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The presence of an error-correction term among a number of co-integrated variables shows that changes in the dependent variable is a function of both the level of disequilibrium in the co-integration relationship (represented by the ECM) and the changes in other explanatory variables.
It should be stressed that while linkage disequilibrium is detected in the population as a whole and in some subpopulations, the values of the index of association are all close to zero (ISA = 0.074 0.095), indicating a limited level of disequilibrium.
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Four loci show very high LD (r2>0.8) with surrounding SNPs, and others present low levels of disequilibrium (Figure 3).
Due to the effects of Ne on the level of linkage disequilibrium, a fast decay of linkage disequilibrium should be generally expected (reviewed in [ 40]), which in turn might preclude hitchhiking and ultimately the observation of genomic islands of divergence.
Genomic herd descriptors were (1) the level of linkage disequilibrium (r2) within specific chromosome segments, and (2) the average allele frequency for single nucleotide polymorphisms in close distance to a functional mutation.
The level of linkage disequilibrium is influenced by a number of factors including genetic linkage, selection, the rate of recombination, genetic drift, and population structure.
genepop software (v.3.1c, http://wbiomed.curtin.edu.au/genepop/; [34]) was used to calculate the level of linkage disequilibrium between all pairs of loci within regions.
The expected strengths of the associations between these variables and fitness should depend on factors such as the intensity of selection for heterozygosity, the level of linkage disequilibrium in the population and the action of genetic drift [17], [18].
The density of markers required for efficient GWA scans in a species is dependent on the average length of chromosome "blocks" possessing a high level of linkage disequilibrium (LD).
In addition, the level of linkage disequilibrium (LD) of rs62106244 in relation to other variants (i.e. haplotype status) has not yet been determined, although the entire DNMT1 gene lies in a large block of LD.
When several SNPs stood within this limit it was decided to filter out lowest frequency variants and polymorphisms showing high level of linkage disequilibrium with other selected SNPs of the same fragment.
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