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Furthermore, wild populations of D. melanogaster show a cline in the frequency of the most common mth haplotype along the latitudinal gradient of the U.S. east coast [24], a pattern that decays with decreasing linkage disequilibrium both 5' and 3' of the mth locus [25].
The performance of haplotyping methods can deteriorate on databases with decreasing linkage disequilibrium (LD) rates.
Data cleaning techniques were further investigated to determine their individual effect in improving or decreasing linkage quality.
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While these disruptions of the imported alleles were observed only in ∼10% of clones, ISR are likely to have an impact on allelic diversity, because they have the potential to significantly decrease linkage between individual polymorphic sites.
If there was any effect at all, it appeared to decrease linkage quality.
Recombination not only reduces interference between QTL, but also decreases linkage disequilibrium between QTL and neighboring neutral loci.
An alternative way to decrease linkage disequilibrium is to intersperse extra generations of neutral mixing between rounds of selection.
This step is critical as non-pre-processed linkage variables result in a decreased linkage proportion because true matches are more frequently missed [ 22].
The LD method is based on the theoretical expectation that when Ne decreases, linkage disequilibrium due to drift will increase [ 59, 60].
These considerations clearly suggest that there is a balance between recombination (always decreases linkage disequilibrium) and selection (convergence to coupling or repulsion haplotypes) in the system.
For example, while recombination decreases linkage between alleles, disrupting the driver passenger paradigm considered here, it would not necessarily prevent application of the method.
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