nvogtvincent / wio_coral

Supplementary data and scripts for Coral reef potential connectivity in the southwest Indian Ocean

Noam S Vogt-Vincent, April J Burt, Rosa M van der Ven, Helen Johnson

This repository contains all (full-size) figures from the manuscript, alternate versions for all five coral species with larval parameters described in Connolly & Baird (2010), and the full raw data (connectivity matrices) described in the paper. The scripts used to generate these figures are also stored here. Note that we use the following acronyms for coral species: PD (Platygyra daedalea), GR (Goniastrea retiformis), AV (Acropora valida), AG (Acropora gemmifera), and AM (Acropora millepora). Large files can be found in the Zenodo repository, here. The interactive Sea the Connectivity web app can be found here.

Repository overview

Figures

Matrices: Contains the explicit connectivity (Fig. 2), explicit connectivity variability (Fig. S3), and implicit connectivity (Fig. 3) matrices. Note that the colour scale for implicit connectivity is different for GR. Generated by CX_CMIC_Matrices.py in the Scripts directory.

Metrics: Contains a variety of connectivity metrics (out-entropy, in-entropy, out-strength, in-strength, out-consistency, in-consistency, and betweeness centrality) for close-up views, and the entire domain. Note that only out-entropy is discussed in the manuscript (Fig. S4). The other metrics are either described in Vogt-Vincent et al. High-frequency variability dominates potential connectivity between remote coral reefs (2023), or in Sea the Connectivity (see below). Generated by Metrics.py in the Scripts directory.

Partitioning: Contains the PCA plot for the meta-clusters (Fig. 4), true Euclidean distance in PCA space (Fig. S5), inertia (Fig. S1), meta-clusters in geographic space (Fig. 5), individual principal components plotted geographically (Figs. S9-11) and discrete partitioning using K-Means with k = 3, 5, and 8 clusters (Figs. S6-7). Generated by Network_partitioning.py in the Scripts directory.

Matrices - note that these data are large, and can be found in the associated Zenodo repository (see top)

Postprocessed subdirectory contains the following:

PROCESSED CONNECTIVITY MATRICES: Raw data for Figs. 2-3 and S3. If you are a marine spatial planner or conservationist in the SWIO, this is probably what you want! Feel free to contact me if you need help opening/using these data.

Metrics/gridded metrics: Various derived metrics averaged over time, for different cells and plotted geographically.

Main directory contains the following:

Drift time: Not used in this study, but contains the drift time of larvae between all pairs of reef groups, in 0.5 day bins.

Flux (source cell): Connectivity matrices containing the climatological flux of larvae between all pairs of reef cells.

Flux (source group): Connectivity matrices containing the flux of larvae between all pairs of reef groups, as a function of spawning day.

Retention strength: Matrices containing the proportion of larvae that were retained at the source reef cell, as a function of spawning day.

Source strength: Matrices containing the proportion of larvae that settle anywhere from a reef cell, as a function of spawning day.

Sink strength:: Matrices containing the proportion/ratio of larvae that settle at a reef cell, as a function of spawning day.

Source entropy: Matrices containing the entropy associated with larval destinations for larvae from a reef cell, as a function of spawning day (see Fig. S4, or contact the author)

Source entropy: Matrices containing the entropy associated with larval sources for larvae for a reef cell, as a function of spawning day.

Scripts

See Figures

Grid data

Model grid used for the WINDS hydrodynamic simulations and larval dispersal simulations. Contains the listing of the 180 reef groups (from the 8088 reef cells), and reef group names.

Reference

Reference files used by the larval dispersal simulations.

Scripts

See above

Sim

Simulation scripts used for larval dispersal simulations (similar to those used in Vogt-Vincent et al. (2023)).

Sea the Connectivity

Files for the web app (developed with Otis Brunner and Julia Janicki).