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McCarthy OS, Contractor K, Figueira WF, Gleason ACR, Viehman TS, Edwards CB, Sandin SA. Closing the gap between existing large-area imaging research and marine conservation needs. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14145. [PMID: 37403804 DOI: 10.1111/cobi.14145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/06/2023] [Accepted: 06/21/2023] [Indexed: 07/06/2023]
Abstract
Emerging technology has immense potential to increase the scale and efficiency of marine conservation. One such technology is large-area imaging (LAI), which relies on structure-from-motion photogrammetry to create composite products, including 3-dimensional (3-D) environmental models, that are larger in spatial extent than the individual images used to create them. Use of LAI has become widespread in certain fields of marine science, primarily to measure the 3D structure of benthic ecosystems and track change over time. However, the use of LAI in the field of marine conservation appears limited. We conducted a review of the coral reef literature on the use of LAI to identify research themes and regional trends in applications of this technology. We also surveyed 135 coral reef scientists and conservation practitioners to determine community familiarity with LAI, evaluate barriers practitioners face in using LAI, and identify applications of LAI believed to be most exciting or relevant to coral conservation. Adoption of LAI was limited primarily to researchers at institutions based in advanced economies and was applied infrequently to conservation, although conservation practitioners and survey respondents from emerging economies indicated they expect to use LAI in the future. Our results revealed disconnect between current LAI research topics and conservation priorities identified by practitioners, highlighting the need for more diverse, conservation-relevant research using LAI. We provide recommendations for how early adopters of LAI (typically Global North scientists from well-resourced institutions) can facilitate access to this conservation technology. These recommendations include developing training resources, creating partnerships for data storage and analysis, publishing standard operating procedures for LAI workflows, standardizing methods, developing tools for efficient data extraction from LAI products, and conducting conservation-relevant research using LAI.
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Affiliation(s)
- Orion S McCarthy
- Scripps Institution of Oceanography, Center for Marine Biodiversity and Conservation, University of California San Diego, La Jolla, California, USA
| | - Kanisha Contractor
- Scripps Institution of Oceanography, Center for Marine Biodiversity and Conservation, University of California San Diego, La Jolla, California, USA
| | - Will F Figueira
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | | | - T Shay Viehman
- National Centers for Coastal Ocean Science, NOAA National Ocean Service, Beaufort, North Carolina, USA
| | - Clinton B Edwards
- Scripps Institution of Oceanography, Center for Marine Biodiversity and Conservation, University of California San Diego, La Jolla, California, USA
- Consolidated Safety Services Inc., under contract to NOAA National Centers for Coastal Ocean Science, Fairfax, Virginia, USA
| | - Stuart A Sandin
- Scripps Institution of Oceanography, Center for Marine Biodiversity and Conservation, University of California San Diego, La Jolla, California, USA
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Pulido Mantas T, Roveta C, Calcinai B, Coppari M, Di Camillo CG, Marchesi V, Marrocco T, Puce S, Cerrano C. Photogrammetry as a promising tool to unveil marine caves' benthic assemblages. Sci Rep 2023; 13:7587. [PMID: 37165208 PMCID: PMC10172382 DOI: 10.1038/s41598-023-34706-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Traditionally, monitoring approaches to survey marine caves have been constrained by equipment limitations and strict safety protocols. Nowadays, the rise of new approaches opens new possibilities to describe these peculiar ecosystems. The current study aimed to explore the potential of Structure from Motion (SfM) photogrammetry to assess the abundance and spatial distribution of the sessile benthic assemblages inside a semi-submerged marine cave. Additionally, since impacts of recent date mussel Lithophaga lithophaga illegal fishing were recorded, a special emphasis was paid to its distribution and densities. The results of SfM were compared with a more "traditional approach", by simulating photo-quadrats deployments over the produced orthomosaics. A total of 22 sessile taxa were identified, with Porifera representing the dominant taxa within the cave, and L. lithophaga presenting a density of 88.3 holes/m2. SfM and photo-quadrats obtained comparable results regarding species richness, percentage cover of identified taxa and most of the seascape metrics, while, in terms of taxa density estimations, photo-quadrats highly overestimated their values. SfM resulted in a suitable non-invasive technique to record marine cave assemblages. Seascape indexes proved to be a comprehensive way to describe the spatial pattern of distribution of benthic organisms, establishing a useful baseline to assess future community shifts.
