DOI: 10.5061/dryad.69p8cz90s
title: Effect of the Central American Isthmus on gene flow and divergence of the American crocodile Crocodylus acutus

description: The final formation of the Central American Isthmus (CAI) about 3.5 Ma
 altered global ocean circulation, connected North and South America
 terrestrial biotas and established the Caribbean Sea. The nature of this
 event creates a natural scenario to test vicariance, divergence, and
 speciation by allopatry. Studies have shown the effect of the CAI on
 marine and terrestrial species, but none have examined a large-bodied
 amphibious taxon. We used RAD sequencing on populations of the American
 crocodile Crocodylus acutus, to study the genomic variation of C.
 acutus on both sides of the CAI, infer its demographic history
 and measure the effect of the opening of the Panama Canal. Our results
 showed three genomic clusters: 1) Caribbean and the Panama Canal, 2)
 Pacific coast, and 3) Coiba island. The estimated divergence times between
 the Caribbean and Pacific populations are about 20 ka, which is two orders
 of magnitude younger than the formation of the CAI, but coincides with the
 Last Glacial Maximum. We hypothesize the glacial/interglacial cycles
 facilitated gene flow between the Caribbean and Pacific crocodile
 populations after the formation of the CAI, masking any genomic divergence
 the CAI may have caused. There is no evidence of gene flow associated with
 the opening of the Panama Canal.
description: We used Single digest Restriction site Associated DNA Sequencing
 (sRAD-Seq) (Baird <i>et al</i>., 2008) to generate Single
 Nucleotide Polymorphisms (SNPs) for genomic scans of crocodile populations
 from Panama.
description: SNP's data Panama_SNPs.vcf - This file
 includes the 17 312 SNPs obtained in this study and used for the
 analysis. DIYABC SNP's data
 DIYABC_SNPs_Panama - This file includes the 686 polymorphic loci
 used for the DIYABC modelling. Frequency Spectrum
 files  BCI_COIdip.sf - This file includes the Frequency
 spectrum data for the paired population comparison between BCI and
 Coiba. BCI_GALdip.sf - This file includes the Frequency
 spectrum data for the paired population comparison between BCI and
 Galeta. BCI_LAGdip.sf - This file includes the
 Frequency spectrum data for the paired population comparison between BCI
 and Lagartero. GAL_COIdip.sf - This file includes the
 Frequency spectrum data for the paired population comparison between
 Galeta and Coiba. GAL_LAGdip.sf - This file includes
 the Frequency spectrum data for the paired population comparison between
 Galeta and Lagartero. LAG_COIdip.sf - This file
 includes the Frequency spectrum data for the paired population comparison
 between Lagartero and Coiba CAR_PAC4460dip.sf - This
 file includes the Frequency spectrum data for the paired population
 comparison between Caribbean and Pacific. Fast
 Structure Analysis Panamastructure.str - This file
 is the structure file used for the clsutering analysis with Fast
 Structure Scripts used for the Pipeline
 Scripts_Panama.txt - This file has the programs and comands used
 for the data processing  DAPC Analysis
 PanamaDAPC.R - This file has the script to run the discriminant
 analysisi of the principal components PanamaDAPC.gen -
 This file  is the .gen file used for the DAPC analysis in R
 DADI analysis Dadicocos.py - This fle has the
 Dadi scipt used for the demographic inference