This repository is structured as follows:
|-- data
|-- scripts
|-- results
|-- plots
|-- figures
In the data directory are the occurrence data (xlsx files) and
the spatial data required for this analysis.
This analysis is implemented in R version 4.2.2 (2022-10-31) and requires the following packages:
# for analysis
-- tidyverse
-- sf
-- terra
-- quadtree
-- ConR
-- WEGE
# for visualisation
-- ggplot2
-- ggarrange
-- ggnewscale
-- ggrepel
-- ggpubr
-- jpeg
The workflow of this study. A. Curation of the literature and the NHMC arthropod collection for the endemic arthropod occurrences. B. PACA for the preliminary assessment of the arthropods and their distributions in Crete. C. Prediction of potential KBAs and endemicity hotspots and D. their overlap with Natura2000 and Land Use Change evaluation for human pressures.
First the script species_assessment.R is executed. It is the main
script that calculates the IUCN AOO and EOO and PACA metrics. Based on the
results the script hotspot_assessment.R generates the hotspots,
threatspots and Key Biodiversity Areas of the endemic arthropods of Crete.
Then the spatial_analysis.R script finds all the overlaps between the species metrics
and spatial data, i.e Natura2000, Corine Land Cover and HILDA+.
Subsequently, the species_assessment_statistict.Rmd
R markdown file generates a report based on these results. The functions.R is a
collection of functions required in all scripts.
The script code_snippets.R contains code and data manipulation of large
files, e.g. Natura2000 sites, elevation maps of Europe. This script is not
meant to be executed but to guide to the original versions of the data as
downloaded from the sources.
The script get_species_info.R is used for exploratory analysis of the
GBIF information of the species in our dataset and for the current IUCN assessments
of arthropod species.
In publication_figures.R we produce the figures and supplementary figures for the publications.
All figures use the color-blind friendly palette Okabe-Ito.
Occurrences of endemic arthropod species in the island of Crete were
compiled by Natural History Museaum of Crete. The data were cureted
from the literature and from Natural History Museaum of Crete specimens.
They are available as Supplementary-material-1.xlsx.
The protected areas of Natura2000 SCI (habitats directive) and Wildlife refuges are used in this analysis.
Spatial data from Copernicus system are also used. These are the CORINE Land Cover and the Digital Elevation Models. CORINE Land Cover data are used to identify human pressures on the Natura2000 regions and on the hotspots of the arthropod endemic taxa.
The land use change in Crete is estimated with the HILDA+ dataset available here.
Full IUCN assessments of the species are downloaded from the IUCN web resource. In advanced search, the Taxonomy, Land regions and Filter on Endemics fields are used to download data. We use the World, Europe, Greece Land regions and endemics to download "Search Results" of 3 different datasets. Crete endemics are not included in the IUCN assessment so we filter from our curated Cretan endemics. These data are used to compare with our preliminary analysis.
The assessment of taxa is based on the critirion B of IUCN; Extend of
Occurrence and Area of Occupancy. All the results of this analysis is
visualised in the plots directory.
Preliminary Automated Conservation Assessments (PACA) is based on critirion B. It is a fast way to estimated the taxa under threat.
Using the European Environment Agency reference grid of 10km X 10km we defined a location as a cell grid that a species has occurrered. The endemic hotspots and the threatened hotspots are the cell grids the 10% highest endemic species and threatened species, respectively.
Giannis Bolanakis, Savvas Paragkamian, Maria Chatzaki, Liubitsa Kardaki and Apostolos Trichas. 2023. The conservation status of the Cretan Endemic Arthropods under Natura 2000 network.