Taxonomics Methods Using DNA

National Library Of Medicine

Investigators

Linked publications & trials

Abstract

Originally, Dr. Spouge was invited to the 2009 Edinburgh Conference Selecting Barcode Loci for Plants, a gathering of a subset of the Plant Working Group within the Consortium for the Barcode of Life, to help select a plant barcode. The other conference participants sequenced 7 candidate barcode loci across a broad range of land plants, so Dr Spouge and Damon Little of the New York Botanical Garden could analyze the resulting data, to permit the conference participants to select markers for a plant barcode. The Edinburgh Conference selected rbcL and matK as the 2 plant barcode markers, from 7 choices. Later, Dr. Spouge performed a similar data analysis for the Fungal Barcode Working Group in Amsterdam (2011), which selected ITS (the Internal Transcribed Spacer between structural ribosomal RNAs) from 4 choices. He offered similar services to the Protist Barcode Working Group in Berlin (2011), but insufficient data prevented a decisive analysis. He had made implementations of his analysis publicly available in user-friendly programs, to permit barcode researchers to carry out their own analyses. More recently, in collaboration with Dr. Martin, he has analyzed the efficacy of barcodes in identifying South-East Asian fungi. Such analyses are likely to be particularly important in selecting secondary markers in different fungal clades. He is also working with Dr Martin to test web tools for automating the evaluation of barcode efficacy. The collaboration is producing statistical tools for the objective evaluation of the accuracy of taxonomic classification. Dr Spouge has developed statistical tests for evaluating the accuracy of taxonomic identification, and Dr Martin is applying the methods and tools to the evaluation of DNA barcodes in the fungal Genus Ramaria. Drs Erickson and Sun, in collaboration with Dr Spouge, have developed alignment-free methods of identifying the source populations and have applied the methods to white oak, a notoriously taxonomically difficult case.