Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 19, Issue 4, Pages 554-562Publisher
OXFORD UNIV PRESS
DOI: 10.1093/oxfordjournals.molbev.a004111
Keywords
genomics; mitochondrial DNA; molecular phylogenetics; molecular systematics; sequence analysis; singular value decomposition
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We recently developed a method for producing comprehensive gene and species phylogenies from unaligned whole,genome data using singular value decomposition (SVD) to analyze character string frequencies. This work provides an integrated gene and species phylogeny for 64 vertebrate mitochondrial genomes composed of 832 total proteins. In addition, to provide a theoretical basis for the method, we present a graphical interpretation of both the original frequency matrix and the SVD-derived matrix. These large matrices describe high-dimensional Euclidean spaces within which biomolecular sequences can be uniquely represented as vectors. In particular, the SVD-derived vector space describes each protein relative to a restricted set of newly defined, independent axes, each of which represents a novel form of conserved motif, termed a correlated peptide motif. A quantitative comparison of the relative orientations of protein vectors in this space provides accurate and straightforward estimates of sequence similarity, which can in turn be used to produce comprehensive gene trees. Alternatively. the vector representations of genes from individual species can be summed, allowing species trees to be produced.
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