The Allele-Frequency Spectrum Conditioned on Information from a Closely-Related Species
Hua Chen 1, Richard E. Green 2, Svante Paabo 2 and Montgomery Slatkin 1*
1 University of California at Berkeley
2 Max-Planck Institute of Evolutionary Anthropology
* To whom correspondence should be addressed. E-mail: slatkin{at}berkeley.edu.
Submitted on January 9, 2007
Revised on April 2, 2007
Accepted on 19 June 2007
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Abstract |
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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.
Key Words:
Neanderthal genomics, diffusion theory, trans-species polymorphism