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Affiliation(s)
- Torcuato Pulido Mantas
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Camilla Roveta
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Barbara Calcinai
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Martina Coppari
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Cristina Gioia Di Camillo
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Veronica Marchesi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Teo Marrocco
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Stefania Puce
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Carlo Cerrano
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
- Fano Marine Center, Viale Adriatico 1/N, 61032, Fano, Italy
- Stazione Zoologica di Napoli Anton Dohrn, Villa Comunale, 80121, Naples, Italy
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Harborne AR, Kochan DP, Esch MM, Fidler RY, Mitchell MD, Butkowski DW, González-Rivero M. Drivers of fine-scale diurnal space use by a coral-reef mesopredatory fish. JOURNAL OF FISH BIOLOGY 2022; 100:1009-1024. [PMID: 35099815 DOI: 10.1111/jfb.15006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
The habitat preferences of many reef fishes are well established, but the use of space within these habitats by non-site-attached species is poorly studied. The authors examined the space use of a functionally important mesopredator, graysby (Cephalopholis cruentata), on six patch reefs in the Florida Keys. A 1 m2 -scale grid was constructed on each reef and 16 individual C. cruentata were tracked diurnally in situ to identify space use. At the patch reef scale, larger C. cruentata were more active and had larger observed home ranges, although home ranges were also affected by fish density and the abundances of prey and predators. The total time in each 1 m2 grid cell was regressed against a range of fine-scale biotic variables, including multiple variables derived from structure-from-motion three-dimensional digital reconstructions of each reef. Nonetheless, time in grid cells (preferred microhabitats) was only significantly positively correlated with the height of carbonate structures, likely because the cavities they enclose are particularly suitable for predator avoidance, resting and ambushing prey. The ongoing flattening of reefs in the region caused by negative carbonate budgets is thus likely to have significant effects on the abundance and space use of C. cruentata. In addition to examining spatial patterns, we analysed C. cruentata waiting times in each grid cell before moving. These times were best approximated by a truncated power-law (heavy-tailed) distribution, indicating a "bursty" pattern of relatively long periods of inactivity interspersed with multiple periods of activity. Such a pattern has previously been identified in a range of temperate ambush predators, and the authors extend this move-wait behaviour, which may optimize foraging success, to a reef fish for the first time. Understanding how C. cruentata uses space and time is critical to fully identify their functional role and better predict the implications of fishing and loss of reef structure.
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Affiliation(s)
- Alastair R Harborne
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - David P Kochan
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Melanie M Esch
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Robert Y Fidler
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
| | - Matthew D Mitchell
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
- Marine Biology Lab, Division of Science, New York University, Abu Dhabi, UAE
| | - Drew W Butkowski
- Institute of Environment, Department of Biological Sciences, Florida International University, North Miami, Florida, USA
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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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Vozzo ML, Cumbo VR, Crosswell JR, Bishop MJ. Wave energy alters biodiversity by shaping intraspecific traits of a habitat‐forming species. OIKOS 2020. [DOI: 10.1111/oik.07590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maria L. Vozzo
- Dept of Biological Sciences, Macquarie Univ. North Ryde NSW 2109 Australia
- Sydney Inst. of Marine Science Mosman NSW 2088 Australia
| | - Vivian R. Cumbo
- Dept of Biological Sciences, Macquarie Univ. North Ryde NSW 2109 Australia
| | | | - Melanie J. Bishop
- Dept of Biological Sciences, Macquarie Univ. North Ryde NSW 2109 Australia
- Sydney Inst. of Marine Science Mosman NSW 2088 Australia
