Bioinformatics for DNA Sequence Analysis.pdf - Index of

84 Jermiin et al.ATBTGGCACACTDTGGCACAFig. 4.13. Tetrahedral plots for: all codon sites (A), first codon sites (B), second codonsites (C), and third codon sites (D). The plots were obtained using the Select Sitescommand from the View menu, and were based on an alignment of protein-codingmitochondrial genes used to infer the evolutionary relationship among 53 species ofanimals (90). Based on these plots, it can be concluded that the nucleotide content at allcodon sites varies greatly among the sequences, especially at third codon sites, implyingthat it would be unwise to assume that the genomes have evolved under stationary,reversible, and homogeneous conditions.Table 4.2Summary of results from matched-pairs tests of symmetry aFirst codon sites Second codon sites Third codon sitesThreshold Number b Proportion Number b Proportion Number b Proportion0.05 1306 0.948 1061 0.770 1364 0.9900.01 1259 0.914 919 0.667 1349 0.9790.005 1233 0.895 859 0.623 1340 0.9720.001 1182 0.858 762 0.553 1331 0.9660.0005 1158 0.840 728 0.528 1327 0.9630.0001 1114 0.808 661 0.480 1316 0.9550.00005 1093 0.793 633 0.460 1307 0.948a The alignment of protein-coding mitochondrial genes from 53 animals was obtained from Bourlat et al. (90).b The number of times that the matched-pairs test of symmetry resulted in a p-value below the threshold(number of tests: 1378).