Organism-environment interactions take place through a multitude of processes that generate patterns across scales in space and time, but our understanding of pattern and processes is traditionally constrained by observational limitations. Contemporary technological advances in remote sensing, explored in this thesis, are extending the power and capability of ecological investigation. Three-dimensional (3D) ecosystem structure can now be analysed across scales from millimetres to kilometres and from minutes to decades, providing insight into scale-dependent patterns and their driving processes in complex and dynamic systems like temperate reefs.
Remote sensing technologies are available for 3D mapping and recent years have seen a rapid expansion in their use in field ecology. In chapter 2, I reviewed the current state of the art in high-resolution 3D ecosystem mapping technologies and their applications, highlighting the emerging era of 3D spatial ecology and identifying potential barriers to widespread uptake. I addressed a paucity of information on the accuracy and practicality of emerging optical remote sensing tools in ecological contexts by testing structure-from-motion photogrammetry and terrestrial laser scanning, in three coastal habitats, over three spatial scales. The accuracy of structure-from-motion photogrammetry, compared to terrestrial laser scanning models, was greatest at fine spatial scales (25 m², < 1 cm resolution) on more stable substrates like rock, with mean ± sd absolute difference of 4 mm ± 14 mm. Accuracy decreased with increasing spatial scale and in less stable vegetated scenes, with a maximum difference of 56 mm ± 111 mm in saltmarsh at a scale of 2500 m² extent and <2 cm resolution. Structure-from-motion photogrammetry was more portable, faster, flexible and lower-cost than terrestrial laser scanning, but was more vulnerable to error propagation.
Capturing sufficient ecologically relevant spatial and temporal variation in 3D structure is challenging in complex, dynamic habitats like intertidal temperate reefs. In chapter 3 I used the tools tested in chapter 2 to investigate spatial and temporal patterns in the structure of biogenic Sabellaria alveolata reef across scales. At a habitat scale (~35,000 m² extent, 10 cm horizontal resolution) most of the variation in reef structural change was explained by a combination of systematic trends with shore height and positive spatial
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autocorrelation up to the scale of colonies (1.5 m) or patches (4 m). Plot-scale mapping (2500 m² extent, 10 cm horizontal resolution) over five years (2014-2019, 6-month intervals) revealed previously undocumented temporal patterns in reef accretion and erosion. The system was highly dynamic at small spatial and temporal scales (<4 m, 6 months), but reef accretion and erosion compensated each other, resulting in stable habitat structure over larger scales (>130 m, 5 years). This scale-dependent variability would have been impossible to capture with conventional methods like quadrat, transect or point-based survey using GPS or theodolite, demonstrating the value of modern 3D mapping technologies to enhance our understanding of ecosystem dynamics across scales.
Subtidal temperate reefs hosting diverse communities are often found in high-energy waters, but these are understudied compared to lower energy seas, and knowledge of reef distribution is lacking. In chapter 4 I used multiscale 3D seafloor data and hydrodynamic information to predict the spatial distribution of geogenic reef and biogenic Sabellaria spinulosa reef habitats in a high tidal energy region. Random Forest models for reef substrate and S. spinulosa reef had balanced accuracy mean ± 95% CI of 80.7% ± 0.8% and 77% ± 1% respectively. Mean bed shear stress was the most important variable in both models, highlighting the importance of including measures of hydrodynamic energy in predictive mapping of high-energy temperate reef habitats.
My research demonstrates the increased power and insight that can be gained with contemporary 3D mapping and monitoring tools in field ecology. I showed that habitat structure in complex systems can be simultaneously highly dynamic and remarkably stable depending on the scale of observation, and that multiscale structural metrics are central to cost-effective mapping of subtidal temperate reef ecosystems. The collective works highlight the need for multiscale and multidisciplinary analysis and the value of embracing technological solutions for ecology in the age of big data. The emerging field of 3D ecosystem mapping and high-resolution remote sensing will have far-reaching implications for research, management and public engagement.