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Li Z, Guo X, Guo Z, Shi X, Zhou J, Liu Z, Xiao Q, Chen Y. 3D Morphological Scanning and Environmental Correlates of Bufo gargarizans in the Yellow River Basin. Animals (Basel) 2024; 14:369. [PMID: 38338012 PMCID: PMC10854707 DOI: 10.3390/ani14030369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/30/2023] [Accepted: 01/15/2024] [Indexed: 02/12/2024] Open
Abstract
Morphology plays a crucial role in understanding the intricacies of biological forms. Traditional morphometric methods, focusing on one- or two-dimensional geometric levels, often fall short of accurately capturing the three-dimensional (3D) structure of organisms. The advent of 3D scanning techniques has revolutionized the study of organismal morphology, enabling comprehensive and accurate measurements. This study employs a 3D structured light scanning system to analyze the morphological variations in the Chinese toad (Bufo gargarizans Cantor, 1842) along the Yellow River Basin. The 3D digital model obtained from the scan was used to calculate various morphological parameters including body surface area, volume, fractal dimensions, and limb size. The research explores geographic variability patterns and identifies environmental drivers affecting the 3D phenotypic variation of B. gargarizans. Results reveal a bimodal pattern of variation in the toad population, with higher elevations exhibiting smaller body sizes, greater appendage proportions, and more complex body structures. Linear regression analyses highlight the influence of elevation and annual mean temperature on the morphological variation of B. gargarizans, with elevation playing a significant role. This study underscores the significance of 3D morphometric analysis in unraveling the intricacies of organismal morphology and understanding the adaptive strategies of species in diverse environments.
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Affiliation(s)
- Zihan Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; (Z.L.); (X.G.); (Z.G.); (X.S.); (J.Z.); (Z.L.); (Q.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuecheng Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; (Z.L.); (X.G.); (Z.G.); (X.S.); (J.Z.); (Z.L.); (Q.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zeguang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; (Z.L.); (X.G.); (Z.G.); (X.S.); (J.Z.); (Z.L.); (Q.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoqin Shi
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; (Z.L.); (X.G.); (Z.G.); (X.S.); (J.Z.); (Z.L.); (Q.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; (Z.L.); (X.G.); (Z.G.); (X.S.); (J.Z.); (Z.L.); (Q.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhidong Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; (Z.L.); (X.G.); (Z.G.); (X.S.); (J.Z.); (Z.L.); (Q.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Xiao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; (Z.L.); (X.G.); (Z.G.); (X.S.); (J.Z.); (Z.L.); (Q.X.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youhua Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; (Z.L.); (X.G.); (Z.G.); (X.S.); (J.Z.); (Z.L.); (Q.X.)
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2
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Engleman A, Cox K, Brooke S. Dead but not forgotten: complexity of Acropora palmata colonies increases with greater composition of dead coral. PeerJ 2023; 11:e16101. [PMID: 37842045 PMCID: PMC10576496 DOI: 10.7717/peerj.16101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/25/2023] [Indexed: 10/17/2023] Open
Abstract
Coral reefs are highly biodiverse ecosystems that have declined due to natural and anthropogenic stressors. Researchers often attribute reef ecological processes to corals' complex structure, but effective conservation requires disentangling the contributions of coral versus reef structures. Many studies assessing the relationships between reef structure and ecological dynamics commonly use live coral as a proxy for reef complexity, disregarding the contribution of dead coral skeletons to reef habitat provision or other biogeochemical reef dynamics. This study aimed to assess the contribution of dead coral to reef complexity by examining structural variations in live and dead Acropora palmata colonies. We used photogrammetry to reconstruct digital elevation models (DEMs) and orthomosaics of the benthic region immediately surrounding 10 A. palmata colonies. These reconstructions were used to quantify structural metrics, including surface rugosity, fractal dimension, slope, planform curvature, and profile curvature, as a function of benthic composition (i.e., live A. palmata, dead A. palmata, or non-A. palmata substrate). The results revealed that dead coral maintained more varied profile curvatures and higher fractal dimensions than live or non-coral substrate. Conversely, A. palmata colonies with a higher proportion of live coral displayed more uniform structure, with lower fractal dimensions and less variability in profile curvature measures. Other metrics showed no significant difference among substrate types. These findings provide novel insights into the structural differences between live and dead coral, and an alternative perspective on the mechanisms driving the observed structural complexity on reefs. Overall, our results highlight the overlooked potential contributions of dead coral to reef habitat provision, ecological processes, and other biogeochemical reef dynamics, and could have important implications for coral reef conservation.
