We measured the mean ΔSSLS and number of significantly convergent sites in each of these three subsets.
To assess the significance of each result, we performed a randomization separately for each subset of loci as follows: 1,000 replicate data sets were simulated by reshuffling the observed values without replacement, and the expected mean ΔSSLS or number of significantly convergent sites for the subset of loci recomputed.
No such relationship is expected for the frequency of observed convergent sites, in the case of an LBA artifact.
Among the six parallel sites and ten convergent sites, which occurred with a significance level of 1%, sites 45, 78, and 123 may be potential adaptive sites.
As these convergent sites should be very rare, the LBA hypothesis can be evaluated, in each case, by comparing the number of observed symplesiomorphy character sites between the rare and common forms of each aaRS.
Thus, our analyses would suggest that the sister group relationship between the single copy RLN gene from New World monkeys and the RLN1 paralog of apes is due to an event of convergent evolution at the sequence level between co-ortholog genes, where changes in a subset of the convergent sites appear to be driven by positive selection.
Comparative analyses based on coding and noncoding sequence suggests an event of convergent evolution at the sequence level between co-ortholog genes, the single-copy RLN gene found in New World monkeys and the RLN1 gene of apes, where changes in a fraction of the convergent sites appear to be driven by positive selection.
It might even be the case that site of convergence later in a feed-forward network might receive more noise from a given input than would a non-convergent site earlier in the network, as might have happened with the L SFG versus the R STG for the left standard stimuli, thus shifting the SR curve toward lower noise levels.
Because these genes do not contain a GC box at the root of mammals, this correlation cannot be explained by conservation, and therefore these genes represent convergent binding site conversions occurring in eutherian mammals independently of birds.
These hosts are all molecules bearing concave surfaces that provide convergent binding sites for another molecule or ion with compatible divergent binding sites.
In all instances, CTCF and cohesin recruitment were lost, and chromatin loops with distal, convergent CTCF sites were disrupted or destabilized.
