README.md

Guppy Colour Polymorphism

Code, scripts and additional data pertaining to "A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy"

These data relate to the Nature Communications Publication which is available here:

https://www.nature.com/articles/s41467-022-28895-4

Please contact me at parisjosephine<@>gmail.com with any queries

Raw data

DNA sequencing data are available at the European Nucleotide Archive (ENA) under the Study Accession PRJEB36506: Pool-seq Iso-Y data (SAMEA6512722-SAMEA6512725); whole-genome sequencing data for Paria (SAMEA8750557-SAMEA8750565); long-read pacbio data for Iso-Y6 (SAMEA8795870-SAMEA8795872). Whole-genome sequencing data for Upper Marianne individuals are available from the ENA under the Study Accession PRJEB10680 (SAMEA3649957-SAMEA3649973).

Please refer to the file sample_metadata.txt for more information on read names and sample accessions

SNP calling

SNP calling was performed using the pipeline described here: https://github.com/josieparis/gatk-snp-calling

Colour phenotype analysis

Colormesh can be found here: https://github.com/J0vid/Colormesh

Publication with example data is published in https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.7992

NB these analyses and scripts were performed and written by Mitchel Daniel

R script for performing DAPC and fish image DAPC loading heatmaps:

This script also creates the components for Figure 1 and Supplementary Figure 1

01_DAPC_heatmaps.R

R script for plotting phenotype data PCAs:

This script also creates the components for Supplementary Figure 2

02_phenotype_data_PCA_plots.R

R script for performing phenotype data permutations

This script also creates the components for Supplementary Figure 3

03_phenotype_perm.R

Genomic data analysis

LG12 coordinate liftover

The LG12 coordinates were lifted over from the genome available in Fraser et al 2020 GBE (https://doi.org/10.1093/gbe/evaa187) to add additional contigs placed by Deborah Charlesworth's genetic maps:

The function for liftover of chr12 coordinates is: update_chr12_liftover.R

The updates to the files are run in an R script (and bash to sort the vcf files afterwards)

chr12_liftover.R

Iso-Y Pool-seq data analysis

Poolfstat to calculate FST and allele frequencies:

Poolfstat is available here: https://cran.r-project.org/web/packages/poolfstat/index.html

Script to calculate pairwise FST and allele freqs using poolfstat: poolfstat_FST_AFs.R

R script for perfoming Z_FST_PCA analysis and figures:

This script also creates figure components for Figure 2a & d, and Supplementary Figures 4,6 and 8

Z_FST_PCA_analysis.R

R script for polarising / folding AFs analysis and figures:

This script also creates figure components for Figure 2b and e

polarise_plot_AFs.R

R script for polarising and plotting density of AFs:

This script also creates figure components for Figure 3, and Supplementary Figures 12, 13 & 14

polarised_AF_densities.R

R script for change point detection analysis:

CPD_analysis.R

R script for pairwise FST:

This script also creates figure components for Supplementary Figures 5 and 7

raw_pairwise_fst.R

R script for performing Z_pi_PCA analysis and figures:

This script also creates figure components for Supplementary Figures 9 & 11

To calculate pi in 10kb windows we use a custom function (written by Jim Whiting) pool_pi.R

To run the function and create the figures: Z_pi_PCA_analysis.R

Natural WGS data analysis

R script for LD analysis:

LDheatmap package can be found here: https://cran.r-project.org/web/packages/LDheatmap/index.html

This script creates figure components for Figure 4a & e, and Supplementary Figure 15

LD_heatmap.R

R script for Lostruct analysis:

Lostruct can be found here: https://github.com/petrelharp/local_pca

This script creates figure components for Figure 4b & f, and Supplementary Figure 21

lostruct_localPCA.R

R script for perfoming popuation genetics stats using PopGenome:

PoopGenome can be found here: https://cran.r-project.org/web/packages/PopGenome/index.html

This script creates figure components for Figure 4c,g,d & h

popgenome_nat_data.R

Scripts for creating inter-chrom LD can be found here:

https://github.com/josieparis/interchromLD

Scripts for creating a genotype plot and haplotype plot as per Figure 5 can be found here:

https://github.com/josieparis/genotype_plot

R Script for performing GO enrichment and KEGG mapping:

GO_KEGG_analysis_LG1.R

Interchrom LD can be found in the file:

interchromLD