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Purging putative siblings from population genetic data sets: a cautionary view.

Robin S Waples1, Eric C Anderson2

  • 1NOAA Fisheries, Northwest Fisheries Science Center, 2725 Montlake Blvd. East, Seattle, WA, 98112, USA.

Molecular Ecology
|January 19, 2017
PubMed
Summary
This summary is machine-generated.

Removing siblings from population genetic data can reduce precision for allele frequency and differentiation estimates. Aggressively removing siblings can bias effective population size (Ne) estimates, highlighting the need for caution in data adjustment.

Keywords:
allele frequencyeffective population sizefamily structuregenetic differentiationprecision

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Area of Science:

  • Population genetics
  • Bioinformatics
  • Conservation genetics

Background:

  • Recent interest in removing siblings from population genetic data sets before downstream analyses.
  • This study evaluates strategies for adjusting samples to account for family structure using coho salmon.
  • Compares performance of estimators for allele frequency (P^), population differentiation (FST), and effective population size (Ne) in full and sibling-reduced samples.

Discussion:

  • Removing siblings generally reduced precision of P^ and FST unless samples included large family groups and unrelated individuals.
  • Effective population size (Ne) estimates were unbiased in full random samples but became upwardly biased with aggressive sibling purging.
  • Nonrandom sampling led to biased Ne estimates; a 'Goldilocks' fraction of sibling removal could yield unbiased estimates, but this varied widely.

Key Insights:

  • Sibling removal can decrease precision of allele frequency and population differentiation estimates.
  • Aggressive sibling purging leads to upward bias in effective population size (Ne) estimates.
  • Weighting individuals by inferred pedigree (BLUE) is precise with correct pedigrees but poor with incorrect ones.

Outlook:

  • No single optimal solution exists for adjusting population genetic data for family structure.
  • A variant of sibling removal that retains small sibling groups is more robust to pedigree inference errors.
  • Caution is advised when adjusting data for siblings without understanding the consequences.