DOI: 10.5061/dryad.4f4qrfjbk
title: Connectivity Matrices from biophysical modelling studies for A. millepora coral larvae in the Great Barrier Reef (Australia); present day and future scenarios

description: These data contain connectivity matrices from biophysical modelling
 simulations of the dispersal of Acropora millepora coral larvae in the
 southern Great Barrier Reef (Australia), under present-day and future
 climate scenarios. The connectivity matrices represent modelled strength
 of larval transfer from one reef to another, and were obtained using a
 coupled reef-scale, high-resolution, depth-integrated finite element
 hydrodynamic model (SLIM) of water currents in the Great Barrier Reef, and
 Individual-Based particle tracking module. Biological parameters to model
 larval acquisition and loss of competency and mortality were based on the
 results of experiments detailed in the related journal article. We include
 connectivity matrices for 2 different water temperature scenarios
 representing current and future climates, for three different recent
 spawning seasons (2008, 2009, 2010), and also for scenarios where
 low-frequency currents through the domain are modulated to mimic the
 likely effects from future changes to large-scale circulation extracted
 from CMIP5 global climate models. We also include files summarising the
 relative changes, per reef, to certain key connectivity metrics between
 the 2 temperature scenarios (dispersal distance, local retention, number
 of incoming connections, "source index", and present day
 "source index" - all metrics are defined in the related journal
 article and Methods section of this metadata), averaged over all 3
 spawning seasons modelled, as plotted in Figs 1a-e in the related journal
 article. Additionally, we include a separate file summarising changes to
 reef recovery times following a disturbance to coral cover between the 2
 temperature scenarios, per reef, as modelled using the meta-population
 model described in the related journal article, and as shown in Fig 2 of
 the article.
description: These connectivity matrices were generated by an Individual-Based
 (Lagrangian) Model to simulate the dispersal of coral larvae during
 different spawning seasons in the Great Barrier Reef. Details of the
 Hydrodynamic and Individual-Based models can be found in the linked
 journal article. The matrices themselves have been normalised by the total
 number of particles seeded in each simulation. As well as the connectivity
 matrices describing the (normalised) strength of larval dispersal from
 source reef (indexed by the matrix row) to the destination reef (matrix
 column), we include an associated matrix giving the (normalised) quantity
 of larvae seeded at each reef, again normalised by the total number of
 larvae seeded; all matrices are therefore directly equivalent.
 The present-day matrix was obtained using hydrodynamics
 calibrated to present-day conditions, and an assumed water temperature of
 27 degrees Celsius; the 29 degree Celsius matrix was obtained assuming the
 effects of a 2 degree Celsius increase in water temperature with respect
 to the present day scenario. The future hydrodynamics scenarios, with
 modulated water inflow quantities, were carried out using biological
 parameters for 27 degree Celsisus water temperature. Each scenario is
 repeated for the 3 spawning seasons. Validation plots and metrics for the
 hydrodynamic model are detailed in the related journal article.
 To calculate changes in connectivity metrics (such as local
 retention, or dispersal distance) with respect to the present day, we
 advise looking at the difference separately for each of the 3 spawning
 seasons and then averaging, such that each season is given equal weight,
 to make the results more robust to particular annual changes in larval
 dispersal patterns, whether on a small scale affecting only a small number
 of reefs, or at the larger, regional scale. We also
 include 2 additional files containing the data represented in the 2 main
 plots in the related journal article - Figs 1a-e and Fig 2, which
 respectively show relative percentage changes between the 2 temperature
 scenarios, by reef, to certain key connectivity metrics, and to recovery
 times following disturbances, averaged over the 3 spawning seasons. The
 data for Figs 1a-e were created by processing the connectivity matrices in
 the way described in the journal article, specifically:
 dispersal distance is calculated as the average
 distance between source and destination reefs, averaged over all larvae
 released at the source reef which settled on any other reef during the
 simulation. This is calculated and shown by source reef.
 local retention is calculated as the proportion of larvae
 released over the source reef which settled over that same reef during the
 course of the simulation. number of incoming
 connections is the number of reefs from which a reef has received settlers
 (i.e. settled larvae) during the course of the simulation.
 source index is defined as the product of the number of larvae
 released at a given reef which settled on any other reef, and the number
 of outgoing connections from this reef to any other reef; it is designed
 to measure the relative importance of a reef as a source of larvae to
 other reefs. The data contain the source index averaged over the 27C
 simulation, to show the geographical distribution of the most important
 reefs under "present day" conditions, as well as the relative
 change in source index, by reef, between the 27C and 29C simulations. The
 source index is normalised by the value of the reef with the highest
 source index in the domain so it varies between 0 and 1, since it is
 purely a relative measure to compare different reefs within the same
 simulation domain. The data file for
 "Fig 2" contains the relative percentage changes to recovery
 times following a) single-reef and b) multi-reef simultaneous disturbances
 in initial coral cover, by reef, using the methodology described in the
 related journal article to simulate the evolution of coral cover in time
 following these initial disturbances. Reefs which never fully recovered
 initial coral cover do not contain any value. Relative
 changes for all data in the Figs 1a-e and Fig 2 datasets are first
 calculated by reef and by spawning season, and then averaged, by reef,
 over all three spawning seasons to obtain single value by reef. They
 represent the percentage change at 29C relative to the 27C temperature
 scenario.
description: Please refer to the 2 README files for specific details about the
 content of the individual files included and a description of the file
 naming convention used. The 00_README file describes the connectivity
 matrices, whilst the 01_README_Figs1and2_data file describes the
 "Figs 1 and 2" datasets in more detail. Note
 that some rows of the connectivity matrix are blank; any rows/columns
 which are blank in both the connectivity matrix and the associated
 "reefs seeded" matrix should be ignored, as these were not
 included in the simulations. We also include a file containing the
 geographical coordinates of the central position of each reef referred to
 in the connectivity matrix (same indexing, ie the coordinates in row N
 correspond to row N/column N in the connectivity matrices); these can be
 used to compute dispersal distances.