DOI: 10.16904/envidat.85
title: Simulated and observed prevalence of dispersal-related traits in tropical reef fish assemblages worldwide

description: This dataset contains all data and R codes (R Development Core Team, https://www.R-project.org) used in the following publication: Donati GFA, Parravicini V, Leprieur F, Hagen O, Gaboriau T, Heine C, Kulbicki M, Rolland J, Salamin N, Albouy C, Pellissier L. "A process-based model supports an association between dispersal and the prevalence of species traits in tropical reef fish assemblages" accepted by Ecography in August 2019. When using this data and R scripts the above publication should be cited. 
The interaction of habitat dynamics with species dispersal abilities could generate gradients
in species diversity and prevalence of life-history and ecological traits, when the latter are associated with dispersal potential. In this dataset, we use a spatial mechanistic model of speciation, extinction and dispersal, constrained by a dispersal parameter. This model allows to simulate the interplay between reef habitat dynamics over the past 140 million years and dispersal, shaping lineage diversification history and global assemblage composition of over 6000 tropical reef fish species. Global trait distribution data of tropical reef fish are used to evaluate the congruence between simulations and observations.
description: Resource Title: Global species distribution of tropical reef fish species
 Size: 3224423 bytes
 Format: text/csv
 URL: https://www.envidat.ch/dataset/6b06ad48-bd85-47a8-b478-0850b6def1a4/resource/f554c199-621c-4c60-9566-e3ae1d9479b0/download/fishnet_gaspar_code.csv
 Description: Each species corresponds to a "Gaspar_code" gathered from the General Approach to Species Abundance Relationships (GASPAR) database (Kulbicki et al. 2013, Parravicini et al. 2013) and is linked to a specific Fishned ID corresponding to a specific Latitude and Longitude.
description: Resource Title: Dispersal parameter value d per simulation
 Size: 124575 bytes
 Format: text/plain
 URL: https://www.envidat.ch/dataset/6b06ad48-bd85-47a8-b478-0850b6def1a4/resource/f895d8b6-3eff-4479-892b-8cc86b476a22/download/d_param_sim.txt
 Description: Dispersal parameter value d per simulation starting with a minimum dispersal value, where each species is able to colonise each adjacent cell, and ending with the value of d for which all the extant habitats, including the most remote Pacific islands, have been colonised (d ∈ [1.75°: 5.45°]).
description: Resource Title: Global simulated distribution of species under a range of dispersal parameter values
 Size: 30514436 bytes
 Format: text/plain
 URL: https://www.envidat.ch/dataset/6b06ad48-bd85-47a8-b478-0850b6def1a4/resource/471350ea-cbf8-409e-a8cc-55a84fe4a8cd/download/matrix_sim_sprichness.txt
 Description: Global distribution of simulated species richness under a range of dispersal parameter values d 
d ∈ [1.75°: 5.45°].
description: Resource Title: Coral reef grid cells (shape, dbf, etc. files)
 Size: 12441 bytes
 Format: application/zip
 URL: https://www.envidat.ch/dataset/6b06ad48-bd85-47a8-b478-0850b6def1a4/resource/7b6a4981-0f00-432c-9ed8-502c43126613/download/grid_4326_files.zip
 Description: Grid cells of 5 × 5°, corresponding to circa 555 × 555 km at the Equator (see Parravicini et al. 2013, Leprieur et al. 2016)

Parravicini, V. et al. 2013. Global patterns and predictors of tropi- cal reef sh species richness. – Ecography 36: 1254–1262.

