DOI: 10.5061/dryad.gqnk98sw0
title: Widespread and diverging patterns of change in local phylogenetic diversity

description: 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.
description: The data and analyses for this study includes time series data
 from the BioTIME database from four taxonomic groups: fish, birds, mammals
 and plants. It also includes phylogenetic and biome data. Analyses and R
 scripts include spatial harmonization, rarefaction, Bayesian hierarchical
 models, and main analyses and figures.
description: # Widespread and diverging patterns of change in local phylogenetic
 diversity [Access this dataset on
 Dryad](https://doi.org/10.5061/dryad.gqnk98sw0) 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: 1. **Rarefaction and Spatial Harmonization**: *
 `01_rarefyID_gridcell.R` * `02a_rarefaction_cluster_array.R` *
 `02b_rarefied_medians.R` * `02c_update_rarefied_medians.R` 2.
 **Generalized Linear Mixed Effects Models (GLMER)**: *
 `02d_glmer_slopes_cluster.R` * `02e_glmer_slopes_plot.R` 3. **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` 4. **Bayesian Modeling:
 Fish Ecoregions**: * `05a_brm_SR_taxabiome.R` * `05b_brm_PD_taxabiome.R` *
 `05c_brm_MPD_taxabiome.R` * `05d_brm_MNTD_taxabiome.R` 5. **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` 6. **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](https://doi.org/10.1111/geb.12729)
 This dataset integrates WWF ecoregion data: * [Terrestrial Ecoregions of
 the
 World](https://c402277.ssl.cf1.rackcdn.com/publications/15/files/original/official_teow.zip) * [Marine Ecoregions of the World](https://c402277.ssl.cf1.rackcdn.com/publications/351/files/original/MEOW_FINAL.zip) --- ## Code/Software Analyses were conducted using R version 4.2. Cluster computing was conducted using [Alliance Canada](https://alliancecan.ca). Shell scripts provide memory and wall-time information for job requests.