Data from: Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices

Implied weighting, a method for phylogenetic inference that actively seeks
to downweight supposed homoplasy, has in recent years begun to be widely
utilized in palaeontological datasets. Given the method's purported
ability at handling widespread homoplasy/convergence, we investigate the
effects of implied weighting on modelled phylogenetic data. We generated
100 character matrices consisting of 55 characters each using a Markov
Chain morphology model of evolution based on a known phylogenetic tree.
Rates of character evolution in these datasets were variable and generated
by pulling from a gamma distribution for each character in the matrix.
These matrices were then analysed under equal weighting and four settings
of implied weights (k = 1, 3, 5, and 10). Our results show that implied
weighting is inconsistent in its ability to retrieve a known phylogenetic
tree. Equally weighted analyses are found to generally be more
conservative, retrieving higher frequency of polytomies but being less
likely to generate erroneous topologies. Implied weighting is found to
generally resolve polytomies while also propagating errors, resulting in
an increase in both correctly and incorrectly resolved nodes with a
tendency towards higher rates of error compared to equal weighting. Our
results suggest that equal weights may be a preferable method for
parsimony analysis.