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Researchers found that recent population peaks followed by collapses in demographic history reconstructions are often artifacts. Adjusting parameters in the pairwise sequentially Markovian coalescent (PSMC) method can resolve these false signals, improving accuracy for evolutionary studies.

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Area of Science:

  • Evolutionary biology
  • Population genetics
  • Genomics

Background:

  • Inferring historical population sizes is crucial for understanding ecological and evolutionary change.
  • The pairwise sequentially Markovian coalescent (PSMC) method revolutionized demographic history reconstruction from single genomes.
  • Accurate demographic inference is vital for predicting species' responses to global change.

Purpose of the Study:

  • To identify and resolve a common artifact in PSMC and related methods.
  • To investigate the causes of false recent population peaks followed by collapses.
  • To provide recommendations for improving demographic inference accuracy.

Main Methods:

  • Analysis of real and simulated genomic data.
  • Systematic testing and adjustment of PSMC and related method parameters.
  • Comparison of artifact patterns across different methods and datasets.

Main Results:

  • A common artifact of false recent population peaks followed by collapses was detected in PSMC analyses.
  • Ill-set default parameters, not true population dynamics, were identified as the primary cause of these false peaks.
  • Adjusting parameter settings effectively resolved the artifact in tested datasets.
  • Newer methods like Beta-PSMC show improvement but do not entirely eliminate the artifact.

Conclusions:

  • Recent population peaks followed by collapses in demographic histories derived from PSMC are frequently artifacts.
  • Careful parameter testing, particularly for the initial time window, is essential before interpreting such patterns.
  • Development of more robust demographic inference methods is needed to avoid these artifacts.