Abstract
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 omit autapomorphies (unique derived character states), which are considered uninformative. There has been no study of the effect 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 (Mkparsinf), 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.
Highlights
In parsimony phylogenetic analyses, the only data informative for reconstructing the tree topology are those with grouping information: potentially shared, derived character states
Tipdating analyses might be expected to be sensitive to autapomorphies: all autapomorphies occur on terminal branches by definition, so their exclusion will shorten the morphological branchlengths of terminal branches, and perhaps increase estimated branch-wise rate variation
The summary Maximum Clade Credibility (MCC) trees were plotted with 95% highest posterior densities (HPDs) on inferred node and tip dates using BEASTmasteR functions and custom R scripts
Summary
The only data informative for reconstructing the tree topology are those with grouping information: potentially shared, derived character states (synapomorphies; Hennig, Davis & Zangerl, 1999). An autapomorphy—a state unique to one terminal taxon or Operational Taxonomic Unit (OTU; Mishler, 2005)—contributes one step to any possible topology. In model-based inference, autapomorphies can be informative (Lewis, 2001; Wright & Hillis, 2014), because autapomorphies contribute information about the overall rate of change in the character matrix and site-specific rate heterogenetity. An insufficiently recognized point is that autapomorphies might be important in ‘‘tipdating’’ analyses, where terminal taxa include fossils with ages older than the present day (Alexandrou et al, 2013; Pyron, 2011; Ronquist et al, 2012; Wood et al, 2013). Tipdating analyses might be expected to be sensitive to autapomorphies: all autapomorphies occur on terminal branches by definition, so their exclusion will shorten the morphological branchlengths of terminal branches (and presumably their time branchlengths), and perhaps increase estimated branch-wise rate variation
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
