The making of calibration sausage exemplified by recalibrating the transcriptomic timetree of jawed vertebrates

Marjanović, David

doi:10.1101/2019.12.19.882829

Cited by 8 publications

(19 citation statements)

References 309 publications

(744 reference statements)

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“…The choices of hard vs. soft bounds do not seem to make a great difference to the big picture. Due to practical constraints, a set of calibration ages mostly identical to the present ones was analyzed twice, with all bounds treated as soft or as hard, in the first preprint of this work (Marjanović, 2019); the results were quite similar to each other (Marjanović, 2019: figure 1 and table 2). Even so, however, in the run where all bounds were soft, most divergence dates were younger than in the run where all bounds were hard (usually negligibly so, but by 20 Ma in the extreme cases); the mean ages of some calibrated nodes even ended up younger than their minimum ages.…”

Section: Hard and Soft Minima And Maximamentioning

confidence: 52%

“…More likely, Lethiscus and the other aïstopods are rather early-branching stem-stegocephalians [PN] (Pardo et al, 2017(Pardo et al, , 2018Clack et al, 2019; further discussion in Marjanović and Laurin, 2019). Whether Casineria from a geographically (southeastern Scotland) and stratigraphically close site (mid-late Viséan: Paton et al, 1999;Smithson et al, 2012) can replace it in that function depends on two unresolved issues: its own phylogenetic position, for which estimates range from very close to Amniota (within Tetrapoda) into Temnospondyli (Marjanović and Laurin, 2019, and references therein;Clack et al, 2019;Daza et al, 2020: supplementary figure S15), and the controversial phylogenetic position of Lissamphibia [PN] in the stegocephalian tree (Marjanović andLaurin, 2013a, 2019;Danto et al, 2019;Laurin et al, 2019;Daza et al, 2020;Pardo et al, 2020; and references in all five), which determines whether the temnospondyls are tetrapods or quite rootward stem-stegocephalians by determining which node of the otherwise largely stable tree of early stegocephalians bears the name Tetrapoda. Anderson et al (2015) reported a number of isolated anthracosaur [PN] (embolomere or eoherpetid) bones from a mid-Tournaisian site (the Tournaisian preceded the Viséan and began at the Devonian/Carboniferous boundary 358.9 ± 0.4 Ma ago: ICSC).…”

Section: Calibrationsmentioning

confidence: 99%

“…There appears to be pan-mammalian material from the same site (Carroll, 1964;Mann et al, 2020), which has also yielded various "microsaurs" that Pardo et al (2017) included in Sauropsida (see also Marjanović andPardo et al, 2020). I should also emphasize that the next younger sauropsids and pan-mammals (and "microsaurs") older than 288 Ma come from several sites in each following geological stage (Moscovian through Artinskian) and represent a considerable diversity; from the Moscovian alone, four sites of successive ages are known that present more or less complete skeletons of uncontroversial amniotes, namely, sauropsids closely related to Diapsida and Hylonomus (Anthracodromeus, Brouffia, Cephalerpeton, Paleothyris), the oldest "parareptile" (Carbonodraco) as well as what appears to be the sister-group to most other sauropsids (Coelostegus), and, on the pan-mammalian side, ophiacodontids (Echinerpeton; Archaeothyris from two sites).…”

Section: Calibrationsmentioning

confidence: 99%

“…This may be supported by the body size increase in snakes: their oldest sampled node (Macrostomata or Afrophidia: Node 136) is placed around the Early/Late Cretaceous boundary, followed by the origin of Endoglyptodonta (Node 138) in the Late Cretaceous, while any Late Cretaceous caenophidians (a clade containing Endoglyptodonta) remain unknown, all potential Cretaceous total-group macrostomates are beset with phylogenetic uncertainty, and considerably younger dates were found by Burbrink et al (2020) despite the use of a mid-Cretaceous potential macrostomate as a minimum-age-only calibration. Similarly, the fact that the entire credibility interval for Supraprimates/Euarchontoglires (Node 155) was younger than its calibrated minimum age when all bounds were treated as soft in Marjanović (2019) may be due to the fact that one of the two sampled supraprimates is Homo, the second-largest sampled mammal and the one with the second-longest generation span. Whelan and Halanych (2016) found that the CAT-GTR model (at least as implemented in PhyloBayes) is prone to inferring inaccurate branch lengths, especially in large datasets; this may turn out to be another cause of the results described above.…”

Section: Changes In the Divergence Datesmentioning

confidence: 99%

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The Making of Calibration Sausage Exemplified by Recalibrating the Transcriptomic Timetree of Jawed Vertebrates

Marjanović

2021

Front. Genet.

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Molecular divergence dating has the potential to overcome the incompleteness of the fossil record in inferring when cladogenetic events (splits, divergences) happened, but needs to be calibrated by the fossil record. Ideally but unrealistically, this would require practitioners to be specialists in molecular evolution, in the phylogeny and the fossil record of all sampled taxa, and in the chronostratigraphy of the sites the fossils were found in. Paleontologists have therefore tried to help by publishing compendia of recommended calibrations, and molecular biologists unfamiliar with the fossil record have made heavy use of such works (in addition to using scattered primary sources and copying from each other). Using a recent example of a large node-dated timetree inferred from molecular data, I reevaluate all 30 calibrations in detail, present the current state of knowledge on them with its various uncertainties, rerun the dating analysis, and conclude that calibration dates cannot be taken from published compendia or other secondary or tertiary sources without risking strong distortions to the results, because all such sources become outdated faster than they are published: 50 of the (primary) sources I cite to constrain calibrations were published in 2019, half of the total of 280 after mid-2016, and 90% after mid-2005. It follows that the present work cannot serve as such a compendium either; in the slightly longer term, it can only highlight known and overlooked problems. Future authors will need to solve each of these problems anew through a thorough search of the primary paleobiological and chronostratigraphic literature on each calibration date every time they infer a new timetree, and that literature is not optimized for that task, but largely has other objectives.

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“…It provides useful, if partly outdated, information to generate calibration constraints for more than 200 clades and does so on a transparent forum that is open to the whole scientific community. Note however that knowledge about fossil data is constantly evolving (see e.g., Marjanović, 2019) and databases such as the Fossil Calibration Database require ongoing and constant efforts in order to remain relevant.…”

Section: Pre-processing Of Fossil Datamentioning

confidence: 99%

Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods

Guindon

2020

Front. Genet.

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The making of calibration sausage exemplified by recalibrating the transcriptomic timetree of jawed vertebrates

Cited by 8 publications

References 309 publications

The Making of Calibration Sausage Exemplified by Recalibrating the Transcriptomic Timetree of Jawed Vertebrates

Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods

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