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Abstract Detail

Systematics Section/ASPT

Burleigh, Gordon [1], Endara, Lorena [2], Nagalingum, Nathalie [3], Cui, Hong [4].

Semi-automated approaches for extracting phylogenetically informative phenomic datasets from the taxonomic descriptions.

Taxonomic descriptions in the legacy natural history literature provide a wealth of phylogenetically informative phenomic data. We describe new software and approaches, developed as part of the NSF-funded AVAToL Next Generation Phenomics project, to extract phenomic datasets from taxonomic descriptions for use in phylogenetics and evolutionary inference. First, phenomic data are extracted from taxonomic descriptions, and the terms that are not recognized are manually classified by the user. The dataset is then re-analyzed, and the resulting file is converted into a taxon-character matrix. These steps are performed using software available on the Explorer of Taxon Concepts (ETC) website ( MatrixConverter software facilitates the evaluation of character state homology, and it provides tools to enable the characters to be converted into a discrete character matrix for use in phylogenetic analyses. We also discuss the development of a new plant glossary with nearly 10,000 terms from the Flora of North America and Flora of China that has been incorporated into the ETC website to help phenomic character extraction on botanical datasets. We demonstrate these new tools on generic and species descriptions of the Cycadales (Cycads) from the Cycad pages ( The phenomic supermatrix built from these new tools can complement molecular datasets to provide a credible, comprehensive phylogeny of cycads.

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1 - University Of Florida, P.O. Box 118526, Gainesville, FL, 32611, USA
2 - University of Florida, Department of Biology, Gainesville, FL, 32609, USA
3 - Royal Botanic Garden, Sydney, Australia
4 - University of Arizona, School of Information Resources & Library Science, Tucson, AZ, USA


Presentation Type: Oral Paper:Papers for Sections
Session: 18
Location: Salon 3/The Shaw Conference Centre
Date: Monday, July 27th, 2015
Time: 1:30 PM
Number: 18001
Abstract ID:1062
Candidate for Awards:None

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