Investigation and integration of spatial analyses in benthic habitat mapping with application to nearshore Arctic environments

The field of benthic habitat mapping has entered an era of automated statistical methods that have increased the capacity to produce maps as marine management tools. Spurred by a confluence of advances in acoustic remote sensing, open-source statistical tools, GIS, and computing power, these methods facilitate quick and objective mapping of habitats and physical seabed characteristics. Their performance and accessibility have led to widespread uptake, yet key spatial issues associated with these methods have not fully translated into the benthic habitat mapping workflow. Towards establishing “best practices”, this thesis explores the application of several spatial concepts to benthic habitat mapping using three Canadian Arctic case studies. Relationships between seabed morphology and benthic habitats are well-established. Though recognized as a critical element in the field of geomorphometry, the scale dependence of these relationships is commonly neglected in habitat mapping. Chapter 2 provides evidence of the scale dependence of benthic terrain variables and demonstrates methods for testing and selecting from among many variables and scales for modelling the distribution of sediment grain size near Qikiqtarjuaq, Nunavut. Given challenges associated with marine data collection that are pronounced in the Arctic, benthic habitat maps commonly utilize multi-year and multisource datasets. Despite apparent advantages, there can be substantial challenges associated with the compatibility and spatial properties of such data. Chapter 3 demonstrates that spatially autocorrelated samples are likely to inflate estimates of predictive performance and uses a spatial resampling strategy to estimate and correct for inflation in a multi-model Arctic clam habitat map near Qikiqtarjuaq, Nunavut. Classified seabed maps are a common requirement for marine management and one of two broad approaches are often selected to produce them. Chapter 4 examines differences between classification and continuous modelling approaches in a spatial context to produce classified seabed sediment maps for inner Frobisher Bay, Nunavut. Non-spatial methods failed to indicate whether models could extrapolate to unsampled areas, which was a requirement for this study. When evaluated in a spatial context, the qualities of the classification approach made it more suitable, which was a function of ground-truth dataset characteristics and the predictive goals of the model. Non-spatial techniques may be appropriate for interpolation, but the ability to extrapolate needs to be examined in a spatial context

Seafloor morphology and substrate mapping in the Gulf of St Lawrence, Canada, using machine learning approaches

Detailed maps of seafloor substrata and morphology can act as valuable proxies for predicting and understanding the distributions of benthic communities and are important for guiding conservation initiatives. High resolution acoustic remote sensing data can facilitate the production of detailed seafloor maps, but are cost-prohibitive to collect and not widely available. In the absence of targeted high resolution data, global bathymetric data of a lower resolution, combined with legacy seafloor sampling data, can provide an alternative for generating maps of seafloor substrate and morphology. Here we apply regression random forest to legacy data in the Gulf of St Lawrence, Canada, to generate a map of seabed sediment distribution. We further apply k-means clustering to a principal component analysis output to identify seafloor morphology classes from the GEBCO bathymetric grid. The morphology classification identified most morphological features but could not discriminate valleys and canyons. The random forest results were in line with previous sediment mapping work done in the area, but a large proportion of zero values skewed the explained variance. In both models, improvements may be possible with the introduction of more predictor variables. These models prove useful for generating regional seafloor maps that may be used for future management and conservation applications

A multiscale approach to mapping seabed sediments

Benthic habitat maps, including maps of seabed sediments, have become critical spatialdecision support tools for marine ecological management and conservation. Despite the increasing recognition that environmental variables should be considered at multiple spatial scales, variables used in habitat mapping are often implemented at a single scale. The objective of this study was to evaluate the potential for using environmental variables at multiple scales for modelling and mapping seabed sediments. Sixteen environmental variables were derived from multibeam echosounder data collected near Qikiqtarjuaq, Nunavut, Canada at eight spatial scales ranging from 5 to 275 m, and were tested as predictor variables for modelling seabed sediment distributions. Using grain size data obtained from grab samples, we tested which scales of each predictor variable contributed most to sediment models. Results showed that the default scale was often not the best. Out of 129 potential scale dependent variables, 11 were selected to model the additive log-ratio of mud and sand at five different scales, and 15 were selected to model the additive log-ratio of gravel and sand, also at five different scales. Boosted Regression Tree models that explained between 46.4 and 56.3% of statistical deviance produced multiscale predictions of mud, sand, and gravel that were correlated with cross-validated test data (Spearman's ρmud = 0.77, ρsand = 0.71, ρgravel = 0.58). Predictions of individual size fractions were classified to produce a map of seabed sediments that is useful for marine spatial planning. Based on the scale-dependence of variables in this study, we concluded that spatial scale consideration is at least as important as variable selection in seabed mapping

Evaluating the suitability of multi-scale terrain attribute calculation approaches for seabed mapping applications

