Phylogenetic trees were constructed by the neighbor-joining method with the help of MEGA4 software and a maximum likelihood model with 500 bootstrap replicates and pairwise nucleotide deletion options.
All pairs of orthologs showing fixed differences were saved as pairwise nucleotide sequence alignments and subsequently used for the maximum-likelihood estimation of pairwise d N /d S ratios [ 109] using estimated transition to transversion ratios (model M1) in codeml of the PAML package v4.6 [ 110].
A parameter b denoting the internal branch lengths is varied between 0.005, 0.015, 0.05, and 0.1, which gives a maximum pairwise divergence along the tree of about 0.1, 0.3, 1.0, and 2.0 nucleotides per site, respectively.
The number of pairwise nucleotide differences between members of the three major bonobo haplogroups was 1.5 times higher than the maximum pairwise differences between modern humans, placing the time of the most recent common ancestor of today's bonobos somewhat between that of modern humans and the Neandertals.
Mean pairwise (nucleotide) differences between the two clades of T. taeniaeformis were approximately 11%, 10%and13%3% in partial rrnS (182 bp), cox1 (371 bp) and nad1 (459 bp) genes, respectively.
Pairwise nucleotide substitution rates of gpd were as much as 2.2 times higher than those in rps4 and 2.8 times higher than in trnL.
The pairwise nucleotide identity across all sequences in each set is roughly normally distributed around mean 52.8% (minimum mean identity 35.3%, maximum mean identity 93.9%, standard deviation 8%).
Genetic distances between species are reported as minimum pairwise distances, while intraspecific variation is reported as maximum pairwise distances.
Moreover, 97.5% of all the P1-P2 pairs from distinct serotypes had >9% pairwise nucleotide divergence.
The pairwise nucleotide divergence in the VP4/VP2 region ranged from 0 to 72.2%.
