Data from: Measuring stratigraphic congruence across trees, higher taxa, and time

The congruence between the order of cladistic branching and the first
appearance dates of fossil lineages can be quantified using a variety of
indices. Good matching is a prerequisite for the accurate time calibration
of trees, while the distribution of congruence across large samples of
cladograms has underpinned claims about temporal and taxonomic patterns of
completeness in the fossil record. The most widely used stratigraphic
congruence indices are the stratigraphic consistency index, the modified
Manhattan stratigraphic measure, and the gap excess ratio (plus its
derivatives; the topological gap excess ratio and the modified gap excess
ratio). Many factors are believed to variously bias these indices, with
several empirical and simulation studies addressing some subset of the
putative interactions. This study combines both approaches to quantify the
effects (on all five indices) of eight variables reasoned to constrain the
distribution of possible values (the number of taxa, tree balance, tree
resolution, range of first occurrence dates, center of gravity of first
occurrence dates, the variability of first occurrence dates, percentage of
extant taxa, and percentage of taxa with no fossil record). Our empirical
data set comprised 647 published vertebrate and invertebrate cladograms
spanning the entire Phanerozoic, and for these data we also modelled the
effects of mean age of first occurrences (as a proxy for clade age), the
taxonomic rank of the clade, and the higher taxonomic group to which it
belonged. The center of gravity of first occurrence dates had not been
investigated hitherto, and this was found to correlate most strongly with
some measures of stratigraphic congruence in our empirical study
(top-heavy clades had better congruence). The modified gap excess ratio
was the index least susceptible to bias. We found significant differences
across higher taxa for all indices; arthropods had lower congruence and
tetrapods higher congruence. Stratigraphic congruence – however measured –
also varied throughout the Phanerozoic, reflecting the taxonomic
composition of our sample. Notably, periods containing a high proportion
of arthropods had poorer congruence overall than those with higher
proportions of tetrapods.