DOI: 10.5061/dryad.m6t1m
title: Data from: Using more than the oldest fossils: dating Osmundaceae with three Bayesian clock approaches

description: 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.
description: Main matrices and dating
 resultsThis archive includes
 the basic matrix files and the main result files of the various dating
 analyses. For a comprehensive phylogenetic analyses of these data, see
 Benjamin Bomfleur, Guido W Grimm, Stephen McLoughlin (2014) Osmunda
 pulchella sp. nov. from the Jurassic of Sweden—reconciling molecular and
 fossil evidence in the phylogeny of Osmundaceae. bioRxiv, doi:
 http://dx.doi.org/10.1101/005777.Matrices&Trees.zipFigure S1The ML tree for Osmundaceae from the same data as used for the tree in Fig. 1 with bootstrap support at the nodes.FigS1_Tree_from_Fig_with_support.pdfFigure S2Chronograms obtained with the FBD approach and 19 fossil rhizomes or 17 fossil fronds, and with the TE approach and 19 fossil rhizomes.FigS2_subset_analyses UPDATED.pdfTableS1_FossilListForDatingFossils of modern Osmundaceae used in the analyses.Table S2List of all osmundaceous frond fossils evaluated.TableS2_Fossil_record_compressions.odsTable S3Divergence times with 95% highest posterior densities obtained from the fossilized birth-death (FBD) approach, node dating (ND) with oldest fossils, and total evidence (TE), using all 36 fossils, only the 19 fossil rhizomes, or only the 17 fossil fronds.TableS3_ComparisonDatingResults.pdfTable S4Full results of the resampling analyses.TableS4_ResamplingResults.pdf