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Affiliation(s)
- Abigail Engleman
- Department of Biological Science, Florida State University, Tallahassee, United States of America
- Coastal and Marine Laboratory, Florida State University, St. Teresa, FL, United States of America
- Marine Station, Smithsonian, Fort Pierce, FL, United States of America
| | - Kieran Cox
- Marine Station, Smithsonian, Fort Pierce, FL, United States of America
- Biology Department, University of Victoria, Victoria, British Columbia, Canada
- Hakai Institute, Calvert Island, British Columbia, Canada
| | - Sandra Brooke
- Coastal and Marine Laboratory, Florida State University, St. Teresa, FL, United States of America
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3
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Martínez-Quintana Á, Lasker HR, Wilson AM. Three-dimensional species distribution modelling reveals the realized spatial niche for coral recruitment on contemporary Caribbean reefs. Ecol Lett 2023; 26:1497-1509. [PMID: 37380335 DOI: 10.1111/ele.14281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/06/2023] [Accepted: 05/05/2023] [Indexed: 06/30/2023]
Abstract
The three-dimensional structure of habitats is a critical component of species' niches driving coexistence in species-rich ecosystems. However, its influence on structuring and partitioning recruitment niches has not been widely addressed. We developed a new method to combine species distribution modelling and structure from motion, and characterized three-dimensional recruitment niches of two ecosystem engineers on Caribbean coral reefs, scleractinian corals and gorgonians. Fine-scale roughness was the most important predictor of suitable habitat for both taxa, and their niches largely overlapped, primarily due to scleractinians' broader niche breadth. Crevices and holes at mm scales on calcareous rock with low coral cover were more suitable for octocorals than for scleractinian recruits, suggesting that the decline in scleractinian corals is facilitating the recruitment of octocorals on contemporary Caribbean reefs. However, the relative abundances of the taxa were independent of the amount of suitable habitat on the reef, emphasizing that niche processes alone do not predict recruitment rates.
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Affiliation(s)
| | - Howard R Lasker
- Department of Environment and Sustainability, University at Buffalo, Buffalo, New York, USA
- Department of Geology, University at Buffalo, Buffalo, New York, USA
| | - Adam M Wilson
- Department of Geography, University at Buffalo, Buffalo, New York, USA
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4
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Ferreira SB, Burns JHR, Pascoe KH, Kapono CA, Reyes AJ, Fukunaga A. Prediction of habitat complexity using a trait-based approach on coral reefs in Guam. Sci Rep 2023; 13:11095. [PMID: 37422484 PMCID: PMC10329656 DOI: 10.1038/s41598-023-38138-1] [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: 01/09/2023] [Accepted: 07/04/2023] [Indexed: 07/10/2023] Open
Abstract
Scleractinian corals are primary contributors to the structural complexity of coral reef ecosystems. The structure derived from their carbonate skeletons underpins the biodiversity and myriad of ecosystem services provided by coral reefs. This study used a trait-based approach to provide new insights into the relationships between habitat complexity and coral morphology. Three-Dimensional (3D) photogrammetry techniques were used to survey 208 study plots on the island of Guam, from which structural complexity metrics were derived and physical traits of corals were quantified. Three traits at the individual colony level (e.g., morphology, size, and genera) and two site-level environmental characteristics (e.g., wave exposure and substratum-habitat type) were examined. Standard taxonomy-based metrics were also included at the reef-plot level (e.g., coral abundance, richness, and diversity). Different traits disproportionately contributed to 3D metrics of habitat complexity. Larger colonies with a columnar morphology have the highest contribution to surface complexity, slope, and vector ruggedness measure, whereas branching and encrusting columnar colonies have the highest contribution to planform and profile curvature. These results highlight the importance of considering colony morphology and size in addition to conventional taxonomic metrics for the understanding and monitoring reef structural complexity. The approach presented here provides a framework for studies in other locations to predict the trajectory of reefs under changing environmental conditions.
