Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling

The genome-wide ranking of genes whose rates are positively associated with the subterranean branches was identified on the basis of the Mann-Whitney U test p-values (column 2) that were significant at a FDR of 15% under a permutation-based FDR correction procedure (column 3). Other columns list brief gene descriptions (4), known biological function (5), tissue specificity if any (6), known disease links (7), the predominant evolutionary mode on subterranean branches as decided with codon models (8, see Materials and methods), and the subterranean species containing genetic lesions in the corresponding protein-coding sequences (9).

The subterranean-accelerated genes were strongly associated with specific Gene Ontology terms representing functional categories. This table presents the GO term identifier (column 1), description (column 2), the p-value representing the significance of the degree of enrichment of genes in that category among mole-accelerated genes relative to the entire set (3), the multiple test-corrected p-value (4), the degree of enrichment in the accelerated set relative to the entire set (5), the number of genes in that category in the entire analyzed gene set (6), the number of genes in the accelerated set (7), the number of genes in that category in the accelerated gene set (8), and the corresponding gene names (9).

The genome-wide ranking of genes whose rates are negatively associated with the subterranean branches was identified based on the Mann-Whitney U test p-values (column 2) that are significant at a FDR of 15% under a permutation-based FDR correction procedure (column 3). Column 4 lists brief gene descriptions.

The specific Gene Ontology terms representing functional categories with which subterranean-decelerated genes were strongly associated. This table presents the GO term identifier (column 1), description (column 2), the p-value representing the significance of the degree of enrichment of genes in that category among mole-accelerated genes relative to the entire set (3), the multiple test-corrected p-value (4), the degree of enrichment in the accelerated set relative to the entire set (5), the number of genes in that category in the entire analyzed gene set (6), the number of genes in the accelerated set (7), the number of genes in that category in the accelerated gene set (8), and the corresponding gene names (9).

This table presents the results for the mole-accelerated genes from five codon models and the likelihood ratio tests between them. Columns B – T present the branch-site models and tests with their log likelihood values, the likelihood ratio tests between them (see Materials and methods), and some of the estimated parameters for background (conserved) and foreground (subterranean) branches (Zhang et al., 2005). Columns V – AC present the results of the pan-mammalian tests for positive selection using the sites models (M8A and M8) (Swanson et al., 2003; Yang, 2007).

This table lists the pseudogene status of mole-accelerated genes' orthologs in the set of species utilized for the study.

This table presents the evolutionary rates of the 71 eye developmental genes. For each gene (column 1), we performed a branch-site selection model analysis to estimate two different values of dN/dS – one for the four subterranean branches on the tree (3), and one for the rest of the branches (2, see Materials and methods). The mole-acceleration is calculated as the difference between these two values (4). Column 5 indicates whether the gene was identified as a subterranean-accelerated gene using the RER methods, and column 6 lists the refSeq summary.

This table presents the 150 non-coding regions scanned near Pax6 and their relative rate acceleration in subterranean mammals. The first three columns represent the hg19 coordinates of the region. Column 4 represents the mole-acceleration calculated as the negative logarithm to the base 10 of the Mann-Whitney U test p-value. Column 5 provides additional information about the overlap of the region with known tissue-specific enhancers of Pax6.

This table presents the two sets of transcription factor genes used to scan for convergently accelerated non-coding elements. TF genes in the Eye set, were compiled based on a literature survey of their eye developmental role (column 2). Column 3 lists the refSeq summary. Similarly, the tissue-specificity of TF genes belonging to the ‘Other’ set is provided in column 2 of the second table.

This table presents the 17 subterranean-accelerated non-coding regions scanned near the 40 TF genes listed in Supplementary file 9, significant at a FDR of 10%. Columns 1–3 list their hg19 coordinates. Column 4 presents the mole-acceleration calculated as the Mann-Whitney U test p-value. Column 5 lists the permutation-based FDR q-value.

This table presents the 62 subterranean-accelerated putative FANTOM5 enhancers significant at a FDR of 15%. Fantom5 element names containing the word 'eye' correspond to FANTOM5 enhancers identified as eye enhancers in this analysis. Columns 2 and 3 list each region's mm9 and hg19 coordinates respectively. Column 4 represents the mole-acceleration calculated as the Mann-Whitney U test p-value. Column 4 lists the permutation-based FDR q-value.