The Shape and Dimensionality of Phylogenetic Tree-Space Based on Mitochondrial Genomes

James Wilgenbusch,Kyle Gallivan,Wen Huang

doi:10.1038/npre.2010.4605.1

Abstract

AbstractPhylogenetic analyses of large and diverse data sets generally result in large sets of competing phylogenetic trees. Consensus tree methods used to summarize sets of competing trees discard important information regarding the similarity and distribution of competing trees. A more fine grain approach is to use a dimensionality reduction method to project tree-to-tree distances in 2D or 3D space. In this study, we systematically evaluate the performance of several nonlinear dimensionality reduction (NLDR) methods on tree-to-tree distances obtained from independent nonparametric bootstrap analyses of genes from three mid- to large-sized mitochondrial genome alignments.

Highlights

The Shape and Dimensionality of Phylogenetic Tree-Space Based on Mitochondrial Genomes
Representing phylogenetic trees supported by different genes or by other a priori defined data partitions in 2- or 3-Dimensional (D) space can be a useful way for investigators to gain a better perspective on potential problems sometimes associated with the analysis of large multi-source data sets (Hillis et al, 2005)
Dimensionality reduction methods and evaluation criteria were performed using software developed by the authors (GPL: http://bpd.sc.fsu.edu/index.php/component/content/article/64), while bootstrap analyses and tree-to-tree distances were calculated using PAUP* (Swofford, 2002)

Summary

Introduction

Representing phylogenetic trees supported by different genes or by other a priori defined data partitions in 2- or 3-Dimensional (D) space can be a useful way for investigators to gain a better perspective on potential problems sometimes associated with the analysis of large multi-source data sets (Hillis et al, 2005). The Shape and Dimensionality of Phylogenetic Tree-Space Based on Mitochondrial Genomes Wilgenbusch, Department of Scientific Computing, Florida State University Wen Huang, Department of Mathematics, Florida State University Kyle A.

Results

Conclusion