Estimates of the time of divergence in numbers of generations, T, were of the same order of magnitude for the three taxa: 968≤T≪3,104 for P. phylax, 712≤T≪2,503 for C. mckeyi, and 619≤T≪2,774 for their host-plant.
Finally, the mutation rate per site per year was estimated by where d ij is the genetic distance between sequence i and j, t ij is twice their divergence time (in number of days), and n is the number of sequences.
The resampling-based approach compared values of population-based statistics such as heterozygosity and population divergence in a number of adjacent SNPs, to the distribution of values obtained by the resampling of the same number of SNPs from random locations along each chromosome.
But because of the small number of TFBSs found within each CNE (the average number of TFBSs found in each CNE was 5.9), it is difficult to perform robust tests of divergence in the number of binding sites for individual transcription factors.
Our screen identified sequence divergence in a number of proteins that are important during HIV infection, such as APOBEC3C (91.6%) and BST2 (also known as tetherin, 95.1%), as well as pattern-recognition receptors (MBL2, CLEC4A, CLEC4D and CLEC6A), the antiviral sensor cyclic GMP AMP synthase (cGAS (also known as MB21D1)) and other immune mediators (Extended Data Table 1).
Overall, these results suggest there has been parallel divergence in the number of MHC alleles per individual between stickleback populations foraging in littoral and pelagic habitats (Figure 1).
Our results indicate parallel divergence in the number of MHC alleles between sympatric stickleback species, possibly resulting from the contrasting parasite communities in littoral and pelagic habitats of lakes.
If so, T-cell depletion would not be a likely cause for the low levels of individual allelic richness in limnetics, and would probably not cause the observed divergence in allele number between sympatric species.
The parallel divergence in the number of MHC class II alleles per individual between limnetic and benthic species in two lakes with species pairs is not observed in the allelic richness of microsatellites, and is unlikely to have occurred by drift.
Previous comparative studies of development between C. elegans and P. pacificus have also demonstrated that sequence divergence is correlated with divergence in a number of developmental processes [ 8– 10].
These results suggested that there were at least 24 Hsf genes in the common ancestor of these grass species and that the divergence in gene number in these species was the result of gene duplication and/or loss.
