ArticleScientific reports2013
TreeParser-aided Klee diagrams display taxonomic clusters in DNA barcode and nuclear gene datasets.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed.
- PyKleeBarcode: Enabling representation of the whole animal kingdom in information space.PloS one · 2023Article
- Article
- Bridging two scholarly islands enriches both: COI DNA barcodes for species identification versus human mitochondrial variation for the study of migrations and pathologies.Ecology and evolution · 2016Article
- Interbreeding among deeply divergent mitochondrial lineages in the American cockroach (Periplaneta americana).Scientific reports · 2015Article
- The Application of DNA Barcodes for the Identification of Marine Crustaceans from the North Sea and Adjacent Regions.PloS one · 2015Article
- DNA barcoding works in practice but not in (neutral) theory.PloS one · 2014Article
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2 authors.
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Abstract
Indicator vector analysis of a nucleotide sequence alignment generates a compact heat map, called a Klee diagram, with potential insight into clustering patterns in evolution. However, so far this approach has examined only mitochondrial cytochrome c oxidase I (COI) DNA barcode sequences. To further explore, we developed TreeParser, a freely-available web-based program that sorts a sequence alignment according to a phylogenetic tree generated from the dataset. We applied TreeParser to nuclear gene and COI barcode alignments from birds and butterflies. Distinct blocks in the resulting Klee diagrams corresponded to species and higher-level taxonomic divisions in both groups, and this enabled graphic comparison of phylogenetic information in nuclear and mitochondrial genes. Our results demonstrate TreeParser-aided Klee diagrams objectively display taxonomic clusters in nucleotide sequence alignments. This approach may help establish taxonomy in poorly studied groups and investigate higher-level clustering which appears widespread but not well understood.
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