For such an assumption, a heuristic justification without rigorous theoretical proof is as follows: Given each randomly produced ancestor sequence, each nucleotide (event) LogPr on the non-reference sequences acts as an independently and identically distributed random variable, and the summation of these LogPrs follows the central limit theorem for a large sample size (sequence length).
This mechanism is the basis for the "correction or conversion" of any mutated nucleotide sequences engineered into either arm of the palindrome and the incorporation of "illegitimate recombination" (addition or deletion of nucleotides) events that are commonly observed at the Ori of other RCR biological systems during DNA replication.
These models vary in complexity, ranging from the treatment of insertion and deletion events (indels) as single-nucleotide events [ 13] to the modeling of complex length distributions for indels [ 9, 14, 15], but all allow for evolutionary inference without assuming a single alignment.
The ratios of nucleotide substitution events to indel events (S/I) for different pairwise comparisons showed that, among the five Camellia cp genomes, the S/I ratio varied from 2.67 (PETE vs. RETI) to 5.00 (ASSA vs. OLEI) (Table 5).
Using the computer program, Dawg version 1.2 [ 30] we simulated DNA evolution along a 16-taxon model tree, incorporating both nucleotide substitution events and insertion and deletion (indel) events (the latter as a function of the substitution rate).
Their length varied considerably, from the IND-35 that involves the insertion/deletion of 11 nucleotides to events involving a unique nucleotide (IND-745, IND-717, IND-658, IND-649, IND643 and IND1100).
The identity and number of nucleotide extension events were determined by automated measurement of the amount of light generated after incorporation of each dNTP.
We restricted our analysis to the 4099 high confidence single nucleotide polymorphism events that were called identically in at least two out of three lanes.
Nucleotide insertion/deletion events were not reported.
Three distinct nucleotide deletion events occurred across RacPyV5 and RacPyV10.
