Same trait, different genes: pelvic spine loss in three brook stickleback populations in Alberta

The genetic basis of phenotypic or adaptive parallelism can reveal much about constraints on evolution. This study investigated the genetic basis of a canonically parallel trait: pelvic spine reduction in sticklebacks. Pelvic reduction has a highly parallel genetic basis in threespine stickleback in populations around the world, always involving a deletion of the pel1 enhancer of Pitx1. In three populations of brook stickleback in Alberta, Canada, pelvic reduction did not involve Pitx1. Instead, pelvic reduction in one population involved a mutation in an exon of Tbx4, and it involved a mutation in an intron of Lmbr1 in the other two populations. Hence, the parallel phenotypic evolution of pelvic spine reduction across stickleback genera, and among brook stickleback populations, has a non-parallel genetic basis. This suggests that there is redundancy in the genetic basis of this adaptive polymorphism, but it is not clear whether this indicates a lack of constraint on the evolution of th..., , , # Same trait, different genes: pelvic spine loss in three brook stickleback populations in Alberta

## Description of the data and file structure

The raw DNA sequence data is not included here, but is accessible on the Short Read Archive (SRA) database: accession numbers PRJNA895038 (Astotin Lake), PRJNA838068 (Muir Lake), and PRJNA838194 (Shunda Lake).

The raw sequence data was used to call SNPs in each lake using the SNP-calling pipeline available at [https://github.com/jon-mee/culaea_wgs_SNPs](https://github.com/jon-mee/culaea_wgs_SNPs)

The SNP data for all three lakes is provided here in vcf format and Plink binary format. There are three versions of the SNP data: 1) not filtered for minimum allele frequency (MAF), 2) filtered for MAF, and 3) LD-pruned. There are also files containing a genetic relatedness matrix (GRM) for each lake. 

For each lake, there is also a vcf (variant call format) file and Plink binary files with just the SNPs in the outlier region (these are much smal...