DOI: 10.6084/m9.figshare.c.3602828_d1
title: Additional file 1: Table S1. of Differences in molecular evolutionary rates among microRNAs in the human and chimpanzee genomes

description: Statistics for miRNA tested in Tajima’s Relative Rate Test and HyPHY analyses. Type, Mapping result in PT4 (100 means perfect match). L.hg19, length of miRNAs in humans. True_length, Length trully informative. Median p-value indicates the median of 100 p-values obtained from HyPHY analysis. pVal.Tajimas indicates the p-value of the Tajima’s RRT. Qvalue, q-value calculation of the previous distribution of p-values. Type indicates whether miRNA map using BLAT in all all species (TOTAL), only in chimpanzee (NOMAP_PA2) or only in orang-utan (NOMAP_PT4). Mut, number of substitutions found in each branch. Categories: Number of copies (M), primate-specificity (P), localization in genome (L1), localization within genes (L2) and clustering (C). Table S2. Functional enrichment analysis of TargetScan predicted target genes for miRNAs with significant results on Tajima’s test. The classic Fisher’s test and 1000 randomizations of groups of ten miRNAs was used for the analysis of hsa-mir-3691, hsa-mir-4267 and hsa-mir-4686. Table S3. Linear models tested and their p-values. The number of miRNAs tested in each model is indicated in bold. B stands for BLAST and L for Liftover. Final subset: The subset of miRNAs described in the manuscript. BLAST filtered: Primate-specific miRNAs showing BLAST hits in other non-primate species are removed. Only in miRBase miRNAs whose predicted chimpanzee orthologs are also described in miRBase for chimpanzees. With many-to-one: A subset containing miRNAs presenting multiple human versions assigned to the same chimpanzee or orang-utan ortholog. Categories: Number of copies (M), primate-specificity (P), localization in genome (L1), localization within genes (L2) and clustering (C). Table S4. Statistical test for miRNA categories and results for the Tajima’s test. Effective length indicates sequence (number of base pairs) effectively analysed (i.e. No gaps nor INDELs). First pval column contains the p-value for Tajima’s test for Human-Chimpanzee comparison. The second pval column indicates the p-value for Tajima’s test using information on transitions (ts) and transversions (tv), contained in the previous four fields. subs, substitutions in the indicated lineage; rate, substitution rate in the indicated lineage. Sd columns contain the standard deviations of substitution rates from 100 bootstraps from miRNAa and flanking regions. Table S5. Statistical test of substitution rates of miRNA categories. Green cells indicate significant comparisons at 0.025 tails (see Methods). Two groups of miRNAs are analysed. 1) 1,241 all, miRNAs. 2) 1,139, only miRNAs doing BLAT and Liftover. The number in cells indicates the percentile that any observed value for categories, in rows, occupies in the distribution of 100 bootstraps values for any other category, in columns. Table S6. Substitutions found in seed regions in all miRNA analysed. Categories: Number of copies (M), primate-specificity (P), localization in genome (L1), localization within genes (L2) and clustering (C). Subs, substitutions in the indicated lineage. Table S7. Analysis of the proportion of C to T transitions in CpG dinucleotides in each miRNA category. Subs, substitutions in the indicated lineage. Prop. CpG, proportion of substitutions in CpG sites. Table S8. Analysis of the contribution of GC-BGC in each miRNA category. P = PValue, W = Weak, S = Strong. Table S9. Rates of substitutions observed for each type of nucleotide in the human lineage. Table S10. Median p-values for 100 repetitions of the Hyphy analysis for different categories of miRNAs. Either ARs or flanking regions were used as neutral reference sequence. Table S11. miRNAs present in clusters of chromosomes 14 and 19. In yellow miRNAs that have been excluded from the study and the reason to do so. Table S12. Presence of ALUs near-by miRNAs and diversity in miRNAs and flanking regions for each chromosome. P-values and correlation coefficient for divergence measures versus number of ALUs (below). (XLSX 408 kb)