Speciation, dispersal, and the build-up of fern diversity in the American tropics

This dataset supports an investigation into the temporal dynamics of speciation and dispersal in ferns (Polypodiopsida) across the American tropics. It includes 378,115 georeferenced occurrence records compiled from GBIF, cleaned and taxonomically standardised using the 'CoordinateCleaner' and 'taxastand' R packages. Species were matched to a time-calibrated phylogenetic tree comprising 5850 fern species, from which 56 clades predominantly distributed in the American tropics were retrieved. These clades encompass 1530 species coded for presence/absence across nine biogeographically defined regions and a global category. Using biogeographical stochastic mapping (BSM) in BioGeoBEARS, we estimated the frequency and type of biogeographic events (e.g., dispersal, extinction, speciation) across 1-million-year time slices. The dataset also includes lineage-through-time (LTT) counts, regional species pool compositions at four time points (0, 5, 10, and 30 Ma), and pairwise compositional similar..., , # Speciation, dispersal, and the build-up of fern diversity in the American tropics

This DRYAD repository contains scripts for reconstructing the biogeographical history of ferns in the American tropics and output data, as presented in the paper \"Speciation, dispersal and the build-up of fern diversity in the American tropics\" in the scientific journal Ecography.

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## Before you start

To reconstruct our analyses, we used a combination of R Studio on a PC and a High Performance Computer (HPC). We recommend using an HPC due to the computational intensity of the analyses. The HPC we used was set up with Slurm Workload Manager.

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## Installation and startup

You need to install some programs on the HPC. We used the package manager Conda for installation.

* Rstudio version 4.1.3 (RStudio Team 2023; [http://www.rstudio.com/](http://www.rstudio.com/))
* BioGeoBEARS (Matzke 2013; [https://github.com/nmatzke/BioGeoBEARS?tab=readme-ov-file](https://github.com/nmatzke/BioGeoBEARS?tab=re...,