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McDonald RA, Neuhausler R, Robinson M, Larsen LG, Harrington HA, Bruna M. Zigzag persistence for coral reef resilience using a stochastic spatial model. J R Soc Interface 2023; 20:20230280. [PMID: 37608713 PMCID: PMC10445017 DOI: 10.1098/rsif.2023.0280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
A complex interplay between species governs the evolution of spatial patterns in ecology. An open problem in the biological sciences is characterizing spatio-temporal data and understanding how changes at the local scale affect global dynamics/behaviour. Here, we extend a well-studied temporal mathematical model of coral reef dynamics to include stochastic and spatial interactions and generate data to study different ecological scenarios. We present descriptors to characterize patterns in heterogeneous spatio-temporal data surpassing spatially averaged measures. We apply these descriptors to simulated coral data and demonstrate the utility of two topological data analysis techniques-persistent homology and zigzag persistence-for characterizing mechanisms of reef resilience. We show that the introduction of local competition between species leads to the appearance of coral clusters in the reef. We use our analyses to distinguish temporal dynamics stemming from different initial configurations of coral, showing that the neighbourhood composition of coral sites determines their long-term survival. Using zigzag persistence, we determine which spatial configurations protect coral from extinction in different environments. Finally, we apply this toolkit of multi-scale methods to empirical coral reef data, which distinguish spatio-temporal reef dynamics in different locations, and demonstrate the applicability to a range of datasets.
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Affiliation(s)
- R. A. McDonald
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK
| | - R. Neuhausler
- Department of Geography, University of California, Berkeley, CA 94720, USA
| | - M. Robinson
- Computer Science Department, University of Oxford, Oxford OX1 3QG, UK
| | - L. G. Larsen
- Department of Geography, University of California, Berkeley, CA 94720, USA
| | - H. A. Harrington
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - M. Bruna
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge CB3 0WA, UK
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Komyakova V, Jaffrés JBD, Strain EMA, Cullen-Knox C, Fudge M, Langhamer O, Bender A, Yaakub SM, Wilson E, Allan BJM, Sella I, Haward M. Conceptualisation of multiple impacts interacting in the marine environment using marine infrastructure as an example. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154748. [PMID: 35337877 DOI: 10.1016/j.scitotenv.2022.154748] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/12/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
The human population is increasingly reliant on the marine environment for food, trade, tourism, transport, communication and other vital ecosystem services. These services require extensive marine infrastructure, all of which have direct or indirect ecological impacts on marine environments. The rise in global marine infrastructure has led to light, noise and chemical pollution, as well as facilitation of biological invasions. As a result, marine systems and associated species are under increased pressure from habitat loss and degradation, formation of ecological traps and increased mortality, all of which can lead to reduced resilience and consequently increased invasive species establishment. Whereas the cumulative bearings of collective human impacts on marine populations have previously been demonstrated, the multiple impacts associated with marine infrastructure have not been well explored. Here, building on ecological literature, we explore the impacts that are associated with marine infrastructure, conceptualising the notion of correlative, interactive and cumulative effects of anthropogenic activities on the marine environment. By reviewing the range of mitigation approaches that are currently available, we consider the role that eco-engineering, marine spatial planning and agent-based modelling plays in complementing the design and placement of marine structures to incorporate the existing connectivity pathways, ecological principles and complexity of the environment. Because the effect of human-induced, rapid environmental change is predicted to increase in response to the growth of the human population, this study demonstrates that the development and implementation of legislative framework, innovative technologies and nature-informed solutions are vital, preventative measures to mitigate the multiple impacts associated with marine infrastructure.
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Affiliation(s)
- Valeriya Komyakova
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia; Centre for Marine Socioecology, University of Tasmania, Hobart, Tasmania 7053, Australia.
