Including autapomorphies is important for paleontological tip-dating with clocklike data, but not with non-clock data

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dc.contributor.author Matzke, Nicholas en
dc.contributor.author Irmis, RB en
dc.date.accessioned 2018-10-25T23:53:04Z en
dc.date.issued 2018-04-06 en
dc.identifier.citation PeerJ 6:e4553 Jan 2018 en
dc.identifier.issn 2167-8359 en
dc.identifier.uri http://hdl.handle.net/2292/43488 en
dc.description.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. en
dc.publisher PeerJ Inc. en
dc.relation.ispartofseries PeerJ en
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. en
dc.rights.uri https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm en
dc.rights.uri https://creativecommons.org/licenses/by/4.0/ en
dc.title Including autapomorphies is important for paleontological tip-dating with clocklike data, but not with non-clock data en
dc.type Journal Article en
dc.identifier.doi 10.7717/peerj.4553 en
pubs.volume 6 en
dc.rights.holder Copyright: The authors en
dc.identifier.pmid 29637019 en
pubs.author-url https://peerj.com/articles/4553/ en
dc.rights.accessrights http://purl.org/eprint/accessRights/OpenAccess en
pubs.subtype Article en
pubs.elements-id 735647 en
pubs.org-id Science en
pubs.org-id Biological Sciences en
dc.identifier.eissn 2167-8359 en
pubs.record-created-at-source-date 2018-04-09 en
pubs.online-publication-date 2018-04-06 en
pubs.dimensions-id 29637019 en


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