DOI: 10.5061/dryad.w9ghx3g1p
title: Modelling coastal connectivity in the Mediterranean Sea: Similar effects of changes in hydrodynamics and reduction in planktonic duration

description: Climate change can affect the dispersal of marine organisms and the
 connectivity of their populations through changes in hydrodynamics and the
 reduction of the planktonic duration of propagules. Few studies have
 investigated these effects over regional to global scales across a variety
 of release dates and sites. Here, we use hydrodynamic Lagrangian modelling
 to investigate these effects, their seasonal variation, and how they are
 modulated by the planktonic duration of dispersing propagules. Marine
 coastal organisms with planktonic propagules dispersed passively by ocean
 currents (e.g., seagrasses, mussels, sea urchins). Simulations of
 propagule dispersal were carried out using particle tracking model
 simulations driven by sea current velocity fields derived from the POLCOMS
 hydrodynamic model, under the Representative Concentration Pathway 8.5. We
 released propagules over three decades and followed their transport for
 planktonic durations up to 60 days. We quantified connectivity using three
 site-level variables (i.e., dispersal distance, coastal retention, and
 netflow) and a clustering approach. Changes in hydrodynamics and reduction
 in planktonic duration had similar effects on connectivity, leading to
 changes of up to 60% of the values of the 2020s. While the largest effects
 of changes in hydrodynamics were confined to a few areas, the effects of
 the reduction in planktonic duration were less variable spatially and
 seasonally. The effects of hydrodynamic changes were larger and more
 variable in species with longer planktonic durations. Because they had
 similar magnitudes, both the effects of changes in hydrodynamics and the
 reduction in planktonic duration should be considered in future studies.
 The expected changes in connectivity have potential consequences for
 genetic structure, the effectiveness of protected areas, and biological
 invasions. The dispersal dataset produced here is openly accessible and
 will support further research in these critical areas.
description: # Modelling coastal connectivity in the Mediterranean Sea: Similar effects
 of changes in hydrodynamics and reduction in planktonic duration Dataset
 DOI: [10.5061/dryad.w9ghx3g1p](10.5061/dryad.w9ghx3g1p) ## Description of
 the data and file structure Results of the particle tracking simulation of
 propagule dispersal for Mediterranean coastal species, and code to analyse
 the results and produce the figures of the paper. ### Archives:
 Cmatrix_RCP85_XXXXs.zip and Distance_RCP85_XXXXs.zip Each .zip archive
 contains the results of particle tracking simulations for the given decade
 (2020s, 2050s, 2090s). Archives named **Cmatrix_RCP85_XXXXs.zip** contain
 dispersal matrices. Archives named **Distance_RCP85_XXXXs.zip** contain
 dispersal distances. Particle tracking simulations were performed by
 releasing virtual propagules on the first day of each month for each of
 the ten years of each decade (except for the last two months of the
 decade), for a total of 118 release dates per decade. For example, for the
 decade 2020s, the first propagule release was on Jan 1st, 2020, and the
 last one was on Oct 1st, 2029. For each release date, results were
 calculated for different planktonic durations, from 5 days to 60 days in
 increments of 5 days (i.e, a total of 12 planktonic durations). Therefore,
 each .zip archive contains 118*12=1416 distinct files. #### File:
 Cmatrix_RCP85_2020s.zip #### File: Cmatrix_RCP85_2050s.zip #### File:
 Cmatrix_RCP85_2090s.zip **Description:** Dispersal probability matrices in
 RData format. Each file is named with the same pattern:
 Cmatrix_RCP85_YYYY_MM_KPLD.RData, where YYYY is the year, MM is the month
 (from 01 to 12), and K is the planktonic duration (from 5 to 60 in
 increments of 5). Each file contains an R matrix object named
 Cmatrix_temp, whose elements Cmatrix_temp[i,j] give the number of
 propagules released from site *j* (column) that end up in site *i* (row)
 at the end of their planktonic duration. Note that the dispersal matrix is
 oriented so that *Cij* is dispersal from *j* to *i*, whereas in other
 datasets, dispersal matrices might be oriented so that Cij is dispersal
 from *i* to *j*. This choice of orientation is arbitrary, but one must
 always be consistent. From *j* to *i* is more common in population
 dynamics. Sites are sorted in the same order as in the polygons.shp
 shapefile. One hundred propagules were released at each site. To get
 probability out of the Cmatrix_temp, one must divide each element by 100,
 i.e. ``` Cmatrix_temp / 100 ``` #### File: Distance_RCP85_2020s.zip ####
 File: Distance_RCP85_2050s.zip #### File: Distance_RCP85_2090s.zip
 **Description:** Dispersal distance data in.RData format. Each file is
 named with the same pattern: Distance_RCP85_YYYY_MM_KPLD.RData, where YYYY
 is the year, MM is the month (from 01 to 12), and K is the planktonic
 duration (from 5 to 60 in increments of 5). Each file contains a dataframe
 with 5055 rows (one per site) and 6 columns: *ID.polygon*: the ID of the
 release site *dist_median*: median great circle distance (in km) travelled
 by the 100 propagules released in that site at the end of their planktonic
 duration *dist_IQR*: interquartile range of the great circle distance (in
 km) travelled by the 100 propagules released in that site at the end of
 their planktonic duration *PLD*: planktonic duration (days) *year*: Year
 of propagule release *month*: Month of propagule release Note that the
 *PLD*, *year, *and *month* columns do not contain useful information as
 they are all constant within the same file, but were retained to
 facilitate binding the dataframes of different files together. ###
 Archive: polygons.zip **Description:** The archive contains the shapefile
 of the 5055 square polygons used as release sites. ### Archive:
 velocity.zip **Description:** This .zip archive contains raster files of
 the zonal (uo) and meridional (vo) components of velocity, and for the
 resultant (vel) velocity, for each month of each decade. The raster files
 are named as: uo_surf_01_2020.tif, where "uo" indicates the
 zonal velocity, 01 indicates the month of January, and 2020 indicates the
 2020 decade. Each raster file is the average velocity over the years of
 the decade, for the given month. These rasters are generated with the
 01-Read_oceanographic_data.R script. ### Archive: Temperature.zip
 **Description:** This .zip archive contains raster files of temperature
 for each month of each decade. The raster files are named as:
 to_surf_01_2020.tif, where 01 indicates the month of January and 2020
 indicates the 2020 decade. Each raster file is the average temperature
 over the years of the decade, for the given month. These raster are
 generated with the 01-Read_oceanographic_data.R script. ### Archive:
 Cmatrix_decade_PD.zip **Description:** This .zip archive contains RData
 files of dispersal matrices for each decade and planktonic duration. The
 RData files contain a matrix object analogous to those contained in the
 Cmatrix_RCP85_2020s.zip archive. These files are generated with the
 02-Collate_data.R script. ## Code/software The dispersal matrices and the
 dispersal distance files are.RData file that can be opened with
 [R](https://cran.r-project.org/). The polygons shapefile and the velocity
 raster files can be opened with [QGis](https://qgis.org/) or with R using
 the R packages [sf](https://cran.r-project.org/web/packages/sf/index.html)
 or [terra](https://cran.r-project.org/web/packages/terra/index.html).