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Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms

DOI: 10.1186/1471-2148-9-61

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Abstract:

We performed maximum likelihood bootstrap analyses of the complete, 3-gene 567-taxon data matrix and the incomplete, 5-gene 567-taxon data matrix. Although the 5-gene matrix has more missing data (27.5%) than the 3-gene data matrix (2.9%), the 5-gene analysis resulted in higher levels of bootstrap support. Within the 567-taxon tree, the increase in support is most evident for relationships among the 170 taxa for which both matK and 26S rDNA sequences were added, and there is little gain in support for relationships among the 119 taxa having neither matK nor 26S rDNA sequences. The 5-gene analysis also places the enigmatic Hydrostachys in Lamiales (BS = 97%) rather than in Cornales (BS = 100% in 3-gene analysis). The placement of Hydrostachys in Lamiales is unprecedented in molecular analyses, but it is consistent with embryological and morphological data.Adding available, and often incomplete, sets of sequences to existing data sets can be a fast and inexpensive way to increase support for phylogenetic relationships and produce novel and credible new phylogenetic hypotheses.Molecular data have had an enormous impact on angiosperm phylogenetic hypotheses (e.g. [1-5]), and the abundance of new sequence data provides the potential for further resolving angiosperm relationships. Still, molecular phylogenetic studies across all angiosperms have utilized only a small fraction of the available sequence data. While GenBank currently contains over 1.7 million core nucleotide sequences from angiosperms, with over 160,000 of these being from often phylogenetically useful plastid loci [6], few phylogenetic analyses of angiosperms have included more than a thousand sequences. We examine whether augmenting existing plant data matrices with incomplete data assembled from publicly available sources can enhance the understanding of the backbone phylogenetic relationships across angiosperms.The sampling strategies of phylogenetic studies across angiosperms demonstrate a tradeoff betw

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