On a molecular level, the sequence divergence is caused by replacements of amino acids by other amino acids.
Using the logic of molecular divergence employed above, sequence divergence between P. euryzonus and P. stonei (10.1%, Table 3) would support a divergence time of about 10.1 MYA.
Molecular sequence estimates place the divergence between the two orders around 55 60 Myr ago [ 32, 33, 48].
Because the 5′-UTR is the target of most molecular diagnostic assays, this sequence divergence needs to be taken into account in future studies.
Assuming a molecular clock of 2% sequence divergence per million years [ 4, 44] the 4.8% within sequence divergence observed in P. hypselopterus would correspond to ~4.8 MYBP or roughly in the mid-Pliocene.
Conservatively assuming an exceptionally fast molecular clock rate, the sequence divergence of 5% among the most similar MOTU2 and 3 suggested that these lineages diverged at least 1 million years ago (Table 2).
Molecular analysis has revealed substantial sequence divergence at mitochondrial loci [ 8, 25, 38, 39] though, to date, no multi-gene analysis of this variation has been conducted.
Partitioning of the molecular sequence alignment may impact on divergence time estimates [ 56, 57].
In our molecular analyses, pairwise sequence divergences between G. indicus and G. tenuirostris are similar to their respective divergence estimates from G. coprotheres (Table 1), and to those reported between various other broadly recognized species within the family Accipitridae [ 35].
If a molecular clock is applied to the sequence divergence, we estimate an initial divergence from a common ancestor approximately 2 mya.
