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Effect of the Central American Isthmus on gene flow and divergence of the American crocodile Crocodylus acutus

Citation

Avila-Cervantes, Jose et al. (2020), Effect of the Central American Isthmus on gene flow and divergence of the American crocodile Crocodylus acutus, Dryad, Dataset, https://doi.org/10.5061/dryad.69p8cz90s

Abstract

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.

Methods

We used Single digest Restriction site Associated DNA Sequencing (sRAD-Seq) (Baird et al., 2008) to generate Single Nucleotide Polymorphisms (SNPs) for genomic scans of crocodile populations from Panama.

Usage Notes

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

Funding

Canadian Foundation of Innovation - Integrated Quantitative Biology Initiative, Award: 33122

Consejo Nacional de Ciencia y Tecnología, Award: 217923-313487

IUCN-SSC Crocodile Specialist Group, Award: Student Research Assistance Scheme (SRAS) grant

McGill University, Award: Biology Department Mobility Award Travel award

McGill University, Award: Neotropical environment program

Natural Sciences and Engineering Research Council of Canada, Award: Discovery Grant

NSERC-BESS Biodiversity, Ecosystem Services and Sustainability

Quebec Centre for Biodiversity and Science, Award: Excellence award

Secretaría de Educación Pública, Award: Complementary Scholarship

Smithsonian Tropical Research Institute, Award: Short term fellowship

Canadian Foundation of Innovation - Integrated Quantitative Biology Initiative, Award: 33122

IUCN-SSC Crocodile Specialist Group, Award: Student Research Assistance Scheme (SRAS) grant

NSERC-BESS Biodiversity, Ecosystem Services and Sustainability

Quebec Centre for Biodiversity and Science, Award: Excellence award