An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)

Arcila, Dahiana; Pyron, R. Alexander; Tyler, James C.; Ortı́, Guillermo; Betancur‐R, Ricardo

doi:10.1016/j.ympev.2014.10.011

Cited by 143 publications

(145 citation statements)

References 80 publications

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“…We thus propose balancing different lines of evidence, including information from standard substitution rates, results generated using secondary calibrations, and data based on the morphology of the fossil and related taxa (Lóriga et al, 2014;Heinrichs et al, 2015;Schneider et al, 2015Schneider et al, , 2016Feldberg et al, 2017). The recently proposed fossilized birth-death approach was designed to overcome the problem of assigning fossils to certain nodes in divergence time analyses (Heath et al, 2014); however, this approach requires a dense fossil record and numerous morphological character states of both fossils and extant taxa to be coded (Arcila et al, 2015;Warnock et al, 2015). We were unable to successfully employ this approach because of the small number of Radula fossils, their incomplete preservation, and the monotonous morphology of both the majority of extant and fossil species (Grolle, 1987;Renner and Braggins, 2004;Renner, 2015;Heinrichs et al, 2016b;Kaasalainen et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

A Burmese amber fossil of <i>Radula</i> (Porellales, Jungermanniopsida) provides insights into the Cretaceous evolution of epiphytic lineages of leafy liverworts

et al. 2017

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Abstract. DNA-based divergence time estimates suggested major changes in the composition of epiphyte lineages of liverworts during the Cretaceous; however, evidence from the fossil record is scarce. We present the first Cretaceous fossil of the predominantly epiphytic leafy liverwort genus Radula in ca. 100 Myr old Burmese amber. The fossil's exquisite preservation allows first insights into the morphology of early crown group representatives of Radula occurring in gymnosperm-dominated forests. Ancestral character state reconstruction aligns the fossil with the crown group of Radula subg. Odontoradula; however, corresponding divergence time estimates using the software BEAST lead to unrealistically old age estimates. Alternatively, assignment of the fossil to the stem of subg. Odontoradula results in a stem age estimate of Radula of 227.8 Ma (95 % highest posterior density (HPD): 165.7-306.7) and a crown group estimate of 176.3 Ma (135.1-227.4), in agreement with analyses employing standard substitution rates (stem age 235.6 Ma (142.9-368.5), crown group age 183.8 Ma (109.9-289.1)). The fossil likely belongs to the stem lineage of Radula subg. Odontoradula. The fossil's modern morphology suggests that switches from gymnosperm to angiosperm phorophytes occurred without changes in plant body plans in epiphytic liverworts. The fossil provides evidence for striking morphological homoplasy in time. Even conservative node assignments of the fossil support older rather than younger age estimates of the Radula crown group, involving origins for most extant subgenera by the end of the Cretaceous and diversification of their crown groups in the Cenozoic.

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Section: Discussionmentioning

confidence: 99%

A Burmese amber fossil of <i>Radula</i> (Porellales, Jungermanniopsida) provides insights into the Cretaceous evolution of epiphytic lineages of leafy liverworts

et al. 2017

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“…They also did not find the increase in precision noted by Ronquist et al [2012a]. Arcila et al [2015] examined the diversification of tetraodontiform fishes using node-and tip-dating calibrations. In a set of extensive comparisons using BEAST and MrBayes, they also found that tip-dating approaches yielded older age estimates.…”

Section: Node-age Differences Based On Tip-dating and Node-datingmentioning

confidence: 99%

Xenopus in Space and Time: Fossils, Node Calibrations, Tip-Dating, and Paleobiogeography

Cannatella

2015

Cytogenet Genome Res

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Published data from DNA sequences, morphology of 11 extant and 15 extinct frog taxa, and stratigraphic ranges of fossils were integrated to open a window into the deep-time evolution of Xenopus. The ages and morphological characters of fossils were used as independent datasets to calibrate a chronogram. We found that DNA sequences, either alone or in combination with morphological data and fossils, tended to support a close relationship between Xenopus and Hymenochirus, although in some analyses this topology was not significantly better than the Pipa + Hymenochirus topology. Analyses that excluded DNA data found strong support for the Pipa + Hymenochirus tree. The criterion for selecting the maximum age of the calibration prior influenced the age estimates, and our age estimates of early divergences in the tree of frogs are substantially younger than those of published studies. Node-dating and tip-dating calibrations, either alone or in combination, yielded older dates for nodes than did a root calibration alone. Our estimates of divergence times indicate that overwater dispersal, rather than vicariance due to the splitting of Africa and South America, may explain the presence of Xenopus in Africa and its closest fossil relatives in South America.

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“…Finally, tip-dating is computationally demanding [66], and has only thus far been applied to relatively small genetic datasets [39,42,67]. Efficient, highly parallelised algorithms for analysing genomic-scale data do not yet simultaneously infer topology and divergence dates, although some can accommodate morphological data in (undated) simultaneous analyses [68].…”

Section: Reviewmentioning

confidence: 99%

Morphological Phylogenetics in the Genomic Age

2015

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Evolutionary trees underpin virtually all of biology, and the wealth of new genomic data has enabled us to reconstruct them with increasing detail and confidence. While phenotypic (typically morphological) traits are becoming less important in reconstructing evolutionary trees, they still serve vital and unique roles in phylogenetics, even for living taxa for which vast amounts of genetic information are available. Morphology remains a powerful independent source of evidence for testing molecular clades, and - through fossil phenotypes - the primary means for time-scaling phylogenies. Morphological phylogenetics is therefore vital for transforming undated molecular topologies into dated evolutionary trees. However, if morphology is to be employed to its full potential, biologists need to start scrutinising phenotypes in a more objective fashion, models of phenotypic evolution need to be improved, and approaches for analysing phenotypic traits and fossils together with genomic data need to be refined.

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An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)

Cited by 143 publications

References 80 publications

A Burmese amber fossil of <i>Radula</i> (Porellales, Jungermanniopsida) provides insights into the Cretaceous evolution of epiphytic lineages of leafy liverworts

A Burmese amber fossil of <i>Radula</i> (Porellales, Jungermanniopsida) provides insights into the Cretaceous evolution of epiphytic lineages of leafy liverworts

Xenopus in Space and Time: Fossils, Node Calibrations, Tip-Dating, and Paleobiogeography

Morphological Phylogenetics in the Genomic Age

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An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)

Cited by 143 publications

References 80 publications

A Burmese amber fossil of &lt;i&gt;Radula&lt;/i&gt; (Porellales, Jungermanniopsida) provides insights into the Cretaceous evolution of epiphytic lineages of leafy liverworts

A Burmese amber fossil of &lt;i&gt;Radula&lt;/i&gt; (Porellales, Jungermanniopsida) provides insights into the Cretaceous evolution of epiphytic lineages of leafy liverworts

Xenopus in Space and Time: Fossils, Node Calibrations, Tip-Dating, and Paleobiogeography

Morphological Phylogenetics in the Genomic Age

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Product

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A Burmese amber fossil of <i>Radula</i> (Porellales, Jungermanniopsida) provides insights into the Cretaceous evolution of epiphytic lineages of leafy liverworts

A Burmese amber fossil of <i>Radula</i> (Porellales, Jungermanniopsida) provides insights into the Cretaceous evolution of epiphytic lineages of leafy liverworts