DOI: 10.5061/dryad.9s4mw6mpr
title: Data from: Phylogenetic and biogeographic history of the Snooks (Centropomidae: Carangiformes) spanning the closure of the Isthmus of Panama

description: Aim: Amphiamerican New World fishes provide a unique opportunity to
 explore the impact of geological processes and the formation of geographic
 barriers on biological diversification across both spatial and temporal
 dimensions. We employed phylogenetic and biogeographic methods to assess
 the impact of the emergence of the isthmus of Panama on the evolutionary
 history of snooks. Location: Eastern tropical Pacific and western Atlantic
 Oceans. Methods: Bayesian methods were used for phylogenetic inference and
 divergence time estimation, incorporating the fossil record of Carangidae,
 Centropomidae, Istiophoriformes, Latidae, and Sphyraenidae to establish a
 timeline using the methods of stratigraphic intervals for node calibration
 density specification. Biogeographic models were fitted to test the
 hypothesis that transisthmian vicariant events are coeval with the Isthmus
 closure. To estimate ancestral range probability and perform stochastic
 mapping, we utilized BioGeoBears and the parameters from the best-fitting
 model. This allowed us to estimate the quantity and kind of
 biogeographical events. Results: Our results suggest a sister relationship
 between Centropomidae and Sphyraenidae with a common ancestor that
 originated in the Upper Cretaceous (~78.51 Ma). The biogeographic model
 BAYAreaLIKE + j indicated speciation in sympatry and dispersal (founder
 effect) as the primary modes of speciation in the genus Centropomus. The
 dispersion in the family Centropomidae was estimated from the Tropical
 Eastern Pacific to the tropical western Atlantic since the Oligocene. Main
 conclusions: The alignment of divergence times with ancestral species
 distributions suggests a possible synchrony between the current
 distribution in Centropomus species and the processes of the formation of
 the Isthmus of Panama during the Miocene. However, the evidence of only
 two transisthmic pair suggests that this event was not determinant in
 allopatric interbasin speciation. Furthermore, recent diversification
 events within each basin imply an influence of post-closure environmental
 conditions on the evolution of this group of fishes.
description: We collected specimens at local fish markets and landing areas
 across Caribbean and Pacific localities. All specimens collected were
 preserved and stored at the fish collection of Universidad del Valle
 (CIR-UV). Fishes were photographed, and a small fragment of the right
 pectoral fin was preserved in 96% ethanol and stored at -20 °C.
 We extracted DNA following the Salting Out protocol (Sambrook et
 al. 1989). Four mitochondrial genes (12SrRNA, 16SrRNA, Cytochrome oxidase
 subunit I - COI, and cytochrome b -CYB) and one nuclear marker, a
 single-copy locus TMO-4c4 were amplified. The PCR amplification reactions
 were conducted in a final volume of 15µl containing 1 µl of DNA of stock
 concentration, 1.5 µl 10X reaction buffer BD (0.8M Tris -HCL, 0.2
 M(NH<sub>4</sub>)<sub>2</sub>SO<sub>4</sub>; Solis Bio Dyne), 1.2 µl of 2.0 mM MgCl<sub>2</sub>, 0.4 mM premixed deoxynucleotide triphosphates, 0.1 µl of 5Uml <em>Taq </em>FIREPOL DNA polymerase (Solis Bio Dyne), and 0.2 µl of each oligonucleotide primer, each at 20mM concentration.
description: # Data from: Phylogenetic and biogeographic history of the Snooks
 (Centropomidae: Carangiformes) spanning the closure of the Isthmus of
 Panama
 [https://doi.org/10.5061/dryad.9s4mw6mpr](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.](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 Fig*Treein* 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](https://doi.org/10.5281/zenodo.10535162)) as well as on [https://github.com/gaballench/centropomidae_divtime.](https://github.com/gaballench/centropomidae_divtime.) ## Code/Software The code for the biogeographical analyses were taken and adapted from [http://phylo.wikidot.com/biogeobears](http://phylo.wikidot.com/biogeobears), Author: Nicholas J. Matzke.