%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 }