Abstract
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.
Highlights
Genetic study of biodiversity has been hampered by the relatively small number of species represented in databases
We first considered 12 animal groups, using COI sequences deposited in barcode sequence alignments deposited in (BOLD) taxon-specific projects (Table 2)
This paper describes a mathematical approach to comparative analysis of nucleotide sequences using digital transformation in vector space
Summary
Genetic study of biodiversity has been hampered by the relatively small number of species represented in databases. The largest set of alignable sequences in GenBank (small subunit ribosomal RNA) represents fewer than 21,000 species and the second largest (cytochrome b) includes fewer than 14,000 [1]. This is modest coverage compared to the approximately 1.9 million named species of plants and animals and likely much larger numbers of protozoa, fungi, bacteria, and archaea [2]. A primary goal of comparative genetic study is assembling a Tree of Life that represents the temporal sequence of evolutionary divergences. Potential limitations to tree representations include difficulty in representing discontinuities among species or groups of species, as all taxa are linked in a continuous structure; visualizing horizontal affinities across groups, as taxa within each group are joined in a single branch; and comparing data sets such as from ecological surveys, as branching diagrams challenge visual comparison
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