Widespread and diverging patterns of change in local phylogenetic diversity

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..., 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., , # 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.

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## 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_P...