Data and R code for paper: Diversity patterns of threatened decapod species in Brazil/https://doi.org/10.1007/s10750-025-05964-5
Description
In this study, we compared spatial patterns of species richness (SR), phylogenetic diversity (PD), and phylogenetic endemism (PE) of crustaceans, based on the two most recent assessment periods (2016 and 2022) under the International Union for Conservation of Nature (IUCN) criteria. The analyses were conducted within a phylogenetic framework based on mitogenomic markers.
Files
Steps to reproduce
Files: Coordenadas 2016 GBIF OK.xlsx Description: Species coordinates from the 2016 dataset. Alin_Concatenado_2014_phy.phy.varsites.phy.treefile Description: Maximum likelihood (ML) tree including all species from the 2016 dataset. Coordenadas GBIF OK.xlsx Description: Species coordinates from the 2022 dataset. Alin_Concatenado_2022_phy.phy.varsites.phy.treefile Description: Maximum likelihood (ML) tree including all species from the 2022 dataset. R scripts: Script Diversity patterns 2016.R Description: Workflow to compute SR, PD and PE indices for the 2016 dataset using picante, phyloraster, and phylobase. The plots were executed using ggplot2. Script Diversity patterns 2022.R Description: Workflow to compute SR, PD and PE indices for the 2022 dataset using picante, phyloraster, and phylobase. The plots were executed using ggplot2. Diversity_Metrics_Correlation.R Description: Correlation analysis among diversity indices (SR, PD, and PE) using Pearson correlation. Software: R (v4.3.2) – For all data processing, spatial analysis and plotting Geneious Prime (v2024.0) – Sequence alignment and tree construction IQ-TREE 2 – Maximum likelihood phylogenetic tree generation Required R packages: Data Processing & Cleaning: tidyverse, dplyr, CoordinateCleaner, readxl. Spatial Analysis & Mapping: leaflet, terra, rgdal. Phylogenetic & Biodiversity Analysis: picante, phyloraster, ape, phylobase, LetsR, SESraster. Visualization: ggplot2, gridExtra, ggpubr Workflow Overview Data Import & Cleaning: Occurrence data were compiled and cleaned using CoordinateCleaner. Phylogenetic Analysis: Mitochondrial sequences aligned in Geneious; ML phylogenetic trees generated with IQ-TREE 2. Diversity Metrics: SR, PD and PE computed using phyloraster, picante, and phylobase. Statistical Analysis: Pearson correlation using "lm" function. Mapping: Figures created using ggplot2.
Institutions
- Universidade de Sao Paulo