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.

化石在演化研究中的应用价值，取决于其能否被精准安置于系统发育框架（phylogenetic frameworks）中，但固有的、普遍存在的缺失数据使得这一工作极具挑战性。化石形成过程中发生的复杂埋藏学（taphonomic）过程，极易让人难以区分“物种原本不存在该特征”与“特征未被保存下来”，对于保存异常完好的软组织化石（soft-tissue fossils）而言尤为如此：某一化石中缺失的特定形态特征（如附肢、触手或神经），究竟是该物种本就不具备该特征（系统发育缺失，phylogenetic absence），还是仅仅未被保存下来（埋藏学丢失，taphonomic loss）？目前学界尚未在非现存解剖结构的解读，以及演化亲缘关系的定向偏移与偏差分析中，对缺失数据展开相关检验。本研究中，我们通过将现存特征编码（1）替换为缺失编码（？）或缺失特征编码（0）的方式，对模拟及实测的完整分类群（taxa）施加数据丢失处理。两种替换方式均会导致分类群从其在系统发育树上的原始位置向根部方向滑移。对于人为引入的缺失特征而言，引发显著下移的绝对阈值极低：仅需替换2个现存特征（占现存特征总量的6%）即可触发显著下移。而实测化石类群的阈值恰好相反：将2个预设的缺失特征替换为现存特征时，会导致化石类群向系统发育树的顶端方向上移。由此可见，仅需少数未被保存的特征被误判为物种本就缺失的特征，就会使得化石物种被错误解读为比其实际生存状态更为原始的类群。这种对非现存形态特征编码的敏感性，给所有试图利用化石重建演化速率或解析形态变化序列的演化研究带来了共性难题。所谓向茎类群滑移（stem-ward slippage），即埋藏过程导致生物体被人为判定为更为原始的类群，这一现象似乎是缺失数据所固有的、普遍存在且极具挑战性的问题，即便不存在腐烂偏差亦是如此。因此，对于缺失特征的解读，必须辅以明确的论证依据与埋藏学分析框架方能成立。