Main Analysis Pipelines
Main analysis pipelines for the Palm Warbler subspcies (Setophaga palmarum) hybrid zone project.
1_Genotyping_Pipeline: calls genotypes in VCF format from demultiplexed genotype-by-sequencing data
2_STRUCTURE_Pipeline: runs STRUCTURE from the VCF genotype calls
3_PCoA_Cline_FST_Pipeline: runs principal coordinate analysis (PCoA), performs kriging and fits a geographic cline to the STRUCTURE admixture proportions, and calculates per-site Weir and Cockerham's FST from the VCF genotype calls
4_Cline_Plumage_Pipeline: performs kriging and fits a geographic cline to the plumage hybrid index
5A_2POP_fastsimcoal2_Pipeline: coalescent modelling of subspecies divergence using fastsimcoal2. From the two chosen non-admixed "parental" populations, calls genotypes, down-samples, calculates the site frequency spectrum (SFS), and finds the best fitting divergence model for the empirical SFS
5B_3POP_fastsimcoal2_Pipeline: tests alternate models of genetic swamping post-divergence using fastsimcoal2. Given three populations (two pure parental populations and one admixed population), finds the best fit model between scenarios in which gene flow has predominantly occurred from one of the parents into the admixed population.
6_EEMS: generates estimated effective migration surfaces (EEMS) using the STRUCTURE admixture proportions (Petkova et al. 2016)