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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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Quantifying Coral Reef Composition of Recreational Diving Sites: A Structure from Motion Approach at Seascape Scale. REMOTE SENSING 2019. [DOI: 10.3390/rs11243027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recreational diving is known to have both direct and indirect impacts on coral habitats. Direct impacts include increasing sedimentation, breaks and diseases that lead to a decrease in the richness and abundances of hard corals. Indirect impacts include urban development, land management and sewage disposal. The ecological effects of scuba diving on the spatial composition metrics of reef benthic communities are less well studied, and they have not been investigated at seascape scale. In this study, we combine orthomosaics derived from Structure from Motion (SfM) photogrammetry and data-mining techniques to study the spatial composition of reef benthic communities of recreational diving sites at seascape scale (>25 m 2 ). The study focuses on the case study area of Ponta do Ouro Partial Marine Reserve (Mozambique). Results showed that scuba-diving resistant taxa (i.e., sponges and algae) were abundant at small (>850 m 2 ) and highly dived sites (>3000 dives yr − 1 ), characterized by low diversity and density, and big organisms with complex shapes. Fragile taxa (i.e., Acropora spp.) were abundant at low (365 dives yr − 1 ) and moderately dived sites (1000–3000 dives yr − 1 ) where the greater depth and wider coral reef surfaces attenuate the abrasive effect of waves and re-suspended sediments. Highest taxa diversity and density, and lowest abundance of resistant taxa were recorded at large (>2000 m 2 ) and rarely dived sites. This study highlights the potential applications for a photogrammetric approach to support monitoring programs at Ponta do Ouro Partial Marine Reserve (Mozambique), and provides some insight to understand the influence of scuba diving on benthic communities.
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8
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An Under-Ice Hyperspectral and RGB Imaging System to Capture Fine-Scale Biophysical Properties of Sea Ice. REMOTE SENSING 2019. [DOI: 10.3390/rs11232860] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Sea-ice biophysical properties are characterized by high spatio-temporal variability ranging from the meso- to the millimeter scale. Ice coring is a common yet coarse point sampling technique that struggles to capture such variability in a non-invasive manner. This hinders quantification and understanding of ice algae biomass patchiness and its complex interaction with some of its sea ice physical drivers. In response to these limitations, a novel under-ice sled system was designed to capture proxies of biomass together with 3D models of bottom topography of land-fast sea-ice. This system couples a pushbroom hyperspectral imaging (HI) sensor with a standard digital RGB camera and was trialed at Cape Evans, Antarctica. HI aims to quantify per-pixel chlorophyll-a content and other ice algae biological properties at the ice-water interface based on light transmitted through the ice. RGB imagery processed with digital photogrammetry aims to capture under-ice structure and topography. Results from a 20 m transect capturing a 0.61 m wide swath at sub-mm spatial resolution are presented. We outline the technical and logistical approach taken and provide recommendations for future deployments and developments of similar systems. A preliminary transect subsample was processed using both established and novel under-ice bio-optical indices (e.g., normalized difference indexes and the area normalized by the maximal band depth) and explorative analyses (e.g., principal component analyses) to establish proxies of algal biomass. This first deployment of HI and digital photogrammetry under-ice provides a proof-of-concept of a novel methodology capable of delivering non-invasive and highly resolved estimates of ice algal biomass in-situ, together with some of its environmental drivers. Nonetheless, various challenges and limitations remain before our method can be adopted across a range of sea-ice conditions. Our work concludes with suggested solutions to these challenges and proposes further method and system developments for future research.
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Werth AJ, Kosma MM, Chenoweth EM, Straley JM. New views of humpback whale flow dynamics and oral morphology during prey engulfment. MARINE MAMMAL SCIENCE 2019; 35:1556-1578. [PMID: 32863564 PMCID: PMC7449129 DOI: 10.1111/mms.12614] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The rise of inexpensive, user-friendly cameras and editing software promises to revolutionize data collection with minimal disturbance to marine mammals. Video sequences recorded by aerial drones and GoPro cameras provided close-up views and unique perspectives of humpback whales engulfing juvenile salmon at or just below the water surface in Southeast Alaska and Prince William Sound. Although humpback feeding is famous for its flexibility, several stereotyped events were noted in the 47 lunges we analyzed. Engulfment was rapid (mean 2.07 s), and the entrance through which the tongue inverts into the ventral pouch was seen as water rushes in. Cranial elevation was a major contributor to gape, and pouch contraction sometimes began before full gape closure, with reverberating waves indicating rebounding flow of water within the expanded pouch. Expulsion of filtered water began with a small splash at the anterior of the mouth, followed by sustained excurrent flow in the mouth's central or posterior regions. Apart from a splash of rebounding water, water within the mouth was surprisingly turbulence-free during engulfment, but submersion of the whale's head created visible surface whirlpools and vortices which may aggregate prey for subsequent engulfment.
