Pervasive and recurrent hybridisation prevents inbreeding depression in Europe's most threatened seabirds

Introduction

This git repository contains those scripts used during the population genomics analyses performed with Puffinus mauretanicus by the Molecular Evolutionary Genetics Group, University of Barcelona.

Structure

1. SNP_calling: SNP calling pipeline for WGS resequencing data that uses a combination of freebayes and GATK HaplotypeCaller. Includes VCF filtering and phasing.
2. SNP_calling_mitogenome: SNP calling pipeline which uses freebayes - adapted for mitogenomic data.
3. Population_structure: includes those analyses performed to visualize population structure within P. mauretanicus and P. yelkouan. Among these, we include: PCAs, Struct-f4, TreeMix and haplotype genealogy graphs for mitogenomes (using Fitchi).
4. Dated_phylogeny: inference of time-callibrated species trees using SNAPP.
5. Demographic_modelling: scripts for demographic modelling using dadi, alongside custom models.
6. Genome_scans: performance of genome-wide scans for signatures of selection, including detailed analyses of the main outlier windows.
7. Conservation_genomics: scripts to calculate heteroziogsity, LROHs, ...
8. Forward_simulations: scripts to use SLiM simulations to investigate the plausibility of mito-nuclear discordance in our model and to assess the effects of migration/demography in the species heterozygosity/FROH.
9. Others: smaller tasks, such as finding fixed differences between populations, calculating the SFS, ...