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Stepping-stone spatial structure causes slow decay of linkage disequilibrium and shifts the site frequency spectrum.

Publication ,  Journal Article
De, A; Durrett, R
Published in: Genetics
June 2007

The symmetric island model with D demes and equal migration rates is often chosen for the investigation of the consequences of population subdivision. Here we show that a stepping-stone model has a more pronounced effect on the genealogy of a sample. For samples from a small geographical region commonly used in genetic studies of humans and Drosophila, there is a shift of the frequency spectrum that decreases the number of low-frequency-derived alleles and skews the distribution of statistics of Tajima, Fu and Li, and Fay and Wu. Stepping-stone spatial structure also changes the two-locus sampling distribution and increases both linkage disequilibrium and the probability that two sites are perfectly correlated. This may cause a false prediction of cold spots of recombination and may confuse haplotype tests that compute probabilities on the basis of a homogeneously mixing population.

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Published In

Genetics

DOI

EISSN

1943-2631

ISSN

0016-6731

Publication Date

June 2007

Volume

176

Issue

2

Start / End Page

969 / 981

Related Subject Headings

  • Probability
  • Population Density
  • Models, Genetic
  • Linkage Disequilibrium
  • Kinetics
  • Genetics, Population
  • Gene Frequency
  • Emigration and Immigration
  • Developmental Biology
  • Chromosomes
 

Citation

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ICMJE
MLA
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De, A., & Durrett, R. (2007). Stepping-stone spatial structure causes slow decay of linkage disequilibrium and shifts the site frequency spectrum. Genetics, 176(2), 969–981. https://doi.org/10.1534/genetics.107.071464
De, Arkendra, and Richard Durrett. “Stepping-stone spatial structure causes slow decay of linkage disequilibrium and shifts the site frequency spectrum.Genetics 176, no. 2 (June 2007): 969–81. https://doi.org/10.1534/genetics.107.071464.
De, Arkendra, and Richard Durrett. “Stepping-stone spatial structure causes slow decay of linkage disequilibrium and shifts the site frequency spectrum.Genetics, vol. 176, no. 2, June 2007, pp. 969–81. Epmc, doi:10.1534/genetics.107.071464.

Published In

Genetics

DOI

EISSN

1943-2631

ISSN

0016-6731

Publication Date

June 2007

Volume

176

Issue

2

Start / End Page

969 / 981

Related Subject Headings

  • Probability
  • Population Density
  • Models, Genetic
  • Linkage Disequilibrium
  • Kinetics
  • Genetics, Population
  • Gene Frequency
  • Emigration and Immigration
  • Developmental Biology
  • Chromosomes