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Gene flow analysis method, the D-statistic, is robust in a wide parameter space.

Yichen Zheng1, Axel Janke2

  • 1Biodiversität und Klima Forschungszentrum, Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt, Germany. yzheng2@uni-koeln.de.

BMC Bioinformatics
|January 10, 2018
PubMed
Summary
This summary is machine-generated.

The D-statistic effectively detects gene flow but is sensitive to population size. Researchers should use this method cautiously in species with large populations relative to divergence times to ensure accurate gene flow detection.

Keywords:
Gene flowParameter spacePopulation sizeSensitivitySimulationThe D-statistic

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Area of Science:

  • Population Genetics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • The D-statistic is a parsimony-like method for detecting gene flow between closely related species.
  • Its application across diverse taxa and divergence times necessitates a systematic study of its parameter space.
  • Previous studies have not comprehensively explored the factors influencing the D-statistic's sensitivity.

Purpose of the Study:

  • To systematically evaluate the sensitivity of the D-statistic to various parameters.
  • To understand the limitations and applicability of the D-statistic in gene flow detection.
  • To investigate the influence of divergence time, population size, gene flow timing, outgroup distance, and number of loci.

Main Methods:

  • A sensitivity analysis was conducted on the D-statistic.
  • Key parameters examined included divergence time, population size, gene flow timing, outgroup distance, and the number of loci.
  • The f-statistics ([Formula: see text] and [Formula: see text]) were also assessed for estimating gene flow fractions.

Main Results:

  • Relative population size is the primary determinant of the D-statistic's sensitivity.
  • Incomplete lineage sorting significantly confounds gene flow detection, especially in large populations.
  • The D-statistic's sensitivity is also influenced by gene flow direction, population size, and the number of loci.

Conclusions:

  • The D-statistic is robust to genetic distance but sensitive to population size.
  • Application of the D-statistic requires critical reservation for taxa with large population sizes relative to divergence times.
  • The f-statistics can be used for comparative analyses in similar demographic backgrounds.