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

  title={The Making of Calibration Sausage Exemplified by Recalibrating the Transcriptomic Timetree of Jawed Vertebrates},
  author={David Marjanovi{\'c}},
  journal={Frontiers in Genetics},
  • D. Marjanović
  • Published 27 December 2019
  • Environmental Science
  • Frontiers in Genetics
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… 

Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)

The most comprehensive non-supertree phylogeny of shorebirds to date is presented, based on a total-evidence dataset comprising 336 ingroup taxa, 24 loci, and 69 morphological characters, which consistently support a mid-Paleocene origin for the Charadriiformes and an early diversification for most major subclades.

Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods

  • S. Guindon
  • Environmental Science
    Frontiers in Genetics
  • 2020
It is argued that the fossilized birth-death process relies on assumptions about the mechanisms underlying fossilization and the data collection process that may negatively impact the date estimates, and node-dating approaches make better use of the data available, even though they rest on paleontologists' intervention to prepare raw fossil data.

The First Age of Reptiles? Comparing Reptile and Synapsid Diversity, and the Influence of Lagerstätten, During the Carboniferous and Early Permian

  • N. Brocklehurst
  • Environmental Science, Biology
    Frontiers in Ecology and Evolution
  • 2021
An examination of local species richness (alpha diversity) of synapsids and reptiles during the Pennsylvanian and Cisuralian at different spatial scales shows that these taxonomic revisions have substantial impacts on relative diversity patterns of synapid and reptiles.

Giant lungfish genome elucidates the conquest of land by vertebrates

The chromosome-quality genome of the Australian lungfish is determined, known to have the largest genome of any animal, and phylogenomic analyses confirm that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods.

Iguanian lizards from the Split Rock Formation, Wyoming: exploring the modernization of the North American lizard fauna

Terrestrial ecosystems in North America changed substantially during the Neogene. Previous authors have documented changes in plants and mammals but squamates have received comparatively little



Fossils, molecules, divergence times, and the origin of lissamphibians.

A review of the paleontological literature shows that the early dates of appearance of Lissamphibia recently inferred from molecular data do not favor an origin of extant amphibians from

An updated paleontological timetree of lissamphibians, with comments on the anatomy of Jurassic crown-group salamanders (Urodela)

The conclusion that the fossil record of Lissamphibia is dense enough to provide reliable calibration constraints for molecular divergence dating is upheld and some of the divergence dates the authors infer from the tree are up to 15 Ma younger than previously published.

Best Practices for Justifying Fossil Calibrations

  • JamesF. Benton
  • Environmental Science
    Systematic biology
  • 2012
Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining

Completeness of the eutherian mammal fossil record and implications for reconstructing mammal evolution through the Cretaceous/Paleogene mass extinction

The completeness of the eutherian fossil record through geological time is evaluated and supports the “explosivemodel” of early placental evolution, whereby placentalmammals originated around the time of the K/Pg boundary and diversified soon after.

Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses

Predictive models are developed that demonstrate that the possession of distinctive character state combinations is the primary predictor of the degree of induced topological change, and that the relative impact of taxa (fossil and extant) can be predicted to some extent before any analysis.

Phylogenetic relationships of the Cretaceous frog Beelzebufo from Madagascar and the placement of fossil constraints based on temporal and phylogenetic evidence

A metric is derived, Δt, to quantify temporal divergence among chronograms and finds that errors resulting from mis‐specified calibrations are localized when additional nodes throughout the tree are properly calibrated.

Phylogeny and systematic history of early salamanders

While this study has not resolved the relationships between salamander families it has allowed a deeper understanding of the data, and assesses the confidence with which the placement of key fossils can be made in a new way.

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

  • D. Cannatella
  • Environmental Science, Geography
    Cytogenetic and Genome Research
  • 2015
The 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.

Effects of phylogenetic uncertainty on fossil identification illustrated by a new and enigmatic Eocene iguanian

A skull fossil of a new pleurodontan lizard taxon is described from the Eocene deposits of the Willwood Formation, Wyoming, and used as a case-study to explore the effects of phylogenetic uncertainty on fossil identification.


A series of rigorously vetted calibration fossils for arthropod evolutionary history, taking into account recently published guidelines for best practice in fossil calibration are presented, resulting in 80 fossil calibrations for 102 clades.