Comparison of Hierarchical Clustering Methods for Binary Data From SSR and ISSR Molecular Markers

Data from molecular markers, which are used to construct dendrograms based on genetic distances between different plant species, are encoded as binary data. For the construction of the dendrograms, the most commonly used linkage method is the UPGMA (Unweighted Pair Group Method with Arithmetic Mean) in combination with the squared Euclidean distance. It seems that in this scientific field, this is, the “golden standard” clustering method. In this study, a comparison of 189 clustering methods (except the “golden standard”), that is seven linkage methods in the sense that this methodological scheme is used in the vast majority of the corresponding studies by 27 appropriate distances along with the Benzécri’s chi-squared distance in combination with the Ward’s linkage method, is attempted using data originating from molecular markers applied on pear trees species and Sinapis arvensis populations. Fruit trees cluster analysis was performed using SSR markers, while for Sinapis arvensis populations’ clustering, ISSR markers were used. The results showed that the “golden standard” is not the only appropriate method for dendrogram construction based on binary data derived from molecular markers. Ten other hierarchical clustering methods could be used for the construction of dendrograms from SSR markers and thirty-seven other hierarchical clustering methods could be used for the construction of dendrograms using binary data resulted from ISSR markers.