In addition, the low plating densities of spores of the high relatedness populations could be more susceptible to drift.
Remarkably, the same allele of the EDA gene, which carries just four amino acid differences compared to that found in fully plated fish, was identified in all the low plated morphs obtained from Europe, and from both the American coasts.
In contrast, at the lowest plating density tested (20,000 cells cm−2), the entire culture contains squamous amniotic ectoderm-like cysts on day 4 (Fig. 2b).
Furthermore, by tracking individuals in the low-plate population we determined that the two additional regions had strong, but not complete linkage.
A total of 3 million and 3.7 million reads were obtained from the low-plate and complete-plate F2 pools, respectively, yielding an average of 16 or 20 RAD tags per polymorphic marker.
For the bulk-segregant stickleback study, linked markers with fewer than three tags from the RS parent were counted in each bin of 10 markers in the low-plate pool and fewer than three markers from the BP parent were counted in the complete-plate pool.
We therefore expected that linked markers in the low-plate F2 pool should be almost exclusively from the BP parent, while the high plate pool, with heterozygous and RS-homozygous individuals, should show a strong bias towards markers from the RS parent.
For studies involving the stickleback EcoRI RAD tags, 10 contiguous markers were binned and the numbers of linked markers were counted (i.e. number of markers lacking RS-specific RAD tags in the low-plate population, or having fewer than three BP-specific RAD tags in the high-plate population).
Cells with the highest RNA levels correspond to those with the highest plating efficiency, and those with intermediate RNA levels are those with the lowest plating efficiency.