| | - Jasmine B D Jaffrés
- C&R Consulting, Townsville, Australia; College of Science and Engineering, James Cook University, Townsville, Australia
| | - Elisabeth M A Strain
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia; Centre for Marine Socioecology, University of Tasmania, Hobart, Tasmania 7053, Australia
| | - Coco Cullen-Knox
- Centre for Marine Socioecology, University of Tasmania, Hobart, Tasmania 7053, Australia
| | - Maree Fudge
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia; Centre for Marine Socioecology, University of Tasmania, Hobart, Tasmania 7053, Australia; College of Business and Economics, University of Tasmania, Australia
| | - Olivia Langhamer
- Division of Electricity, Department of Electrical Engineering, Uppsala University, Sweden
| | - Anke Bender
- Division of Electricity, Department of Electrical Engineering, Uppsala University, Sweden
| | - Siti M Yaakub
- Sustainability & Climate Solutions Department, DHI Water & Environment (S), Singapore
| | - Eloise Wilson
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia; Centre for Marine Socioecology, University of Tasmania, Hobart, Tasmania 7053, Australia
| | - Bridie J M Allan
- Department of Marine Science, University of Otago, Dunedin 9016, New Zealand
| | | | - Marcus Haward
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia; Centre for Marine Socioecology, University of Tasmania, Hobart, Tasmania 7053, Australia; Blue Economy Cooperative Research Centre, PO Box 897, Launceston, Tasmania 7250, Australia
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3
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Strickland WC, Battista NA, Hamlet CL, Miller LA. Planktos: An Agent-Based Modeling Framework for Small Organism Movement and Dispersal in a Fluid Environment with Immersed Structures. Bull Math Biol 2022; 84:72. [PMID: 35689123 DOI: 10.1007/s11538-022-01027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/06/2022] [Indexed: 11/25/2022]
Abstract
Multiscale modeling of marine and aerial plankton has traditionally been difficult to address holistically due to the challenge of resolving individual locomotion dynamics while being carried with larger-scale flows. However, such problems are of paramount importance, e.g., dispersal of marine larval plankton is critical for the health of coral reefs, and aerial plankton (tiny arthropods) can be used as effective agricultural biocontrol agents. Here we introduce the open-source, agent-based modeling software Planktos targeted at 2D and 3D fluid environments in Python. Agents in this modeling framework are relatively tiny organisms in sufficiently low densities that their effect on the surrounding fluid motion can be considered negligible. This library can be used for scientific exploration and quantification of collective and emergent behavior, including interaction with immersed structures. In this paper, we detail the implementation and functionality of the library along with some illustrative examples. Functionality includes arbitrary agent behavior obeying either ordinary differential equations, stochastic differential equations, or coded movement algorithms, all under the influence of time-dependent fluid velocity fields generated by computational fluid dynamics, experiments, or analytical models in domains with static immersed mesh structures with sliding or sticky collisions. In addition, data visualization tools provide images or animations with kernel density estimation and velocity field analysis with respect to deterministic agent behavior via the finite-time Lyapunov exponent.
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Affiliation(s)
- W C Strickland
- Department of Mathematics, University of Tennessee, Knoxville, 227 Ayres Hall, Knoxville, TN, 37996-1320, USA.
| | - N A Battista
- Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, 08628, USA
| | - C L Hamlet
- Department of Mathematics, Bucknell University, Lewisburg, PA, 17837, USA
| | - L A Miller
- Department of Mathematics, University of Arizona, 617 N. Santa Rita Ave., Tuscon, AZ, 85721-0089, USA
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Carturan BS, Parrott L, Pither J. Functional Richness and Resilience in Coral Reef Communities. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.780406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Within the Anthropocene the functional diversity of coral communities is changing rapidly, putting the resilience of many coral reef ecosystems in jeopardy. A better understanding of the relationship between coral functional diversity and reef resilience could reveal practical ways to achieve increased resilience. However, manipulating coral diversity experimentally is challenging, and consequently the links between coral functional diversity, resilience, and ecosystem functioning remain obscure. We used an ecologically detailed agent-based model to conduct a virtual experiment in which functional diversity was manipulated over the entire trait space of scleractinian corals. Using an imputed trait dataset of 798 coral species and eight key functional traits, we assembled 245 functionally distinct coral communities, which we subjected to a cyclone and bleaching event. We then measured four different aspects of their resilience and quantified for each measure the respective effect of (i) the functional richness (FRic), and (ii) community-weighted means (CWM) of four types of trait: effect, resistance, recovery, and competitive. FRic represents the volume occupied by a community in the functional space, while CWM indicates the location of the communities’ centroid in the functional space. We found a significant and positive effect of FRic on three measures of resilience: communities with higher FRic recovered surface cover faster and had more rugosity and cover 10 years after the disturbances. In contrast, the resistance of the coral community—i.e., the capacity to maintain surface cover when subjected to the disturbances—was independent of FRic and was determined primarily by the CWM of resistance traits. By analyzing community dynamics and functional trade-offs, we show that FRic increases resilience via the selection and the insurance effects due to the presence of competitive species in the functional space, i.e., those highly dominant species that contribute the most to the complexity of the habitat and recover quickly from disturbances. Building from the results of our experiment and the trait correlation analysis, we discuss the potential for FRic to serve as a proxy measure of resilience and we present a strategy that can provide direction to on-going reef restoration efforts, and pave the way for sustaining coral communities in a context of rapid global change.
