Code from: Comparative phylogeography reveals the demographic patterns of neotropical ancient mountain species

Mountains are renowned for their bountiful biodiversity. Explanations on the origin of such abundant life are usually regarded to their orogenic history. However, ancient mountain systems with geological stability also exhibit astounding levels of number of species and endemism, as illustrated by the Brazilian Quartzitic Mountains (BQM) in Eastern South America. Thus, cycles of climatic changes over the last couple of million years are usually assumed to play impotant role in the origin of mountainous biota. These climatic oscillations potentially isolated and reconnected adjacent populations, a phenomenon known as flickering connectivity, accelerating speciation events due to range fragmentation, dispersion, secondary contact, and hybridization. To evaluate the role of the climatic fluctuations on the diversification of the BQM biota, we estimated the ancient demography of distinct endemic species of animals and plants using hierarchical approximate Bayesian computation analysis and Ec..., See the associated article for how the dataset was collected and processed.
, , # Code from: Comparative phylogeography reveals the demographic patterns of neotropical ancient mountain species

In this dataset, you can find all scripts used in the paper [Dantas-Queiroz et al., 2023](https://onlinelibrary.wiley.com/doi/10.1111/mec.16929)

## Description of the data and file structure

The scripts are distributed in three folders. Each of them contains one or more R scripts that were used for that particular analysis.

### ABC

This is the folder for all Approximate Bayesian Computation simulations and analyses conducted with PipeMaster. Each species have it's own script (e.g., \"PipeMaster_Vriesea.R\"), and all of them can be analysed with the script \"abc_posterior_parameters_inference.R\".

For more details on how PipeMaster works, please refer to Marcelo Gehara's GitHub (https://github.com/gehara/PipeMaster).

### hABC

In this script, I included all steps needed to run the hierarchical ABC (hABC). It works using the PipeMaster package, which you can find in Marcelo ..., ,