Code from: Comparative phylogeography reveals the demographic patterns of neotropical ancient mountain species
Data files
Mar 02, 2026 version files 7.58 MB
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README.md
1.84 KB
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submissao_dryad_comp_phylogeo.zip
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Abstract
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 Ecological Niche Modeling. Additionally, we evaluated if climatic oscillations have driven a genetic spatial congruence in the genetic structure of co-distributed species from the Espinhaço Range, one of the main BQM areas. Our results show that the majority of plant lineages underwent a synchronous expansion over the Last Glacial Maximum (LGM, ca. 21 thousand years ago), although we could not obtain a clear demographic pattern for the the animal lineages.We also obtained a signal of congruent phylogeographic break between lineages endemic to the Espinhaço Range, suggesting how ancient climatic oscillations might have driven the evolutionary history of the Espinhaço’s biota.
In this dataset, you can find all scripts used in the paper Dantas-Queiroz et al., 2023
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 Gehara's GitHub (https://github.com/gehara/PipeMaster).
bGYMC
This script was used to standardized the analysis of population structure by using a Bayesian generalized mixed yule coalescent approach.
The inputs are ultrametric trees for each species. Please, refer to the original source of this script (https://github.com/gehara/ME_caatinga_scripts/blob/master/ME_caatinga_scripts/GMYC.R) for more details
ENM
In this script, I included all steps needed to run an Ecological Niche Modeling (ENM) in the notebook named "enm_notebook.html". Note that some steps require a large amount of processing, so they will not perform adequately in a regular desktop/notebook. I expressly indicate when are those cases with a begin sentence. These computationally intensive analyses were ran in GridUnesp, a High-perfomance computing cluster.
See the associated article for how the dataset was collected and processed.
