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Dr. John Burns
University of Hawaii at Hilo - Marine Science and Data Science UHH-CNHS 200 W. Kawili St., Hilo, HI 96720, USA

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0 GIS
0 3D Reconstruction
0 Ecosystem functions
0 Quantitative Ecology
0 Coral reef ecology

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3D Reconstruction

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Journal article
Published: 15 November 2020 in Diversity
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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.

ACS Style

Atsuko Fukunaga; Randall K. Kosaki; Kailey H. Pascoe; John H. R. Burns. Fish Assemblage Structure in the Northwestern Hawaiian Islands Is Associated with the Architectural Complexity of Coral-Reef Habitats. Diversity 2020, 12, 430 .

AMA Style

Atsuko Fukunaga, Randall K. Kosaki, Kailey H. Pascoe, John H. R. Burns. Fish Assemblage Structure in the Northwestern Hawaiian Islands Is Associated with the Architectural Complexity of Coral-Reef Habitats. Diversity. 2020; 12 (11):430.

Chicago/Turabian Style

Atsuko Fukunaga; Randall K. Kosaki; Kailey H. Pascoe; John H. R. Burns. 2020. "Fish Assemblage Structure in the Northwestern Hawaiian Islands Is Associated with the Architectural Complexity of Coral-Reef Habitats." Diversity 12, no. 11: 430.

Journal article
Published: 19 August 2020 in Remote Sensing
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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.

ACS Style

Atsuko Fukunaga; John Burns. Metrics of Coral Reef Structural Complexity Extracted from 3D Mesh Models and Digital Elevation Models. Remote Sensing 2020, 12, 2676 .

AMA Style

Atsuko Fukunaga, John Burns. Metrics of Coral Reef Structural Complexity Extracted from 3D Mesh Models and Digital Elevation Models. Remote Sensing. 2020; 12 (17):2676.

Chicago/Turabian Style

Atsuko Fukunaga; John Burns. 2020. "Metrics of Coral Reef Structural Complexity Extracted from 3D Mesh Models and Digital Elevation Models." Remote Sensing 12, no. 17: 2676.

Letter
Published: 21 March 2020 in Remote Sensing
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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.

ACS Style

Atsuko Fukunaga; John H. R. Burns; Kailey H. Pascoe; Randall K. Kosaki. Associations between Benthic Cover and Habitat Complexity Metrics Obtained from 3D Reconstruction of Coral Reefs at Different Resolutions. Remote Sensing 2020, 12, 1011 .

AMA Style

Atsuko Fukunaga, John H. R. Burns, Kailey H. Pascoe, Randall K. Kosaki. Associations between Benthic Cover and Habitat Complexity Metrics Obtained from 3D Reconstruction of Coral Reefs at Different Resolutions. Remote Sensing. 2020; 12 (6):1011.

Chicago/Turabian Style

Atsuko Fukunaga; John H. R. Burns; Kailey H. Pascoe; Randall K. Kosaki. 2020. "Associations between Benthic Cover and Habitat Complexity Metrics Obtained from 3D Reconstruction of Coral Reefs at Different Resolutions." Remote Sensing 12, no. 6: 1011.

Journal article
Published: 21 February 2019 in Scientific Reports
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Structural complexity underpins the ecological functioning of coral reefs. However, rising ocean temperatures and associated coral bleaching threaten the structural integrity of these important ecosystems. Despite the increased frequency of coral bleaching events, few studies to date have examined changes in three-dimensional (3D) reef structural complexity following severe bleaching. The influence of local stressors on reef complexity also remains poorly understood. In the wake of the 2015-2016 El Niño-induced mass coral bleaching event, we quantified the effects of severe heat stress on 3D reef structural complexity across a gradient of local human disturbance. Using Structure-from-Motion photogrammetry we created 3D reconstructions of permanent reef plots and observed substantial declines in reef structural complexity, measured as surface rugosity and terrain ruggedness, and a detectable loss of habitat volume one year after the bleaching event. 3D reef complexity also declined with increasing levels of human disturbance, and with decreasing densities of branching and massive corals. These findings improve our understanding of the effects of local and global stressors on the structural foundation of coral reef ecosystems. In the face of accelerating climate change, mitigating local stressors may increase reef structural complexity, thereby heightening reef resilience to future bleaching events.

