The Joint Allele-Frequency Spectrum in Closely Related Species Export

@article{citeulike:1683059, abstract = {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. 10.1534/genetics.107.070730}, author = {Chen, Hua and Green, Richard E. and Paabo, Svante and Slatkin, Montgomery}, citeulike-article-id = {1683059}, citeulike-linkout-0 = {http://dx.doi.org/10.1534/genetics.107.070730}, citeulike-linkout-1 = {http://www.genetics.org/cgi/content/abstract/177/1/387}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17603120}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17603120}, doi = {10.1534/genetics.107.070730}, journal = {Genetics}, keywords = {allele, frequency, related-species}, month = {September}, number = {1}, pages = {387--398}, posted-at = {2008-04-10 21:51:46}, priority = {2}, title = {The Joint Allele-Frequency Spectrum in Closely Related Species}, url = {http://dx.doi.org/10.1534/genetics.107.070730}, volume = {177}, year = {2007} }

TY - JOUR ID - citeulike:1683059 L3 - citeulike-article-id:1683059 N2 - 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. 10.1534/genetics.107.070730 IS - 1 JF - Genetics EP - 398 TI - The Joint Allele-Frequency Spectrum in Closely Related Species VL - 177 SP - 387 KW - allele KW - frequency KW - related-species AU - Chen, Hua AU - Green, Richard AU - Paabo, Svante AU - Slatkin, Montgomery PY - 2007/09/01/ UR - http://dx.doi.org/10.1534/genetics.107.070730 ER -