Genetic diversity, FST and genome scan
We calculated genetic diversity (π and θ) following the methods outlined
in Pieri et al. (2024) and C. Wang, Liu, Yin, Eller, Brix, Wang,
Salojärvi, et al. (2021). Briefly, ancestral alleles were first
annotated by mapping the fastq files of six Poaceae species to the
reference genome. The ancestral state of the alleles was determined by
selecting the most common bases using ANGSD (Korneliussen, Albrechtsen,
& Nielsen, 2014). Based on this ancestral information, we calculated π
and θ from the unfolded site frequency spectra using the bam files.
Additionally, we estimated F ST between the AU and
CN populations, as well as between the brackish water and freshwater
populations within the CN lineage, using ANGSD with a window size of
10kb. We selected SNPs with F ST values in the top
1%, considering these as potential sites under selection.