Estimates of nucleotide divergence for candidate and control genes varied among species (Table 1) but were consistent with their phylogenetic position relative to P. taeda (Gernandt et al. 2008; Eckert and Hall 2006; Willyard et al. 2007).
Although highly diverse, young (less or equal to 12 mya), middle (12 to 25 mya) and old chains (more than 25 mya) as dated by LTR divergence, the majority of candidate CfERV-Fc chains (n = 28) could be used in Pol phylogenies.
To estimate the synonymous sequence divergence between pairs of candidate L. polyphemus paralogous gene pairs and L. polyphemus genes and their T. tridentatus orthologs, we constructed codon alignments of predicted coding sequence for estimation of synonymous sequence divergence.
To estimate the synonymous sequence divergence between pairs of candidate L. polyphemus paralogous gene pairs, and between L. polyphemus genes and their T. tridentatus orthologs, we followed the following protocol.
The depth of divergences among candidate species of Crenadactylus (and within other pygopodoid genera such as Diplodactylus, Lucasium and Salturius [ 27- 29]) are comparable with vertebrate radiations noted for their extreme morphological conservatism (e.g. Plethodon salamanders) [ 30].
A model of directional selection best explained the patterns of polymorphism to divergence of the 17 variant candidate genes for domestication and improvement relative to 38 neutral loci (mean log likelihood ratio test statistic = 372; P < 0.0001 for all comparisons; Additional file 2: Table S3).
Thus, 16 out of 26 groups of features that display significant divergence of gene expression in candidate adaptive features differ in the direction of the change between juveniles and adults (16) or between adult muscle and liver tissue (3) [see Additional file 3].
In general, using the AIC model should imply less computational time than the most complex model but depending among other things on the number of candidate models, sequence divergence, and number of sequences.
The masking strategy employed in this study can be applied to any species and will assist in answering more fundamental questions such as: 1) phenotypic effects of candidate gene sequence divergence and gene expression patterns, 2) the roles of gene duplication, 3) the relative importance of cis- and trans-acting mutations, and 4) gene expression vs. structural changes for future adaptation.
To further determine whether the divergence of orthology in NMD candidates also led to functional divergence, we compared the functional distributions of human and mouse NMD candidates using the FatiGO web tool [ 67], which is able to detect particular GO terms for which the two lists of genes have different proportions of genes.
