10.5061/DRYAD.7DQ0J
Congreve, Curtis R.
Pennsylvania State University
Lamsdell, James C.
Yale University
American Museum of Natural History
Data from: Implied weighting and its utility in palaeontological datasets:
a study using modelled phylogenetic matrices
Dryad
dataset
2017
Cladistics
parsimony
character weights
Homoplasy
2017-02-18T00:00:00Z
en
https://doi.org/10.1111/pala.12236
12953241 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
Appendix S1 - TNT filesZip file containing all 100 matrices generated from
our MK model of morphological change.S1 - TNT files.zipAppendix S2 –
TreesZip file containing pdfs of all consensus trees generated from equal
and implied weighting analyses for all 100 matrices. The files have been
commented on to denote correct and incorrect node relationships with
checks and x's respectively.S2 - Trees.zipAppendix S3 - Spreadsheet
of Node CountsExcel spreadsheet with raw counts of correct, incorrect, and
unknown relationships for all runs of equal and implied weighting, as well
standardized counts of implied weighting relative to equal weighting, and
overall counts of the relative proportions of the data which increase or
decrease error.S3 - Spreadsheet of Node Counts.xlsxAppendix S4 – Run
Counts of Repeated ErrorsA checklist of the 100 runs counting off the
number of times an error in equal weighting was repeated in 1, 2, 3, and
all 4 implied weights runs.S4 - Run Counts of repeated errors.xlsxAppendix
S5 - Character Weights Test NEXUS filesZip folder containing all 100 nexus
files used in the character weights tests. These matrices contain the same
4 characters (Character 56-59), generated with known rates of evolution.S5
- Character Weights Test NEXUS files.zipAppendix S6 - Character
WeightsExcel spreadsheet of the weights/fits generated for our four
characters in all 100 matrices for four values of k (1,3,5,10).S6 -
Character Weights.xlsx