Originally published as Genetics Published Articles Ahead of Print on June 11, 2007.

Genetics, Vol. 176, 2405-2420, August 2007, Copyright © 2007
doi:10.1534/genetics.107.071779

A Covariance Structure Model for the Admixture of Binary Genetic Variation

Mark N. Grote1

Department of Anthropology, University of California, Davis California 95616

1 Address for correspondence: Department of Anthropology, University of California, 1 Shields Ave., Davis, CA 95616.
E-mail: mngrote{at}ucdavis.edu

I derive a covariance structure model for pairwise linkage disequilibrium (LD) between binary markers in a recently admixed population and use a generalized least-squares method to fit the model to two different data sets. Both linked and unlinked marker pairs are incorporated in the model. Under the model, a pairwise LD matrix is decomposed into two component matrices, one containing LD attributable to admixture, and another containing, in an aggregate form, LD specific to the populations forming the mixture. I use population genetics theory to show that the latter matrix has block-diagonal structure. For the data sets considered here, I show that the number of source populations can be determined by statistical inference on the canonical correlations of the sample LD matrix.