Leprieur, F. et al. 2016. Plate tectonics drive tropical reef biodiver- sity dynamics. – Nat. Commun. 7: 11461.
description: Resource Title: Global coast files from https://www.ngdc.noaa.gov/mgg/shorelines/gshhs.html
 Size: 566907 bytes
 Format: application/zip
 URL: https://www.envidat.ch/dataset/6b06ad48-bd85-47a8-b478-0850b6def1a4/resource/a14c6b25-180d-42d8-a863-e13574487a03/download/coast_files.zip
 Description: Global coast files from https://www.ngdc.noaa.gov/mgg/shorelines/gshhs.html used in the Figures
description: Resource Title: Simulated rates of speciation and extinction under a range of dispersal parameters.
 Size: 8135 bytes
 Format: .rds
 URL: https://www.envidat.ch/dataset/6b06ad48-bd85-47a8-b478-0850b6def1a4/resource/3b9df6ee-3cc3-4760-a51c-8241db1fa78c/download/rates.rds
 Description: Simulated rates of speciation and extinction under a range of dispersal parameters. Net diversification rates are calculated from the difference between speciation and extinction rates. This data allows the creation of Figure A4 in Supporting information, Appendix 1.
description: Resource Title: 
 Size: 17762 bytes
 Format: .rdata
 URL: https://www.envidat.ch/dataset/6b06ad48-bd85-47a8-b478-0850b6def1a4/resource/95d1d60f-7dc9-4c51-992e-baaca842c296/download/cong_sim_obs_trait_prop.rdata
 Description: Input for spatial congruence test overlap between proportions of low and high dispersal and observed low- and high- dispersal-related traits in assemblages (30-50% threshold). see Table 2.
description: Resource Title: Input for the Global distribution maps for proportions of species richness for (a) simulated dispersal parameter value (b) observed dispersal-related traits
 Size: 45638 bytes
 Format: text/csv
 URL: https://www.envidat.ch/dataset/6b06ad48-bd85-47a8-b478-0850b6def1a4/resource/2115cb5b-7557-4897-8892-f109a15eb0c1/download/grid_pl_sim_obs_trait_prop_cong.csv
 Description: Geographic distribution data (species richness and proportions of high/low dispersal-related traits) on predominantly low dispersing and high dispersing species expected based on the simulations, and those where low- and high- dispersal related traits values are observed for the five investigated traits.
description: Resource Title: Functions used in R scripts in: Donati et al. 2019 "A process-based-model supports an association between # dispersal and the prevalence of species traits in tropical reef fish assemblages" accepted in Ecography, August 2019
 Size: 8444 bytes
 Format: .r
 URL: https://www.envidat.ch/dataset/6b06ad48-bd85-47a8-b478-0850b6def1a4/resource/eed003d7-c661-42ab-bafb-c2fd2290d94e/download/donati_et_al_dispersal_global_prevalence_traits_functions.r
 Description: Functions for Figures illustrated in Donati et al. 2019 "A process-based-model supports an association between dispersal and the prevalence of species traits in tropical reef fish assemblages" accepted in Ecography, August 2019.
description: Resource Title: Donati et al. main script
 Size: 9040 bytes
 Format: .r
 URL: https://www.envidat.ch/dataset/6b06ad48-bd85-47a8-b478-0850b6def1a4/resource/e00d3cf8-4845-4de0-8eb6-33243506c274/download/donati_et_al_dispersal_global_prevalence_traits_main.r
 Description: Main script used in : Donati et al. 2019 "A process-based-model supports an association between dispersal and the prevalence of species traits in tropical reef fish assemblages"
accepted in Ecography, August 2019
description: Resource Title: Main text figures
 Size: 15475 bytes
 Format: .r
 URL: https://www.envidat.ch/dataset/6b06ad48-bd85-47a8-b478-0850b6def1a4/resource/c0870690-1143-4ac8-957a-2bfd2d6c96e3/download/donati_et_al_dispersal_global_prevalence_traits_figures_main_text.r
 Description: R Script used for figures in main text in: Donati et al. 2019: "A process-based-model supports an association between dispersal and the prevalence of species traits in tropical reef fish assemblages" accepted in Ecography, August 2019.
description: Resource Title: Supplementary material Appendix 1 Figures
 Size: 26270 bytes
 Format: .r
 URL: https://www.envidat.ch/dataset/6b06ad48-bd85-47a8-b478-0850b6def1a4/resource/2946e2c8-9f5c-4ed8-bce2-13069fcb6faf/download/donati_et_al_dispersal_global_prevalence_traits_figures_supp_mat.r
 Description: Supplementary material Appendix 1 Figures illustrated in Donati et al. 2019 "A process-based-model supports an association between dispersal and the prevalence of species traits in tropical reef fish assemblages". accepted in Ecography, August 2019
description: Resource Title: Tropical reef fish trait data
 Size: 428195 bytes
 Format: text/csv
 URL: https://www.envidat.ch/dataset/6b06ad48-bd85-47a8-b478-0850b6def1a4/resource/a5227230-5514-4bdc-b81d-b38d5aaea5cb/download/sp_ecological_trait_data.csv
 Description: Species trait (i.e. adult body size, home range mobility behaviour, circadian activity and schooling) data gathered from the General Approach to Species Abundance Relationships (GASPAR) database (Kulbicki et al. 2013, Parravicini et al. 2013). 

Kulbicki, M. et al. 2013. Global biogeography of reef shes: a hier- archical quantitative delineation of regions. – PLoS One 8: e81847.

Parravicini, V. et al. 2013. Global patterns and predictors of tropi- cal reef sh species richness. – Ecography 36: 1254–1262.

To complement the trait data with Pelagic Larval Duration information refer to the following publication:

Luiz, Osmar J., et al. "Adult and larval traits as determinants of geographic range size among tropical reef fishes." Proceedings of the National Academy of Sciences 110.41 (2013): 16498-16502.

In Donati et al. "A process-based model supports an association between dispersal and the prevalence of species traits in tropical reef fish assemblages" accepted in Ecography in August 2019, we used the PLD gathered from Luiz et al. 2013 as described in the methods - section "Species trait data".