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Estimating divergence times from DNA sequences.

Per Sjödin1, James McKenna1, Mattias Jakobsson1,2

  • 1Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18 A, Uppsala 752 36, Sweden.

Genetics
|March 26, 2021
PubMed
Summary
This summary is machine-generated.

We developed two new methods, Two-Two (TT) and Two-Two-outgroup (TTo), to estimate when populations diverged using genetic data. These computationally efficient approaches provide robust estimates of divergence times, even with migration.

Keywords:
divergence timeeffective population sizehuman evolutionpopulation divergence

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Area of Science:

  • Population Genetics
  • Evolutionary Biology
  • Genomics

Background:

  • Genetic variation patterns reveal evolutionary forces.
  • Inferring evolutionary history relies on population genetic approaches.

Purpose of the Study:

  • Introduce the Two-Two (TT) and Two-Two-outgroup (TTo) methods for estimating population divergence times.
  • Provide a computationally efficient and transparent approach to infer evolutionary history.

Main Methods:

  • Utilize coalescent theory and sequence data from two populations.
  • Derive probabilities of sample configurations under a simple population-divergence model.
  • Solve equations to estimate model parameters, including population split times.

Main Results:

  • The TT and TTo methods estimate divergence times directly from sequence data.
  • The approach allows time estimation in generations, independent of genetic drift.
  • Simulations show robustness to migration and TTo's ability to correct for ancestral population size changes.

Conclusions:

  • The TT and TTo methods offer a reliable way to estimate population divergence.
  • These methods can be applied to human population splits and archaic hominin relationships.
  • The approaches enhance our understanding of evolutionary timelines and population dynamics.