Phylogeographic-analysis-of-nine-spined-sticklebacks

Scripts and code used in manuscript "Complex population history affects admixture analyses in nine-spined sticklebacks" (https://doi.org/10.1111/mec.16651).

Content

Pipeline and associated scripts for each of the analyses in the manuscript.

1. Mapping of raw reads and variant calling
2. Population structure and phylogentic analyses
3. Symmetry statistics and admixture tests
4. Estimation of the divergence times with MSMC2, moments and data simulation with msprime
5. Sex chromosome related analysis

Contigs included in nine-spine stickleback reference v6b can be found here

Detailed results of f4-statistics, qpWave and f4-ratio tests can be found here