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Peer-reviewedCC BYProceedings. Biological sciences

Competing methods of divergence time estimation recover diverse evolutionary timescales.

  • Sidney E L Davies1
  • Alessia Tasca2
  • Sandra Álvarez-Carretero3
  • Christopher Brochu4
  • Davide Pisani5
  • Philip C J Donoghue1
5 affiliations
  1. 1Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol , Bristol BS8 1TQ, UK.
  2. 2Department of Biotechnology and Biosciences, University of Milano-Bicocca , Milan, 20126, Italy.
  3. 3Department of Genetics, Evolution and Environment, University College London , London WC1E 6BT, UK.
  4. 4School of Earth, Environment and Sustainability, University of Iowa , IA, 52242, USA.
  5. 5Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol , Bristol BS8 1TQ, UK.
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Abstract

Molecular clocks convert evolutionary distances into geological times to infer time-scaled phylogenies. Methods differ in terms of fossil calibration strategy (node versus tip) and whether they use molecular and/or morphological data, but their relative performance remains unclear. Given their well preserved fossil record, we use Crocodylia to interrogate common approaches to timescale estimation using a combination of calibration strategies and datatypes in MrBayes. We found that calibration strategies had a much greater impact than datatype, with node-calibrated timescales producing younger ages than tip calibration. The older ages recovered by tip-calibrated approaches imply an Early Cretaceous origin (approx. 125-102 Ma) of Crocodylia, inconsistent with the biostratigraphic record, while node calibration produces more credible estimates, including a Late Cretaceous origin (approx. 95-78 Ma). Performing tip calibration with a fossilized birth-death process produced an intermediate timescale, estimating an Early-Late Cretaceous origin (approx. 118-95 Ma). These timescales support materially distinct scenarios for crocodylian evolution. We show that these disparities among calibration strategies are driven by differences in the structure of their underlying priors, with tip-calibrated timescales biased toward unrealistically ancient ages. Our results highlight the need for future analyses to explore hybrid calibration strategies that treat node and tip calibration as complementary, rather than competing, approaches.

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Cite

BibTeXRIS
BibTeX
@article{davies2026competing,
  title = {{Competing methods of divergence time estimation recover diverse evolutionary timescales.}},
  author = {Sidney E L Davies and Alessia Tasca and Sandra Álvarez-Carretero and Christopher Brochu and Davide Pisani and Philip C J Donoghue},
  journal = {Proceedings. Biological sciences},
  year = {2026},
  month = oct,
  doi = {10.1098/rspb.2026.0635},
  url = {https://europepmc.org/article/MED/42838565},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Competing methods of divergence time estimation recover diverse evolutionary timescales.
AU  - Sidney E L Davies
AU  - Alessia Tasca
AU  - Sandra Álvarez-Carretero
AU  - Christopher Brochu
AU  - Davide Pisani
AU  - Philip C J Donoghue
PY  - 2026
DA  - 2026/10/01
JO  - Proceedings. Biological sciences
DO  - 10.1098/rspb.2026.0635
UR  - https://europepmc.org/article/MED/42838565
AB  - Molecular clocks convert evolutionary distances into geological times to infer time-scaled phylogenies. Methods differ in terms of fossil calibration strategy (node versus tip) and whether they use molecular and/or morphological data, but their relative performance remains unclear. Given their well preserved fossil record, we use Crocodylia to interrogate common approaches to timescale estimation using a combination of calibration strategies and datatypes in MrBayes. We found that calibration strategies had a much greater impact than datatype, with node-calibrated timescales producing younger ages than tip calibration. The older ages recovered by tip-calibrated approaches imply an Early Cretaceous origin (approx. 125-102 Ma) of Crocodylia, inconsistent with the biostratigraphic record, while node calibration produces more credible estimates, including a Late Cretaceous origin (approx. 95-78 Ma). Performing tip calibration with a fossilized birth-death process produced an intermediate timescale, estimating an Early-Late Cretaceous origin (approx. 118-95 Ma). These timescales support materially distinct scenarios for crocodylian evolution. We show that these disparities among calibration strategies are driven by differences in the structure of their underlying priors, with tip-calibrated timescales biased toward unrealistically ancient ages. Our results highlight the need for future analyses to explore hybrid calibration strategies that treat node and tip calibration as complementary, rather than competing, approaches.
SN  - 0962-8452
SN  - 1471-2954
ER  -