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In the studied population of single-colony isolates that colonized the 90-year old patient, most isolates contained the same alleles of futA and futB at these two loci (type A and B, Figure 7, Table 1).
Only 2 types of epistasis exist based on functional relationships between or among loci (Table S4): epistasis between alleles at upstream loci and their regulated downstream loci (type I in scenarios 3, 4), and epistasis between alleles at different segregating loci within the same unit in each level of the system (type II in scenarios 5 7).
Second, positive selection in the direction of the pathway effect will result in 2 types of weak positive linkage disequilibrium (LD), one between the upstream loci and their regulated downstream loci (type I, scenarios 3 and 4) and between different segregating loci within the same units in each level of the signaling pathway (scenarios 5 7).
First, many R-gene loci (Type II R-genes) show presence/absence polymorphism in different genotypes.
Breed-defining loci (type 1) and large effect QTL (type 2) were identified from the literature and the Online Inheritance in Animals database [ 10].
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Ray et al. (2010), on the other hand, considered 401 autosomal microsatellite loci typed in 29 native American populations.
For HLA donor centers/registries the cost of HLA typing currently is a major constriction limiting the resolution and number of loci typed at registration.
Analyses in large panel of plant species covering plant kingdom revealed that a huge diversity of phasiRNA-generating loci types in plants (Zheng et al. 2015; Xia et al. 2013).
Multilocus heterozygosity (MLH) is calculated as the proportion of heterozygote loci among loci typed (varied between 27 and 31).
Since the variance in all heterozygosity measures tended to decrease with the number of loci typed (see results), we calculated normalised estimates to make our loci statistically comparable.
Simulations for CERVUS were run with: 10000 cycles, 50% of candidate parents sampled, 100% of loci typed and a genotyping error rate of 1%.
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