Using More Than the Oldest Fossils: Dating Osmundaceae with Three Bayesian Clock Approaches

• Published in: Systematic biology 2015-05, Vol.64 (3), p.396-405
• Main Authors: Grimm, Guido W., Kapli, Paschalia, Bomfleur, Benjamin, McLoughlin, Stephen, Renner, Susanne S.
• Format: Article
• Language: English
• Subjects: Aquatic plants; Bayes Theorem; Bayesian analysis; Bayesian dating methods; Calibration; Classification - methods; Deoxyribonucleic acid; DNA; Ecosystems and species history; Ekosystem och arthistoria; Extinction; Extinction, Biological; Ferns; Ferns - classification; Fosilized birth-death dating; Fossils; Genetic Speciation; Genetics; Molecular clocks; Neogene; Node dating; Osmunda; Osmundastrum; Paleozoic; Phylogeny; Royal ferns; Speciation; Systematic biology; Time; Total evidence dating; Triassic
• ISSN: 1063-5157; 1076-836X; 1076-836X
• DOI: 10.1093/sysbio/syu108

A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved—"node dating" (ND) in BEAST, "total evidence" (TE) dating in MrBayes, and the "fossilized birth-death" (FBD) in FDPPDiv—to infer divergence times in the royal ferns. Osmundaceae have 16-17 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ~17 genera. For ND, we used the five oldest fossils, whereas for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils, we included up to 36 rhizomes and frond compression/impression fossils, which for TE dating were scored for 33 morphological characters. We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence ages were generally greater than those inferred from ND; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We prefer the FBD-derived ages because they best fit the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Paleozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, the FBD approach yielded speciation and extinction rates that overlapped those obtained from just neontological data. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling; therefore, these estimates should be treated with caution.