https://doi.org/10.5061/dryad.9s4mw6mpr

Code and data for the Phylogenetic and biogeographic history of the Snooks (Centropomidae: Carangiformes) spanning the closure of the Isthmus of Panama (Ossa-Hernández, Ballen, Acero-P, & Tavera, 2024).

This repository has the following structure:

├── divtime │   ├── clock_modsel │   │   ├── gbm │   │   │   ├── 1..64 │   │   └── iln │   │   ├── 1..64 │   ├── mcmctree1_GBM │   ├── mcmctree1_ILN │   ├── mcmctree2_GBM │   ├── mcmctree2_ILN │   ├── mcmctree3_GBM │   ├── mcmctree3_ILN │   ├── mcmctree4_GBM │   ├── mcmctree4_ILN │   └── phylips ├── mrbayes ├── sequences ├── strat_intervals

sequences

This directory stores the DNA sequences in fasta format used in this study, along with the substitution model selected for each locus. Concatenated versions in both fasta and nexus formats are available along with a file identifying the partition positions in the concatenated dataset.

**Concatenate_snooks_NF **Corresponds to the concatenated matrix composed of five partitions, used for the construction of the phylogenetic hypothesis.

mrbayes

Here we will find the MrBayes script (concatenated.mb) and the output of four independet runs as well as the summarised files.

strat_intervals

The posterior of the origination time for each of the groups used is found here. The files in tsv format include the fossil occurrences. The script strat_interval_posteriors.R will call the code provided in Wang et al. (2016) for the calculations of the posterior density and then return and plot the posterior along with the fossil occurrences used in Figure 1.

The posteriors on the origination time for each group are then used as calibrations on their respective nodes using the truncated Cauchy distribution.

divtime

The maximum credibility tree found in the previous step was used for clock model selection and divergence time estimation using MCMCtree.

phylips

Data in phylip format. Necessary for MCMCtree.

clock_modsel

The file in.BV is the approximation of the multilocus dataset using the gradient and Hessian matrix for use in the approximate likelihood calculations, as generated by MCMCtree.

The stepping stones method used for clock model selection will be found here, under iln for the independent lognormal clock, and under gbm for the geometric Brownian motion model (also known as autocorrelated model). Each of these directories will have three important scripts: step_stones.R, mcmctree.ctl, and run_stepstones.sh. The first one will used the second one in order to generate each of the 64 stones, whereas the third one will iterate over each of the stone directories and submit them.

After finishing the stone runs, the script ../summarise_models.R was used in order to calculate the marginal likelihood for each model and carry out model selection.

Four independent analyses using either the iln or gbm models were carried out (mcmctreeN_MOD where N is the run number 1--4 and MOD is the model, ILN for independent lognormal and GBM for the autocorrelated clock). However, only those of the best model are presented and discussed in the article.

BioGeoBEARS

Biogeographical analyses were performed using the R package "BioGeoBEARs" authored by Nicholas J. Matzke. The scripts were adjusted to our data based on what Nicholas J. Matzke published at http://phylo.wikidot.com/biogeobears.  The following tex files were used as inputs for the analysis:

Areas Snooks.txt: A PHYLIP-formatted geography file specifying the geographic areas of the species for the analysis. 

**Time_periods.txt:**A file represent a time periods file for a time-stratified analysis. The oldest age correspond to the age of the root of your tree, and there can only be one such age.

**Manual_dispersal_multipliers_OLD.txt: **This file defines the areas permitted during each time period specified in the Time_periods.txt file.

TREE: 

The files FigTreein Ma and FigTree are the philogenetic reconstruction in .tree format.

Reference

Ossa‐Hernández, N., Ballen, G. A., P, A. A., & Tavera, J. (2025). Phylogenetic and biogeographic history of the Snooks (Centropomidae: Carangiformes) spanning the closure of the Isthmus of Panama. Journal of Biogeography, 52(1), 232-244.

+: Shared first authorship *: Corresponding author

Sharing/Access information

Links to other publicly accessible locations of the data:

• All the code and data necessary for reproducing the results are available on Zenodo (DOI https://doi.org/10.5281/zenodo.10535162) as well as on https://github.com/gaballench/centropomidae_divtime.

Code/Software

The code for the biogeographical analyses were taken and adapted from http://phylo.wikidot.com/biogeobears, Author: Nicholas J. Matzke.