The scale dependence of benthic terrain attributes is well-accepted, and multi-scale methods are increasingly applied for benthic habitat mapping. There are, however, multiple ways to calculate terrain attributes at multiple scales, and the suitability of these approaches depends on the purpose of the analysis and data characteristics. There are currently few guidelines establishing the appropriateness of multi-scale raster calculation approaches for specific benthic habitat mapping applications. First, we identify three common purposes for calculating terrain attributes at multiple scales for benthic habitat mapping: (i) characterizing scale-specific terrain features, (ii) reducing data artefacts and errors, and (iii) reducing the mischaracterization of ground-truth data due to inaccurate sample positioning. We then define criteria that calculation approaches should fulfill to address these purposes. At two study sites, five raster terrain attributes, including measures of orientation, relative position, terrain variability, slope, and rugosity were calculated at multiple scales using four approaches to compare the suitability of the approaches for these three purposes. Results suggested that specific calculation approaches were better suited to certain tasks. A transferable parameter, termed the ‘analysis distance’, was necessary to compare attributes calculated using different approaches, and we emphasize the utility of such a parameter for facilitating the generalized comparison of terrain attributes across methods, sites, and scales

MultiscaleDTM : an open‐source R package for multiscale geomorphometric analysis

Digital terrain models (DTMs) are datasets containing altitude values above or below a reference level, such as a reference ellipsoid or a tidal datum over geographic space, often in the form of a regularly gridded raster. They can be used to calculate terrain attributes that describe the shape and characteristics of topographic surfaces. Calculating these terrain attributes often requires multiple software packages that can be expensive and specialized. We have created a free, open‐source R package, MultiscaleDTM , that allows for the calculation of members from each of the five major thematic groups of terrain attributes: slope, aspect, curvature, relative position, and roughness, from a regularly gridded DTM. Furthermore, these attributes can be calculated at multiple spatial scales of analysis, a key feature that is missing from many other packages. Here, we demonstrate the functionality of the package and provide a simulation exploring the relationship between slope and roughness. When roughness measures do not account for slope, these attributes exhibit a strong positive correlation. To minimize this correlation, we propose a new roughness measure called adjusted standard deviation. In most scenarios tested, this measure produced the lowest rank correlation with slope out of all the roughness measures tested. Lastly, the simulation shows that some existing roughness measures from the literature that are supposed to be independent of slope can actually exhibit a strong inverse relationship with the slope in some cases

Applying a Multi-Method Framework to Analyze the Multispectral Acoustic Response of the Seafloor

Improvements to acoustic seafloor mapping systems have motivated novel marine geological and benthic biological research. Multibeam echosounders (MBES) have become a mainstream tool for acoustic remote sensing of the seabed. Recently, “multispectral” MBES backscatter, which is acquired at multiple operating frequencies, has been developed to characterize the seabed in greater detail, yet methods for the use of these data are still being explored. Here, we evaluate the potential for seabed discrimination using multispectral backscatter data within a multi-method framework. We present a novel MBES dataset acquired using four operating frequencies (170, 280, 400, and 700 kHz) near the Doce River mouth, situated on the eastern Brazilian continental shelf. Image-based and angular range analysis methods were applied to characterize the multifrequency response of the seabed. The large amount of information resulting from these methods complicates a manual seabed segmentation solution. The data were therefore summarized using a combination of dimensionality reduction and density-based clustering, enabling hierarchical spatial classification of the seabed with sparse ground-truth. This approach provided an effective solution to synthesizing these data spatially to identify two distinct acoustic seabed classes, with four subclasses within one of the broader classes, which corresponded closely with seafloor sediment samples collected at the site. The multispectral backscatter data also provided information in likely, unknown, sub-surface substrate differences at this site. The study demonstrates that the adoption of a multi-method framework combining image-based and angular range analysis methods with multispectral MBES data can offer significant advantages for seafloor characterization and mapping

Harmonizing Multi-Source Sonar Backscatter Datasets for Seabed Mapping Using Bulk Shift Approaches

The development of multibeam echosounders (MBES) as a seabed mapping tool has resulted in the widespread uptake of backscatter intensity as an indicator of seabed substrate properties. Though increasingly common, the lack of standard calibration and the characteristics of individual sonars generally produce backscatter measurements that are relative to a given survey, presenting major challenges for seabed mapping in areas that comprise multiple MBES surveys. Here, we explore methods for backscatter dataset harmonization that leverage areas of mutual overlap between surveys for relative statistical calibration—referred to as “bulk shift” approaches. We use three multispectral MBES datasets to simulate the harmonization of backscatter collected over multiple years, and using multiple operating frequencies. Results suggest that relatively simple statistical models are adequate for bulk shift harmonization procedures, and that more flexible approaches may produce inconsistent results that risk statistical overfitting. While harmonizing datasets collected using the same operating frequency from separate surveys is generally feasible given reasonable temporal limitations, results suggest that the success at harmonizing datasets of different operating frequencies partly depends on the extent to which the frequencies differ. We recommend approaches and diagnostics for ensuring the quality of harmonized backscatter mosaics, and provide an R function for implementing the methods presented here

Supplementary_material_1.xlsx

This dataset accompanies the pre-print "Benthic habitat mapping: A review of three decades of mapping biological patterns on the seafloor" submitted to EarthArXiv, which is currently under review in Estuarine Coastal and Shelf Science. It contains data from a quantitative review of 624 benthic habitat mapping studies, each of which present mapped results of benthic mapping initiatives. </p