Cell number and viability for each sample was assessed using 0.4% Trypan blue solution and a hemocytometer.
Quality of the sequenced reads for each individual sample was assessed using the FastQC program (see Code availability 1).
Samples were assessed using methods described by Bland and Altman for repeated measures.
The concentration and integrity of all RNA samples were assessed using the NanoDrop ND-2000 spectrophotometer (NanoDrop Technologies).
Paired samples were assessed using the paired t-test.
Significance for each pathway across samples was assessed using the Fisher's Omnibus [49] and adjusted for multiple comparisons using the Bonferoni method.
Population structure for the two samples was assessed using STRUCTURE V2.3.1 [17]–[18], based on the 25 microsatellite markers.
Convergence of the Gibbs sampler was assessed using the Gelman-Rubin criterion for parallel runs from a Gibbs sampler [ 31].
Normal distribution within samples was assessed using the one-sample Kolmogorov-Smirnov test for normal distribution.
Before library preparation, the quality of the genomic DNA samples was assessed using a Bioanalyzer DNA 7500 Chip (Agilent Technologies).