ACS Style

Jennifer M. T. Magel; John H. R. Burns; Ruth D. Gates; Julia K. Baum. Effects of bleaching-associated mass coral mortality on reef structural complexity across a gradient of local disturbance. Scientific Reports 2019, 9, 2512 .

AMA Style

Jennifer M. T. Magel, John H. R. Burns, Ruth D. Gates, Julia K. Baum. Effects of bleaching-associated mass coral mortality on reef structural complexity across a gradient of local disturbance. Scientific Reports. 2019; 9 (1):2512.

Chicago/Turabian Style

Jennifer M. T. Magel; John H. R. Burns; Ruth D. Gates; Julia K. Baum. 2019. "Effects of bleaching-associated mass coral mortality on reef structural complexity across a gradient of local disturbance." Scientific Reports 9, no. 1: 2512.

Journal article
Published: 28 January 2019 in Journal of Marine Science and Engineering
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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.

ACS Style

Atsuko Fukunaga; John H. R. Burns; Brianna K. Craig; Randall K. Kosaki. Integrating Three-Dimensional Benthic Habitat Characterization Techniques into Ecological Monitoring of Coral Reefs. Journal of Marine Science and Engineering 2019, 7, 27 .

AMA Style

Atsuko Fukunaga, John H. R. Burns, Brianna K. Craig, Randall K. Kosaki. Integrating Three-Dimensional Benthic Habitat Characterization Techniques into Ecological Monitoring of Coral Reefs. Journal of Marine Science and Engineering. 2019; 7 (2):27.

Chicago/Turabian Style

Atsuko Fukunaga; John H. R. Burns; Brianna K. Craig; Randall K. Kosaki. 2019. "Integrating Three-Dimensional Benthic Habitat Characterization Techniques into Ecological Monitoring of Coral Reefs." Journal of Marine Science and Engineering 7, no. 2: 27.

Journal article
Published: 01 October 2016 in Journal of Invertebrate Pathology
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Diseases have caused significant reductions in coral populations throughout the global ocean. Despite a substantial effort to thoroughly characterize the epizootiology and etiology of coral diseases, little is known about the distribution and spatial clustering of disease lesions on affected coral colonies. This study investigated spatial clustering of the coral disease, growth anomaly (GA), which exhibits high levels of prevalence and severity in Montipora capitata and other corals at Wai'ōpae, southeast Hawai'i Island. Like many other coral diseases, the patterns of disease spread and transmissibility of GA remains unknown. We utilized cutting-edge 3D reconstruction techniques to map the precise spatial distribution of GAs on affected coral colonies. Three statistical measures, Ripley's K, Moran's I, and the Kolmogorov-Smirnov test were used to determine if the GA lesions were distributed in a non-random pattern. Each measure showed the GA lesions exhibited distinct spatial clustering on all ten affected colonies analyzed in this study. Our study is not only the first 3D analysis of intra-colony disease clustering, but also provides a novel approach for investigating and quantifying levels of disease clustering in order to improve our understanding of coral disease epizootiology, transmission, and etiology.

ACS Style

John H.R. Burns; Theodore Alexandrov; Ekaterina Ovchinnikova; Ruth D. Gates; Misaki Takabayashi. Investigating the spatial distribution of growth anomalies affecting Montipora capitata corals in a 3-dimensional framework. Journal of Invertebrate Pathology 2016, 140, 51 -57.

AMA Style

John H.R. Burns, Theodore Alexandrov, Ekaterina Ovchinnikova, Ruth D. Gates, Misaki Takabayashi. Investigating the spatial distribution of growth anomalies affecting Montipora capitata corals in a 3-dimensional framework. Journal of Invertebrate Pathology. 2016; 140 ():51-57.

Chicago/Turabian Style

John H.R. Burns; Theodore Alexandrov; Ekaterina Ovchinnikova; Ruth D. Gates; Misaki Takabayashi. 2016. "Investigating the spatial distribution of growth anomalies affecting Montipora capitata corals in a 3-dimensional framework." Journal of Invertebrate Pathology 140, no. : 51-57.

