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Linkage disequilibrium under recurrent bottlenecks.

E Schaper1, A Eriksson, M Rafajlovic

  • 1Department of Physics, University of Gothenburg, SE-41296 Gothenburg, Sweden.

Genetics
|November 4, 2011
PubMed
Summary

Understanding neutral genetic variation is key to modeling selection. This study examines two-locus gene genealogies under recurrent population bottlenecks, revealing how recombination and demographic fluctuations impact genetic association.

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Area of Science:

  • Population genetics
  • Evolutionary biology
  • Genomics

Background:

  • Understanding neutral genetic variation is crucial for modeling selection.
  • Patterns of neutral variation at multiple loci provide insights into linkage and gene genealogies.
  • The effects of recombination and demographic fluctuations on multilocus genealogies are poorly understood.

Purpose of the Study:

  • To investigate the combined effects of recombination and recurrent population bottlenecks on two-locus gene genealogies.
  • To derive coalescent approximations for the covariance of coalescence times at two loci.
  • To analyze how these factors influence linkage disequilibrium and gene association.

Main Methods:

  • Utilized a two-locus Wright-Fisher model with recurrent bottlenecks.
  • Derived coalescent approximations for the covariance of times to the most recent common ancestor.
  • Analyzed linkage disequilibrium measures and their relationship to physical distance and demographic history.

Main Results:

  • An effective population-size approximation accurately describes locus association when recombination rates are extreme relative to population fluctuations.
  • Under specific bottleneck and recombination patterns, gene history association becomes independent of physical distance.
  • A common linkage disequilibrium measure (σ²(d)) can underestimate long-range associations due to canceling terms.

Conclusions:

  • Recurrent bottlenecks and recombination interact in complex ways to shape genetic variation patterns.
  • The findings provide a more nuanced understanding of linkage disequilibrium in fluctuating populations.
  • New analytical tools, like the Xi coalescent, may be needed to fully capture complex demographic histories.