The mean pairwise diversity within the Dallas populations was higher than the mean pairwise diversity within the Montgomery populations (Table 2, Clade II: P < 0.05).
The mean pairwise diversity at ospC was much greater than at the other loci analyzed (π = 0.207).
The overall nucleotide diversity of each repertoire, summarized in Table 4, shows both the percentage of nucleotides in different loci that are polymorphic (% S) as well as the mean pairwise diversity.
To summarize the overall diversity of these repertoires, we calculated the proportion of segregating sites (%S) and the mean pairwise diversity of each of the 12 nucleotide alignments and 9 amino acid alignments.
Reflecting the subtype diversity, the mean pairwise diversity among all reverse transcriptase nucleotide sequences from each country ranged from 1.39% (Libya) to 13.85% (Djibouti), with an average of 8.12% (Supplementary Table 2).
Common summary statistics applicable in this context include the time to the most common ancestor (TMRCA) of the sample and the mean pairwise diversity of the sample, which is the average branch length distance between pairs of tips on the tree.
Both the rate, 2 Nλ, and the fitness effect, s, of recurrent selection are estimated based upon their relationship with the means and standard deviations of common polymorphism summary statistics (the mean average pairwise diversity, the number of segregating sites (S), θH, and ZnS (Jensen, Thornton, and Andolfatto 2008)).
Both the rate, 2 Nλ, and the fitness effect, s, of recurrent selection are estimated based upon their relationship with the means and standard deviations of common polymorphism summary statistics (the mean average pairwise diversity, the number of segregating sites (S), θ H, and Zn S; see Jensen, Thornton, and Andolfatto 2008).
Tajima's D tests the departure from neutral by comparing the estimations of nucleotide diversity derived from the average pairwise diversity and the total number of polymorphic sites.
Full details of substitution parameters and evolutionary models are given in Additional file 2. N = sample size, Hn = number of haplotypes, S = number of polymorphic sites, H d = gene diversity, π = nucleotide diversity (Nei 1987), k = mean pairwise nucleotide diversity (Tajima 1993) Weighted parsimony analyses generated 95 equally parsimonious trees (length = 272, CI = 0.871, RI = 0.967).
The mean pairwise nucleotide diversity of the 50 E. cloacae complex isolates was higher within clade 2 than clade 1 (0.047+/−0.003 vs. 0.014+/−0.002), suggesting that isolates from clade 2 are older than isolates from clade 1.
