In order to retain intronic sequences conserved among the species in each of the four groups, but not conserved between the groups, we removed ECRs that are found in orthologous introns as well as in any of the pairwise alignments of reference genomes; a minimum overlap of one base pair was used as a criterion for removal.
To ensure comparable injuries between the study groups, we removed the liver and identified the number of hepatic vessels injured.
To exclude the possibility that allometry explains most of the shape differences between the two groups, we removed its effect from shape analyses using allometry-free residuals.
In an attempt to simplify the task so that performance of rats with hippocampal lesions was not at floor, possibly obscuring differences between the lesion groups, we removed every other arm of the maze, converting it to a 6-arm maze, and confronted the rats with a 3/6 working/reference memory task.
In the teen and adult groups, we removed foods eaten by < 1% of the restricted sample, whereas we removed foods eaten by < 5% of the restricted child sample.
Before comparing median values of Ka and Ks between different groups of genes, we removed data points of 70 ribosomal genes (that are extremely slow-evolving genes that lack divergence information), 228 sex-chromosomal genes (that are under different strength of selection compared with autosomal genes), and 1,997 pseudogenes listed in http://Pseudogene.org/ (Karro et al. 2007).
Because the frogs spleens were pooled between tanks, we removed tank-level effects.
To examine the functional connectivity between regions, we removed the stimulus-driven activity (Fig. 3).
All transcript clusters with high differential exonic expression (> 5-fold change) between groups were removed, as they have a tendency to produce false positive results for alternative splicing [ 18].
When two terms were almost identical (Jaccard index between gene groups being above 0.95), we removed the term with smaller number of synonymous SNPs, resulting in 130 GO terms.