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Affiliation(s)
| | - Madison M. Kosma
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, Alaska 99801, U.S.A
| | - Ellen M. Chenoweth
- College of Natural Science and Mathematics, University of Alaska Fairbanks, Sitka, Alaska 99835, U.S.A
| | - Janice M. Straley
- Department of Natural Sciences, University of Alaska Southeast, Sitka, Alaska 99835, U.S.A
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Loh T, Archer SK, Dunham A. Monitoring program design for data-limited marine biogenic habitats: A structured approach. Ecol Evol 2019; 9:7346-7359. [PMID: 31380055 PMCID: PMC6662303 DOI: 10.1002/ece3.5261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/16/2019] [Accepted: 04/23/2019] [Indexed: 11/07/2022] Open
Abstract
Marine biogenic habitats-habitats created by living organisms-provide essential ecosystem functions and services, such as physical structuring, nutrient cycling, biodiversity support, and increases in primary, secondary, and tertiary production. With the growing trend toward ecosystem approaches to marine conservation and fisheries management, there is greater emphasis on rigorously designed habitat monitoring programs. However, such programs are challenging to design for data-limited habitats for which underlying ecosystem processes are poorly understood. To provide guidance in this area, we reviewed approaches to benthic assessments across well-studied marine biogenic habitats and identified common themes related to indicator selection, sampling methods, and survey design. Biogenic habitat monitoring efforts largely focus on the characteristics, distribution, and ecological function of foundation species, but may target other habitat-forming organisms, especially when community shifts are observed or expected, as well as proxies of habitat status, such as indicator species. Broad-scale methods cover large spatial areas and are typically used to examine the spatial configuration of habitats, whereas fine-scale methods tend to be laborious and thus restricted to small survey areas, but provide high-resolution data. Recent, emerging methods enhance the capabilities of surveying large areas at high spatial resolution and improve data processing efficiency, bridging the gap between broad- and fine-scale methods. Although sampling design selection may be limited by habitat characteristics and available resources, it is critically important to ensure appropriate matching of ecological, observational, and analytical scales. Drawing on these common themes, we propose a structured, iterative approach to designing monitoring programs for marine biogenic habitats that allows for rigorous data collection to inform management strategies, even when data and resource limitations are present. A practical application of this approach is illustrated using glass sponge reefs-a recently discovered and data-limited habitat type-as a case study.
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Affiliation(s)
- Tse‐Lynn Loh
- Quest University CanadaSquamishBritish ColumbiaCanada
| | - Stephanie K. Archer
- Fisheries and Oceans Canada, Pacific Biological StationNanaimoBritish ColumbiaCanada
| | - Anya Dunham
- Fisheries and Oceans Canada, Pacific Biological StationNanaimoBritish ColumbiaCanada
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Underwater photogrammetry in Antarctica: long-term observations in benthic ecosystems and legacy data rescue. Polar Biol 2019. [DOI: 10.1007/s00300-019-02480-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Integrating Three-Dimensional Benthic Habitat Characterization Techniques into Ecological Monitoring of Coral Reefs. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2019. [DOI: 10.3390/jmse7020027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Long-term ecological monitoring of reef fish populations often requires the simultaneous collection of data on benthic habitats in order to account for the effects of these variables on fish assemblage structure. Here, we described an approach to benthic surveys that uses photogrammetric techniques to facilitate the extraction of quantitative metrics for characterization of benthic habitats from the resulting three-dimensional (3D) reconstruction of coral reefs. Out of 92 sites surveyed in the Northwestern Hawaiian Islands, photographs from 85 sites achieved complete alignment and successfully produced 3D reconstructions and digital elevation models (DEMs). Habitat metrics extracted from the DEMs were generally correlated with one another, with the exception of curvature measures, indicating that complexity and curvature measures should be treated separately when quantifying the habitat structure. Fractal dimension D64, calculated by changing resolutions of the DEMs from 1 cm to 64 cm, had the best correlations with other habitat metrics. Fractal dimension was also less affected by changes in orientations of the models compared to surface complexity or slope. These results showed that fractal dimension can be used as a single measure of complexity for the characterization of coral reef habitats. Further investigations into metrics for 3D characterization of habitats should consider relevant spatial scales and focus on obtaining variables that can complement fractal dimension in the characterization of reef habitats.
