Using more than the oldest fossils: dating osmundaceae with three Bayesian clock approaches

Guido W Grimm¹, Paschalia Kapli², Benjamin Bomfleur², Stephen McLoughlin², Susanne S Renner³

Affiliations

¹ Department of Palaeobiology, Swedish Museum of Natural History, Svante Arrhenius Väg 7, 10405 Stockholm, Sweden; Department of Palaeontology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria; Natural History Museum of Crete and Biology Department, University of Crete, PO Box 2208, 71409 Heraklion, Crete, Greece, and Scientific Computing, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35. 69118 Heidelberg, Germany; and Institute of Systematic Botany and Mycology, University of Munich, Menzinger Str. 67, 80638 Munich, Germany Department of Palaeobiology, Swedish Museum of Natural History, Svante Arrhenius Väg 7, 10405 Stockholm, Sweden; Department of Palaeontology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria; Natural History Museum of Crete and Biology Department, University of Crete, PO Box 2208, 71409 Heraklion, Crete, Greece, and Scientific Computing, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35. 69118 Heidelberg, Germany; and Institute of Systematic Botany and Mycology, University of Munich, Menzinger Str. 67, 80638 Munich, Germany.
² Department of Palaeobiology, Swedish Museum of Natural History, Svante Arrhenius Väg 7, 10405 Stockholm, Sweden; Department of Palaeontology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria; Natural History Museum of Crete and Biology Department, University of Crete, PO Box 2208, 71409 Heraklion, Crete, Greece, and Scientific Computing, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35. 69118 Heidelberg, Germany; and Institute of Systematic Botany and Mycology, University of Munich, Menzinger Str. 67, 80638 Munich, Germany.
³ Department of Palaeobiology, Swedish Museum of Natural History, Svante Arrhenius Väg 7, 10405 Stockholm, Sweden; Department of Palaeontology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria; Natural History Museum of Crete and Biology Department, University of Crete, PO Box 2208, 71409 Heraklion, Crete, Greece, and Scientific Computing, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35. 69118 Heidelberg, Germany; and Institute of Systematic Botany and Mycology, University of Munich, Menzinger Str. 67, 80638 Munich, Germany renner@lmu.de.

PMID: 25503771
DOI: 10.1093/sysbio/syu108

Using more than the oldest fossils: dating osmundaceae with three Bayesian clock approaches

Guido W Grimm et al. Syst Biol. 2015 May.

. 2015 May;64(3):396-405.

doi: 10.1093/sysbio/syu108. Epub 2014 Dec 9.

Authors

Guido W Grimm¹, Paschalia Kapli², Benjamin Bomfleur², Stephen McLoughlin², Susanne S Renner³

Affiliations

¹ Department of Palaeobiology, Swedish Museum of Natural History, Svante Arrhenius Väg 7, 10405 Stockholm, Sweden; Department of Palaeontology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria; Natural History Museum of Crete and Biology Department, University of Crete, PO Box 2208, 71409 Heraklion, Crete, Greece, and Scientific Computing, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35. 69118 Heidelberg, Germany; and Institute of Systematic Botany and Mycology, University of Munich, Menzinger Str. 67, 80638 Munich, Germany Department of Palaeobiology, Swedish Museum of Natural History, Svante Arrhenius Väg 7, 10405 Stockholm, Sweden; Department of Palaeontology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria; Natural History Museum of Crete and Biology Department, University of Crete, PO Box 2208, 71409 Heraklion, Crete, Greece, and Scientific Computing, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35. 69118 Heidelberg, Germany; and Institute of Systematic Botany and Mycology, University of Munich, Menzinger Str. 67, 80638 Munich, Germany.
² Department of Palaeobiology, Swedish Museum of Natural History, Svante Arrhenius Väg 7, 10405 Stockholm, Sweden; Department of Palaeontology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria; Natural History Museum of Crete and Biology Department, University of Crete, PO Box 2208, 71409 Heraklion, Crete, Greece, and Scientific Computing, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35. 69118 Heidelberg, Germany; and Institute of Systematic Botany and Mycology, University of Munich, Menzinger Str. 67, 80638 Munich, Germany.
³ Department of Palaeobiology, Swedish Museum of Natural History, Svante Arrhenius Väg 7, 10405 Stockholm, Sweden; Department of Palaeontology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria; Natural History Museum of Crete and Biology Department, University of Crete, PO Box 2208, 71409 Heraklion, Crete, Greece, and Scientific Computing, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35. 69118 Heidelberg, Germany; and Institute of Systematic Botany and Mycology, University of Munich, Menzinger Str. 67, 80638 Munich, Germany renner@lmu.de.

PMID: 25503771
DOI: 10.1093/sysbio/syu108

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 "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.

Keywords: Bayesian inference; fossilized birth–death dating; molecular clock calibration; node dating; royal ferns; total evidence dating.

PubMed Disclaimer

Publication types

Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

LinkOut - more resources

Full Text Sources
- Ovid Technologies, Inc.
- Silverchair Information Systems
Other Literature Sources
- Dryad Digital Repository
- scite Smart Citations

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Using more than the oldest fossils: dating osmundaceae with three Bayesian clock approaches

Affiliations

Using more than the oldest fossils: dating osmundaceae with three Bayesian clock approaches

Authors

Affiliations

Abstract

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources

Other Literature Sources