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Kayal M, Adjeroud M. The war of corals: patterns, drivers and implications of changing coral competitive performances across reef environments. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220003. [PMID: 35719881 PMCID: PMC9198512 DOI: 10.1098/rsos.220003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/24/2022] [Indexed: 05/03/2023]
Abstract
Amidst global environmental changes, predicting species' responses to future environments is a critical challenge for preserving biodiversity and associated human benefits. We explored the original idea that coral competitive performances, the ability of corals to preempt ecological space on the reef through territorial warfare, serve as indicators of species' ecological niches and environmental windows, and therefore, responses to future environments. Our surveys indicated that coral performances varied with taxonomic identity, size and position along environmental gradients, highlighting complex interplays between life-history, warfare-strategy and niche segregation. Our results forewarn that growing alterations of coastal environments may trigger shifts in coral dominance, with the decline of major reef-building taxa like acroporids, and emphasize the importance of limiting human impacts for coastal resilience. Our empirical approach untangles the complexity of species' battle-like interactions and can help identify winners and losers in various communities caught in the interplay between ecological niches, environmental windows and global changes.
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Affiliation(s)
- Mohsen Kayal
- ENTROPIE, IRD, CNRS, IFREMER, Université de la Nouvelle-Calédonie, Université de la Réunion, Noumea, New Caledonia
- Laboratoire d'Excellence ‘CORAIL’, Paris, France
| | - Mehdi Adjeroud
- Laboratoire d'Excellence ‘CORAIL’, Paris, France
- ENTROPIE, IRD, CNRS, IFREMER, Université de la Nouvelle-Calédonie, Université de la Réunion, Perpignan, France
- PSL Université Paris, USR 3278 CRIOBE - EPHE-UPVD-CNRS, Perpignan, France
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Peck SL, Heiss A. Can constraint closure provide a generalized understanding of community dynamics in ecosystems? OIKOS 2021. [DOI: 10.1111/oik.07621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Andrew Heiss
- Dept of Public Management and Policy/Andrew Young School of Policy Studies, Georgia State Univ. Atlanta GA USA
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Carturan BS, Pither J, Maréchal JP, Bradshaw CJA, Parrott L. Combining agent-based, trait-based and demographic approaches to model coral-community dynamics. eLife 2020; 9:e55993. [PMID: 32701058 PMCID: PMC7473774 DOI: 10.7554/elife.55993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 07/23/2020] [Indexed: 11/26/2022] Open
Abstract
The complexity of coral-reef ecosystems makes it challenging to predict their dynamics and resilience under future disturbance regimes. Models for coral-reef dynamics do not adequately account for the high functional diversity exhibited by corals. Models that are ecologically and mechanistically detailed are therefore required to simulate the ecological processes driving coral reef dynamics. Here, we describe a novel model that includes processes at different spatial scales, and the contribution of species' functional diversity to benthic-community dynamics. We calibrated and validated the model to reproduce observed dynamics using empirical data from Caribbean reefs. The model exhibits realistic community dynamics, and individual population dynamics are ecologically plausible. A global sensitivity analysis revealed that the number of larvae produced locally, and interaction-induced reductions in growth rate are the parameters with the largest influence on community dynamics. The model provides a platform for virtual experiments to explore diversity-functioning relationships in coral reefs.
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Affiliation(s)
| | - Jason Pither
- Department of Biology, University of British ColumbiaKelownaCanada
- Institute for Biodiversity, Resilience, and Ecosystem Services, University of British ColumbiaKelownaCanada
- Department of Earth, Environmental and Geographic Sciences, University of British ColumbiaKelownaCanada
| | | | - Corey JA Bradshaw
- Global Ecology, College of Science and Engineering, Flinders UniversityAdelaideAustralia
| | - Lael Parrott
- Department of Biology, University of British ColumbiaKelownaCanada
- Institute for Biodiversity, Resilience, and Ecosystem Services, University of British ColumbiaKelownaCanada
- Department of Earth, Environmental and Geographic Sciences, University of British ColumbiaKelownaCanada
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