Conservative and non-conservative indel events. a) Examples of 3 bp insertions in a protein coding region. An insertion can either occur between two codons (phase 0), between the first and second nucleotide of a codon (phase 1), or between the second and third nucleotide (phase 2). Phase 1 and 2 insertions can thereby be divided into conservative events, which only insert a new amino acid without changing the translated amino acid of the ancestral codon (phase 1- and 2-), or non-conservative events that additionally change it (phase 1+, 2+). Insertions in phase 0 are always conservative. In a similar manner deletions can be partitioned into the 5 different categories (reversing time arrows in the figure yields the corresponding examples). Notice that the indel in phase 1-could have also been assigned as a phase 0 or phase 2 indel depending on where the alignment algorithm prefers to place the gap (all three gap placements have equal numbers of matches and gaps and therefore equal alignment scores). b) Measured frequencies of non-conservative insertion and deletion events in observed data and simulations.