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Originally published as Genetics Published Articles Ahead of Print on July 1, 2007.

Genetics, Vol. 177, 387-398, September 2007, Copyright © 2007
doi:10.1534/genetics.107.070730

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The Joint Allele-Frequency Spectrum in Closely Related Species

Hua Chen*, Richard E. Green{dagger}, Svante Pääbo{dagger} and Montgomery Slatkin*,1

* Department of Integrative Biology, University of California, Berkeley, California 94720 and {dagger} Max-Planck Institute of Evolutionary Anthropology, Leipzig, Germany D-04103

1 Corresponding author: Department of Integrative Biology, 3060 VLSB, University of California, Berkeley, CA 94720-3140.
E-mail: slatkin{at}berkeley.edu

We develop the theory for computing the joint frequency spectra of alleles in two closely related species. We allow for arbitrary population growth in both species after they had a common ancestor. We focus on the case in which a single chromosome is sequenced from one of the species. We use classical diffusion theory to show that, if the ancestral species was at equilibrium under mutation and drift and a chromosome from one of the descendant species carries the derived allele, the frequency spectrum in the other species is uniform, independently of the demographic history of both species. We also predict the expected densities of segregating and fixed sites when the chromosome from the other species carries the ancestral allele. We compare the predictions of our model with the site-frequency spectra of SNPs in the four HapMap populations of humans when the nucleotide present in the Neanderthal DNA sequence is ancestral or derived, using the chimp genome as the outgroup.


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