In many species, spatial genetic variation displays patterns of isolation-by-distance. Characterized by locally correlated allele frequencies, these patterns are known to create periodic shapes in geographic maps of principal components which confound signatures of specific migration events and influence interpretations of principal component analyses (PCA). In this study, we introduced models combining probabilistic PCA and kriging models to infer population genetic structure from genetic data while correcting for effects generated by spatial autocorrelation. The corresponding algorithms are based on singular value decomposition and low rank approximation of the genotypic data. As their complexity is close to that of PCA, these algorithms scale with the dimension of the data. To illustrate the utility of these new models, we simulated isolation-by-distance patterns and broad-scale geographic variation using spatial coalescent models. Our methods remove the horseshoe patterns usually observed in PC maps and simplify intrepretations of spatial genetic variation. We demonstrate our approach by analyzing single nucleotide polymorphism data from the Human Genome Diversity Panel, and provide comparisons with other recently introduced methods.
%0 Journal Article
%1 10.3389/fgene.2012.00254
%A Frichot, Eric
%A Schoville, Sean D
%A Bouchard, Guillaume
%A Fran\cois, Olivier
%D 2012
%J Frontiers in Genetics
%K Morans_I PCA genetic_maps spatial_structure
%N 254
%R 10.3389/fgene.2012.00254
%T Correcting principal component maps for effects of spatial autocorrelation in population genetic data
%U http://www.frontiersin.org/applied_genetic_epidemiology/10.3389/fgene.2012.00254/abstract
%V 3
%X In many species, spatial genetic variation displays patterns of isolation-by-distance. Characterized by locally correlated allele frequencies, these patterns are known to create periodic shapes in geographic maps of principal components which confound signatures of specific migration events and influence interpretations of principal component analyses (PCA). In this study, we introduced models combining probabilistic PCA and kriging models to infer population genetic structure from genetic data while correcting for effects generated by spatial autocorrelation. The corresponding algorithms are based on singular value decomposition and low rank approximation of the genotypic data. As their complexity is close to that of PCA, these algorithms scale with the dimension of the data. To illustrate the utility of these new models, we simulated isolation-by-distance patterns and broad-scale geographic variation using spatial coalescent models. Our methods remove the horseshoe patterns usually observed in PC maps and simplify intrepretations of spatial genetic variation. We demonstrate our approach by analyzing single nucleotide polymorphism data from the Human Genome Diversity Panel, and provide comparisons with other recently introduced methods.
@article{10.3389/fgene.2012.00254,
abstract = {In many species, spatial genetic variation displays patterns of isolation-by-distance. Characterized by locally correlated allele frequencies, these patterns are known to create periodic shapes in geographic maps of principal components which confound signatures of specific migration events and influence interpretations of principal component analyses (PCA). In this study, we introduced models combining probabilistic PCA and kriging models to infer population genetic structure from genetic data while correcting for effects generated by spatial autocorrelation. The corresponding algorithms are based on singular value decomposition and low rank approximation of the genotypic data. As their complexity is close to that of PCA, these algorithms scale with the dimension of the data. To illustrate the utility of these new models, we simulated isolation-by-distance patterns and broad-scale geographic variation using spatial coalescent models. Our methods remove the horseshoe patterns usually observed in PC maps and simplify intrepretations of spatial genetic variation. We demonstrate our approach by analyzing single nucleotide polymorphism data from the Human Genome Diversity Panel, and provide comparisons with other recently introduced methods.},
added-at = {2013-09-21T23:27:19.000+0200},
author = {Frichot, Eric and Schoville, Sean D and Bouchard, Guillaume and Fran{\c}ois, Olivier},
biburl = {https://www.bibsonomy.org/bibtex/25c36dafde17218c57f7dc432a6602c2d/peter.ralph},
doi = {10.3389/fgene.2012.00254},
interhash = {b378b5631fba216180bdff0a54091054},
intrahash = {5c36dafde17218c57f7dc432a6602c2d},
issn = {1664-8021},
journal = {Frontiers in Genetics},
keywords = {Morans_I PCA genetic_maps spatial_structure},
number = 254,
timestamp = {2013-09-21T23:27:19.000+0200},
title = {Correcting principal component maps for effects of spatial autocorrelation in population genetic data},
url = {http://www.frontiersin.org/applied_genetic_epidemiology/10.3389/fgene.2012.00254/abstract},
volume = 3,
year = 2012
}