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.