As can be noted visually, very accurate estimates of the unascertained allele frequency distribution are recovered from the divergence ascertained data.
It is also worth noting that this skew in the frequency spectrum will lead to an increase or decrease in the expected number of segregating sites recovered from divergence ascertained loci.
This ascertainment corrected version of the likelihood function is also useful in a Bayesian setting, for an example see Katzman et al. [14], where it was used in a Bayesian Hierarchical model for estimating distributions of selection coefficients from divergence ascertained data.
In this study I offer simple corrections for those biases which may be used to estimate the unascertained site frequency spectrum of divergence ascertained data as well as for estimation of evolutionary parameters when the sequence used for ascertainment is included in the population sample.
Increasing SNP density should resolve fragmentation of the haplotype structure in congenic regions of BN.GK-Nidd/gk1 and ascertain segments of genetic divergence and conservation between strains, thus providing information for selecting functional and positional candidate genes.
Using computational methods, we have identified putative orthologs among these species and generated a phylogenetic tree to ascertain the relationship and sequence divergence among these species.
It is often difficult to ascertain whether these differences were caused by divergence during the course of evolution or were brought about through adaptive differentiation.
However, species boundaries of closely related taxa, in the initial stages of divergence, can be difficult to ascertain using multilocus phylogenetic methods because gene trees of recently diverged taxa can differ substantially in their evolutionary histories [ 10].
This is because any uncertainty in ascertaining the true initial conditions leads to divergence in the model behavior from the system behavior (Smith 2003); and, there is no way to reduce this uncertainty to zero (e.g., Bishop 2003).
However, reconstruction of historical relationships between closely related species is not a simple task, because these species usually have low levels of genetic divergence, and it is difficult to ascertain whether the recent divergence is the consequence of lineage sorting of ancestral polymorphisms or introgressive hybridization.
Information on the function of wing pigmentation during courtship would be relevant to ascertaining which of these scenarios occurred during the divergence of these two species.
