The core haplotype is defined on a 1689 base region spanning the Cyp6m2, from chromosome arm 3R, starting at position 6928858 and ending at position 6930547. This region was selected to ensure a 1:1 haplotype correspondence with that used in the hierarchical clustering analysis. Extended haplotype homozygosity (EHH) was computed across all core haplotypes in all populations as described in Sabeti et al. [45] using scikit-allel version 1.1.9 [46]. EHH composite plots were made using the matplotlib Python package version 3.1.2 [40].
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