Biology subjects

Staples, T. L.

Publications and source records attributed to Staples, T. L..

3 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↗

bioRxiv2026

Two decades of Novel Ecosystems: Literature analysis of topics, trends and connectivity

1. As human-driven climate change and other anthropogenic forces produce widespread impacts on biodiversity and ecosystem functioning, many ecosystems are shifting into unprecedented, novel states. The Novel Ecosystem Concept (NEC), formalized in 2006, was developed as an alternative framework for managing "novel ecosystems", human-altered systems that are challenging to restore to their historical state. In the years since, the NEC has been proposed as a broader lens for ecosystem management under ongoing global change. 2. We evaluated how the uptake and potential of the NEC have been realized over time using a bibliometric and linguistic toolkit. Using bibliometric data from the Web of Science, we clustered 40,914 applied ecology papers published between 2006 and 2025 into twenty research topics based on language use. We quantified the volume of NEC research within each topic, rates of publication over time, and cross-topic connectivity proxied by citations. 3. We found NEC research in most of the topics of applied ecology, particularly invasion biology, ecosystem services, soil research and studies of freshwater, urban and marine systems. In contrast, several major conservation-focused topics, including protected areas, threatened species, and human-wildlife interactions, contained little research with an explicit link to novel ecosystems. Publication rates increased across all topics, although growth slowed over time. At the same time, NEC research became more focused into ecosystem-specific topics, especially marine ecosystems. NEC research across different topics was well-connected by citations, with papers more likely to cite each other when they used similar language. 4. Overall, the NEC does not appear to have expanded beyond its origins in restoration to become a broadly applied framework across conservation and ecosystem management. Instead, the concepts behind the NEC have been integrated into restoration and management frameworks grappling with climate and other anthropogenic change, while "novelty" is emerging as a powerful quantitative variable for measuring ecological change over space and time. Our results highlight the potential value of bibliometric and linguistic tools to deconstruct the ecological literature to inform what we can, or should, do to intervene for benefit of nature and people.

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↗