title: Bayesian Morphological Clock Methods Resurrect Placoderm Monophyly and Reveal Rapid Early Evolution in Jawed Vertebrates.
abstract: The phylogeny of early gnathostomes provides an important framework for understanding one of the most significant evolutionary events, the origin and diversification of jawed vertebrates. A series of recent cladistic analyses have suggested that the placoderms, an extinct group of armoured fish, form a paraphyletic group basal to all other jawed vertebrates. We revised and expanded this morphological data set, most notably by sampling autapomorphies in a similar way to parsimony-informative traits, thus ensuring this data (unlike most existing morphological data sets) satisfied an important assumption of Bayesian tip-dated morphological clock approaches. We also found problems with characters supporting placoderm paraphyly, including character correlation and incorrect codings. Analysis of this data set reveals that paraphyly and monophyly of core placoderms (excluding maxillate forms) are essentially equally parsimonious. The two alternative topologies have different root positions for the jawed vertebrates but are otherwise similar. However, analysis using tip-dated clock methods reveals strong support for placoderm monophyly, due to this analysis favoring trees with more balanced rates of evolution. Furthermore, enforcing placoderm paraphyly results in higher levels and unusual patterns of rate heterogeneity among branches, similar to that generated from simulated trees reconstructed with incorrect root positions. These simulations also show that Bayesian tip-dated clock methods outperform parsimony when the outgroup is largely uninformative (e.g., due to inapplicable characters), as might be the case here. The analysis also reveals that gnathostomes underwent a rapid burst of evolution during the Silurian period which declined during the Early Devonian. This rapid evolution during a period with few articulated fossils might partly explain the difficulty in ascertaining the root position of jawed vertebrates.
authors.affiliation: School of Biological Sciences, Flinders University, PO Box 2100, Adelaide, South Australia 5001, Australia.
authors.forename: Benedict
authors.initials: B
authors.lastname: King
authors.affiliation: Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, PO Box 643, Beijing 100044, China.
authors.forename: Tuo
authors.initials: T
authors.lastname: Qiao
authors.affiliation: School of Biological Sciences, Flinders University, PO Box 2100, Adelaide, South Australia 5001, Australia.|Earth Sciences Section, South Australian Museum, North Terrace, Adelaide 5000, Australia.
authors.forename: Michael S Y
authors.initials: MSY
authors.lastname: Lee
authors.affiliation: Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, PO Box 643, Beijing 100044, China.
authors.forename: Min
authors.initials: M
authors.lastname: Zhu
authors.affiliation: School of Biological Sciences, Flinders University, PO Box 2100, Adelaide, South Australia 5001, Australia.
authors.forename: John A
authors.initials: JA
authors.lastname: Long
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D005075:Biological Evolution; D002965:Classification / Q000379:methods*; D005580:Fossils; D008954:Models, Biological; D010802:Phylogeny; D014714:Vertebrates
keywords: BEAST; Bayesian; monophyly; morphological clock; morphology; phylogenetics; placoderms; tip dating; tree topology