Phylogenetic Tree Construction for Y-DNA Haplogroups

Male Y-chromosome is currently used to estimate the paternal ancestry and migratory patterns of humans. Y-chromosomal Short Tandem Repeat(STR) segments provide important data for reconstructing phylogenetic trees. However, STR data is not widely used for phylogeny because there is not enough appropriate methodology. We propose a three-step method for analyzing large numbers of STR data and constructing phylogenetic trees. We implement our method on 145 samples from the Y-DNA Haplogroup G. We use distance matrix based phylogeny so we find genetic distance between each sample first. Then samples are partitioned into a number of clusters. Finally we construct phylogenetic trees for each cluster by using Neighbor-Joining (NJ) method. We also propose a new partitioning based clustering algorithm. We compare several partitioning based (e.g. FCM) and density based (e.g. FN-DBSCAN) clustering algorithms with our algorithm. We use Multi-Dimensional Scaling (MDS) to visualize samples and compare results of MDS with results of NJ method.