Structural Analysis of Biodiversity.

Sirovich, Lawrence; Stoeckle, Mark Y.; Yu Zhang

Large, recently-available genomic databases cover a wide range of life forms, suggesting opportunity for insights into genetic structure of biodiversity. In this study we refine our recently-described technique using indicator vectors to analyze and visualize nucleotide sequences. The indicator vector approach generates correlation matrices, dubbed Klee diagrams, which represent a novel way of assembling and viewing large genomic datasets. To explore its potential utility, here we apply the improved algorithm to a collection of almost 17000 DNA barcode sequences covering 12 widely-separated animal taxa, demonstrating that indicator vectors for classification gave correct assignment in all 11000 test cases. Indicator vector analysis revealed discontinuities corresponding to species- and higher-level taxonomic divisions, suggesting an efficient approach to classification of organisms from poorly-studied groups. As compared to standard distance metrics, indicator vectors preserve diagnostic character probabilities, enable automated classification of test sequences, and generate high-information density single-page displays. These results support application of indicator vectors for comparative analysis of large nucleotide data sets and raise prospect of gaining insight into broad-scale patterns in the genetic structure of biodiversity.

BIODIVERSITY; GENOMES; GENETICS; NUCLEOTIDE sequence; VECTOR analysis; BIOLOGICAL classification; NUCLEIC acid analysis; QUALITATIVE research

PLoS ONE, 2010, Vol 5, Issue 2, p1

1932-6203

Academic Journal

10.1371/journal.pone.0009266