Supplementary information for: A biased fossil record can preserve reliable phylogenetic signal

Abstract.­­––The fossil record is notoriously imperfect and biased in
representation, hindering our ability to place fossil specimens into an
evolutionary context. For groups with fossil records mostly
consisting of disarticulated parts (e.g., vertebrates, echinoderms,
plants), the limited morphological information preserved sparks concerns
about whether fossils retain reliable evidence of phylogenetic
relationships, and lends uncertainty to analyses of diversification,
paleobiogeography, and biostratigraphy in Earth history. To
address whether a fragmentary past can be trusted, we need to assess
whether incompleteness affects the quality of phylogenetic information
contained in fossil data. Herein, we characterize skeletal incompleteness
bias in a large dataset (6,585 specimens; 14,417 skeletal
elements) of fossil squamates (lizards, snakes, amphisbaenians,
and mosasaurs). We show that jaws + palatal bones, vertebrae, and ribs
appear more frequently in the fossil record than other parts of the
skeleton. This incomplete anatomical representation in the fossil record
is biased against regions of the skeleton that contain the majority of
morphological phylogenetic characters used to assess squamate evolutionary
relationships. Despite this bias, parsimony- and model-based comparative
analyses indicate that the most frequently-occurring parts of the skeleton
in the fossil record retain similar levels of phylogenetic signal as parts
of the skeleton that are rarer. These results demonstrate that the biased
squamate fossil record contains reliable phylogenetic information, and
support our ability to place incomplete fossils in the Tree of
Life.