NOO3D: A procedure to perform 3D species distribution models

• Published in: Ecological informatics 2019-11, Vol.54, p.101008, Article 101008
• Main Authors: Pérez-Costas, Elisa, Guisande, Cástor, González-Vilas, Luis, García-Roselló, Emilio, Heine, Jürgen, González-Dacosta, Jacinto, Lobo, Jorge M.
• Format: Article
• Language: English
• Subjects: Alpha shape 3D; Biogeography; Macroecology; MaxEnt; Niche of occurrence
• ISSN: 1574-9541
• DOI: 10.1016/j.ecoinf.2019.101008

There is consensus surrounding the need to include a third dimension when estimating Species Distribution Models (SDMs), which is of special interest for marine species. Application of the third dimension is, however, rarely available, thus users are obliged to manually combine 2D SDM outputs (i.e., suitability or presence/absence maps) for 3D distribution generation. Herein, the Niche of Occurrence 3D (NOO3D) is presented, which is a new, simple modelling procedure that provides 3D distributions using both 3D occurrence samples and environmental datasets that consist of one layer per depth value. NOO3D performance was evaluated using five virtual marine species to avoid errors associated with real data sets (three pelagic species, with wide, medium, and narrow distributions, respectively, a mesopelagic species and an abyssal species). These virtual species are distributed across the North Atlantic Ocean and were built to a 0.5° x 0.5° resolution and considering 49 depth levels (from 0.43 m to an undersea depth of 5274.7 m). NOO3D results were also compared to those provided by 3D Alpha Shapes and Maximum Entropy (MaxEnt). The True Positive Rate (TPR), or sensitivity, True Negative Rate (TNR), or specificity, False Positive Rate (FPR), or commission error, and False Negative Rate (FNR), or omission error, were employed in order to facilitate comparison between methods. MaxEnt performed best for TPR, TSS and FNR, and Alpha Shape 3D performed best for FPR and TNR. NOO3D was always the second-ranked method for all metrics considered, which indicates that it was the most suitable method. The provided results indicate that NOO3D can be considered a viable alternative in achieving three-dimensional species distribution models. •NOO3D is presented, which is a modelling procedure that provides 3D distributions.•NOO3D performance was compared with 3D Alpha Shapes and MaxEnt using virtual species.•NOO3D was the most suitable method considering all metrics examined.•The results indicate that NOO3D is an alternative for performing 3D SDM.