Fig 1.
Flow chart of the array redesign process.
The steps of redesigning the array (blue) are described in more detail in the text. Application of the array (red) was done after each subsequent step to assess the effects of the according step on the frequency spectrum.
Fig 2.
Derived allele frequency spectra for the different SNP sets.
For the remodeled sets, areas show the modelling according to the original array [21] while grey lines represent the 50 random population groupings.
Fig 3.
Derived allele frequency spectra within the population groups.
Fig 4.
Impact of a varying number of discovery populations (A) or target density (B) on the derived allele frequency spectrum.
For A, blue indicates the spectra after the discovery step and red after the equal spacing step. For B, only the equal spacing step is shown and blue indicates that the algorithm including the initial backbone, while red shows the results without the backbone included in the algorithm. Different numbers of populations in the discovery set (4 to 40) or the increase in the target density are indicated by an intensifying color gradient and only one representative and randomly picked run per population number/ target density is shown. As the differences in the color gradients are hard to distinguish, arrows in the respective color are indicating the shift of the spectra with increasing numbers of discovery populations.
Fig 5.
Expected Heterozygosity (Hexp) by population and SNP set.
Populations are ordered by the Hexp of the unfiltered WGS SNP set. Only the reference sets and relevant steps of the array design are shown. Discovery populations are shaded with a darker background.
Table 1.
OHE of the SNP sets from the first run.
Table 2.
OHE of the SNP sets out of the 50 random population groupings.
Fig 6.
Relation of the OHE as a function of the number of discovery populations.
A—discovery, B—equal spacing. While the number of discovery populations was varied from 4 to 40 by increments of one, the Boxplots are only shown for a subset of the number of discovery populations to avoid a crowded figure. The smoothing lines, which show the trend, are calculated from all observations. Plots for all five steps can be found in S9 Fig.
Fig 7.
OHE after equal spacing (step 3) by target density in SNPs/cM and population group.
The smoothing lines show the trend and the dashed lines the target density of 667 SNPs/cM, used for the remodeling according to the original array [21]. The algorithm was run including the initial backbone SNPs (A) or not including them (B). Gallus varius is not included, as it is constantly underestimated.