The population sizes and global extinction risk of reef-building coral species at biogeographic scales

Full description

This dataset and code supports the 2021 Nature Ecology and Evolution publication by Andreas Dietzel, Michael Bode, Sean Connolly and Terry Hughes, entitled "The population sizes and global extinction risk of reef-building coral species at biogeographic scales"

Abstract:

Knowledge of a species’ abundance is critically important for assessing its risk of extinction, but for the vast majority of wild animal and plant species such data are scarce at biogeographic scales. Here, we estimate the total number of reef-building corals, and the population sizes of more than 300 individual species, on reefs spanning the Pacific Ocean biodiversity gradient, from Indonesia to French Polynesia. Our analysis suggests that approximately half a trillion corals (0.3 x 10¹² – 0.8 x 10¹²) inhabit these coral reefs, similar to the number of trees in the Amazon. Two thirds of the examined species have population sizes exceeding 100 million colonies, and one fifth of the species even have population sizes greater than 1 billion colonies. Our findings suggest that, while local depletions pose imminent threats that can have ecologically devastating impacts to coral reefs, the global extinction risk of most coral species is lower than previously estimated.

Folder structure:

The file "Population_Sizes.Rproj" sets the directory and work environment.

R scripts can be found in subfolder "R", numbered in sequence.

Input data can be found in subfolder "data". Most input files are contained in the RData file "Input_Files.RData" in the subfolder "RData".

Figures are automatically stored in the subfolder "figures".

Files saving intermediate results are stored in the subfolder "RData".

Input files:

 File "LIT_data.csv"

Species abundance data collected across the Indo-Pacific biodiversity gradient

 File "TaxoOverview.csv"

Overview over inconsistencies in scleractinian taxonomies between species abundance data, IUCN Red List and the World Register of Marine Species

 File "Input_Files.RData" in subfolder RData

 - bbx: bounding box delineating the geographic extent of the study

- CoralCover: coral cover measurements from Bruno et al. (2016)

- grd.global: spatial grid across the global tropics

- grd.IP:  spatial grid of the Indo-Pacific

- HabitatMaps: habitat data collated from various sources

- HabMaps_LookUp: additional information about habitat data

- LOF: additional habitat data from the Khaled bin Sultan Living Oceans foundation. Proportional habitat data were extracted from the website of the LOF

- Interc: line-intercept transect data of species abundances collected in five regions and three habitats

- Locations: GPS coordinates and description of survey locations where species abundance data were collected

- MEOW: spatial polygon data frame of the Marine Ecoregions of the World according to Spalding et al.

- Ranges: spatial polygon data frame of the geographic ranges of all Indo-Pacific coral species (Hughes et al. )

- reefs.rast.CEIP: raster file of the study domain (Central and Eastern Indo-Pacific as defined by Spalding) specifying the percentage of each grid cell covered by coral reefs.

- reefs.rast.global and reefs.rast.IP: same as above but for the whole world and the entire Indo-Pacific respectively.

- ReefArea.byCountry: reef area estimate for each country used for sensitivity analysis.

- SupportData: data file using auxiliary information for each species such as its growth form, taxonomy and current IUCN threat status.

- proj_CEA: cyclindrical equal area projection used for all spatial files: "+proj=cea +lon_0=-160 +lat_ts=0 +x_0=0 +y_0=0 +datum=WGS84 +units=m +no_defs"

- res: the resolution/dimensions of each grid cell in m

File "OUT3_Relative_Species_Abundances.RData" in subfolder Data

Script "3-Calculate_relative_abundances.R" takes a long time to run. This file allows skipping this part of the analysis and continuing with subsequent steps.

File "Appendix_terSteege2015.csv" in subfolder data

Appendix from ter Steege et al. (2015) listing the population size estimates of Amazonian tree species.