Data from: Using supermatrices for phylogenetic inquiry: an example using the sedges

In this article, we use supermatrix data-mining methods to reconstruct a
large, highly inclusive phylogeny of Cyperaceae from nucleotide data
available on GenBank. We explore the properties of these trees and their
utility for phylogenetic inference, and show that even the highly
incomplete alignments characteristic of supermatrix approaches may yield
very good estimates of phylogeny. We present a novel pipeline for
filtering sparse alignments to improve their phylogenetic utility by
maximizing the partial decisiveness of the matrices themselves through a
technique we call “phylogenetic scaffolding,” and we present a new method
of scoring tip instability (i.e. “rogue taxa”) based on the I statistic
implemented in the software Mesquite. The modified statistic, which we
call IS, is somewhat more straightforward to interpret than similar
statistics, and our implementation of it may be applied to large sets of
large trees. The largest sedge trees presented here contain more than 1500
tips (about one quarter of all sedge species) and are based on multigene
alignments with more than 20 000 sites and more than 90% missing data.
These trees match well with previously supported phylogenetic hypotheses,
but have lower overall support values and less resolution than more
heavily filtered trees. Our best-resolved trees are characterized by
stronger support values than any previously published sedge phylogenies,
and show some relationships that are incongruous with previous studies.
Overall, we show that supermatrix methods offer powerful means of pursuing
phylogenetic study and these tools have high potential value for many
systematic biologists.