A fundamental question in the field is therefore whether patterns of molecular evolution are best understood by taking the global network context of the genes of interest into account or whether taking a locus-by-locus approach is sufficient.
The allelic frequencies for a locus was estimated by taking a sample pool composed of all the genotypes distinguished by all loci except the one being estimated and this procedure was repeated for each locus in a round robin fashion.
The LocusByTypeService was created to take in a locus type and return a list of all map symbols of that type.
Further, assumption 5 enables us to take a product across loci, as genotypes at separate loci are independent.
For the purpose of annotation and filtering, Biofilter takes a list of loci or a list of regions, and then either filters that list by another list (whether provided as input or using information from LOKI), or annotates the list provided.
We set up three models, in which: (i) α is constrained to zero at all loci, i.e. no adaptive evolution; (ii) α is a free-parameter common to all loci; and (iii) α can take a different value at each locus.
For all three models, the expected neutral divergence (λ=µ t) and neutral diversity (θ=4 N eµ) each took a single value at all loci, and selective constraint was allowed to vary between loci.
To test the presence of H3K9ac and H3K14ac over bivalent promoters, we took a subset of randomly selected loci and successfully validated them by ChIP-qPCR.
For each model, we only varied the parameter α, and kept the remaining parameters constant as follows: the neutral diversity per site (θ=4Neμ) took a single value at all loci for each of the two Daphnia species, and finally, the proportion of mutations at non-synonymous sites that are under strong purifying, positive or no selection (f) was estimated at each locus.
We took a pragmatic approach to these loci: if a gene appeared to be intact except for one frameshift site or one internal stop codon, we annotated it and assumed that the problem was a sequencing error; if a gene contained more than one such site, we assumed that it is a pseudogene.
Indeed, Th2-specific chromatin remodeling and demethylation takes place in a locus control region that flanks a number of Th2 cytokines [ 17].
