Tip-dating, where fossils are included as dated terminal taxa in Bayesian dating inference, is an increasingly popular method. Data for these studies often come from morphological character matrices originally developed for non-dated, and usually parsimony, analyses. In parsimony, only shared derived characters (synapomorphies) provide grouping information, so many character matrices have an ascertainment bias: they leave out autapomorphies (unique derived character states), which are

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... uninformative. There has been no study of the affect of this ascertainment bias in tip-dating, but autapomorphies can be informative in model-based inference. We expected that excluding autapomorphies would shorten the morphological branchlengths of terminal branches, and thus bias downwards the time branchlengths inferred in tip-dating. We tested for this effect using a matrix for Carboniferous-Permian eureptiles where all autapomorphies had been deliberately coded. Surprisingly, date estimates are virtually unchanged when autapomorphies are excluded, although we find large changes in morphological rate estimates and small effects on topological and dating confidence. We hypothesized that the puzzling lack of effect on dating was caused by the non-clock nature of the eureptile data. We confirm this explanation by simulating strict clock and non-clock datasets, showing that autapomorphy exclusion biases dating only for the clocklike case. A theoretical solution to ascertainment bias is computing the ascertainment bias correction (Mk parsinf ), but we explore this correction in detail, and show that it is computationally impractical for typical datasets with many character states and taxa. Therefore we recommend that palaeontologists collect autapomorphies whenever possible when assembling character matrices. PeerJ reviewing PDF | (12 13 Abstract 14 Tip-dating, where fossils are included as dated terminal taxa in Bayesian dating inference, is an 15 increasingly popular method. Data for these studies often come from morphological character 16 matrices originally developed for non-dated, and usually parsimony, analyses. In parsimony, 17 only shared derived characters (synapomorphies) provide grouping information, so many 18 character matrices have an ascertainment bias: they leave out autapomorphies (unique derived 19 character states), which are considered uninformative. There has been no study of the affect of 20 this ascertainment bias in tip-dating, but autapomorphies can be informative in model-based 21 inference. We expected that excluding autapomorphies would shorten the morphological 22 branchlengths of terminal branches, and thus cause artificially shortened time branchlengths PeerJ reviewing PDF | (Manuscript to be reviewed 23 inferred in tip-dating. We tested for this effect using a matrix for Carboniferous-Permian 24 eureptiles where all autapomorphies had been deliberately coded. Surprisingly, date estimates 25 are virtually unchanged when autapomorphies are excluded, although we find large changes in 26 morphological rate estimates and small effects on topological and dating confidence. We 27 hypothesized that the puzzling lack of effect on dating was caused by the non-clock nature of 28 the eureptile data. We confirm this explanation by simulating strict clock and non-clock 29 datasets, showing that autapomorphy exclusion biases dating only for the clocklike case. A 30 theoretical solution to ascertainment bias is computing the ascertainment bias correction 31 (Mk parsinf ), but we explore this correction in detail, and show that it is computationally 32 impractical for typical datasets with many character states and taxa. Therefore we recommend 33 that palaeontologists collect autapomorphies whenever possible when assembling character 34 matrices. 35 36 37 38 PeerJ reviewing PDF | (