Data from: Bias and sensitivity in the placement of fossil taxa resulting from interpretations of missing data

The utility of fossils in evolutionary contexts is dependent on their
accurate placement in phylogenetic frameworks, yet intrinsic and
widespread missing data make this problematic. The complex taphonomic
processes occurring during fossilization can make it difficult to
distinguish absence from non-preservation, especially in the case of
exceptionally preserved soft-tissue fossils: is a particular morphological
character (e.g. appendage, tentacle or nerve) missing from a fossil
because it was never there (phylogenetic absence), or just happened to not
be preserved (taphonomic loss)? Missing data has not been tested in the
context of interpretation of non-present anatomy nor in the context of
directional shifts and biases in affinity. Here, complete taxa, both
simulated and empirical, are subjected to data loss through the
replacement of present entries (1s) with either missing (?s) or absent
(0s) entries. Both cause taxa to drift down trees, from their original
position, toward the root. Absolute thresholds at which downshift is
significant are extremely low for introduced absences (2 entries replaced,
6 % of present characters). The opposite threshold in empirical fossil
taxa is also found to be low; two absent entries replaced with presences
causes fossil taxa to drift up trees. As such, only a few instances of
non-preserved characters interpreted as absences will cause fossil
organisms to be erroneously interpreted as more primitive than they were
in life. This observed sensitivity to coding non-present morphology
presents a problem for all evolutionary studies that attempt to use
fossils to reconstruct rates of evolution or unlock sequences of
morphological change. Stem-ward slippage, whereby fossilization processes
cause organisms to appear artificially primitive, appears to be a
ubiquitous and problematic phenomenon inherent to missing data, even when
no decay biases exist. Absent characters therefore require explicit
justification and taphonomic frameworks to support their interpretation.