This level of divergence is similar to the genetic divergence found between other species of potoo, pointing the possibility for 'cryptic' species within the Great Potoo lineage.
The magnitude of this problem obviously depends on the level of divergence between the (ignored) subpopulations, which in case of modern human mtDNA data usually is relatively small in Europe.
Although the level of divergence varied among replicates, some lineages evolved reproductive isolation via genetic incompatibilities.
Once however this level of divergence is reached, the scatter immediately covers the entire, available outcome space.
Depending on the level of divergence one of the following steps is being executed: 1. Update the ILU-decomposition using the current pattern and values of A. 2.
Although this level of divergence is still very high for microsatellite data.
The high level of divergence, 21%, implied a substantial amount of multiple hits.
The lack of reliability of both models at low level of divergence might be partly explained by a clear underestimation of population specific FST at low level of divergence (FST<0.05) (Figure S2).
However, the genomic sequence within the 5' region of JV ORF1 (5'GS) displays a high level of divergence.
Although phylogenetic footprinting is a powerful tool for identifying novel regulatory elements, the appropriate level of divergence among species is critical [51].
We compared our scoring matrices with the typically used BLOSUM62 scoring matrix with ours scaled to the same level of divergence (62% expected sequence identity).
