Recalibrating clade origins, part 1

Marjanovic 2019 reports on
the origin of several clades based on the fossil literature and molecules.

From the abstract:
“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.”

Testing has shown molecular testing leads to false positives over deep time. Phylogenetic testing using the large reptile tree (LRT, 1630+ taxa) has also shown the fossil record to be, at this date, more complete than Marjanovic (and, no doubt, others) imagine with no new clades appearing for quite some time and all known clades demonstrating a gradual accumulation of traits in the LRT.

“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.”

Ideally, but unrealistically, paleontologists would be better off omitting genomics and focusing on taxon exclusion within phenomics (trait-studies).

“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.”

To their detriment and the deliver of false positives.

“Using a recent example of a large timetree inferred from molecular data, I demonstrate that calibration dates cannot be taken from published compendia without risking strong distortions to the results, because compendia become outdated faster than they are published.”

It is strongly recommended that no one infer anything from molecular data, including Dr. Marjanovic.

“The present work cannot serve as such a compendium either; in the slightly longer term, it can only highlight known and overlooked problems.”

The number one overlooked problem is genomics.

“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; over 40% of the sources I cite were published after mid-2016. Treating all calibrations as soft bounds results in younger nodes than treating all calibrations as hard bounds.”

All calibrations involving genomics are going to have to be validated with last common ancestors recovered from phenomics. So, why not skip a step and just use phenomics?

“The unexpected exception are nodes calibrated with both minimum and maximum ages, further demonstrating the widely underestimated importance of maximum ages in divergence dating.”

Now let’s see what Marjanovic discovered, because his abstract does not give a clue. It’s an introduction, not a boiled-down synthesis. Comparisons with the LRT will be noted. Marjanovic’s cladogram is the first to include as wide a gamut as the LRT while employing only generic taxa. Unfortunately no fossil taxa are included. Only ten mammals and six birds are included.

Distinct from the LRT, the Marjanovic cladogram
nests turtles with archosaurs (creating the invalid clade, Archelosauria).

More tomorrow…


References
Marjanovic D 2019. Recalibrating the transcriptomic timetree of jawed vertebrates.
bioRxiv 2019.12.19.882829 (preprint)
doi: https://doi.org/10.1101/2019.12.19.882829
https://www.biorxiv.org/content/10.1101/2019.12.19.882829v1

1 thought on “Recalibrating clade origins, part 1

  1. Hi! Thank you for your engagement with my preprint. It would have been nice to drop me an e-mail, though; if a colleague hadn’t told me about it, I’d never have noticed. That would be a pity, because at the very least this part

    Now let’s see what Marjanovic discovered, because his abstract does not give a clue. It’s an introduction, not a boiled-down synthesis.

    is exactly the kind of valuable feedback I was looking for!

    This, however, is a misunderstanding:

    Marjanovic’s cladogram is the first to include as wide a gamut as the LRT while employing only generic taxa. Unfortunately no fossil taxa are included. Only ten mammals and six birds are included.

    I did not conduct a phylogenetic analysis. (This is clear from the text.) Consequently, “my cladogram” is simply the cladogram of my source, Irisarri et al. (2017). I deliberately kept my work very narrow: the basic question is whether, given their tree, the calibrations they used are correct.

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