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Affiliation(s)
- Sofia B Ferreira
- MEGA Lab, College of Natural and Health Sciences, University of Hawaii at Hilo, Hilo, HI, 96720, USA.
| | - John H R Burns
- MEGA Lab, College of Natural and Health Sciences, University of Hawaii at Hilo, Hilo, HI, 96720, USA
| | - Kailey H Pascoe
- MEGA Lab, College of Natural and Health Sciences, University of Hawaii at Hilo, Hilo, HI, 96720, USA
- Center for Global Discovery and Conservation Science, Arizona State University, Hilo, HI, 96720, USA
| | - Clifford A Kapono
- MEGA Lab, College of Natural and Health Sciences, University of Hawaii at Hilo, Hilo, HI, 96720, USA
- Center for Global Discovery and Conservation Science, Arizona State University, Hilo, HI, 96720, USA
| | - Andres J Reyes
- Marine Scientist, NAVFAC Systems Command Marianas, Joint Region Marianas, Santa Rita, GU, 96915, USA
| | - Atsuko Fukunaga
- MEGA Lab, College of Natural and Health Sciences, University of Hawaii at Hilo, Hilo, HI, 96720, USA
- Center for Global Discovery and Conservation Science, Arizona State University, Hilo, HI, 96720, USA
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5
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Madin JS, Asbury M, Schiettekatte N, Dornelas M, Pizarro O, Reichert J, Torres-Pulliza D. A word on habitat complexity. Ecol Lett 2023; 26:1021-1024. [PMID: 36964971 DOI: 10.1111/ele.14208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/05/2023] [Indexed: 03/27/2023]
Abstract
In their recent synopsis, Loke and Chisholm (Ecology Letters, 25, 2269-2288, 2022) present an overview of habitat complexity metrics for ecologists. They provide a review and some sound advice. However, we found several of their analyses and opinions misleading. This technical note provides a different perspective on the complexity metrics assessed.
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Affiliation(s)
- Joshua S Madin
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Hawai'i, Kāne'ohe, USA
| | - Mollie Asbury
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Hawai'i, Kāne'ohe, USA
| | - Nina Schiettekatte
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Hawai'i, Kāne'ohe, USA
| | - Maria Dornelas
- Centre for Biological Diversity, Scottish Oceans Institute, University of St Andrews, St Andrews, UK
- MARE, Guia Marine Laboratory, University of Lisbon, Cascais, Portugal
| | - Oscar Pizarro
- Department of Marine Technology, Norwegian University of Science and Technology, Trondheim, Norway
- Australian Centre for Field Robotics, University of Sydney, Sydney, Australia
| | - Jessica Reichert
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Hawai'i, Kāne'ohe, USA
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Damaris Torres-Pulliza
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Hawai'i, Kāne'ohe, USA
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6
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Miao L, Dai X, Song H, Backes AR, Song H. A new index for quantifying the ornamentational complexity of animals with shells. Ecol Evol 2022; 12:e9247. [PMID: 36035271 PMCID: PMC9412138 DOI: 10.1002/ece3.9247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/03/2022] [Accepted: 07/29/2022] [Indexed: 11/11/2022] Open
Abstract
Morphological complexity reflects the biological structure of an organism and is closely linked to its associated functions and phylogenetics. In animals with shells, ornamentation is an important characteristic of morphological complexity, and it has various functions. However, because of the variations in type, shape, density, and strength of ornamentation, a universal quantitative measure of morphological complexity for shelled animals is lacking. We propose an ornamentation index (OI) derived from 3D scanning technology and a virtual model for quantifying ornamentation complexity. This index is designed to measure the extent of folding associated with ornamentation, regardless of shape and size. Ornamentation indices were measured for 15 ammonite specimens from the Permian to Cretaceous, 2 modern bivalves, 2 gastropods from the Pliocene to the present, and a modern echinoid. Compared with other measurements, such as the fractal dimension, rugosity, and surface-volume ratio, the OI displayed superiority in quantifying ornamentational complexity. The present study demonstrates that the OI is suitable for accurately characterizing and quantifying ornamentation complexity, regardless of shape and size. Therefore, the OI is potentially useful for comparing the ornamentational complexity of various organisms and can be exploited to provide further insight into the evolution of conchs. Ultimately, the OI can enhance our understanding of morphological evolution of shelled organisms, for example, whether shell ornaments simplify under ocean acidification or extinction, and how predation pressure is reflected in ornamentation complexity.
