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Reconstructing evolution at the community level: A case study on Mediterranean amphibians.

Sarah Ehl1, Miguel Vences2, Michael Veith1

  • 1Trier University, Department of Biogeography, Universitätsring 15, 54296 Trier, Germany.

Molecular Phylogenetics and Evolution
|February 25, 2019
PubMed
Summary

Reconstructing evolutionary timescales requires combining nuclear and mitochondrial DNA data. A two-step calibration method using secondary calibrations improves the accuracy of time trees for Mediterranean amphibians.

Keywords:
Bayesian analysisBiogeographical plausibility test (BP-test)Fossil calibrationMolecular datingPlio-Pleistocene climatic fluctuationsVicariant events

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Area of Science:

  • Evolutionary biology
  • Biogeography
  • Molecular evolution

Background:

  • Accurate species evolution timescales are crucial for biogeography.
  • Estimating divergence times is complex, with significant uncertainty in time trees.
  • Combining slow-evolving nuclear DNA and fast-evolving mitochondrial DNA presents a 'genome-timescale-dilemma' for time tree construction.

Purpose of the Study:

  • To address the challenge of integrating nuclear and mitochondrial DNA markers in time tree analysis.
  • To empirically compare strategies for inferring shallow and deep divergences within a single time tree.
  • To reconstruct and validate evolutionary timescales for Mediterranean amphibians.

Main Methods:

  • Analysis of 202 lineages of western Palearctic amphibians using four nuclear and five mitochondrial genes.
  • Reconstruction of time trees using primary fossil calibrations and a novel two-step protocol involving secondary calibrations.
  • Statistical comparison of alternative time trees using a biogeographical plausibility test focusing on vicariance events.

Main Results:

  • The two-step calibration protocol significantly outperformed the alternative approach in terms of spatial and temporal plausibility.
  • Reconstructed time trees revealed Plio-Pleistocene climatic fluctuations as a dominant driver of intrageneric evolution in Mediterranean amphibians.
  • Identified multiple tectonic and climatic events contributing to amphibian divergences across eight geographic provinces.

Conclusions:

  • The proposed two-step protocol is recommended for future molecular clock analyses integrating diverse genetic markers.
  • Understanding the interplay of geological and climatic events is key to explaining amphibian diversification patterns.
  • This study provides a robust framework for inferring evolutionary histories at both shallow and deep time scales.