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House JE, Brambilla V, Bidaut LM, Christie AP, Pizarro O, Madin JS, Dornelas M. Moving to 3D: relationships between coral planar area, surface area and volume. PeerJ 2018; 6:e4280. [PMID: 29435392 PMCID: PMC5806594 DOI: 10.7717/peerj.4280] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/29/2017] [Indexed: 11/20/2022] Open
Abstract
Coral reefs are a valuable and vulnerable marine ecosystem. The structure of coral reefs influences their health and ability to fulfill ecosystem functions and services. However, monitoring reef corals largely relies on 1D or 2D estimates of coral cover and abundance that overlook change in ecologically significant aspects of the reefs because they do not incorporate vertical or volumetric information. This study explores the relationship between 2D and 3D metrics of coral size. We show that surface area and volume scale consistently with planar area, albeit with morphotype specific conversion parameters. We use a photogrammetric approach using open-source software to estimate the ability of photogrammetry to provide measurement estimates of corals in 3D. Technological developments have made photogrammetry a valid and practical technique for studying coral reefs. We anticipate that these techniques for moving coral research from 2D into 3D will facilitate answering ecological questions by incorporating the 3rd dimension into monitoring.
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Affiliation(s)
- Jenny E House
- Center for Biological Diversity, Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Viviana Brambilla
- Center for Biological Diversity, Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Luc M Bidaut
- Clinical Research Imaging Facility, University of Dundee, Dundee, United Kingdom.,College of Science, University of Lincoln, Lincoln, United Kingdom
| | - Alec P Christie
- Center for Biological Diversity, Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Oscar Pizarro
- Australian Centre for Field Robotics, University of Sydney, Sydney, NSW, Australia
| | - Joshua S Madin
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kaneohe, HI, USA.,Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Maria Dornelas
- Center for Biological Diversity, Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, United Kingdom
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14
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Ferrari R, Figueira WF, Pratchett MS, Boube T, Adam A, Kobelkowsky-Vidrio T, Doo SS, Atwood TB, Byrne M. 3D photogrammetry quantifies growth and external erosion of individual coral colonies and skeletons. Sci Rep 2017; 7:16737. [PMID: 29196651 PMCID: PMC5711843 DOI: 10.1038/s41598-017-16408-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/01/2017] [Indexed: 11/21/2022] Open
Abstract
Growth and contraction of ecosystem engineers, such as trees, influence ecosystem structure and function. On coral reefs, methods to measure small changes in the structure of microhabitats, driven by growth of coral colonies and contraction of skeletons, are extremely limited. We used 3D reconstructions to quantify changes in the external structure of coral colonies of tabular Acropora spp., the dominant habitat-forming corals in shallow exposed reefs across the Pacific. The volume and surface area of live colonies increased by 21% and 22%, respectively, in 12 months, corresponding to a mean annual linear extension of 5.62 cm yr-1 (±1.81 SE). The volume and surface area of dead skeletons decreased by 52% and 47%, respectively, corresponding to a mean decline in linear extension of -29.56 cm yr-1 (±7.08 SE), which accounted for both erosion and fragmentation of dead colonies. This is the first study to use 3D photogrammetry to assess fine-scale structural changes of entire individual colonies in situ, quantifying coral growth and contraction. The high-resolution of the technique allows for detection of changes on reef structure faster than other non-intrusive approaches. These results improve our capacity to measure the drivers underpinning ecosystem biodiversity, status and trajectory.
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Affiliation(s)
- Renata Ferrari
- School of Life and Environmental Sciences, Edgeworth David Building, Science Road, The University of Sydney, Sydney, NSW 2006, Australia.
