Supplementary material for "Zonal rather than linear: bathymetric structuring of shallow-deep faunal transitions in the Arctic Ocean"

The supplementary materials include: ST1 – Supplementary Table 1. Raw data used in the analyses presented in the article. ST2 – Supplementary Table 3. Results of the Kruskal–Wallis test comparing the distribution of faunal boundaries across defined bathymetric ranges (upper, middle and lower bathyal, and abyssal) for the full dataset, the Nordic Seas, and the Arctic Basin. Output generated by script 9_Sl-grid_Kruskal.r. ST3 – Supplementary Table 4. Results of the Wilcoxon signed-rank test assessing shifts in maximum, median, and minimum species depth limits across different basins. Output generated by script 10_Sl_Species-depth.r Supplementary Figures – a file containing additional and program-generated versions of figures. Maps folder – includes a QGIS project (Arctic_bathyal.qgs) with layer display settings matching those used in the figures of the article (where applicable), along with associated cartographic materials: Slope.csv – file with coordinates of occurrence records (copy of Supplementary Table 1). ALL_species_areas.xxx – files containing range boundaries for all species used in the analysis of range-boundary condensation. Output generated by script Sl_bathymetric polygons.r grid_boundary_condensation_depth250m.gpkg – grid file containing the number of range boundaries per cell. Output generated by scripts 6_Sl_species_borders_light.r and 7_Sl_depth_filter_for_grid.r Scripts folder – R scripts used for data analysis. 1_Sl_Regions_and_ranges.r – This script defines global settings used across analyses, including depth thresholds (depth_controls) and the list of seas assigned to the Nordic seas group. It also implements the function split_regions(), which partitions the dataset into three subsets: All, Nordic seas, and Arctic Basin (i.e. all areas not included in the Nordic seas group). Its primary purpose is to centralize regional definitions, ensuring that all dependent scripts operate with consistent boundaries and depth ranges. It is used as a supporting script for subsequent analyses and may be executed multiple times within the pipeline under different parameter settings. 2_Sl_Depth_graph_Dendros.r – This script reads Slope.csv, filters records deeper than 150 m, and bins depth values into intervals defined by depth_step (50 m by default). For the full dataset and two regional subsets (Nordic seas and Arctic Basin), it produces two types of bar plots (observed species richness and range-based richness based on min–max depth limits) and two dendrograms showing similarity among depth bins in terms of species composition (Bray–Curtis dissimilarity). All 12 panels are combined and saved as a single output file: outputs/depth_plots.pdf. 3_Sl_Cumulative_curves.R generates cumulative species-accumulation curves for four bathymetric zones. It reads Slope.csv, automatically detects the CSV delimiter, and retains records with valid species names and depth values of at least 150 m, excluding records assigned to the Shelf region. The records are divided into the depth intervals min–450 m, 450–1500 m, 1500–2900 m, and 2900 m–max 4_Sl_moving_window.r – This script calculates beta diversity along the depth gradient using a moving window approach, partitioning it into turnover and nestedness components (Jaccard-based indices from the betapart package). It builds species presence matrices by depth bins (two variants: record-based and range-based), compares adjacent windows, and performs the analysis separately for All, Nordic seas, and Arctic Basin. Outputs include CSV files with results for each region and matrix type, as well as a combined figure (moving_window_6panel.pdf), where turnover is plotted above zero and nestedness below zero. 5_Sl_bathymetric polygons.r – This script loads species occurrence data and ETOPO bathymetry, filters species based on minimum number of records and spatial coverage (latitude/longitude extent), and estimates the plausible depth range for each species. Based on this range, it generates a mask of suitable depths, constrains it using the spatial geometry of occurrences (concave hull with buffer), and produces a final polygon representing the potential distribution. Results are saved as individual shapefiles for each species, a combined shapefile for all species, and a summary table containing parameters and processing status. 6_Sl_species_borders_light.r – This script generates a map of species range boundary condensation by counting, for each grid cell, the number of unique species polygon boundaries intersecting it. It uses a combined layer of species polygons, converts them into boundary lines, and overlays a regular grid (10 km resolution). Grid cells are filtered by depth using ETOPO data (Depth_m > 150 m), and the number of intersecting species boundaries (N_species_boundaries) is calculated. The output is a single GPKG file containing the filtered grid with attributes Depth_m and N_species_boundaries, suitable for further analysis in QGIS or downstream scripts. 7_Sl_depth_filter_for_grid.r – This auxiliary script filters the output of Sl_species_borders_light.r by depth. It retains only grid cells deeper than a specified threshold (Depth_m > depth_min_m, 450 m by default). The script reads the input GPKG file, verifies the presence of the Depth_m column, removes NA values and shallow cells, and writes a new filtered GPKG file with a depth-specific suffix in the filename. 8_Sl_grid_border_distribution.r – This script analyses the depth distribution of grid cells in relation to their “boundary density” (i.e. the number of species boundaries, N_species_boundaries). It reads grid_boundary_condensation_depth450m.gpkg, assigns each cell to a marine region via spatial intersection with World_Seas_IHO_v3, and bins depths into 50 m intervals. For each region (All, Nordic seas, Arctic Basin), it quantifies cells above and below the 85th percentile (P85) of N_species_boundaries. Outputs include two PDF files with bar plots (cells above/below P85 and cells above P85 only) and a CSV file with P85 thresholds for each region. 9_Sl-grid_Kruskal.r – This script tests whether the number of species boundaries per grid cell (N_species_boundaries) differs among depth-defined zones. It reads the grid GPKG, assigns cells to regions based on marine polygons, partitions the data into All, Nordic seas, and Arctic Basin, and applies a Kruskal–Wallis test followed by pairwise Wilcoxon tests (with Holm correction) using depth zones defined in depth_controls. Outputs include two CSV files: one with statistical test results (grid_boundary_kruskal_by_depth.csv) and one summarizing values by depth zone (grid_border_summary.scv; note the current typo in the file extension). 10_Sl_Species-depth.r – This script compares species depth distributions between the Nordic seas and the Arctic Basin for species occurring in both regions. It generates scatter plots of Nordic vs Arctic depth values (minimum, median, and maximum) and saves the figure as species_depth_scatter.pdf. In addition, paired Wilcoxon tests are performed for these three metrics, with results saved to species_depth_wilcoxon.csv.