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.
%0 Journal Article
%1 de2007steppingstone
%A De, A
%A Durrett, R
%D 2007
%J Genetics
%K linkage_disequilibrium site_frequency_spectrum coalescent_theory spatial_coalescent
%N 2
%P 969-981
%R 10.1534/genetics.107.071464
%T Stepping-stone spatial structure causes slow decay of linkage disequilibrium and shifts the site frequency spectrum
%U http://www.ncbi.nlm.nih.gov/pubmed/17409067?dopt=Abstract
%V 176
%X 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.
@article{de2007steppingstone,
abstract = {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.},
added-at = {2014-01-02T02:37:40.000+0100},
author = {De, A and Durrett, R},
biburl = {https://www.bibsonomy.org/bibtex/222de120cc6e89652182b13d859f84c35/peter.ralph},
doi = {10.1534/genetics.107.071464},
interhash = {a329f6adb0d0b6b2b679d9f2666e616c},
intrahash = {22de120cc6e89652182b13d859f84c35},
journal = {Genetics},
keywords = {linkage_disequilibrium site_frequency_spectrum coalescent_theory spatial_coalescent},
month = jun,
number = 2,
pages = {969-981},
pmid = {17409067},
timestamp = {2014-09-14T17:43:51.000+0200},
title = {Stepping-stone spatial structure causes slow decay of linkage disequilibrium and shifts the site frequency spectrum},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17409067?dopt=Abstract},
volume = 176,
year = 2007
}