Because these are largely due to transitions resulting from deamination of cytosine residues in the Neandertal DNA, we restricted the divergence estimates to transversions.
In this paper, the black-border constraints naturally restrict such divergence to a very small value.
Irrespective of whether local or global alignments are used, the seed restricts the divergence of the read to the reference genome.
These data are also consistent with the possibility that the genes of the second mini-clade turned into pseudogenes and are, therefore, neither expressed nor subjected to natural selection that restricts their divergence process.
Previous studies have demonstrated a positive relationship between tissue specificity of expression and evolutionary rate, presumably due to selection against the deleterious pleiotropic effect of mutation restricting the divergence of broadly expressed genes [ 40- 42].
To avoid issues of excessive divergence resulting in saturation, we restricted the average divergence calculation to those genes with d S <2, following the example of Axelsson et al. (2008).
Genomes of such hybridizing species may be expected to exhibit a mosaic structure, with high levels of divergence restricted to "speciation islands," which contain the loci responsible for species differences (Wu 2001).
Following the divergence, each lineage was restricted in situ and diverged independently without distinct population expansion.
Our analyses reveal that initial divergence is restricted to a small fraction of the genome, largely clustered around known wing-patterning genes.
Beam divergence was restricted with a 0.15 mm silt on the source side.
