Parallel evolution despite low genetic diversity in three-spined sticklebacks

The three-spined stickleback (Gasterosteus aculeatus) is a model organism for studies of parallel evolution in the wild; marine stickleback populations have repeatedly colonized and adapted to different brackish and freshwater habitats. Population genetic studies of European three-spined sticklebacks have usually been conducted only in high-latitude areas. Here, we analysed southern and northern European samples of marine and freshwater three-spined stickleback to test two hypotheses. First, southern European freshwater populations – which currently lack or have limited connection to marine populations – have lost genetic diversity due to population bottlenecks and inbreeding compared to their northern European counterparts. Second, the degree of genetic parallelism in response to freshwater colonisation is higher among northern than southern European populations as the latter have been isolated and likely subjected to strong genetic drift. The results show that southern populations exh..., , , # Parallel evolution despite low genetic diversity in three-spined sticklebacks

[https://doi.org/10.5061/dryad.fxpnvx102](https://doi.org/10.5061/dryad.fxpnvx102)

The raw data for this manuscript can be found in the NCBI Short Reads Archive (Bioproject  PRJNA1074927, runs SRR27925730-SRR27925878 ). In this DRYAd repository you can find the scripts used to analyse the raw data, as well as the called genotype data in Variant Call Format (VCF):

1- The entire analytical pipeline, consisting of ten bash scripts, starting from genome indexing and ending with genotype calling and filtering. These scripts allow the recreation of the main VCF data files that are used in the analyses reported in the manuscript (see *5-VCF.zip* folder).

2- Scripts for Runs of Homozygosity Analyses. These include a bash script to run the ROH analyses in *bcftools* and an R script to run the geographic test reported in the paper.

3- The R scripts to replicate the Principal Component Analyses and the Quadratic...