- Australian Institute of Marine Sciences, PMB No. 3, Townsville, Queensland, 4810, Australia.
| | - Will F Figueira
- School of Life and Environmental Sciences, Edgeworth David Building, Science Road, The University of Sydney, Sydney, NSW 2006, Australia
| | - Morgan S Pratchett
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
| | - Tatiana Boube
- School of Life and Environmental Sciences, Edgeworth David Building, Science Road, The University of Sydney, Sydney, NSW 2006, Australia
| | - Arne Adam
- School of Life and Environmental Sciences, Edgeworth David Building, Science Road, The University of Sydney, Sydney, NSW 2006, Australia
| | - Tania Kobelkowsky-Vidrio
- School of Life and Environmental Sciences, Edgeworth David Building, Science Road, The University of Sydney, Sydney, NSW 2006, Australia
| | - Steve S Doo
- School of Life and Environmental Sciences, Edgeworth David Building, Science Road, The University of Sydney, Sydney, NSW 2006, Australia
| | - Trisha Brooke Atwood
- Department of Watershed Sciences and Ecology Center, Utah State University, Logan, UT, USA
- Global Change Institute, The University of Queensland, St. Lucia, QLD, Australia
| | - Maria Byrne
- School of Life and Environmental Sciences, Edgeworth David Building, Science Road, The University of Sydney, Sydney, NSW 2006, Australia
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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15
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Application of Low-Cost UASs and Digital Photogrammetry for High-Resolution Snow Depth Mapping in the Arctic. REMOTE SENSING 2017. [DOI: 10.3390/rs9111144] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Murfitt SL, Allan BM, Bellgrove A, Rattray A, Young MA, Ierodiaconou D. Applications of unmanned aerial vehicles in intertidal reef monitoring. Sci Rep 2017; 7:10259. [PMID: 28860645 PMCID: PMC5579233 DOI: 10.1038/s41598-017-10818-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/15/2017] [Indexed: 11/09/2022] Open
Abstract
Monitoring of intertidal reefs is traditionally undertaken by on-ground survey methods which have assisted in understanding these complex habitats; however, often only a small spatial footprint of the reef is observed. Recent developments in unmanned aerial vehicles (UAVs) provide new opportunities for monitoring broad scale coastal ecosystems through the ability to capture centimetre resolution imagery and topographic data not possible with conventional approaches. This study compares UAV remote sensing of intertidal reefs to traditional on-ground monitoring surveys, and investigates the role of UAV derived geomorphological variables in explaining observed intertidal algal and invertebrate assemblages. A multirotor UAV was used to capture <1 cm resolution data from intertidal reefs, with on-ground quadrat surveys of intertidal biotic data for comparison. UAV surveys provided reliable estimates of dominant canopy-forming algae, however, understorey species were obscured and often underestimated. UAV derived geomorphic variables showed elevation and distance to seaward reef edge explained 19.7% and 15.9% of the variation in algal and invertebrate assemblage structure respectively. The findings of this study demonstrate benefits of low-cost UAVs for intertidal monitoring through rapid data collection, full coverage census, identification of dominant canopy habitat and generation of geomorphic derivatives for explaining biological variation.
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Affiliation(s)
- Sarah L Murfitt
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, P.O. Box 423, Warrnambool, 3280, Victoria, Australia
| | - Blake M Allan
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, P.O. Box 423, Warrnambool, 3280, Victoria, Australia.,Victorian UAS Training, 57 Koroit-Woolsthrope Road, Koroit, 3282, Victoria, Australia
| | - Alecia Bellgrove
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, P.O. Box 423, Warrnambool, 3280, Victoria, Australia
| | - Alex Rattray
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, P.O. Box 423, Warrnambool, 3280, Victoria, Australia
| | - Mary A Young
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, P.O. Box 423, Warrnambool, 3280, Victoria, Australia
| | - Daniel Ierodiaconou
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology, P.O. Box 423, Warrnambool, 3280, Victoria, Australia.
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17
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How Reliable Is Structure from Motion (SfM) over Time and between Observers? A Case Study Using Coral Reef Bommies. REMOTE SENSING 2017. [DOI: 10.3390/rs9070740] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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