Data article
Published: 19 September 2016 in Data in Brief
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Ten annotated 3D reconstructions of Montipora capitata coral colonies contain x,y,z coordinates for all growth anomaly (GA) lesions affecting these corals. The 3D reconstructions are available as Virtual Reality Modeling Language (VRML) files, and the GA lesions coordinates are in accompanying text files. The VRML models and GA lesion coordinates can be spatially analyzed using Matlab. Matlab scripts are provided for three spatial statistical procedures in order to assess clustering of the GA lesions across the coral colony surfaces in a 3D framework: Ripley׳s K, Moran׳s I, and the Kolmogorov–Smirnov test. Please see the research article, “Investigating the spatial distribution of Growth Anomalies affecting Montipora capitata corals in a 3-dimensional framework” (J.H.R. Burns, T. Alexandrov, E. Ovchinnikova, R.D. Gates, M. Takabayashi, 2016) [1], for further interpretation and discussion of the data.

ACS Style

John H.R. Burns; Theodore Alexandrov; Katya Ovchinnikova; Ruth D. Gates; Misaki Takabayashi. Data for spatial analysis of growth anomaly lesions on Montipora capitata coral colonies using 3D reconstruction techniques. Data in Brief 2016, 9, 460 -462.

AMA Style

John H.R. Burns, Theodore Alexandrov, Katya Ovchinnikova, Ruth D. Gates, Misaki Takabayashi. Data for spatial analysis of growth anomaly lesions on Montipora capitata coral colonies using 3D reconstruction techniques. Data in Brief. 2016; 9 ():460-462.

Chicago/Turabian Style

John H.R. Burns; Theodore Alexandrov; Katya Ovchinnikova; Ruth D. Gates; Misaki Takabayashi. 2016. "Data for spatial analysis of growth anomaly lesions on Montipora capitata coral colonies using 3D reconstruction techniques." Data in Brief 9, no. : 460-462.

Journal article
Published: 01 April 2016 in Methods in Oceanography
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ACS Style

J.H.R. Burns; D. Delparte; L. Kapono; M. Belt; R.D. Gates; M. Takabayashi. Assessing the impact of acute disturbances on the structure and composition of a coral community using innovative 3D reconstruction techniques. Methods in Oceanography 2016, 15-16, 49 -59.

AMA Style

J.H.R. Burns, D. Delparte, L. Kapono, M. Belt, R.D. Gates, M. Takabayashi. Assessing the impact of acute disturbances on the structure and composition of a coral community using innovative 3D reconstruction techniques. Methods in Oceanography. 2016; 15-16 ():49-59.

Chicago/Turabian Style

J.H.R. Burns; D. Delparte; L. Kapono; M. Belt; R.D. Gates; M. Takabayashi. 2016. "Assessing the impact of acute disturbances on the structure and composition of a coral community using innovative 3D reconstruction techniques." Methods in Oceanography 15-16, no. : 49-59.

Journal article
Published: 07 July 2015 in PeerJ
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The structural complexity of coral reefs plays a major role in the biodiversity, productivity, and overall functionality of reef ecosystems. Conventional metrics with 2-dimensional properties are inadequate for characterization of reef structural complexity. A 3-dimensional (3D) approach can better quantify topography, rugosity and other structural characteristics that play an important role in the ecology of coral reef communities. Structure-from-Motion (SfM) is an emerging low-cost photogrammetric method for high-resolution 3D topographic reconstruction. This study utilized SfM 3D reconstruction software tools to create textured mesh models of a reef at French Frigate Shoals, an atoll in the Northwestern Hawaiian Islands. The reconstructed orthophoto and digital elevation model were then integrated with geospatial software in order to quantify metrics pertaining to 3D complexity. The resulting data provided high-resolution physical properties of coral colonies that were then combined with live cover to accurately characterize the reef as a living structure. The 3D reconstruction of reef structure and complexity can be integrated with other physiological and ecological parameters in future research to develop reliable ecosystem models and improve capacity to monitor changes in the health and function of coral reef ecosystems.

ACS Style

Jhr Burns; Donna M Delparte; Ruth D Gates; Misaki Takabayashi. Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs. PeerJ 2015, 3, e1077 .

AMA Style

Jhr Burns, Donna M Delparte, Ruth D Gates, Misaki Takabayashi. Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs. PeerJ. 2015; 3 ():e1077.

Chicago/Turabian Style

Jhr Burns; Donna M Delparte; Ruth D Gates; Misaki Takabayashi. 2015. "Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs." PeerJ 3, no. : e1077.

