Evolution of the Insertion-Deletion Mutation Rate Across the Tree of Life

Supplemental Material for Sung, et al, 2016

Files in this Data Supplement:

  • Figure S1 - Average depth of coverage in Staphylococcus epidermidis, Agrobacterium tumefaciens, and Vibrio cholerae, mutation-accumulation experiments. (.pdf, 73 KB)
  • Figure S2 - Estimate of Θs from minor allele counts (Escherichia coli data shown). (.pdf, 75 KB)
  • Figure S3 - A) Distribution of the read frequency for insertion-deletion mutation calls using BWA mapping. B) Bimodal distribution displaying the proportion of MA lines sharing the same (size and motif) putative insertion-deletion mutation call using BWA mapping for same organisms. (.pdf, 84 KB)
  • Figure S4 - The r2 value of the regression between Ne and Uid under the null hypothesis, as a function of the root mean square error (RMSE) of estimates of ubs. (.pdf, 92 KB)
  • Figure S5 - The r2 value of the regression between Ne and Uid under the null hypothesis, as a function of the correlation between errors in estimate of ubs and uid. (.pdf, 93 KB)
  • Figure S6 - A scatter-plot of effective genome size (Ge) against silent site diversity (πs). (.pdf, 99 KB)
  • Figure S7 - A scatter-plot of base-substitution mutation rate (ubs) against silent site diversity (πs). (.pdf, 97 KB)
  • File S1 - Supplemental Materials and Methods. (.pdf, 184 KB)
  • Table S1 - Limit of selection to fix antimutators that reduce uid in each species. (.pdf, 106 KB)
  • Table S2 - Regression coefficients of the variables relating effective population size to deleterious mutation rate. (.pdf, 71 KB)
  • Dataset S1 - Base-substitution and insertion-deletion (indel) mutation summary statistics for the prokaryotes Agrobacterium tumefaciens (Agt), Bacillus subtilis (Bs), Escherichia coli (Ec), Mesoplasma florum (Mf), and Vibrio cholerae (Vc). (.pdf, 265 KB)
  • Dataset S2 - Caenorhabditis elegans N2 insertion-deletion (indel) summary statistics after an average of 250 generations (Gen). (.pdf, 39 KB)
  • Dataset S3 - List of base-substitution mutation calls for Agrobacterium tumefaciens (Agt), Bacillus subtilis (Bs), Escherichia coli (Ec), Mesoplasma florum (Mf), and Vibrio cholerae (Vc). (.pdf, 693 KB)
  • Dataset S4 - List of insertion-deletion mutation calls for Agrobacterium tumefaciens (Agt), Bacillus subtilis (Bs), Escherichia coli (Ec), Mesoplasma florum (Mf), Vibrio cholerae (Vc), and Caenorhabditis elegans (Ce). (.pdf, 230 KB)