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Affiliation(s)
- Luyi Miao
- State Key Laboratory of Biogeology & Environmental Geology, School of Earth Sciences China University of Geosciences Wuhan China
| | - Xu Dai
- State Key Laboratory of Biogeology & Environmental Geology, School of Earth Sciences China University of Geosciences Wuhan China
| | - Hanchen Song
- State Key Laboratory of Biogeology & Environmental Geology, School of Earth Sciences China University of Geosciences Wuhan China
| | - André Ricardo Backes
- School of Computer Science Federal University of Uberlândia Uberlândia MG Brazil
| | - Haijun Song
- State Key Laboratory of Biogeology & Environmental Geology, School of Earth Sciences China University of Geosciences Wuhan China
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7
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Urbina‐Barreto I, Elise S, Guilhaumon F, Bruggemann JH, Pinel R, Kulbicki M, Vigliola L, Mou‐Tham G, Mahamadaly V, Facon M, Bureau S, Peignon C, Dutrieux E, Garnier R, Penin L, Adjeroud M. Underwater photogrammetry reveals new links between coral reefscape traits and fishes that ensure key functions. Ecosphere 2022. [DOI: 10.1002/ecs2.3934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Isabel Urbina‐Barreto
- UMR 9220 ENTROPIE, Université de la Réunion, CNRS, IRD, IFREMER, Université de la Nouvelle‐Calédonie Saint‐Denis France
- Creocean OI Sainte Clotilde France
| | - Simon Elise
- UMR 9220 ENTROPIE, Université de la Réunion, CNRS, IRD, IFREMER, Université de la Nouvelle‐Calédonie Saint‐Denis France
| | - François Guilhaumon
- MARBEC, IRD, CNRS, Université de Montpellier, Ifremer Montpellier France
- IRD Saint‐Denis France
| | - J. Henrich Bruggemann
- UMR 9220 ENTROPIE, Université de la Réunion, CNRS, IRD, IFREMER, Université de la Nouvelle‐Calédonie Saint‐Denis France
- Laboratoire d'Excellence CORAIL Perpignan France
| | | | - Michel Kulbicki
- Laboratoire d'Excellence CORAIL Perpignan France
- UMR 9220 ENTROPIE, Université de la Réunion, CNRS, IRD, IFREMER, Université de la Nouvelle‐Calédonie, Université de Perpignan Nouméa France
| | - Laurent Vigliola
- Laboratoire d'Excellence CORAIL Perpignan France
- UMR 9220 ENTROPIE, Université de la Réunion, CNRS, IRD, IFREMER, Université de la Nouvelle‐Calédonie Nouméa New Caledonia
| | - Gerard Mou‐Tham
- UMR 9220 ENTROPIE, Université de la Réunion, CNRS, IRD, IFREMER, Université de la Nouvelle‐Calédonie Nouméa New Caledonia
| | | | | | - Sophie Bureau
- UMR 9220 ENTROPIE, Université de la Réunion, CNRS, IRD, IFREMER, Université de la Nouvelle‐Calédonie Saint‐Denis France
| | - Christophe Peignon
- UMR 9220 ENTROPIE, Université de la Réunion, CNRS, IRD, IFREMER, Université de la Nouvelle‐Calédonie Nouméa New Caledonia
| | | | | | - Lucie Penin
- UMR 9220 ENTROPIE, Université de la Réunion, CNRS, IRD, IFREMER, Université de la Nouvelle‐Calédonie Saint‐Denis France
- Laboratoire d'Excellence CORAIL Perpignan France
| | - Mehdi Adjeroud
- Laboratoire d'Excellence CORAIL Perpignan France
- UMR 9220 ENTROPIE, Université de la Réunion, CNRS, IRD, IFREMER, Université de la Nouvelle‐Calédonie, Université de Perpignan Nouméa France
- PSL Université Paris, USR 3278 CRIOBE—EPHE‐UPVD‐CNRS Perpignan France
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Chen GK, Dai CF. Using 3D photogrammetry to quantify the subtle differences of coral reefs under the impacts of marine activities. MARINE POLLUTION BULLETIN 2021; 173:113032. [PMID: 34689075 DOI: 10.1016/j.marpolbul.2021.113032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/02/2021] [Accepted: 10/02/2021] [Indexed: 06/13/2023]
Abstract