Journal article
Published: 09 April 2015 in ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences
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The structural complexity of coral reefs profoundly affects the biodiversity, productivity, and overall functionality of reef ecosystems. Conventional survey techniques utilize 2-dimensional metrics that are inadequate for accurately capturing and quantifying the intricate structural complexity of scleractinian corals. A 3-dimensional (3D) approach improves the capacity to accurately measure architectural complexity, topography, rugosity, volume, and other structural characteristics that play a significant role in habitat facilitation and ecosystem processes. This study utilized Structure-from-Motion (SfM) photogrammetry techniques to create 3D mesh models for several Hawaiian corals that represent distinct morphological phenotypes. The orthophotos and digital elevation models generated from the SfM process were imported into geospatial analysis software in order to quantify several metrics pertaining to 3D complexity that are known to affect ecosystem biodiversity and productivity. The 3D structural properties of the reconstructed coral colonies were statistically analyzed to determine if the each species represents a unique morpho-functional group. The SfM reconstruction techniques described in this paper can be utilized for an array of research purposes to improve our understanding of how changes in coral composition affect habitat structure and ecological processes in coral reef ecosystems.

ACS Style

J. H. R. Burns; D. Delparte; R. D. Gates; M. Takabayashi. UTILIZING UNDERWATER THREE-DIMENSIONAL MODELING TO ENHANCE ECOLOGICAL AND BIOLOGICAL STUDIES OF CORAL REEFS. ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences 2015, XL-5/W5, 61 -66.

AMA Style

J. H. R. Burns, D. Delparte, R. D. Gates, M. Takabayashi. UTILIZING UNDERWATER THREE-DIMENSIONAL MODELING TO ENHANCE ECOLOGICAL AND BIOLOGICAL STUDIES OF CORAL REEFS. ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences. 2015; XL-5/W5 ():61-66.

Chicago/Turabian Style

J. H. R. Burns; D. Delparte; R. D. Gates; M. Takabayashi. 2015. "UTILIZING UNDERWATER THREE-DIMENSIONAL MODELING TO ENHANCE ECOLOGICAL AND BIOLOGICAL STUDIES OF CORAL REEFS." ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XL-5/W5, no. : 61-66.

Journal article
Published: 02 May 2011 in Coral Reefs
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This study investigated the morphology, severity, and distribution of growth anomalies (GAs) in the coral, Montipora capitata, from Wai‘ōpae tide pools, southeast Hawai‘i Island. A macro-image analysis of skeletal microstructure placed GAs into two definable categories; Type A and Type B. Type A GAs had polyp density reduced by 43.05 ± 0.80% (mean ± SE) compared to healthy M. capitata tissue, with many fused and protrusive tuberculae. Type B GAs had no discernable polyps or calices and fused protuberant coenosteum. The prevalence of Type A and Type B GAs among all M. capitata colonies (n = 1,093) in 8 tide pools at Wai‘ōpae was 22.1% (range 2.8–33.7%) and 8.2% (range 0.0–16.9%), respectively. The proportion of colony surface area occupied by GA (relative GA cover) was quantified to assess the severity of this disease among all surveyed colonies. The relative GA cover was significantly greater on colonies larger than 1 m in diameter than smaller colonies and in the central portion of colonies than in the periphery. Furthermore, relative GA cover was negatively related to water motion (R 2 = 0.748, P < 0.01). Developing field diagnostic criteria of M. capitata GA allowed for a detailed epizootiological assessment that determined several cofactors associated with disease severity. Such epizootiological analysis is applicable to future studies of GAs elsewhere.

ACS Style

J. H. R. Burns; N. K. Rozet; M. Takabayashi. Morphology, severity, and distribution of growth anomalies in the coral, Montipora capitata, at Wai‘ōpae, Hawai‘i. Coral Reefs 2011, 30, 819 -826.

AMA Style

J. H. R. Burns, N. K. Rozet, M. Takabayashi. Morphology, severity, and distribution of growth anomalies in the coral, Montipora capitata, at Wai‘ōpae, Hawai‘i. Coral Reefs. 2011; 30 (3):819-826.

Chicago/Turabian Style

J. H. R. Burns; N. K. Rozet; M. Takabayashi. 2011. "Morphology, severity, and distribution of growth anomalies in the coral, Montipora capitata, at Wai‘ōpae, Hawai‘i." Coral Reefs 30, no. 3: 819-826.