Phylogenetic clades of 7 haplotypes (H_3, H_4, H_5, H_11, H_22, H_23, and H_29), derived directly or indirectly from the network torso structure and ancient haplotypes or lost potential haplotypes, and these haplotypes were the most recent miRNAs (Figure 1A, black circles).
The most ancestral haplotypes derived many recent haplotypes, but many of them had lost dominant positions except for H_1, which still was the most dominant haplotype and shared by many animal species (Figure 2).
As a calibration point we set the geological age of Réunion to 2.1 Ma [ 60] as a normally distributed prior with mean of 1Ma and extremes of standard deviation reaching 2.1, thus in effect setting the maximal age of the most recent common ancestor of Réunion haplotypes.
The time of most recent common ancestor for all the haplotypes was dated to 8.11 Mya (Table 1).
The time of the most recent common ancestor (tmrca) for all haplotypes of A. morrisonia was estimated back to 11.66 Mya (Table 1).
This overestimation may occur because the most recent common ancestor (MRCA) of the haplotypes (their coalescent) does not necessarily correspond to the real temporal split of the populations but may precede the actual divergence of the populations [ 52].
Thus, the most recent common ancestor of P. diabolicus haplotypes is estimated to have existed between 1.6 and 1.0 million years ago, relative to between 1.8 and 1.2 million years ago for P. plicatus.
The average sequence divergence of the haplotypes to their most recent common ancestor, accompanied by a heuristic estimate of the standard error, was calculated as fully described before [ 58, 59].
Therefore, each short haplotype was assigned the most recent common ancestor of all the haplogroups that share the same short haplotype.
The most recent common ancestor of the two haplotype clades was estimated to predate the human/chimpanzee/gorilla split (Ferguson et al. 2012).