Marine activities may cause the degradation of coral reefs. The composition of benthic communities and seawater quality have been commonly used as the proxies to assess the impacts of marine activities. However, these proxies may not be able to detect the subtle differences within homogeneous environment. We used photogrammetry to quantify the subtle differences of structural complexity between heavily and lightly trafficked sites at Wanlitong, southern Taiwan. Our study demonstrated that the impacts of marine activities can be detected within tens of meters through quantifying structural complexity of coral reefs. Vector ruggedness measure (VRM) is a more suitable metric than conventional linear rugosity to detect such impacts. The correlations between structural complexity and coral cover have variances while comparing with previous studies. The results show that using photogrammetry to quantify the structure of coral reefs can provide a novel aspect to evaluate the subtle differences caused by marine activities.
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Affiliation(s)
| | - Chang Feng Dai
- Institute of Oceanography, National Taiwan University, Taipei 10617, Taiwan
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9
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Jungwirth A, Nührenberg P, Jordan A. On the importance of defendable resources for social evolution: Applying new techniques to a long‐standing question. Ethology 2021. [DOI: 10.1111/eth.13143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Arne Jungwirth
- Department of Interdisciplinary Life Sciences Konrad Lorenz Institute of EthologyUniversity of Veterinary Medicine Vienna Vienna Austria
| | - Paul Nührenberg
- Department of Collective Behaviour Max Planck Institute of Animal Behavior Konstanz Germany
- Centre for the Advanced Study of Collective Behaviour University of Konstanz Konstanz Germany
| | - Alex Jordan
- Department of Collective Behaviour Max Planck Institute of Animal Behavior Konstanz Germany
- Centre for the Advanced Study of Collective Behaviour University of Konstanz Konstanz Germany
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10
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George EE, Mullinix JA, Meng F, Bailey BA, Edwards C, Felts B, Haas AF, Hartmann AC, Mueller B, Roach TN, Salamon P, Silveira C, Vermeij MJ, Rohwer F, Luque A. Space-filling and benthic competition on coral reefs. PeerJ 2021; 9:e11213. [PMID: 34249480 PMCID: PMC8253116 DOI: 10.7717/peerj.11213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/15/2021] [Indexed: 12/28/2022] Open
Abstract
Reef-building corals are ecosystem engineers that compete with other benthic organisms for space and resources. Corals harvest energy through their surface by photosynthesis and heterotrophic feeding, and they divert part of this energy to defend their outer colony perimeter against competitors. Here, we hypothesized that corals with a larger space-filling surface and smaller perimeters increase energy gain while reducing the exposure to competitors. This predicted an association between these two geometric properties of corals and the competitive outcome against other benthic organisms. To test the prediction, fifty coral colonies from the Caribbean island of Curaçao were rendered using digital 3D and 2D reconstructions. The surface areas, perimeters, box-counting dimensions (as a proxy of surface and perimeter space-filling), and other geometric properties were extracted and analyzed with respect to the percentage of the perimeter losing or winning against competitors based on the coral tissue apparent growth or damage. The increase in surface space-filling dimension was the only significant single indicator of coral winning outcomes, but the combination of surface space-filling dimension with perimeter length increased the statistical prediction of coral competition outcomes. Corals with larger surface space-filling dimensions (Ds > 2) and smaller perimeters displayed more winning outcomes, confirming the initial hypothesis. We propose that the space-filling property of coral surfaces complemented with other proxies of coral competitiveness, such as life history traits, will provide a more accurate quantitative characterization of coral competition outcomes on coral reefs. This framework also applies to other organisms or ecological systems that rely on complex surfaces to obtain energy for competition.
