DOI: 10.5061/dryad.dncjsxkz4
title: Population structure and demographic analyses of Acanthocybium solandri from the Indo-Pacific and Atlantic oceans

description: This repository contains scripts, data and results for a populaton
 genomics study of genetic structure and demography of
 wahoo, Acanthocybium solandri, published in Journal of
 Biogeography: Haro-Bilbao et al. (2021) Global connections with some
 genomic differentiation occur between Indo-Pacific and Atlantic Ocean
 wahoo, a large circumtropical pelagic fish. Journal of
 Biogeography. doi.org/10.1111/jbi.14135 In this work, we generated
 population allele frequencies for wahoo sampled at 11 locations around the
 globe using a pooled ezRAD approach. Using thousands of genome-wide SNPs,
 we demonstrated a significant (but subtle) genetic divide between wahoo
 from the Indo-Pacific and those from the Atlantic. This genetic
 differentiation likely occurs against a background of high gene glow
 throughout the evolutionary history of wahoo, as we inferred from
 demographic analysis of select population pairs within and
 between oceanic regions. Analyses contained in this repository are for:
 (1) Filtering pooled ezRAD allele counts (assembled with dDocent
 and imputed using poolne_estim); (2) Estimation of genetic differentiation
 among globally sampled wahoo populations; (3) Estimation of site frequency
 spectra from joint allele frequencies among select population
 pairs; (4) Inference of demographic parameters (using δaδi); and
 (5) Generations of demographic simulation summary statistics. Most of the
 analyses are performed in R and can be run directly from within the
 repository directory, this includes: allele filtering,
 estimation of genetic differentiation, estimaiton of site
 frequency spectra, and generation of demographic summary statistics.
 Demographic inference using δaδi requires setup of a
 Unix environment: input data files and execution scripts are provided, but
 their implementation needs to be customised.
description: Allele frequency data was obtained through a pooled ezRAD
 approach. <em>De novo</em> assembly of RAD contigs and variant
 calling was performed using the <em>dDocent</em> pipeline.
 Population allele frequencies were imputed
 using <em>poolne_estim</em>. Additional quality filtering was
 performed in R. Analysis of genetic differentiation was performed in R,
 which include: estimates
 of <em>F</em><sub>ST</sub> and AMOVA (analysis of
 molecular variance). Generation of site frequency spectra and summary of
 demographic analyses was performed in R. Demographic inference was
 performed using <em>δaδi</em>, originally on an
 HPC. 
description: All R code can be run from within the respository directory using
 the R project file, <em>Wahoo_PROJ.Rproj</em>.
 Demographic analyses using <em>δaδi </em>must be run
 in a Unix environment. The
 scripts <em>Wahoo_DADI_Demog_Models.py</em>
 and <em>Wahoo_DADI_Generic_Execute.py</em> can be used to set
 up a pipeline for executing demographic simulations in a local system or
 on an HPC cluster.
description: # Population structure and demographic analyses of Acanthocybium solandri
 from the Indo-Pacific and Atlantic oceans
 [https://doi.org/10.5061/dryad.dncjsxkz4](https://doi.org/10.5061/dryad.dncjsxkz4) ## Description of the data This repository contains scripts, data and results for a population genomics study of genetic structure and demography of wahoo, Acanthocybium solandri, published in Journal of Biogeography: Haro-Bilbao et al. (2021) Global connections with some genomic differentiation occur between Indo-Pacific and Atlantic Ocean wahoo, a large circumtropical pelagic fish. *Journal of Biogeography*. doi.org/10.1111/jbi.14135 In this work, we generated population allele frequencies for wahoo sampled at 11 locations around the globe using a pooled ezRAD approach. Using thousands of genome-wide SNPs, we demonstrated a significant (but subtle) genetic divide between wahoo from the Indo-Pacific and those from the Atlantic. This genetic differentiation likely occurs against a background of high gene glow throughout the evolutionary history of wahoo, as we inferred from demographic analysis of select population pairs within and between oceanic regions. Analyses contained in this repository are for: (1) Filtering pooled ezRAD allele counts (assembled with dDocent and imputed using poolne_estim); (2) Estimation of genetic differentiation among globally sampled wahoo populations; (3) Estimation of site frequency spectra from joint allele frequencies among select population pairs; (4) Inference of demographic parameters (using δaδi); and (5) Generations of demographic simulation summary statistics. Most of the analyses are performed in R and can be run directly from within the repository directory, this includes: allele filtering, estimation of genetic differentiation, estimaiton of site frequency spectra, and generation of demographic summary statistics. Demographic inference using δaδi requires setup of a Unix environment: input data files and execution scripts are provided, but their implementation needs to be customised. ## Files and variables Download the *Thia_2021_Wahoo_PopGenomics.zip* file to access all the data related to the R analyses. Analytical scripts include a combination of R and python scripts. These data include everything after the bioinformatic anlaysis of pooled ezRAD data to generate pooled allele frequencies.  Read the *Project_info.pdf* file for more information about the scripts and data. ## Code/software **Wahoo_CODE_01_FST_Analyses.R** is used to perform analyses of population genetic structure. **Wahoo_CODE_03a_Dadi_Sims_HPC_PBS_Gen.R** and **Wahoo_CODE_03b_Dadi_Sims_HPC_Slurm_Gen.R** are used to generate automated scripts for running δaδi simulations on a high performance computer (HPC) cluster. **Wahoo_CODE_04_Dadi_Outputs.R** is used to summarise δaδi simulations. **Wahoo_CODE_05_Dadi_Plot_SFS.py** is used to generate plots of site frequency spectra from δaδi simulations. **Wahoo_CODE_06_Posthoc_FST_Shared_Loci.R** is used to perform posthoc analyses of loci used in this pipeline. ## Access information The genomic data used in this study is derived from pooled DNA samples of wahoo, with each sample representing a population. Each sample was sequenced in duplicate to provide an estimate of variance in pool-seq allele frequency estimation. Raw ezRAD pool-seq reads have been uploaded to NCBI's SRA as has the relevant BioSample information: BioProject [PRJNA683059](http://www.peptideatlas.org/PASS/PRJNA683059 "Link to external resource: PRJNA683059"). Additional metadata for these pool-seq reads are available through GeOME ([https://n2t.net/ark:/21547/DhI2](https://n2t.net/ark:/21547/DhI2)).