate how the framework integrates these indicators for detailed assessments of reef habitat condition and its potential role in management. Based on these case studies, we discuss important considerations for applying this framework worldwide, acknowledging current limitations related to data availability, resolution, and the length of time series.

ecology↗

bioRxiv2022

High-latitude marginal reefs support fewer but bigger corals than their tropical counterparts

AimDespite the awareness that climate change impacts are typically detrimental to tropical coral reefs, the effect of increasing environmental stress and variability on the population size structure of coral species remains poorly understood. This gap in knowledge limits our ability to effectively conserve coral reef ecosystems because size specific dynamics are rarely incorporated. Our aim is to quantify variation in the size structure of coral populations along a tropical-to-subtropical environmental gradient. Location20 coral populations along a latitudinal gradient on the east coast of Australia ([~]23{degrees}S to 30{degrees}S). Time PeriodBetween 2010 and 2018. Major taxa studiedScleractinian corals. MethodsWe apply two methods to quantify the relationship between environmental covariates and coral population size structure along a latitudinal environmental gradient. First, we use linear regression with summary statistics, such as median size as response variables; a method frequently favoured by ecologists. The second method is compositional functional regression, a novel method using entire size-frequency distributions as response variables. We then predict coral population size structure with increasing environmental stress and variability. ResultsCompared to tropical reefs, we find fewer but larger coral colonies in marginal reefs, where environmental conditions are more variable and stressful for corals in the former. Our model predicts that coral populations may become gradually dominated by larger colonies (> 148 cm2) with increasing environmental stress. Main conclusionsWith increasing environmental stress and variability, we can expect shifts in coral population size structure towards more larger colonies. Fewer but bigger corals suggest low survival, slow growth, and poor recruitment. This finding is concerning for the future of coral reefs as it implies populations may have low recovery potential from disturbances. We highlight the importance and usefulness of continuously monitoring changes to population structure over large spatial scales. Data availabilityData is supplied in the supplementary information, or upon request. Once accepted for publication it will be made openly available on Dryad.

ecology↗

bioRxiv2021

Coral assemblages at higher latitudes favour short-term potential over long-term performance

The persistent exposure of coral communities to more variable abiotic regimes is assumed to augment their resilience to future climatic variability. Yet, while the determinants of coral population resilience across species remain unknown, we are unable to predict the winners and losers across reef ecosystems exposed to increasingly variable conditions. Using annual surveys of 3171 coral individuals across Australia and Japan (2017-2019), we explore spatial variation across the short- and long-term dynamics of competitive, stress-tolerant, and weedy assemblages to evaluate how thermal variability mediates the structural composition of coral communities. We illustrate how, by promoting short-term potential over long-term performance, coral assemblages can reduce their vulnerability to stochastic environments. However, compared to stress-tolerant, and weedy assemblages, competitive coral taxa display a reduced capacity for elevating their short-term potential. Accordingly, future climatic shifts threaten the structural complexity of coral assemblages in variable environments, emulating the degradation expected across global tropical reefs.

ecology↗

bioRxiv2020

The rise and fall of novel ecological communities

Local and global environmental change is transforming ecological assemblages into new configurations, resulting in ecosystems with novel communities. Here we develop a robust methodology for the identification of novel communities, examine patterns in their natural chance of occurrence, and quantify the probability of local extinction, emigration, local origination and immigration in transitions to and from novel communities. Using a global dataset of Cenozoic marine plankton communities, we found the probability of local extinction, origination and emigration during transitions to a novel community increased up to four times that of background community changes, with the probability of species loss about equal to that of species gain. Although rare, once a novel community state emerged, the chance of shifting into another novel community state was five times greater than expected by chance. Thus, for marine planktonic communities at 100K year time scales, novel communities are particularly sensitive to further extinctions and community shift. One Sentence SummaryOnce developed, novel ecological communities face increased susceptibility to further shifts in species composition, with heightened extinction risk.

ecology↗