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Affiliation(s)
- Emma E. George
- Department of Biology, San Diego State University, San Diego, CA, United States of America
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - James A. Mullinix
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, United States of America
- Computational Science Research Center, San Diego State University, San Diego, CA, United States of America
- Viral Information Institute, San Diego State University, San Diego, CA, United States of America
| | - Fanwei Meng
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, United States of America
| | - Barbara A. Bailey
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, United States of America
- Viral Information Institute, San Diego State University, San Diego, CA, United States of America
| | - Clinton Edwards
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States of America
| | - Ben Felts
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, United States of America
- Viral Information Institute, San Diego State University, San Diego, CA, United States of America
| | - Andreas F. Haas
- NIOZ Royal Netherlands Institute for Sea Research and Utrecht University, Texel, Netherlands
| | - Aaron C. Hartmann
- Department of Biology, San Diego State University, San Diego, CA, United States of America
- Smithsonian National Museum of Natural History, Washington, DC, United States of America
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
| | - Benjamin Mueller
- CARMABI Foundation, Willemstad, Curaçao
- Department of Freshwater and Marine Ecology/Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Ty N.F. Roach
- Department of Biology, San Diego State University, San Diego, CA, United States of America
- Viral Information Institute, San Diego State University, San Diego, CA, United States of America
- Hawai’i Institute of Marine Biology, University of Hawai’i at Mãnoa, Kãne’ohe, HI, United States of America
| | - Peter Salamon
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, United States of America
- Viral Information Institute, San Diego State University, San Diego, CA, United States of America
| | - Cynthia Silveira
- Department of Biology, San Diego State University, San Diego, CA, United States of America
- Viral Information Institute, San Diego State University, San Diego, CA, United States of America
- Department of Biology, University of Miami, Coral Gables, FL, United States of America
| | - Mark J.A. Vermeij
- CARMABI Foundation, Willemstad, Curaçao
- Department of Freshwater and Marine Ecology/Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, CA, United States of America
- Viral Information Institute, San Diego State University, San Diego, CA, United States of America
| | - Antoni Luque
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA, United States of America
- Computational Science Research Center, San Diego State University, San Diego, CA, United States of America
- Viral Information Institute, San Diego State University, San Diego, CA, United States of America
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11
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3D assessment of a coral reef at Lalo Atoll reveals varying responses of habitat metrics following a catastrophic hurricane. Sci Rep 2021; 11:12050. [PMID: 34103641 PMCID: PMC8187721 DOI: 10.1038/s41598-021-91509-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/26/2021] [Indexed: 11/24/2022] Open
Abstract
Extreme disturbances such as hurricanes can cause reductions in coral cover and three-dimensional (3D) structural complexity of coral reefs. We examined changes in structural complexity utilizing 3D reconstruction of a coral-reef site before and after Hurricane Walaka passed through Lalo of the Northwestern Hawaiian Islands. This event resulted in complete destruction of the coral-reef habitat, with dramatic changes in benthic cover from pre-hurricane tabulate coral to post-hurricane rubble. Rugosity and mean slope decreased after the hurricane, while structural complexity, captured by vector ruggedness measure (VRM), showed resolution-specific responses. This metric captured the structural complexity of rubble at a high raster resolution of 1 cm and that of tabulate coral at lower resolutions, resulting in decreases in mean VRM values at 2- and 4-cm resolutions but an increase at 1-cm resolution. Variability in profile and planform curvature was reduced after the hurricane due to a disappearance of extreme curvature values created by the tabulate coral after the hurricane. This study highlights the varying responses of habitat complexity metrics to the complete destruction of a coral reef and provides us with insights into how choices of habitat complexity metrics can affect quantitative assessments of 3D habitat structure.
