Widespread and diverging patterns of change in local phylogenetic diversity

Fernandez-Fournier, Philippe 1 ; Carroll, Tadhg2; Dornelas, Maria3; Mooers, Arne1

Published Nov 26, 2024 on Dryad. https://doi.org/10.5061/dryad.gqnk98sw0

Data files

Nov 26, 2024 version files 329.63 MB

DDI_FernandezFournier_2024.zip

329.62 MB
README.md

4.33 KB

Abstract

Aim: Ecosystems are witnessing drastic changes in biodiversity worldwide. However, it is still unclear whether changes in phylogenetic diversity – a measure of the evolutionary relationships among species – reflect observed changes in species richness. Specifically, we ask whether changes in local phylogenetic diversity correlate with changes in species richness and examine if major taxonomic groups show diverging trends.

Location: Global.

Methods: We estimate how local phylogenetic diversity has changed compared to species richness and whether there were diverging patterns across taxonomic groups. We use a database of compiled assemblage time-series from around the world, BioTIME. We use assemblage total evolutionary history (Faith’s phylogenetic diversity; PD) as well as average relatedness (mean pairwise distance and mean nearest taxon distance; MPD and MNTD, respectively) as measures of phylogenetic diversity and report taxon-level and assemblage-level posterior slope estimates from a Bayesian hierarchical model. We report trends in four major taxonomic groups: fish, birds, terrestrial mammals and terrestrial plants.

Results: We found strong evidence of widespread increases in MPD across fish and bird assemblages, reflecting decreases in average relatedness, and strong evidence of a decrease of MPD in mammals, indicating the opposite. Conversely, we did not find consistent directional change in MNTD, though null average trends included notable positive and negative trends across studies and regions. We also found moderate evidence that SR and PD were increasing in fish assemblages, while they were decreasing in mammals.

Main conclusions: Our findings suggest that changes in species composition are significantly altering the evolutionary makeup of assemblages at the local scale and that overall patterns diverge within and across taxonomic groups. We suggest potential drivers of these changes but highlight that our results are more generalizable for fish and birds than for mammals and plants, given the variation in geographical coverage and sample size.

Access this dataset on Dryad

This dataset supports a study on patterns of change in local phylogenetic diversity over time across four taxonomic groups: fish, birds, mammals, and plants. The data includes time series observations from the BioTIME database, phylogenetic trees for each taxon, and metadata on terrestrial and marine ecoregions from the World Wildlife Fund (WWF). Analyses explore spatial and temporal patterns of biodiversity using metrics such as species richness, phylogenetic diversity (PD), mean pairwise distance (MPD), and mean nearest taxon distance (MNTD). Bayesian hierarchical models were used to assess temporal trends.

Description of the data and file structure

Data Files

data/phylo_birds_PFF.tre: Phylogenetic trees for bird species.
data/phylo_fish_PFF.tre: Phylogenetic trees for fish species.
data/phylo_mamm_PFF.tre: Phylogenetic trees for mammal species.
data/phylo_plants_PFF.tre: Phylogenetic tree for plant species.
data/WWF_biomes_meta.csv: Metadata for WWF biomes.
data/meta_bioTIME_datainfo.pdf: Column information for the BioTIME data files, including abundance and biomass units.
WWF_ecoregions/marine/: GIS dataset for Marine Ecoregions of the World (MEOW), including shapefiles (.shp), spatial indexes (.shx), attribute data (.dbf), projection information (.prj), character encoding (.cpg), and metadata (.xml).
WWF_ecoregions/terrestrial/: GIS dataset for WWF terrestrial ecoregions, including shapefiles (.shp), spatial indexes (.shx, .sbn, .sbx), attribute data (.dbf), projection information (.prj), metadata (.xml, .htm), and layer styles (.lyr).
results/rarefied_medians_ses.csv: Data derived from BioTIME, after taxonomic, spatial and temporal harmonization and after calculating phylogenetic metrics for each year within assemblages.
data/meta_rarefied_medians_ses.csv: Column information for the file rarefied_medians_ses.csv.

Code Files

All analyses were conducted in R version 4.2, with a clear directory structure and scripts named to reflect their purpose. Major workflows include spatial harmonization, rarefaction, Bayesian modeling, and generating figures.

Key R Scripts:

Rarefaction and Spatial Harmonization:
- 01_rarefyID_gridcell.R
- 02a_rarefaction_cluster_array.R
- 02b_rarefied_medians.R
- 02c_update_rarefied_medians.R
Generalized Linear Mixed Effects Models (GLMER):
- 02d_glmer_slopes_cluster.R
- 02e_glmer_slopes_plot.R
Bayesian Modeling:
- 03a_brm_SR_cluster.R (species richness)
- 03b_brm_PD_cluster.R (phylogenetic diversity)
- 03c_brm_MPD_cluster.R (mean pairwise distance)
- 03d_brm_MNTD_cluster.R (mean nearest taxon distance)
- 04a_summary_posteriors_cluster.R
Bayesian Modeling: Fish Ecoregions:
- 05a_brm_SR_taxabiome.R
- 05b_brm_PD_taxabiome.R
- 05c_brm_MPD_taxabiome.R
- 05d_brm_MNTD_taxabiome.R
Standardized Effect Size (SES) Analyses:
- 07_ses_cluster_array.R
- 08_ses_analysis.R
- 09a_brm_sesPD_cluster.R
- 09b_brm_sesMPD_cluster.R
- 09c_brm_sesMNTD_cluster.R
- 10_summary_posteriors_SES_cluster.R
Final Analyses and Figures:
- 11_analysis.R

Shell Scripts for Cluster Submissions:

These scripts automate submission of computationally intensive tasks to a high-performance computing cluster.

Sharing/Access Information

Data was derived from the BioTIME database, which provides publicly available time series data on global biodiversity:

BioTIME database: https://doi.org/10.1111/geb.12729

This dataset integrates WWF ecoregion data:

Code/Software

Analyses were conducted using R version 4.2. Cluster computing was conducted using Alliance Canada. Shell scripts provide memory and wall-time information for job requests.