As a consequence, this kind of asexual reproduction will induce cosegregation of mitochondrial and nuclear genotypes and the consequent linkage disequilibrium among all genetic markers [ 52, 53].
In consequence, both linkage disequilibrium (LD) and population structure in the X chromosome are expected to be stronger than those in autosomes [ 1].
Experiments examining polymorphism of the HLA-DRB1 gene established that these relationships are not a consequence of linkage disequilibrium with HLA-DRB1 alleles implicated in this pathology.
Thus it is more likely that the RsaI negative allele affects the phenotype directly rather than being a consequence of linkage disequilibrium from another mutation or gene.
As a consequence of linkage disequilibrium closely linked SNPs will likely be correlated, which will affect the distribution of the summary statistics, thus to account for this correlation structure we used the following procedure, Figure 1.
Considering that the distribution of summary statistics is affected by a correlation structure of closely linked SNPs, as the consequence of linkage disequilibrium, the following procedure was used for statistical testing.
It is worth noting that this consequence of linkage is not observed for the case d = 0.15 with N = 10 (third column of graphs in Figure 1), suggesting that it depends on the linkage disequilibrium generated in the base population (see Table 1).
This was particularly evident by the Bayesian approach identifying a single marker whereas the SSR approach sometimes identified a cluster of adjacent significant associations for the same location (e.g. chromosome 20 at ~10 MB for cull cow carcass weight); this a consequence of linkage disequilibrium in the genome.
This is probably a consequence of linkage to conserved sites and is likely to be associated with the way that GERP is calculated, since we find that sites with the most negative constraint scores tend to be preferentially located adjacent to runs of conserved sites in non-coding regions (for more details see Additional file 1: Figure S20).
In this work, we investigate the consequences of linkage on inbreeding depression and purging, and on their impact upon genetic diversity.
