To calculate pairwise noncoding region divergence, we first extracted the complete upstream intergenic region between each gene and the coding region of its 5′ neighbor.
The covered region divergence (CRD), defined as the percentage of high-confidence SNPs out of the covered regions of the identified genome, was 0.0042%.
Castillo-Davis et al. (2004) examined the correlation of cis-regulatory region divergence and gene expression in Caenorhabditis elegans and C. briggsae.
Calculated COI region divergence between S. japonica (AP011493) and S. augustata (AP011498) was 4.633 % and estimated divergent rate was 0.9572 %/Ma (4.633 %/4.84 Ma, rounded conservatively) [ 52].
It is noteworthy that in the N-terminal region of the macro domain, which corresponds to the linker region, divergence between these subtypes is extremely high, with only 19% identity.
Our results show that, for a specific conserved region, divergence of TLR1 and TLR6 is limited by gene conversion, most likely because of the need for co-evolution with multiple intracellular and extracellular binding partners.
Because there does not exist a set of TFBS annotations for C. elegans of comparable accuracy with those for yeast, the authors estimated promoter region divergence using alignment programs.
Results were similar to those obtained using the mtDNA control region (divergence between African and Sicilian haplotypes: 95% HPD from 0.164 to 3.603 My (mean: 2.051); split of balearicus/ viridis clades: 95% HPD from 0.18 and 3.795 (mean: 2.123).
Based on the control region, divergence of eastern wolves from coyotes was approximately 3.0%, that of the red wolf sequence from coyotes was 2.0%, and eastern wolves compared to red wolves was 2.7%.
A recent study [ 28], based on 22 X2andnd 46 D4h3 complete mtDNA sequences concluded that although the coding region divergence of these haplogroups shows considerable overlap, their phylogeography in America is strikingly different.