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12
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Peck M, Tapilatu RF, Kurniati E, Rosado C. Rapid coral reef assessment using 3D modelling and acoustics: acoustic indices correlate to fish abundance, diversity and environmental indicators in West Papua, Indonesia. PeerJ 2021; 9:e10761. [PMID: 33614275 PMCID: PMC7877240 DOI: 10.7717/peerj.10761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/22/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Providing coral reef systems with the greatest chance of survival requires effective assessment and monitoring to guide management at a range of scales from community to government. The development of rapid monitoring approaches amenable to collection at community level, yet recognised by policymakers, remains a challenge. Technologies can increase the scope of data collection. Two promising visual and audio approaches are (i) 3D habitat models, generated through photogrammetry from video footage, providing assessment of coral cover structural metrics and (ii) audio, from which acoustic indices shown to correlate to vertebrate and invertebrate diversity, can be extracted. METHODS We collected audio and video imagery using low cost underwater cameras (GoPro Hero7™) from 34 reef samples from West Papua (Indonesia). Using photogrammetry one camera was used to generate 3D models of 4 m2 reef, the other was used to estimate fish abundance and collect audio to generate acoustic indices. We investigated relationships between acoustic metrics, fish abundance/diversity/functional groups, live coral cover and reef structural metrics. RESULTS Generalized linear modelling identified significant but weak correlations between live coral cover and structural metrics extracted from 3D models and stronger relationships between live coral and fish abundance. Acoustic indices correlated to fish abundance, species richness and reef functional metrics associated with overfishing and algal control. Acoustic Evenness (1,200-11,000 Hz) and Root Mean Square RMS (100-1,200 Hz) were the best individual predictors overall suggesting traditional bioacoustic indices, providing information on sound energy and the variability in sound levels in specific frequency bands, can contribute to reef assessment. CONCLUSION Acoustics and 3D modelling contribute to low-cost, rapid reef assessment tools, amenable to community-level data collection, and generate information for coral reef management. Future work should explore whether 3D models of standardised transects and acoustic indices generated from low cost underwater cameras can replicate or support 'gold standard' reef assessment methodologies recognised by policy makers in marine management.
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Affiliation(s)
- Mika Peck
- School of Life Sciences, University of Sussex, Brighton, East Sussex, UK
| | - Ricardo F. Tapilatu
- Marine Science Department and Research Centre of Pacific Marine Resources, University of Papua, Manokwari, West Papua, Indonesia
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Fish Assemblage Structure in the Northwestern Hawaiian Islands Is Associated with the Architectural Complexity of Coral-Reef Habitats. DIVERSITY 2020. [DOI: 10.3390/d12110430] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The architectural complexity of coral-reef habitat plays an important role in determining the assemblage structure of reef fish. We investigated associations between the reef habitats and fish assemblages in the Northwestern Hawaiian Islands (NWHI) using in situ fish counts and data on habitat metrics and benthic community composition that were obtained from three-dimensional (3D) photogrammetric reconstructions of the surveyed sites. The structure of fish assemblage as a whole on the basis of Bray–Curtis dissimilarity, species richness and the abundances of herbivores and piscivores were associated with habitat metrics, with higher levels of architectural complexity generally supporting greater numbers of fish species and individuals. Benthic cover did not explain additional variation in these variables after the effects of habitat metrics were taken into account. Corallivorous fish was the only group that showed positive associations with both habitat metrics and benthic cover (Acropora and Pocillopora corals). The total fish abundance and the abundances of planktivores and invertivores did not show associations with either habitat metrics or benthic cover. This study suggests that an appropriate combination of habitat metrics can be used to account sufficiently for the effects of habitat architecture on fish assemblages in reef monitoring efforts in the NWHI.
