As before, we also observed that λ varied substantially among species with identical divergence times, consistent with lineage specific variation in rearrangement rates.
All 15 models had identical divergence time estimates for the three remaining North American Limenitis species (Additional Files 2 and 4), and all models included hybridization between L. a. arthemis and L. a. astyanax beginning 12,000 ybp, following the recession of the Laurentide ice sheet [ 20].
Similar to the former two isolates, AcNc2 and AcEm2 are also nearly identical (nucleotide divergence π = 0.046%, that is, they are >99.95% identical).
Among Papio representatives the tree topology is identical and divergence ages are similar as previously reported [ 54], depicting paraphyletic relationships in P. ursinus, P. cynocephalus and P. hamadryas, and polyphyletic relationships in P. anubis.
Additionally, these two pairs of species show almost identical sequence divergence (uncorrected pairwise distances in protein-coding genes: 0.388 vs. 0.379 at the amino-acid level and 0.346 vs. 0.356 at the nucleotide level).
We established conservative criteria to identify cases of HT that could be fully analyzed, including >80% identity at the 3′ end, a >400 bp portion of the internal region that is >80% identical, and divergence estimates among species that exclude the possibility of vertical inheritance (supplementary materials and methods, Supplementary Material online).
Further, linR and linE had very little divergence; linR diverged only in one substitution in HDIPO4 (L12P) and linE was 100% identical in all strains.
(For instance, the LTR sequences of D. ananassae are identical despite high divergence in their coding regions, a disagreement that might be explained by gene conversion of the LTR sequences).
Nevertheless, within such a confined bacterial community, individual subclones are not entirely identical, but display divergence through subtle genetic and, consequently, phenotypic variants [13] [19].
The very low divergence between repeat units, even at synonymous positions, suggests that the repeats are kept nearly identical through a process of concerted evolution.
For ATon-I, 146 elements have identical sequences (0% divergence) compared to the consensus sequence of the family and 112 copies have divergence values between 0-1%.
