An analysis of molecular variance (AMOVA) was implemented in ARLEQUIN 3.11 to test whether a significant proportion of genetic variation at both loci in this study was partitioned among the connectivity regions of [9].
We implemented phylogenetic comparative methods to test whether amino acid transporters have proliferated in sternorrhynchan genomes at rates grater than expected by chance.
First, as a heuristic test, reciprocal Shimodaira-Hasegawa (SH) tests [15], as implemented in PAUP*, were used to test whether optimal trees from different partitions were incongruent.
The Shimodaira-Hasegawa maximum likelihood test [69] of competing phylogenetic hypothesis was used with 1,000 RELL pseudo-replicates as implemented in Tree-Puzzle [70] to test whether the difference of likelihoods between the best tree and the competing hypotheses were significantly different from zero (alpha at 0.005 after correcting for multiple trees comparisons).
We next implemented two different statistical approaches to test whether epigenetic modifications can be exclusively utilized to identify functional p63 binding sites.
The χ-goodness-of-fit (exact version implemented in SAS) was applied to test whether the overlap between autosomal fragile sites and evolutionary breakpoint intervals is non-random.
A moderated t-statistic (implemented in limma) was used to test whether each contrast was significantly different from 0 Resulting p-values were corrected for multiple testing with Benjamini-Hochberg (BH) to control for false discovery rates [ 10].
In the site model, codon site models M0, M3, M7, and M8 were implemented, using likelihood ratio tests to test whether variable ω (dN/dS) ratios were present at the amino acid sites.
We used a mean-rank gene set enrichment test MR-GSE test, implemented in LIMMA; [ 59] to test whether the sets of up-regulated or down-regulated significant transcripts showed a tendency to be up- or down-regulated after mating, using the t-values from a contrast between virgin and singly mated females from the same population, from a previously published study [ 44].