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Bayley DTI, Mogg AOM. A protocol for the large‐scale analysis of reefs using Structure from Motion photogrammetry. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13476] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel T. I. Bayley
- Centre for Biodiversity and Environment Research University College London London UK
| | - Andrew O. M. Mogg
- Tritonia Scientific Ltd.Dunstaffnage Marine Laboratories Oban UK
- National Facility for Scientific DivingScottish Association of Marine Science Oban UK
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Metrics of Coral Reef Structural Complexity Extracted from 3D Mesh Models and Digital Elevation Models. REMOTE SENSING 2020. [DOI: 10.3390/rs12172676] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Underwater photogrammetry has been increasingly used in coral-reef research in recent years. Habitat metrics extracted from resulting three-dimensional (3D) reconstructions can be used to examine associations between the structural complexity of the reef habitats and the distribution of reef organisms. We created simulated 3D models of bare surface structures and 3D reconstructions of coral morphologies to investigate the behavior of various habitat metrics that were extracted from both Digital Elevation Models (DEMs) and 3D mesh models. Analyzing the resulting values provided us with important insights into how these metrics would compare with one another in the characterization of coral-reef habitats. Surface complexity (i.e., reef rugosity), fractal dimension extracted from DEMs and vector dispersion obtained from 3D mesh models exhibited consistent patterns in the ranking of structural complexity among the simulated bare surfaces and coral morphologies. The vector ruggedness measure obtained from DEMs at three different resolutions of 1, 2, and 4 cm effectively captured differences in the structural complexity among different coral morphologies. Profile curvature and planform curvature, on the other hand, were better suited to capture the structural complexity derived from surface topography such as walls and overhanging ledges. Our results indicate that habitat metrics extracted from DEMs are generally suitable when characterizing a relatively large plot of a coral reef captured from an overhead planar angle, while the 3D metric of vector dispersion is suitable when characterizing a coral colony or a relatively small plot methodically captured from various angles.
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Associations between Benthic Cover and Habitat Complexity Metrics Obtained from 3D Reconstruction of Coral Reefs at Different Resolutions. REMOTE SENSING 2020. [DOI: 10.3390/rs12061011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Quantifying the three-dimensional (3D) habitat structure of coral reefs is an important aspect of coral reef monitoring, as habitat architecture affects the abundance and diversity of reef organisms. Here, we used photogrammetric techniques to generate 3D reconstructions of coral reefs and examined relationships between benthic cover and various habitat metrics obtained at six different resolutions of raster cells, ranging from 1 to 32 cm. For metrics of 3D structural complexity, fractal dimension, which utilizes information on 3D surface areas obtained at different resolutions, and vector ruggedness measure (VRM) obtained at 1-, 2- or 4-cm resolution correlated well with benthic cover, with a relatively large amount of variability in these metrics being explained by the proportions of corals and crustose coralline algae. Curvature measures were, on the other hand, correlated with branching and mounding coral cover when obtained at 1-cm resolution, but the amount of variability explained by benthic cover was generally very low when obtained at all other resolutions. These results show that either fractal dimension or VRM obtained at 1-, 2- or 4-cm resolution, along with curvature obtained at 1-cm resolution, can effectively capture the 3D habitat structure provided by specific benthic organisms.
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Reef Rover: A Low-Cost Small Autonomous Unmanned Surface Vehicle (USV) for Mapping and Monitoring Coral Reefs. DRONES 2019. [DOI: 10.3390/drones3020038] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In the effort to design a more repeatable and consistent platform to collect data for Structure from Motion (SfM) monitoring of coral reefs and other benthic habitats, we explore the use of recent advances in open source Global Positioning System (GPS)-guided drone technology to design and test a low-cost and transportable small unmanned surface vehicle (sUSV). The vehicle operates using Ardupilot open source software and can be used by local scientists and marine managers to map and monitor marine environments in shallow areas (<20 m) with commensurate visibility. The imaging system uses two Sony a6300 mirrorless cameras to collect stereo photos that can be later processed using photogrammetry software to create underwater high-resolution orthophoto mosaics and digital surface models. The propulsion system consists of two small brushless motors powered by lithium batteries that follow pre-programmed survey transects and are operated by a GPS-guided autopilot control board. Results from our project suggest the sUSV provides a repeatable, viable, and low-cost (<$3000 USD) solution for acquiring images of benthic environments on a frequent basis from directly below the water surface. These images can be used to create SfM models that provide very detailed images and measurements that can be used to monitor changes in biodiversity, reef erosion/accretion, and assessing health conditions.
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