Integration of Clustering and Multidimensional Scaling to Determine Phylogenetic Trees as Spherical Phylograms Visualized in 3 Dimensions

Abstract

Phylogenetic analysis is commonly used to analyze genetic sequence data from fungal communities, while ordination and clustering techniques commonly are used to analyze sequence data from bacterial communities. However, few studies have attempted to link these two independent approaches. In this paper, we propose a method, which we call spherical phylogram (SP), to display the phylogenetic tree within the clustering and visualization result from a pipeline called DACIDR. In comparison with traditional tree display methods, the correlations between the tree and the clustering can be observed directly. In addition, we propose an algorithm called interpolative joining (IJ) to construct and visualize the SP in 3D space. In the experiments, we used the sum of branch lengths to quantify the general fit between the clustering and the phylogenetic tree in SP and Mantel tests to determine how well the same grouping of sequences was preserved between the clustering and the SP. Our results show that DACIDR has a classification accuracy that is similar to a phylogenetic tree generated using a multiple sequence alignment, while having much lower computational cost.

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering

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