DOI: 10.5281/zenodo.17193104
title: Geodiversity correlates with taxonomic diversity, but not with phylogenetic diversity in a Neotropical floodplain

description: Biodiversity is facing anthopogenic pressures. In order to understand biodiversity threats and build a conservation agenda, geodiversity has been suggested as a biodiversity surrogate. We evaluate the relationship of biodiversity and geodiversity for vascular plants in the Tocantins-Araguaia River basin in Brazil. We gathered vascular plants occurrences from online databases. We calculated the taxonomic and phylogenetic sampling completeness and estimated their asymptotic diversities within 0.5º x 0.5º grid cells in the basin. Then, we calculated geodiversity based on water bodies density, and landforms and soil diversities. We evaluated biodiversity-geodiversity relationship through spatial autoregressive models. We found that most grid cells in the basin have sampling completeness lower than 50%, showing a lower sampling completeness for phylogenetic diversity. Asymptotic taxonomic diversity was correlated to geodiversity, which was not found with phylogenetic diversity. By evaluating the relationship between taxonomic and phylogenetic diversity to the variables compounding geodiversity, we found that taxonomic diversity is correlated to landform diversity. Phylogenetic diversity had not been correlated to any compounding variable. Vascular plants in Tocantins-Araguaia River basin need more research efforts to collect and describe its taxonomic and phylogenetic diversity. Geodiversity was related only to taxonomic diversity, despite their weak relationship. These results show that geodiversity has a potential to be a biodiversity surrogate, however, at large spatial grain, studies may show weak correlations.
description: Description of the data and file structure

This repository contains codes and data of the submitted article to Diversity and Distributions.

Data

Vascular plants occurence data and phylogenetic information in Tocantins-Araguaia river basin. Geodiversity variables describing landforms, water bodies and soil diversity. R language scripts to reproduce analyses.

Repository structure

├── araguaia.Rproj

├── base_plot.tif

├── data

│   ├── araguaia_phylogeny_plants.tre

│   ├── araguaia_plants_data.csv

│   ├── completeness_input.csv

│   ├── flora_pts

│   │   ├── Flora_recortado_ARATO_novo.cpg

│   │   ├── Flora_recortado_ARATO_novo.dbf

│   │   ├── Flora_recortado_ARATO_novo.prj

│   │   ├── Flora_recortado_ARATO_novo.shp

│   │   └── Flora_recortado_ARATO_novo.shx

│   ├── incidence_raw.rds

│   ├── incidence.rds

│   ├── pam_araguaia_plants_0.01.csv

│   ├── pam_araguaia_plants.csv

│   ├── pd_completeness.rds

│   ├── rarefaction_min_phylo_coverage.rds

│   ├── raster

│   │   ├── diversity

│   │   │   ├── rarefaction_50_sd.tif

│   │   │   ├── rarefaction_50.tif

│   │   │   ├── rarefaction_min_sd.tif

│   │   │   └── rarefaction_min.tif

│   │   ├── est.tif

│   │   ├── geodiversity.tif

│   │   ├── grid_araguaia

│   │   │   └── araguaia_grid_0.5.tif

│   │   ├── hidrologia

│   │   │   ├── hydrology_araguaia_1km.tif

│   │   │   ├── water_percentage-0000000000-0000000000.tif

│   │   │   └── water_percentage-0000023296-0000000000.tif

│   │   ├── landforms

│   │   │   ├── geomorphons.tif

│   │   │   ├── landform_araguaia_1km.tif

│   │   │   └── landform_diversity_1km.tif

│   │   ├── pd_coverage.tif

│   │   ├── pd_est.tif

│   │   ├── pd_rarefaction_sd.tif

│   │   ├── pd_rarefaction.tif

│   │   ├── pd_sd.tif

│   │   ├── pedologia

│   │   │   ├── Atributos do tema Pedologia.pdf

│   │   │   ├── pedo_area.zip

│   │   │   ├── pedology_araguaia_1km.tif

│   │   │   ├── pedo_ponto.zip

│   │   │   ├── pedo_tabelas.zip

│   │   │   ├── simbologia_pedo_area.zip

│   │   │   └── soil_richness.tif

│   │   ├── sampling_completeness.tif

│   │   └── sd.tif

│   ├── raster_coords_plants_0.01.csv

│   ├── shapes

│   │   ├── Araguaia_Tocantins_ANA

│   │   │   ├── ARAGUAIA_TOCANTINS.cpg

│   │   │   ├── ARAGUAIA_TOCANTINS.dbf

│   │   │   ├── ARAGUAIA_TOCANTINS.prj

│   │   │   ├── ARAGUAIA_TOCANTINS.qmd

│   │   │   ├── ARAGUAIA_TOCANTINS.shp

│   │   │   └── ARAGUAIA_TOCANTINS.shx

│   │   ├── bioma

│   │   │   ├── Biomas

│   │   │   │   ├── lm_bioma_250.CPG

│   │   │   │   ├── lm_bioma_250.dbf

│   │   │   │   ├── lm_bioma_250.prj

│   │   │   │   ├── lm_bioma_250.sbn

│   │   │   │   ├── lm_bioma_250.sbx

│   │   │   │   ├── lm_bioma_250.shp

│   │   │   │   ├── lm_bioma_250.shp.xml

│   │   │   │   └── lm_bioma_250.shx

│   │   │   └── Biomas.zip

│   │   ├── grid_araguaia

│   │   │   ├── grid_araguaia.cpg

│   │   │   ├── grid_araguaia.dbf

│   │   │   ├── grid_araguaia.prj

│   │   │   ├── grid_araguaia.shp

│   │   │   └── grid_araguaia.shx

│   │   ├── plants_araguaia

│   │   │   ├── vascular_plants_araguaia.cpg

│   │   │   ├── vascular_plants_araguaia.dbf

│   │   │   ├── vascular_plants_araguaia.prj

│   │   │   ├── vascular_plants_araguaia.shp

│   │   │   └── vascular_plants_araguaia.shx

│   │   ├── south_america

│   │   │   ├── south_america.dbf

│   │   │   ├── south_america.prj

│   │   │   ├── south_america.shp

│   │   │   └── south_america.shx

│   │   ├── total_points.cpg

│   │   ├── total_points.dbf

│   │   ├── total_points.prj

│   │   ├── total_points.shp

│   │   └── total_points.shx

│   ├── total_points.csv

│   └── tree_flora_names.csv

├── data.zip

├── figura_dados.png

├── figure.R

├── files.zip

├── plot1.png

├── script

│   ├── 01_araguaia.R

│   ├── 02_calculate_pam.R

│   ├── 03_create_grid.R

│   ├── 04_calculate_incidence.R

│   ├── 05_harmonizing_phylogeny.R

│   ├── 06_completeness.R

│   ├── 07_phylo_completeness.R

│   ├── 08_Lanform_diversity.R

│   ├── 09_hydrology_1km.R

│   ├── 10_pedology.R

│   ├── 11_Geodiversity.R

│   ├── 12_regression.R

│   ├── 13_variables_regression.R

│   ├── figure.R

│   └── functions.R

├── v0.1

│   └── ALLMB.tre