Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants

摘要

The ever-larger data matrices resulting from continuing improvements in DNA sequencing techniques require faster and more efficient methods of phylogenetic analysis. Here, a promising new method, parsimony jackknifing, was examined by analysing a matrix comprising 2538 sequences of the chloroplast ribulose-bisphosphate carboxylase large subunit gene rbcL. The sequences included cover a broad taxonomic range, from cyanobacteria to flowering plants. Several parsimony jackknife analyses were performed, both with and without branch-swapping and multiple random addition sequences: (1) including all positions; (2) including only first and second codon positions; (3) including only third positions; and (4) using only transversions. The best resolution was obtained using all positions. Removal of third positions or transitions led to massive loss of resolution, although using only transversions somewhat improved basal resolution. While branch-swapping improved both resolution and the support found for several groups, most of the groups could be recovered by faster simple analyses. Designed to eliminate groups poorly supported by the data, parsimony jackknifing recognized 1400 groups on the basis of all rbcL positions. These included major taxa such as green plants, land plants, flowering plants, monocots and eudicots. Appendices are included of supported angiosperm families, as well as larger groups.