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.
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.
Syst Biol. 2015 May;64(3):396-405. doi: 10.1093/sysbio/syu108. Epub 2014 Dec 9.
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.
分子钟定年的一个主要关注点是如何利用化石记录中的信息来校准 DNA 序列的遗传距离。在这里，我们应用了三种贝叶斯定年方法，它们在实现校准的方式上有所不同——BEAST 中的“节点定年”（ND）、MrBayes 中的“总证据”（TE）定年以及 FDPPDiv 中的“化石出生-死亡”（FBD）定年——以推断皇家羊齿植物的分歧时间。水韭目植物有 16-17 种，分属四个属，两个主要分布在北半球，两个分布在南非和澳大拉西亚；它们是其余的薄囊蕨类植物的姐妹群。它们的化石记录至少包含 150 个种，分布在约 17 个属中。对于 ND，我们使用了五个最古老的化石，而对于 TE 和 FBD 定年，它们不需要将化石强制分配到节点上，因此可以使用更多的化石，我们包括了最多 36 个根茎和蕨叶压缩/印痕化石，对于 TE 定年，这些化石的 33 个形态特征被评分。我们还对 36 个化石进行了 10%、25%和 50%的抽样，以评估模型的敏感性。FBD 推断的分歧年龄通常大于 ND 推断的年龄；七个 TE 推断的年龄中，有两个与 FBD 获得的年龄一致，其余的年龄要么比 ND 或 FBD 年龄年轻得多，要么老得多。我们更喜欢 FBD 推断的年龄，因为它们最符合水韭目的化石记录（包括我们研究中未使用的三叠纪化石）。在首选模型下，包含现存水韭科（和许多化石）的分支可以追溯到晚古生代至早三叠世；现存物种的分歧发生在新近纪。在假定的物种形成和灭绝率不变的情况下，FBD 方法得出的物种形成和灭绝率与仅从新生数据得出的结果重叠。然而，FBD 对物种形成和灭绝的估计对化石连续采样假设的违反很敏感；因此，这些估计应该谨慎对待。
