Population Genetic Data for Drosophila yakuba and Drosophila simulans.
To detect regions of residual heterozygosity, we called SNPs using samtools under a diploid model. Segments with residual heterozygosity were detected using an HMM (HMM;http://cran.r-project.org/web/. The most likely path was calculated using the Viterbi algorithm, and heterozygous segments 10 kb or larger were retained. Heterozygous blocks within 100kb of one another in a sample strain were clustered together as a single segment to define the span of residual heterozygosity within inbred lines.
Further description is available in Rogers et al. 2014.
SNP VCF files are available at http://molpopgen.org/Data
We estimate Theta_pi, Theta_W, and Tajima's D for all SNPs in the D. yakuba and D. simulans genomes, removing sites with missing or ambiguous data as well as heterozygous sites. We calculate:
- Window midpoint
- Number of valid sites with coverage sufficient to assay SNPs
- Theta_pi for the entire window
- Theta_W for the entire window
- Tajima's D
Estimates provided are for 5 kb windows moving in a 500 bp slide across the genome. Positions in each file designate the window midpoint Population genetic parameters were calculated using libsequence module for C++ (Thornton, K. 2003). We exclude all sites with missing data, ambiguous sequence, or heterozygous sites.
Rogers et al. 2014 Tandem duplications and the limits of natural selection in Drosophila yakuba and Drosophila simulans. http://arxiv.org/abs/1405.0518