Data from: A comparison of supermatrix and supertree methods for multilocus phylogenetics using organismal datasets

It has been proposed that supertree approaches should be applied to large
multilocus sequence datasets to achieve computational tractability. Large
datasets such as those derived from phylogenomics studies can be broken
into many locus-specific tree searches and the resulting trees can be
stitched together via a supertree method. Using simulated data, workers
have reported that they can rapidly construct a supertree that is
comparable to the results of heuristic tree search on the entire dataset.
To test this assertion with organismal data, we compared tree length under
the parsimony criterion and computational time for twenty multilocus
datasets using supertree (SuperFine and SuperTriplets) and supermatrix
(heuristic search in TNT) approaches. Tree length and computational times
were compared among methods using the Wilcoxon matched-pairs signed rank
test. Supermatrix searches produce significantly shorter trees than either
supertree approach (SuperFine or SuperTriplets; p < 0.0002 in both
cases). Moreover, the processing time of supermatrix search was
significantly lower than SuperFine+locus-specific search (p < 0.01)
but roughly equivalent to that of SuperTriplets+locus-specific search (p
> 0.4, not significant). In conclusion, we show by using real
rather than simulated data, that there is no basis, either in time
tractability or tree length, for use of supertrees over heuristic tree
search using a supermatrix for phylogenomics.