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An efficient exact algorithm for identifying hybrids using population genomic sequences.

Sneha Chakraborty1, Bruce Rannala2

  • 1Graduate Group in Biostatistics, Department of Statistics, University of California at Davis, Davis, CA 95616, USA.

Genetics
|January 28, 2023
PubMed
Summary
This summary is machine-generated.

Identifying recent hybrid ancestry is crucial. A new Bayesian method, Mongrail, accurately models genetic linkage and recombination, outperforming older methods for inferring hybrid origins in genomic data.

Keywords:
Bayesian inferenceconservation geneticshybridizationrecombinationwhole-genome sequence data

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Area of Science:

  • Genetics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Identifying recent hybrid ancestry has been a long-standing challenge in natural history.
  • Traditional methods using codominant genetic markers assume independent assortment, which is violated by genomic data exhibiting linkage disequilibrium.

Purpose of the Study:

  • To develop a novel, full-likelihood Bayesian method for inferring hybrid ancestry.
  • To explicitly model genetic linkage and recombination in hybrid inference.
  • To assess the performance of the new method against existing composite likelihood approaches.

Main Methods:

  • Development of Mongrail, a Bayesian program implementing a full-likelihood hybrid inference method.
  • Explicit modeling of linkage and recombination between genetic markers.
  • Comparison of Mongrail's statistical performance against the NewHybrids method using simulations.
  • Application to genome sequence data from hybridizing barred and spotted owls.

Main Results:

  • Mongrail generates posterior probabilities for different hybrid genealogical classes (F1, F2, backcross).
  • Simulations demonstrate Mongrail's superior statistical performance compared to composite likelihood methods.
  • The method was successfully applied to real genomic data from owl species.

Conclusions:

  • Mongrail provides a more accurate approach to inferring recent hybrid ancestry by accounting for genetic linkage.
  • The new method advances the analysis of genomic data for understanding hybridization events.
  • Accurate hybrid identification is essential for evolutionary and conservation biology.