The most distant neighbor method "
Complete linkage method", which defines the distance between two clusters by the maximum distance between each item with respect to each formed cluster (Lattin, et al., 2011).
With the application of the
complete linkage cluster hierarchical method to classify calving orders using the ADG, W205 and D160 variables of the calves, the cutoff point was obtained at a height of 20%, with this height being defined for representing the best performance behavior of the calves and heifers as a function of the cows' age (Figure 1A) .
One of three linkage criteria must be selected: single linkage, average linkage, and
complete linkage. We selected the
complete linkage criteria to ensure that the maximum distance between elements of each cluster was under the threshold t.
There is no guarantee that single linkage or
complete linkage will individually give the optimal clusters, because they consider only a single distance between two clusters.
The strains were clustered into four groups at 66% similarity level based on UPGMA with
complete linkage and squared Euclidean Distance, while they were clustered into two main groups at 33% similarity level.
In this research, agglomerative (i.e., bottom-up) hierarchical clustering in the form of
complete linkage clustering was considered.
There is only one value equal to 1 in [r.sup.2,] i.e.,
complete linkage disequilibrium, when the two loci in question have identical allele frequencies.
The results are shown in Figure 8.There was a
complete linkage disequilibrium (r2=1) between g.5368G>A and g.5389A>C.
Based on the cophenetic correlations of hierarchical clustering methods presented (Table 1), the method of average linkage provided better grouping, as it presented the highest cophenetic correlation (0.89), which was expected because the method of average distances produced better partitions than the single linkage,
complete linkage and Ward's methods.
According to the existing [r.sup.2], 23,797 of the 3,385,800 marker pairs were in
complete linkage disequilibrium; 12,225 of these were adjacent pairs.