Using more than the oldest fossils: Dating Osmundaceae by three Bayesian clock approaches

Abstract

Abstract.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 'fossilised birth-death' (FBD) in FDPPDiv-to infer divergence times in the Osmundaceae or royal ferns. Osmundaceae have 13 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 and three extinct families. For ND, we used the five oldest fossils, while for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils, we included up to 36 rhizome 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 dates were generally greater than ages inferred from ND dating; 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 favour the FBD-derived ages because they best match 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 Palaeozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, FBD yielded 0.0299 (0.0099-0.0549) and 0.0240 (0.0039-0.0495) for these rates, whereas neontological data yielded 0.0314 and 0.0339. 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.

The evolutionary history of ferns inferred from 25 low‐copy nuclear genes

“…To date, there are only two analyses of divergent relationships that are based on multiple nuclear loci in ferns: (1) a recent study of Polypodiales (15 taxa) based on 20 markers across 10 distinct nuclear genes (Rothfels et al, 2013); and (2) the green‐plant phylogenomics study of Wickett et al (2014) that included over 800 loci, but only six fern species. Similarly, our understanding of the timescale of fern evolution is based entirely on plastid data (with the rare exception of largely uninformative 18S sequences; Pryer et al, 2004; Schneider et al, 2004b; Janssen et al, 2008; Pryer and Schuettpelz, 2009; Schuettpelz and Pryer, 2009; Smith et al, 2010; Lehtonen et al, 2012; Grimm et al, 2015; Sundue et al, 2014; Rothfels et al, 2015).…”

Puzzling rocks and complicated clocks: how to optimize molecular dating approaches in historical phytogeography

“…Molecular-dated timescales of lineage divergence are a reliable complement to timescales based solely on fossils, if molecular dating is conducted carefully and age estimates are Table 1 Comparisons between pairs of molecular dating (node dating) scenarios that show common-seen bias-introducing effects of certain factors; note that in each line (excluding under-sampling), all parameters except the focal parameter (factor) are exactly the same Scenario 1 Most likely Scenario 1 (S1) < Scenario 2 (S2) Sauquet et al (2012) The crown age of Angiosperm is dated to the early Cretaceous according to an unambiguous fossil record (Friis et al, 2011) but molecular dating suggested a Triassic age (Smith et al, 2010;Zeng et al, 2014), which is in agreement with the recent finding of angiosperm-like pollen grains in the Middle Triassic (Hochuli & Feist-Burkhardt, 2013) Applying priors that comprise a 'soft maximum age constraint' (e.g. a lognormal prior) to calibrate shallow Parham et al, 2012), and comparing dating results from both scenarios, so as to provide justification to follow either scenario with or without outlier fossil calibration(s); note that applying the Fossilized birth-death dating method (Heath et al, 2014;Grimm et al, 2015) will also avoid biases in S1…”

“…It is crucial to note that the 'fossilized birth-death' approach integrates all available fossilized taxa, and therefore avoids potential biased selection and placement of fossil calibrations (Heath et al, 2014;Grimm et al, 2015). There is no need for prior age densities to be applied to fossils as is the case for 'node dating' methods, nor is a morphological data matrix required as for 'total evidence' dating methods (Heath et al, 2014;Grimm et al, 2015). Hence, 'fossilized birth-death' is completely different from 'node dating' and 'total evidence' dating methods, both of which employ only a selected portion of fossils for calibration.…”

“…Hence, 'fossilized birth-death' is completely different from 'node dating' and 'total evidence' dating methods, both of which employ only a selected portion of fossils for calibration. These new developments might lead to improved accuracy of molecular dating, although their merits and shortcomings still require further evaluation (Arcila et al, 2015;Grimm et al, 2015). Time will tell whether their use will help to overcome some of the problems inherent in traditional Bayesian methods of 'node dating'.…”

An overview of extant conifer evolution from the perspective of the fossil record

“…Some analyses have also used fossil‐calibrated molecular clocks to estimate divergence ages in various conifer clades (Wang et al., ; Gernandt et al., ; Biffin et al., , Leslie et al., ; Mao et al., ), and more recent dating techniques promise better (or at least new; see Bapst et al., ) ways in which to integrate fossils into molecular phylogenies by analyzing morphological and molecular data together in a single model (Ronquist et al., ; Heath et al., ; O'Reilly et al., ; Zhang et al., ). These techniques are already being incorporated into analyses that include fossil plants (Grimm et al., ; Renner et al., ; Saladin et al., ) and are likely to become widespread in future analyses of conifers.…”