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Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates.

Pier Francesco Palamara1, Laurent C Francioli2, Peter R Wilton3

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We developed a new method to estimate human genome mutation rates using identical-by-descent (IBD) segments and population history. This approach accurately quantifies mutation and gene conversion rates, even with genotyping errors, providing a higher estimate than previous studies.

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Area of Science:

  • Genetics
  • Population Genetics
  • Genomics

Background:

  • Human genome mutation rates are crucial for understanding evolution and demographics.
  • Accurate estimation of mutation and gene conversion rates is challenging.
  • Existing methods may be limited by genotyping errors and population history assumptions.

Purpose of the Study:

  • To present a novel method for inferring mutation and gene conversion rates using identical-by-descent (IBD) segments and population size history.
  • To validate the method's robustness against genotyping errors using coalescent simulations.
  • To apply the method to a large dataset of Dutch individuals to estimate these rates.

Main Methods:

  • Utilized sequence differences within identical-by-descent (IBD) segments.
  • Incorporated a reconstructed model of recent population-size history.
  • Validated robustness to genotyping error through coalescent simulations.
  • Applied to 498 trio-phased sequenced Dutch individuals.

Main Results:

  • Inferred a point mutation rate of 1.66 × 10(-8) per base per generation and an indel rate of 1.26 × 10(-9) for <20 bp.
  • Estimated the probability of non-crossover gene conversion at 5.99 × 10(-6).
  • Found gene conversion rates reflect recombination rates, with no observable mutagenic effects of recombination post-correction.
  • Detected enrichment of deleterious variation in IBD regions and no significant effect of selection on mutation rate estimates.

Conclusions:

  • The developed method provides robust estimates of mutation and gene conversion rates, accounting for genotyping errors.
  • The inferred mutation rate is higher than previously reported by pedigree-based studies.
  • Results suggest adopting higher mutation rate estimates for DNA-based demographic reconstruction.
  • Gene conversion is a significant factor, and its rates correlate with recombination rates.